Calendar of MRSEC Events

End of Semester Gathering
8:30-9:30am EST | 24 Oxford Street, Room 375 - Classroom 375, Cambridge, MA

TBD abstract

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10am & 1pm EST | Harvard University Science Center, Lecture Hall B, 1 Oxford Street, Cambridge, MA

What is symmetry?
How are crystals formed?
Where can we see patterns in our daily lives?

Beauty and wonder surround us everyday. Our world is full of amazing patterns: from the smallest scale of molecules arranging into crystal structures such as snowflakes, to the stripes on a tiger, to large geological wonders like Devils Postpile. Join us at the 2023 Holiday Science Lecture for Families as we take a close look at some of the amazing patterns observed in nature and the science of their structure and formation. We will use experiments and interactive demonstrations to illustrate ideas of shape, symmetry, packing, and pattern formation!
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End of Semester Gathering
9am-6pm EST | 24 Oxford Street, Geological Lecture Hall, Cambridge, MA

Join us for the 10th Anniversary meeting of the Boston Area Antimicrobial Resistance Network! The program include sessions on Advances in Antibiotics, Advances in Diagnostics, and Alternative Approaches, alongside ample opportunities for networking among colleagues from academia and industry.

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Louison Thorens, Tufts University
6 - 7:30pm | Pierce Hall 209, 29 Oxford Street

Abstract: Many natural and industrial processes rely on the displacement of mixed liquid, gas, and granular materials through confining structures. Specifically, such multi-phase flows through porous geometries play an essential role in engineering applications ranging from oil recovery and CO2 sequestration to filtration. Despite their tremendous potential economic and environmental impact, understanding these three-phase flows remains a formidable challenge. First, we study the formation of granular plugs during the slow drainage of a liquid-grain mixture in a tube illustrating the onset of a “bulldozing” instability. We define a new unstable regime leading to the periodic formation of dunes, analogous to the road “washboarding” instability, where a key element is the strong increase of the frictional forces with the angle of attack of the pushing meniscus at the liquid/air interface. Second, we develop an original method to control the frictional interactions at the origin of this bulldozing instability, by using ferromagnetic particles: submitted to a magnetic field, they acquire a magnetic moment, leading to tunable interactions of pairs of magnetic dipoles. We demonstrate the emergence of a radial force along the walls of the container, whose amplitude and direction are determined by the applied magnetic field. This "magnetic Janssen effect" allows us to control the apparent mass of a granular column, paving the way towards the design of granular meta-materials, for which mechanical (un)jamming properties can be remotely controlled or even programmed.

Bio: Louison Thorens obtained his master's degree in physics from the Ecole Normale Supérieure de Lyon in France, followed by a Ph.D. achieved through a collaborative effort between PoreLab at the University of Oslo in Norway and the Ecole Normale Supérieure de Lyon in France. My doctoral research focused on magnetic granular materials and flow in porous media, which serves as the basis of this talk. I am currently a postdoctoral researcher at Tufts University working with Jeffrey Guasto, my research now primarily explores polymer dynamics and stretching within microfluidic flows.

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Carolyn Elya, MCB
8:30-9:30am EST | 24 Oxford Street, Room 375 - Classroom 375, Cambridge, MA

Many parasites are known to manipulate the behavior of their animal hosts, but how this occurs remains poorly understood. Recently, I discovered a strain of the mind-controlling pathogen Entomophthora muscae in wild fruit flies and developed robust methods to culture the fungus in the model organism Drosophila melanogaster. Before sunset on their final day of life, infected flies perform the “zombie” behaviors characteristic of E. muscae infection: they climb to a high location (a behavior known as “summiting”), extend their proboscises, and raise their wings in a pose that facilitates spore dispersal. Using a combination of approaches that range from behavioral neuroscience to molecular biology, I have established a mechanistic model of summiting behavior in zombie flies. Work in my lab will span multiple disciplines as we identify the fungal inputs to the fly summiting pathway as well as reveal the genetic and circuit underpinnings of additional zombie behaviors driven by E. muscae.

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Adel Djellouli, J.A. Paulson School of Engineering and Applied Sciences, Harvard University
6 - 7:30pm | Pierce Hall 209, 29 Oxford Street

Abstract: The pursuit of materials with enhanced functionality has led to the emergence of metamaterials - artificially engineered materials whose properties are determined by their structure rather than composition. Through careful design of their building blocks, metamaterials with unprecedented electromagnetic, acoustic, thermal and mechanical properties have been realized, with the potential to revolutionize fields ranging from energy harvesting and conversion to sensing and imaging. Although these materials are typically based on a periodic array of solid building blocks, recent studies have demonstrated that the mixing of carefully designed units into a fluid medium can also yield remarkable properties. Such “metafluids” have enabled reconfigurable and adaptable photonic fluids, negative-acoustic-index materials and unconventional thermodynamic properties. Unlike solid metamaterials, metafluids can take the shape of their container, flow, and do not require a precise arrangement of their building blocks. These characteristics make metafluids a promising platform to enhance the functionality of numerous systems that interact with fluids during operation.

Inspired by these recent advances, here we show that by mixing highly deformable shells into an incompressible fluid we can realize a metafluid with programmable elastic response, optical behavior and viscosity. We show that the reversible buckling of the shells radically changes the characteristics of the fluid and provides exciting opportunities for expanding its functionality. First, we experimentally demonstrate both at centimeter and micrometer scale that the buckling of the shells endows the fluid a highly nonlinear behavior. Then, we numerically study how the shells geometry affects such nonlinear response. Finally, we harness the nonlinear fluid behavior to develop smart robotic systems, highly tunable logic gates and optical elements with switchable response. Further, we demonstrate that shell buckling also affects the fluid viscosity, making the flow in the laminar regime dependent not only on the pressure difference between two points but also on the absolute value of pressure at these points. As such, the proposed metafluid provides a promising platform to enhance the functionality of existing fluidic devices by expanding the capabilities of the fluid itself.

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7 pm EST | 1 Oxford Street, Cambridge, MA, Science Center Hall C

Presenter: Mauro Colagreco (@maurocolagreco), Chef and Owner of Mirazur (France)

Dr. Amir Mitchell, UMass Medical School
6 - 7:00pm EST | 24 Oxford Street, Haller Hall, Geo Room 375, Cambridge, MA

Abstract: Numerous non-antibiotic drugs have potent antimicrobial activity at physiological concentrations and can adversely impact the human microbiome. Despite broad recognition of this phenomenon, its mechanistic underpinning remains largely unknown. We investigated the toxicity mechanisms of two hundred antibiotic and non-antibiotic drugs using pooled genetic screens with a collection of thousands of Escherichia coli knockout strains. Analysis of two million gene-drug interactions uncovered the genes and pathways underlying drug-specific toxicity and revealed antibiotics and non-antibiotics leverage on different mechanisms of lethality. This observation suggests non-antibiotics can reveal unexploited targets for novel antimicrobials. Analysis of efflux systems and membrane proteins revealed that they widely impact antibiotics and non-antibiotics alike, implying that many non-antibiotics can inadvertently select for broad antibiotic resistance. Our systematic study suggests overall orthogonality in mechanisms of action and a pervasive risk of inadvertent cross-resistance.

More information about the MSI Seminar

MSI Coffee Hour Sign-Up with Dr. Amir Mitchell for November 17, 10am

Sheila Russo, Assistant Professor, Department of Mechanical Engineering, Boston University
6 - 7:30pm | Pierce Hall 209, 29 Oxford Street

Abstract: Minimally invasive surgical (MIS) procedures pose significant challenges for robots, which need to safely navigate through and manipulate delicate anatomy while performing complex tasks to treat tumors in remote areas. Soft robots hold considerable potential in MIS given their compliant nature, inherent safety, and high dexterity. Yet, a significant breakthrough of soft robots in surgery is impeded by current limitations in the design, manufacturing, and integration of soft materials that combine actuation, sensing, and control. Scientific understanding of medical and surgical robotics is entering an exciting new era where early approaches relying on rigid materials, standard manufacturing, and conventional kinematics are giving way to Soft Material Robotics. Our research at the Material Robotics Lab at Boston University is focused on the design, mechanics, and manufacturing of novel multi-scale and multi-material biomedical robotic systems. This talk will illustrate our work towards achieving safe navigation, distal actuation, integrated sensing, and effective force transmission in MIS by highlighting different classes of soft surgical robots, i.e., soft continuum robots, soft-foldable robots, and soft reactive skins with applications in lung cancer, colorectal cancer, and brain cancer surgery.

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I-Ting Huang, OEB, Cavanaugh Lab
8:30-9:30am EST | 24 Oxford Street, Room 375 - Classroom 375, Cambridge, MA

Qiaobing Xu, Professor Department of Biomedical Engineering, Tufts University
6 - 7:30pm | Pierce Hall 209, 29 Oxford Street

Abstract: Lipid nanoparticles (LNPs) represent the most advanced nonviral nanoparticle delivery systems that have been extensively investigated for nucleic acid delivery. Here I will discuss the design and development of combinatorial synthetic bioreducible and biodegradable LNPs with distinct chemical structures and properties for in vitro and in vivo intracellular mRNA delivery. In the first part of my talk, I will give an overview of the research effort in my group, including various chemistry for synthesis of the lipid library, library screening for organ and cell selective delivery, and application of the delivery for rare diseases, gene editing, and cancer vaccines. In the second part of my talk, I will discuss a specific case that we recently designed a novel lipid-based nanoscale molecular machine to enhance the destabilization and disruption of the endo-lysosomal membrane through nanomechanical action upon light irradiation. Cytosolic transport of biologics with higher efficiency is achieved comparing with conventional delivery systems.

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7 pm EST | 1 Oxford Street, Cambridge, MA, Science Center Hall C

Presenter: Alex Atala (@alexatala), Chef and Owner of the D.O.M. restaurant in São Paulo

Jessica Mark Welch, Forsyth Institute
8:30-9:30am EST | 24 Oxford Street, Room 375 - Classroom 375, Cambridge, MA

TBD abstract

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Brian Timko, Assistant Professor, Department of Biomedical Engineering, Tufts University
6 - 7:30pm | Pierce Hall 209, 29 Oxford Street

Abstract: Hybrid bioelectronic tissues that integrate networks of synthetic devices and living cells offer exciting opportunities to monitor and modulate biological functions. Achieving his goal, however, requires new classes of devices that integrate seamlessly with the surrounding cells. In the first part of this talk, we will discuss our recent work to achieve device-level tissue integration via electrical, magnetic and optical modalities. In the second part of this talk, we will discuss network-level integration through bioelectronic support materials with tunable bioactive and nonlinear mechanical properties. Taken together, these advances could open new routes toward closed-loop tissue integration, with applications in neuroscience and cardiology for disease modeling, bioelectronic medicine, and tissue regeneration.

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Dr. Anthony Hyman, Institute Director - Max Planck Institute of Molecular Cell Biology and Genetics
4 - 5pm | Pierce Hall 209, 29 Oxford Street

Abstract: Prof. Dr. Anthony Hyman is Director and Group Leader at the Max Planck Institute of Molecular Cell Biology and Genetics. 1984 he received his BSc first class in Zoology from the University College in London, where he had also been working as research Assistant in 1981. From 1985 to 1987 he wrote his PhD about “The establishment of division axes in early C.elegans embryos” under the supervision of Dr. John White at the Laboratory of MolecularBiology, MRC in Cambridge, England. After that he moved to San Francisco where he did hispostdoctoral research in the lab of Prof. Tim Mitchison at the University of Californiainvestigating the mechanism of chromosome movement studied in vitro. 1993 he became GroupLeader at the European Molecular Biology Laboratory in Heidelberg, before he moved toDresden in 1999 as a founding director of the Max Planck Institute for Molecular Cell Biologyand Genetics. In 2002 he was named honorary Professor of Molecular Cell Biology at DresdenUniversity of Technology. He is best known for his work on the role of phase separation information of biological compartments.

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7 pm EST | 1 Oxford Street, Cambridge, MA, Science Center Hall C

Presenter: Luciana Bianchi (@lucianabianchi), Chef, Humanist, writer, social entrepreneur. Director of the Galapagos Foundation focused on gastronomy and Founder of MUYU, the first farm, forest and sea to table restaurant in the Galapagos islands

Ethan Garner, Harvard MCB, Professor of Molecular and Cellular Biology
8:30-9:30am EST | 24 Oxford Street, Room 375 - Classroom 375, Cambridge, MA

The process by which bacteria divide in half remains an outstanding biological problem. Our understanding of this system has been furthered by groups with different approaches studying this system. I will discuss the new insights gained from cell biological and biophysical studies into the mechanisms underlying bacterial cell division, as well our recent discovery that the force driving the most energetically difficult part of cell division arises from the simple crowding of filaments on the membrane.

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Nicolas Romeo, University of Chicago
1:00pm EST | 20 Garden Street, Room G10, Cambridge, MA and VIRTUAL

Abstract:
The cell nucleus is enveloped by a complex membrane, whose wrinkling has been implicated in disease and cellular aging. The biophysical dynamics and spectral evolution of nuclear wrinkling during multicellular development remain poorly understood due to a lack of direct quantitative measurements. We characterize the onset and dynamics of nuclear wrinkling during egg development in the fruit fly when nurse cell nuclei increase in size and display stereotypical wrinkling behaviour. A spectral analysis of three-dimensional high-resolution live-imaging data from several hundred nuclei reveals a robust asymptotic power-law scaling of angular fluctuations consistent with renormalization and scaling predictions from a nonlinear elastic shell model. We further demonstrate that nuclear wrinkling can be reversed through osmotic shock and suppressed by microtubule disruption, providing tunable physical and biological control parameters for probing the mechanical properties of the nuclear envelope, highlighting in passing the importance of nonlinear response to biological robustness.

More information about the Center of Mathematical Sciences and Applications Active Matter Seminar

Michael L. Smith, Associate Professor, Department of Biomedical Engineering, Boston University
6 - 7:30pm | Pierce Hall 209, 29 Oxford Street

Abstract: Tensional homeostasis is a phenomenon of fundamental importance in mechanobiology. It refers to the ability of organs, tissues, and cells to respond to external disturbances by maintaining a homeostatic (set point) level of mechanical stress (tension). It is well documented that breakdown in tensional homeostasis is the hallmark of progression of some diseases such as cancer and atherosclerosis. This talk will first survey quantitative studies of tensional homeostasis with the goal of providing characterization of this phenomenon across a broad range of length scales, from the organ level to the subcellular level. Our results, as well as those of other groups, suggest that tensional homeostasis is an emergent phenomenon driven by collective rheostatic mechanisms that build in scale from micrometer focal adhesions to collective actions of cells in multicellular forms. Lastly, this talk will discuss the role of cadherin adhesion molecules and intracellular signaling and scaffolding proteins in regulation of tensional homeostasis, since these molecules specifically link basic science studies of this phenomenon to clinical manifestations of dysregulated cell tension.

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7 pm EST | 1 Oxford Street, Cambridge, MA, Science Center Hall C

Presenter: Bryan Furman (@bs_pitmaster), 2019 & 2020 James Beard Semifinalist, The first Pitmaster to win F&W Best New Chef (class of 2019), Chef in Residency @ Stone Barnes Center for Food & Agriculture

Jason Crawford
6 - 7:00pm EST | 24 Oxford Street, Haller Hall, Geo Room 375, Cambridge, MA

Abstract: Metabolism at the Human-Microbe Interface

The Crawford laboratory focuses on Metabolism at the Human-Microbe Interface. Genome sequencing of bacteria (and fungi) has revealed many highly unusual “orphan” biosynthetic gene clusters suspected of synthesizing novel, structurally diverse, and biologically active small molecules. These types of naturally produced molecules often regulate complex interactions with their animal hosts, hold a rich history of being utilized as human drugs, and serve as excellent molecular probes for identifying new drug targets for a wide variety of diseases. Additionally, there are still many novel metabolites of functional relevance in well-characterized animals, such as humans and mice. Using a blend of small molecule chemistry, protein biochemistry, cell biology, and microbiology, the lab exploits the natural interactions between bacteria and animals to discover new molecules with signaling, antimicrobial, immunomodulatory, and anticancer activities. The lab also connects these products to their underlying biosynthetic genes, characterizes the biosynthetic enzymes involved in their construction, and investigates their roles in biology and medicine. In this talk, I will provide an overview of our approaches and then dig into a few new metabolic systems that are conserved in a variety of gammaproteobacterial pathogens that regulate virulence programming. More information about the MSI Seminar

Michelle Teplensky, Boston University
6 - 7:30pm | Pierce Hall 209, 29 Oxford Street

Abstract: Vaccines potently program the immune system through an adjuvant (activator) and antigen (target), and have been employed to fight various forms of cancer. However, their potential has yet to be fully realized, with many vaccine candidates failing out of clinical trials due to a lack of efficacy. Conventional approaches have focused on the composition with less consideration for the arrangement of the components on a single vaccine structure. This structural consideration becomes increasingly complex when evaluating the immune landscape necessary for potent tumor remission: to be effective against highly mutative aggressive tumors, cancer vaccines must activate multiple immune cell types and overcome immunosuppressive tumor environments. However, design considerations in these areas are underexplored. We highlight the opportunity to uniquely program immunological interactions and positively impact vaccine efficacy across multiple tumor types through rational and molecular antigen placement. This emphasizes the role of nanoscale vaccine structural development to raise complex multi-faceted immunity against future diseases.

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7 pm EST | 1 Oxford Street, Cambridge, MA, Science Center Hall C

Presenter: Betty Petrova (@petrovachocolates), Petrova Chocolates

Jared Mayers, CCB, Balskus Lab
8:30-9:30am EST | 24 Oxford Street, Room 375 - Classroom 375, Cambridge, MA

TBD abstract

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Fred MacKintosh, Rice University
1:00pm EST | 20 Garden Street, Room G10, Cambridge, MA and VIRTUAL

Abstract:
Various processes in living cells depend on contractile forces that are often generated by myosin motors in concert with polar actin filaments. A textbook example of this is the actomyosin contractile ring that forms during cell division. Recent evidence, however, has begun to suggest alternate or redundant mechanisms that do not depend on myosin. Experiments on simplified, reconstituted systems also point to contractility and structure formation in disordered, apolar arrays of filaments. We propose a motor-free mechanism that can generate contraction in biopolymer networks without the need for motors such as myosin or polar filaments such as actin. This mechanism is based on active binding and unbinding of cross-linkers that breaks the principle of detailed balance, together with the asymmetric force-extension response of semiflexible biopolymers. We discuss the resulting force-velocity relation and other implications of this, as well as possible evidence for non-motor force generation.

More information about the Center of Mathematical Sciences and Applications Active Matter Seminar

Kristen Dorsey, Northeastern University
6 - 7:30pm | Pierce Hall 209, 29 Oxford Street

Abstract: Physically-soft mechanical sensors and actuators are poised to unlock exciting new applications in wearable devices, robotics, and human-machine interfaces. A challenge of these soft-material devices is defining and reconfiguring their properties to suit the target application. In this talk, I will discuss challenges and recent work related to designing and controlling origami-patterned sensors and actuators and additive manufacturing approaches for wearable devices and sensors. I will also present work in enhancing the stability and mechanical selectivity of stretchable sensors and discuss applications for such sensors in wearable healthcare applications and soft robotics.

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7 pm EST | 1 Oxford Street, Cambridge, MA, Science Center Hall C

Presenter: Rich Shih (@ourcookquest), Co-author of Koji Alchemy, is one of the key culinary explorers of mold-based fermentation in the United States (Wayne Earl Chinnock Photography)

Marco Jost, HMS, Blavatnick Institute
8:30-9:30am EST | 24 Oxford Street, Room 375 - Classroom 375, Cambridge, MA

Sandra Shefelbine, Northeastern University
6 - 7:30pm | Pierce Hall 209, 29 Oxford Street

Abstract: The skeletal system adapts readily to changes in mechanical load, allowing cartilage and bone to alter shape and structure in response to the mechanical environment. In this talk Dr. Shefelbine will show a snapshot of her current work in which she uses experiments, imaging and computational modeling to probe the link between mechanics and bone growth, maintenance, and aging. From salamander limbs to elite ice hockey players, and mice to paraplegics she combines animal experiments, computational modeling, and clinical observations to examine the role of mechanics in skeletal adaptation.

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7 pm EST | 1 Oxford Street, Cambridge, MA, Science Center Hall C

Presenter: Joanne Chang '91 (@jbchang), Flour Bakery and Café, Myers + Chang, author of "Flour", "Flour Too", "Myers + Chang at Home", and "Baking with Less Sugar"

Max Lavrentovich, Worcester State University
1:00pm EST | 20 Garden Street, Room G10, Cambridge, MA and VIRTUAL

Abstract:
The more prosaic cousin of active matter, driven inactive matter, is still full of unexpected phenomena. I will discuss two projects involving two seemingly mundane systems, a phase-separating colloidal mixture and a lipid membrane, which demonstrate counterintuitive properties when driven out of equilibrium. We will see that the phase separating mixture, when driven by a uniform force, develops (in simulations) an intriguing pattern with a characteristic length scale set by the magnitude of the drive. We will look at some theoretical approaches to understanding the pattern formation and possible experimental realizations. The membrane, when driven by an oscillatory electric field, develops (in experiments) a long-lived metastable state with a decreased capacitance and increased dissipation. This state may have implications for neuronal processing and memory formation.

More information about the Center of Mathematical Sciences and Applications Active Matter Seminar

Margaret McFall-Ngai & Edward Ruby, Carnegie Science, Caltech
6 - 7:00pm EST | 24 Oxford Street, Haller Hall, Geo Room 102, Cambridge, MA

Abstract: Recent research has demonstrated that symbioses between animals and microbes are fundamental to the biology of most, if not all, animal species. The mutualistic association between the Hawaiian bobtail squid, Euprymna scolopes, and its luminous bacterium, Vibrio fischeri, is a powerful model to investigate signaling between the host and its microbial partner. In this system, symbiotic bacteria are acquired by horizontal transmission within hours of hatching and the symbiosis remains dynamically stable throughout the life of the host. We will address how the developmental trajectory of the host, from embryo to adult, fosters the initial colonization of the specific symbiont and maintains the symbiosis through a profound diel rhythm. In addition, we will consider how this partnership has contributed to what we know about the differences between benign or beneficial and pathogenic symbioses.

More information about the MSI Seminar

7 pm EST | 1 Oxford Street, Cambridge, MA, Science Center Hall C

Presenter: Jason Doo (@wusongroad), Chef and Owner of Wusong Road Tiki bar

Nicole Pecora, Brigham & Women
8:30-9:30am EST | 24 Oxford Street, Room 375 - Classroom 375, Cambridge, MA

TBD abstract

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Adnan Syed, MCB, Losick Lab
8:30-9:30am EST | 24 Oxford Street, Room 375 - Classroom 375, Cambridge, MA

TBD abstract

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Herbert Levine, Northeastern University
1:00pm EST | 20 Garden Street, Room G10, Cambridge, MA and VIRTUAL

Abstract:
Cell fate decisions are made by allowing external signals to govern the steady-state pattern adopted by networks of interacting regulatory factors governing transcription and translation. One of these decisions, of importance for both developmental processes and for cancer metastasis, is the epithelial-mesenchymal transition (EMT). In this talk, we will argue that these biological networks have highly non-generic interaction structures such that they allow for phenotypic states with very low frustration, i.e. where most interactions are satisfied. This property has important consequences for the allowed dynamics of these systems.

More information about the Center of Mathematical Sciences and Applications Active Matter Seminar

Michal Caspi Tal, Principal Scientist, Biological Engineering, MIT
12:00pm EST | 52 Oxford Street, Northwest Building, Lecture Hall B103, Cambridge, MA

Abstract:
Lyme disease is a tick-borne disease caused by bacteria of the genus Borrelia. The host factors that modulate susceptibility for Lyme disease have remained mostly unknown. Using epidemiological and genetic data as well as in vitro and in vivo infection assays we show a novel host defense protein in humans present in the skin, sweat, and other secretions which protects against Borrelia bacteria.

More information about the MSI Seminar

Rouzbeh Amini, Department of Mechanical and Industrial Engineering, Northeastern University
6 - 7:30pm | Pierce Hall 209, 29 Oxford Street

Abstract: Mechanics plays a critical role in tissue development, regeneration, and remodeling, as cell–cell interactions and cell–matrix interactions are known to be heavily influenced by changes in the mechanical microenvironment at the extracellular matrix/cellular level. Nuclear shape alteration can be used as a metric for overall cell mechanical deformation. It may also lead to changes in gene expression and protein synthesis that could affect the biomechanics of the tissue extracellular matrix. We used engineering tools to examine how tissue mechanical loading affects the nuclear deformation. In addition, we showed that nuclear deformation is highly sensitive to the micro-structural properties of the extracellular matrix.

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7 pm EST | 1 Oxford Street, Cambridge, MA, Science Center Hall C

Presenters:
Dave Arnold (@CookingIssues), Booker and Dax (NYC), author of "Liquid Intelligence", host of "Cooking Issues," founder of the Museum of Food and Drink

Harold McGee (@Harold_McGee), author of "On Food and Cooking", "Curious Cook", "Nose Dive: A Field Guide to the World's Smells"

Dr. Michael Gilmore, MSI Co-Director
8:30-9:30am EST | 24 Oxford Street, Room 375 - Classroom 375, Cambridge, MA

What enduring properties do specific host-associated microbes have, that have allowed them to be passed generation to generation for eons, and not be displaced by other microbes? Why have some host-associated microbes emerged as leading causes of multidrug resistant infection and not others? Why bacterial species - discrete bins of related genotypes - have to exist. In our quest to understand why two species of enterococci, E. faecalis and E. faecium, emerged as leading causes of human infection, we have wrestled with these and other questions.

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The CMSA will host the ninth annual Conference on Big Data. The 2023 Big Data Conference features speakers from the Harvard community as well as scholars from across the globe, with talks focusing on computer science, statistics, math and physics, and economics.

Organizers: Michael Douglas, CMSA, Harvard University; Yannai Gonczarowski, Economics and Computer Science, Harvard University; Lucas Janson, Statistics and Computer Science, Harvard University; Tracy Ke, Statistics, Harvard University; Horng-Tzer Yau, Mathematics and CMSA, Harvard University; Lu Yue, Electrical Engineering and Applied Mathematics, Harvard University.

Register for Big Data 2023
Registration is required.

Wed, Aug 9–Fri, Aug 11: 8am-4pm @ Harvard
Explore a variety of NGSS-aligned topics like ionic compounds, intermolecular forces, acids and pH, and chemical reactions by making classroom-ready food labs including fresh cheese, caramel, brown butter, and popping boba.

This workshop is primarily intended for high school science chemistry teachers. Since it centers around hands-on labs and discussions, limited space is available and full participation is required. Our application form outlines the expectations for full participation in this virtual format.

Participants will earn:

• PDPs for their work
• a certificate of completion from Harvard University
• a stipend for both completion of the professional development and implementation of activity during the school year

This session is offered by Harvard's MRSEC and Bite Scized Education.

Register for RET PD Workshop, registration is required.   More about Harvard MRSEC RET Workshop

Mon, Aug 7–Tue, Aug 8: 9am-3pm @ Harvard
Explore a variety of NGSS-aligned topics like ionic compounds, intermolecular forces, acids and pH, and chemical reactions by making classroom-ready food labs including fresh cheese, caramel, brown butter, and popping boba.

This workshop is primarily intended for middle school science chemistry teachers. Since it centers around hands-on labs and discussions, limited space is available and full participation is required. Our application form outlines the expectations for full participation in this virtual format.

Participants will earn:

• PDPs for their work
• a certificate of completion from Harvard University
• a stipend for both completion of the professional development and implementation of activity during the school year

This session is offered by Harvard's MRSEC and Bite Scized Education.

Register for RET PD Workshop, registration is required.   More about Harvard MRSEC RET Workshop

Mon, July 31–Tue, Aug 1: Middle School; 9am-3pm on Zoom
Wed, Aug 2–Thur, Aug 3: High School (intended for High School Chemistry); 11am-5pm EST on Zoom

Explore a variety of NGSS-aligned topics like ionic compounds, intermolecular forces, acids and pH, and chemical reactions by making classroom-ready food labs including fresh cheese, caramel, brown butter, and popping boba.

This workshop is primarily intended for middle school science and high school chemistry teachers. Since it centers around hands-on labs and discussions, limited space is available and full participation is required. Our application form outlines the expectations for full participation in this virtual format.

Participants will earn:

• PDPs for their work
• a certificate of completion from Harvard University
• opportunities for stipends after implementation of activities

This session is offered by Harvard's MRSEC and Bite Scized Education.

Register for RET PD Workshop, registration is required.   More about Harvard MRSEC RET Workshop

Pragya Arora, Brandeis University
6 - 7:30pm | Pierce Hall 209, 29 Oxford Street

Abstract: Dense assemblies of active particles are thought to undergo dynamical arrest akin to supercooled equilibrium liquids. However, how activity modifies the approach to a glassy state continues to be debated. Addressing this question is even as essential as a growing body of evidence suggests that dense assemblies of biological cells share hallmark traits of equilibrium glass physics. By designing synthetic active matter systems that capture certain key features of living ones, we systematically investigate active glassy dynamics in this model system. This allowed us to explore the interplay of nature and the degree of activity, shape and topological defects in glassy slowing down. We observed non-trivial relaxation mechanisms unique to active glasses. We anticipate that our experimental strategy will help prune theoretical predictions of active glasses.

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Boaz Yuval, Ph.D., Hebrew University
6 - 7:30pm | Biolabs 1065, 16 Divinity Street, Cambridge, MA and REMOTE

Abstract: Multicellular organisms maintain intimate relationships with diverse communities of microorganisms. These interactions have been studied in depth in many insect species, revealing significant and intricate effects of the microbiome on its host. In my talk, I will focus on the effects of gut symbionts on behavior of the tephritid fruit flies. Specifically, I will describe studies on olive, Oriental, and Mediterranean fruit flies that show how the microbiome affects oviposition choices by females, and foraging decisions by adults and larvae. These studies suggest the presence of an active gut-brain axis, that is modulated by the microbiome to affect sensory and motor pathways adaptively.

Zoom Online Seminar
More information about the Extavour Lab or about the Talk

Conan Wang, University of Queensland, Institute for Molecular Bioscience
6 - 7:30pm | Pierce Hall 209, 29 Oxford Street

Abstract: Proteins are molecular machines that carry out the processes of life. Nature has evolved classes of miniature proteins that have unique complex topologies, constrained through backbone macrocyclization and cystine bonds. These miniature proteins or peptides are found across the major kingdoms of life, including bacteria, plants, and animals. Their highly cross-linked structures engender them with exceptional conformational rigidity, making them excellent scaffolds as drugs. In this talk, I will describe two major approaches used to re-engineer these natural proteins into therapeutics, the first is inspired by structural mimicry of protein surfaces and the second by evolution.

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Kaitlyn Becker, MIT
6 - 7:30pm | Pierce Hall 209, 29 Oxford Street

Abstract: The compliance of soft robots makes them particularly well suited for grasping fragile, compliant, or topologically complex objects, as well as scenarios where target objects have an uncertain size or location. I will talk about three modes in which characteristics of the contact interface between soft grippers and their target objects can be strategically tuned and motivate these with challenging scenarios of deep-sea biological sampling. First, passive digit structures and materials can be tuned to specific contact pressure and varying object sizes. For fluidic soft grippers, the target object size, operating pressure, and payload are not independent but can be tuned separately for a given task. Second, active surface structures can be used to increase dexterity of soft grippers by modulating contact friction. Control over friction and grip force or contact pressure can be independently controlled or strategically coupled. Third, the size of contact area of a grasp can be modulated or broken up into a large collection of discrete and randomly distributed contacts. Application of a stochastic collective of contacts achieved with an array of actuators made of compliant materials and structures enables a highly adaptive grasp. While soft grippers are naturally well suited for gentle grasping, adding each of the three modalities of contact tuning, passive structure, active surface elements, and spatial distribution, can provide more robust, and adept performance. Furthermore, each modality of contact tuning can be applied independently or implemented simultaneously in a hierarchical soft gripper design.

Bio: Kaitlyn Becker is an assistant professor in the Mechanical Engineering Department and recipient of the Doherty Professorship in Ocean Utilization at MIT. She completed her B.S. in Mechanical Engineering at MIT in 2009, after which she worked on subcutaneous defibrillators as a manufacturing engineer for Cameron Health Inc, and then worked on the development of various nanofabrication technologies and UV water treatment as a senior engineer for Nano Terra Inc. She completed her PhD in Professor Wood’s Microrobotics Lab in 2021 and was postdoctoral researcher in Professor Mahadevan’s Soft Math lab at Harvard University. Her primary research thrust is on gentle and adaptive soft robots for grasping and manipulation from the desktop to the deep sea and focuses on novel soft robotic platforms that add functionality through innovations at the intersection of design and fabrication. Her work has been featured on the covers of the journals Soft Robotics and Advanced Functional Materials, and in the Unseen Oceans special exhibit in the American Natural History Museum. Her robotic platforms have also been successfully tested at depths down to 3.5km on research vessels including the Nautilus (Ocean Exploration Trust), Falkor (Schmidt Ocean Institute), and the Rachel Carlson (MBARI). She is a recipient of a Microsoft graduate research scholarship and a NSF Graduate Research Fellowship. Outside of her research and teaching in Mechanical Engineering, she also teaches glassblowing in the Department of Material Science and Engineering at MIT, where she fuses art and applied engineering in her classes.

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Dr. Chuanhua Duan, Boston University
6 - 7:30pm | Pierce Hall 209, 29 Oxford Street

Abstract: Research on solid state nanopores has attracted great attention over the last two decades because of their great potentials in mimicking protein channels in cell membranes. Although significant progress has been made, past research has mainly utilized solid nanopores for translocation-based single bimolecule/particle sensing and ion/molecule transport control. What can we do with solid-state nanopores beyond these two directions? This question can be answered from two different perspectives. On one hand, single nanopores are the basic constitute of nanoporous membranes. It is therefore possible to use single nanopores to study and understand complicated transport phenomena in nanoporous membranes, paving the way for developing nanoporous membranes with better performance. On the other hand, it is worth noting that most of the past nanopore research is focused on molecule/particle translocating through the nanopore. The opposite scenario, i.e. molecules/particles blocking the nanopore, has not been extensively studied. In this talk, I will present my group’s recent efforts on exploring fundamentals and application of solid-state nanopore from these two new aspects.

First, I will present our work on exploring evaporation from single nanopores. We have developed a novel microscope-based optical measurement to measure evaporation rates down to 10 aL/s from single nanopores. I will show that the ultimate evaporation flux from ultrathin silicon nitride nanopores is not limited by liquid transport to the interface and vapor removal from the interface, but by the interfacial evaporation kinetics and shows a strong diameter dependence. I will also show that the kinetically-limited evaporation from graphene nanopores can be much larger than that from silicon nitride nanopores due to edge facilitated evaporation and minimum contaminant accumulation.

Secondly, I will introduce our latest work on studying nanoparticle-blocked nanopore systems. We have found that, when nanoparticles with sizes larger than the diameter of a nanopore are electrophoretically driven towards the nanopore, they can be either electrokinetically trapped near the nanopore or physically block the nanopore based on their surface charge polarity. These two types of nanoparticle blockage modes can respond to various electrical or mechanical stimuli and show stimuli-responsive transport. I will show how we utilize such nanoparticle-blockage-induced stimuli-responsive transport to develop new applications for nanoparticle characterization, nanopore gating as well as bio-sensing.

Bio: Dr. Chuanhua Duan received his B.S. and M.S. degrees in Engineering Thermophysics from Tsinghua University in 2002 and 2004, respectively. He obtained his Ph.D. in Mechanical Engineering from the University of California at Berkeley in 2009 under the guidance of Prof. Arun Majumdar. After staying in Berkeley for two more years as a postdoctoral researcher at the Lawrence Berkeley National Laboratory, Dr. Duan joined the Department of Mechanical Engineering at Boston University as an assistant professor in 2012. He is currently an associate professor at BU ME, leading the Nanoscale Energy-Fluids Transport Laboratory. Among his honors, Dr. Duan received the Defense Advanced Research Project Agency Young Faculty Award (YFA) in 2018, the National Science Foundation Early Faculty Career Development Award (CAREER) in 2017, and the American Chemistry Society Petroleum Research Fund Doctoral New Investigator Award in 2013. His research focuses on the study of micro- and nanofluidic transport phenomena and the development of new fluidic devices/approaches for applications in healthcare, energy systems, and thermal management.

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Jiliang Hu, MIT
6 - 7:30pm | Pierce Hall 209, 29 Oxford Street

Abstract: From tropical forests to gut microbiomes, ecological communities host striking numbers of coexisting species. Beyond high biodiversity, communities exhibit a range of complex dynamics that are difficult to explain under a unified framework. Using bacterial microcosms, we perform the first direct test of theory predicting that simple coarse-grained features dictate emergent behaviors of communities. As either the number of species or the strength of interactions increases, we show that microbial ecosystems transition between three distinct dynamical phases, from a stable equilibrium where all species coexist, to partial coexistence, to emergence of persistent fluctuations in species abundances, in the order predicted by theory. Under fixed conditions, high biodiversity and fluctuations reinforce each other. Our results demonstrate predictable emergent patterns of diversity and dynamics in ecological communities.

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Jacques Fattaccioli, Paris Sciences et Lettres University
6 - 7:30pm | Pierce Hall 209, 29 Oxford Street

Abstract: Response to pathogens and homeostasis is orchestrated by the complex interactions and activities of the large number of diverse cell types involved in the immune response. The innate immune response occurs soon after pathogen exposure and is carried out by phagocytic cells such as neutrophils or macrophages. The subsequent adaptive immune response involves antigen-presenting cells such as macrophages or dendritic cells; and antigen stimulation-dependent cell types such T cell subsets and B cells. As an alternative to polymers or hydrogels that are commonly used when model substrates are needed for uptake or migration studies from the point of view of mechanobiology, we developed ligand-functionalized lipid droplets to address these questions. In this talk, I will present how to make and characterize functional lipid droplets, how they can be used in the context of phagocytosis, cell migration and antigen extraction, and I will present the most recent ongoing results.

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Derin Sevenler, Massachusetts General Hospital, Department of Surgery
6 - 7:30pm | Pierce Hall 209, 29 Oxford Street

Abstract: Intracellular delivery of biomolecules or nanomaterials is a critical step in many bioengineering processes across applications in science, technology, and medicine. In particular, emerging cell and gene therapies can require the genetic manipulation of extremely large numbers of cells (hundreds of trillions of cells, in some cases), and scale-up of conventional methods for delivering genetic material or gene editing complexes into cells (viral vectors, cationic polymers, electroporation) have faced issues with efficiency and/or cytotoxicity. In this talk, we will describe recent work developing a high-throughput method of intracellular delivery which used viscoelastic flow forces within a microfluidic chip to stretch and temporarily permeabilize the plasma membrane of cells, thereby enabling rapid and efficient delivery of large biomolecules including proteins, nucleic acids, and CRISPR-Cas ribonucleoprotein complexes to the cytosol. This method was notably fast, processing over 250 million cells per minute in a single microchannel (100x-1,000x faster than comparable methods) with up to 95% delivery efficiency. Altogether, viscoelastic mechanoporation seems to be a feasible method for high-throughput intracellular delivery for a range of different cell types that includes primary T and NK cells.

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Sahand Hormoz (Harvard Medical School, Dana-Farber Cancer Institute)
1:00pm EST | 20 Garden Street, Room G10, Cambridge, MA and VIRTUAL

Abstract:
Two recent projects from my lab that involve lineage trees of cells (the branching diagram that represents the ancestry and division history of individual cells). In the first project, we reconstructed the lineage trees of individual cancer cells from the patterns of randomly occurring mutations in these cells. We then inferred the age at which the cancer mutation first occurred and the rate of expansion of the population of cancer cells within each patient. To our surprise, we discovered that the cancer mutation occurs decades before diagnosis. For the second project, we developed microfluidic 'mother machines' that allow us to observe mammalian cells dividing across tens of generations. Using our observations, we calculated the correlation between the duration of cell cycle phases in pairs of cells, as a function of their lineage distance. These correlations revealed many surprises that we are trying to understand using hidden Markov models on trees. For both projects, I will discuss the mathematical challenges that we have faced and open problems related to inference from lineage trees.

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Neel Joshi, Northeastern University
6 - 7:30pm | Pierce Hall 209, 29 Oxford Street

Abstract: The intersection between synthetic biology and materials science is an underexplored area with great potential to positively affect our daily lives, with applications ranging from manufacturing to medicine. My group is interested in harnessing the biosynthetic potential of microbes, not only as factories for the production of raw materials, but as fabrication plants that can orchestrate the assembly of complex functional materials. We call this approach “biologically fabricated materials”, a process whose goal is to genetically program microbes to assemble materials from biomolecular building blocks without the need for time consuming and expensive purification protocols or specialized equipment. Accordingly, we have developed Biofilm Integrated Nanofiber Display (BIND), which relies on the biologically directed assembly of biofilm matrix proteins of the curli system in E. coli. We demonstrate that bacterial cells can be programmed to synthesize a range of functional materials with straightforward genetic engineering techniques. The resulting materials are highly customizable and easy to fabricate, and we are investigating their use for practical uses ranging from bioremediation and biodegradable bioplastics to engineered therapeutic probiotics.

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Since its inception in 2004, the Microbial Science Initiative has sponsored and hosted an annual symposium for those in the Harvard and greater Boston communities. The spring event showcases magnificent research across a breadth of microbe-centric topics spanning environmental and biomedical sciences. The MSI Symposium is $20 for the public or $5 for students & postdocs. Welcome to the microbial world! Mid-morning and mid-afternoon breaks with refreshments will be provided, and there will be a 75 minute break for lunch mid-day.

Ticket registration required, $20 or $5 for Students & Postdocs, and is open to the public

Mehran Kardar, MIT
1:00pm EST | 20 Garden Street, Room G10, Cambridge, MA and VIRTUAL

Abstract:
When competing species grow into new territory, the population is dominated by descendants of successful ancestors at the expansion front. Successful ancestry depends on the reproductive advantage (fitness), as well as ability and opportunity to colonize new domains. (1) Based on symmetry considerations, we present a model that integrates both elements by coupling the classic description of one-dimensional competition (Fisher equation) to the minimal model of front shape (KPZ equation). Macroscopic manifestations of these equations on growth morphology are explored, providing a framework to study spatial competition, fixation, and differentiation, In particular, we find that ability to expand in space may overcome reproductive advantage in colonizing new territory. (2) Variations of fitness, as well as fixation time upon differentiation, are shown to belong to distinct universality classes depending on limits to gain of fitness.

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Meni Wanunu, Northeastern University
6 - 7:30pm | Pierce Hall 209, 29 Oxford Street

Abstract: Nanopores have gained a lot of attention recently for their ability to sequence nucleic acids. Recently, however, a surge of interest in the use of nanopores for analyzing proteins has been witnessed. I will talk about two approaches that our lab has taken for characterizing proteins. First, I will describe a method for full-length single-file protein translocation and discrimination using a biological pore. Second, I will describe a method for probing conformational states of a protein and its electrical unfolding. With these tools in mind, it is exciting to think about possibilities in using nanopores for studying protein variants, post-translational modifications, and interactions of proteins with small molecule drugs.

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Sulin Zhang, Pennsylvania State University, Department of Engineering Science and Mechanics
6 - 7:30pm | Pierce Hall 209, 29 Oxford Street

Abstract: In various electro/biochemical processes, mechanical stress generation and transmission pathways exist in parallel and interact in concert with chemical reaction and mass diffusion pathways. How might the mechanics-electrochemistry reciprocity be harnessed for energy storage and energy harvesting, and unharnessed in battery degradation? Similarly, how might the mechanics-biochemistry crosstalk be regulated in development and repair, and dysregulated in disease and injury? These questions have been stimulating new understanding at the interfaces between mechanics and other disciplines including materials, chemistry, biology, and medicine. In this talk, I will show a set of exciting phenomena in rechargeable batteries and living organisms to highlight the crosstalks. Emphasis will be placed on the fundamental mechanics linking to bio/electrochemistry, which underlies materials design, energy storage and harvesting, disease control, and nanomedicine innovation.

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Hemanoel Passareli, Visiting Scholar to Hanage Lab
12-1pm EST | 24 Oxford Street, Room 375 - Classroom 375, Cambridge, MA

Pangenome analysis has become a vital tool to understand bacterial diversity. In this Chalk Talk, we will discuss how we can interpret a pangenome from an ecological perspective to explore the evolution of microorganisms.

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Shane McInally, Brandeis University
1:00pm EST | 20 Garden Street, Room G10, Cambridge, MA and VIRTUAL

Abstract:
The sizes of many subcellular structures are coordinated with cell size to ensure that these structures meet the functional demands of the cell. In eukaryotic cells, these subcellular structures are often membrane-bound organelles, whose volume is the physiologically important aspect of their size. Scaling organelle volume with cell volume can be explained by limiting pool mechanisms, wherein a constant concentration of molecular building blocks enables subcellular structures to increase in size proportionally with cell volume. However, limiting pool mechanisms cannot explain how the size of linear subcellular structures, such as cytoskeletal filaments, scale with the linear dimensions of the cell. Recently, we discovered that the length of actin cables in budding yeast (used for intracellular transport) precisely matches the length of the cell in which they are assembled. Using mathematical modeling and quantitative imaging of actin cable growth dynamics, we found that as the actin cables grow longer, their extension rates slow (or decelerate), enabling cable length to match cell length. Importantly, this deceleration behavior is cell-length dependent, allowing cables in longer cells to grow faster, and therefore reach a longer length before growth stops at the back of the cell. In addition, we have unexpectedly found that cable length is specified by cable shape. Our imaging analysis reveals that cables progressively taper as they extend from the bud neck into the mother cell, and further, this tapering scales with cell length. Integrating observations made for tapering actin networks in other systems, we have developed a novel mathematical model for cable length control that recapitulates our quantitative experimental observations. Unlike other models of size control, this model does not require length-dependent rates of assembly or disassembly. Instead, feedback control over the length of the cable is an emergent property due to the cross-linked and bundled architecture of the actin filaments within the cable. This work reveals a new strategy that cells use to coordinate the size of their internal parts with their linear dimensions. Similar design principles may control the size and scaling of other subcellular structures whose physiologically important dimension is their length.

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12-1pm EST | 24 Oxford Street, classroom #375, Cambridge, MA

Is there an item that's been languishing on your to-do list? Do you have an assignment to do and just can't harness the motivation to take the first step? Register and join the Microbial Sciences Initiative for a Micro-Goal Lunch Hour! Open to all Harvard students and postdocs, especially those with an interest in the microbial world.

Neel Joshi, Northeastern University
6 - 7:30pm | Pierce Hall 209, 29 Oxford Street

Abstract: TBD

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Mark Bowick, Kavli Institute for Theoretical Physics, UCSB
1:00pm EST | 20 Garden Street, Room G10, Cambridge, MA and VIRTUAL

Abstract:
Motivated by the existence of membrane-less compartments in the chemically active environment of living cells, I will discuss the dynamics of droplets in the presence of active chemical reactions. Therefore, I will first introduce the underlying interplay between phase separation and active reactions, which can alter the droplet dynamics compared to equilibrium systems. A key feature of such systems is the emergence of concentration gradients even at steady states. In the second part of this talk, I will discuss how these gradients can trigger instabilities in the core of chemically active droplets, giving rise to a new non-equilibrium steady state of liquid spherical shells. Finally, I will present experimental and theoretical results discussing the existence and energetic cost of this non-equilibrium steady state in a coacervate system.

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Brandy Toner
4 - 5pm EST | William James Hall, Room 105, 33 Kirkland Street, Cambridge, MA

TBD

Bryan Spring, Northeastern University, Dept. of Physics
6 - 7:30pm | Pierce Hall 209, 29 Oxford Street

Abstract: This talk will introduce concepts of targeted photodynamic therapy with microscale fidelity using clinical antibody–photosensitizer (benzoporphyrin derivative monoacid A, verteporfin) conjugates. These initially quenched (“off”) photoimmunoconjugates target tumor cell-surface biomarkers and become activated upon cell-internalization ("on"). Present efforts to further develop these concepts for precision treatment of heterogenous human ovarian cancer will be discussed.

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Invited Speakers:
Corey O'Hern, Yale University
Leslie Shor, University of Connecticut
Ian Wong, Brown University
Evan Wujcik, University of Maine

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Jonathan Bauermann, Max Planck Institute for the Physics of Complex Systems
1:00pm EST | VIRTUAL

Abstract:
Morphogenesis, the process through which genes generate form, establishes tissue scale order as a template for constructing the complex shapes of the body plan. The extensive growth required to build these ordered substrates is fueled by cell proliferation, which, naively, should disrupt order. Understanding how active morphogenetic mechanisms couple cellular and mechanical processes to generate order remains an outstanding question in animal development. I will review the statistical mechanics of orientational order and discuss the observation of a fourfold orientationally ordered phase (tetratic) in the model organism Parhyale hawaiensis. I will also discuss theoretical mechanisms for the formation of orientational order that require both motility and cell division, with support from self-propelled vertex models of tissue. The aim is to uncover a robust, active mechanism for generating global orientational order in a non-equilibrium system that then sets the stage for the development of shape and form.

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Carla Fernandez-Rico, ETH Zurich
6 - 7:30pm | Pierce Hall 209, 29 Oxford Street

Abstract: TBD

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Alexis Jaramillo Cartagema
12-1pm EST | 24 Oxford Street Room 375, Classroom 375, Cambridge, MA

12-1pm EST | 24 Oxford Street, classroom #375, Cambridge, MA

Is there an item that's been languishing on your to-do list? Do you have an assignment to do and just can't harness the motivation to take the first step? Register and join the Microbial Sciences Initiative for a Micro-Goal Lunch Hour! Open to all Harvard students and postdocs, especially those with an interest in the microbial world.

Xin Zhao, Hong Kong Polytechnic University
6 - 7:30pm | Pierce Hall 209, 29 Oxford Street

Abstract: Photocrosslinkable polymers are polymers that can be solidified from liquid upon light exposure. They have been employed to fabricate tissue engineered constructs due to the mild conditions for crosslinking, highly tunable mechanical and structural modifiability, printability, biodegradability and biocompatibility. These biomaterials can maintain their structural integrity after biofabrication and provide topological, biochemical, and physical cues to guide cellular behaviors by creating a biomimetic microenvironment.

The emphasis of this talk is placed on how photocrosslinkable polymers can be used to achieve tissue regeneration, for example, their fabrication into various scaffolds (electrospun fibers, microspheres, and 3D printed scaffolds) to reconstruct bones. Specifically, assisted by microfluidics, we have developed photocrosslinkable methacrylated gelatin (GelMA) based microspheres encapsulating human mesenchymal stem cells (MSCs) for bone repair. Due to the mild crosslinking conditions, we found that the GelMA microspheres can provide a favourable micro-environment for MSC survival, spreading, migration, proliferation and osteogenesis. In another study, we prepared a periosteum mimicking bone aid (PMBA) by electrospinning photocrosslinkable GelMA with L-arginine-based unsaturated poly(ester amide) (Arg-UPEA), and methacrylated hydroxyapatite nanoparticles (nHAMA). Upon light exposure, the resultant hydrogel fibrous scaffolds can solidify within seconds. Via controlling the crosslinking density, we can control the scaffolds’ mechanical and degradation property. The optimal scaffold was found to provide long term structural and functional support and mediation of physiological activity. With the aid of 3D printing, we developed 3D bone scaffolds made of photocrosslinkable nanocomposite ink consisting of tri-block poly (lactide-co-propylene glycol-co-lactide) dimethacrylate (PmLnDMA, m and n respectively represent the unit length of propylene glycol and lactide) and nHAMA. It is discovered that nHAMA can rapidly interact with PmLnDMA upon light exposure within 140 seconds and form an inorganic-organic co-crosslinked nanocomposite network. This bone ink was found to provide good mechanical support and bioactivity (allow for encapsulation and long-term release of growth factors) for bone regeneration.

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Beau Schaeffer
12-1pm EST | 24 Oxford Street Room 375, Classroom 375, Cambridge, MA

Yu Qiu, Department of Earth, Atmospheric, and Planetary Sciences, MIT
6 - 7:30pm | Pierce Hall 209, 29 Oxford Street

Abstract: The displacement of one fluid by another immiscible fluid in confined geometries occurs in many natural and industrial settings from geological CO₂ sequestration to microfluidics. The fluid-solid interactions are key to understanding the combined effects of wetting, capillarity and viscous forces, which, in turn, control the fluid-fluid displacement patterns. One fundamental aspect of fluid-fluid displacement in confined geometries is the wetting transition: the displacement rate above which films of the defending fluid are deposited on the confining surfaces. These films may later dewet, giving rise to complex “residual fluid” patterns. Earlier experiments in our group have shown that the wetting transition results in interface pinch-off that generates disconnected bubbles and drops even in uniform capillaries without external crossflow (Zhao et al., PRL 2018). Here I will present a phase-field model to simulate the two-phase flow with moving contact lines and investigate the interface dynamics in a smooth confinement over a wide range of wettability conditions and viscosity contrast. I will show that the pinch-off of a bubble only occurs when the invading fluid is less viscous. Since real surfaces are rough, we investigate the role of wall roughness on two-phase displacements in confined geometries by means of experiments on a microfluidic fracture with precisely-controlled structured surface. We show that the roughness induces two types of liquid films entrained on the solid surfaces: the classical Bretherton “thick film”, and a new type of “thin film” that is confined within the roughness. Each type is characterized by distinct stability criteria and dewetting dynamics. Our work shed light on the microscale physics and macroscopic displacement patterns in confined geometries that may control long-term biogeochemical reactions.

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Jörn Dunkel, MIT
1:00pm EST | VIRTUAL

Abstract:
Over the last two decades, major progress has been made in understanding the self-organization principles of active matter. A wide variety of experimental model systems, from self-driven colloids to active elastic materials, has been established, and an extensive theoretical framework has been developed to explain many of the experimentally observed non-equilibrium pattern formation phenomena. Two key challenges for the coming years will be to translate this foundational knowledge into functional active materials, and to identify quantitative mathematical models that can inform and guide the design and production of such materials. Here, I will describe joint efforts with our experimental collaborators to realize self-growing bacterial materials [1], and to implement computational model inference schemes for active and living systems dynamics [2,3].

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Andee Wallace
4 - 5pm EST | William James Hall, Room 105, 33 Kirkland Street, Cambridge, MA

The World Health Organization estimates that agricultural productivity will need to increase by 70% by 2050 to meet the food needs of a global population of 10B people. Facing a changing climate and increasing disease pressure, growers today spend nearly $80B on six billion pounds of pesticides each year, and yet still experience yield losses of 20-40% due to pests and disease. Broad-acting, chemically derived pesticides - currently the industry standard - are losing both efficacy and public support as resistance spreads and their negative environmental impacts become clear. At Robigo, we believe in building on nature’s foundation to engineer solutions that work for growers, consumers, and the environment. We have developed a scalable plug and play platform technology that leverages synthetic biology, CRISPR, and data science to engineer microbes that are naturally found out in the fields to protect crops, fight disease, and improve overall yields. Initially targeting three diseases that affect citrus, apples, and tomatoes, our microbes outperform commercial chemical pesticides and reduce disease by over 90% while increasing plant biomass by over 15%. Robigo is unlocking the potential of engineered microbes in agriculture to fundamentally change how the world grows food and create a more sustainable future for agriculture. Founded by MIT synthetic biologists, Robigo is a VC-backed, Seed-stage biotech startup based in Cambridge, MA.

Qiong Zhang, Department of Mechanical Engineering, MIT
6 - 7:30pm | Pierce Hall 301, 29 Oxford Street

Abstract: Sediment transport caused by particles rolling, sliding, and hopping on a river bed is called bedload transport. Semi-empirical formulas to predict bedload sediment flux from the driving factors, known as the transport relation, can be highly inaccurate. Simulations where the sediment particles are fully resolved are carried out to find if the predictions can be improved by considering more particle parameters. After being validated against flume experiments, the numerical scheme is used to simulate bedload transport under many conditions, and its results show that at a fixed relative hydrodynamic driving force, varying river slope (on gentle slopes), fluid depth, mean particle size, particle surface sliding friction coefficient, and grain-grain damping coefficient cause almost no variation of the transport rate. The simulations also shed light on the microscopic mechanisms such as how the fluid torque on particles helps initiate rolling and subsequent grain transport. We further use the numerical scheme to guide development of an alternative framework that can predict the flow profiles for the fast transport as well as the gradual transport beneath the bed surface without resolving the individual particles, which is a more tractable way to model large-scale bedload sediment transport problems.

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Nazim Bouatta, Harvard Medical School
3:30-5:00pm EST | 20 Garden Street Room G10, Cambridge, MA and VIRTUAL

Thursday, February 9, Lecture 1:
A brief intro to protein biology. AlphaFold2 impacts on experimental structural biology. Co-evolutionary approaches. Space of ‘algorithms’ for protein structure prediction. Proteins as images (CNNs for protein structure prediction). End-to-end differentiable approaches. Attention and long-range dependencies. AlphaFold2 in a nutshell.

Thursday, February 16, Lecture 2:
AlphaFold2 architecture. Turning the co-evolutionary principle into an algorithm: EvoFormer. Structure module and symmetry principles (equivariance and invariance). OpenFold: retraining AlphaFol2 and insights into its learning mechanisms and capacity for generalization. Applications of variants of AlphaFold2 beyond protein structure prediction: AlphaFold Multimer for protein complexes, RNA structure prediction.

Thursday, March 9, Lecture 3:
Limitations of AlphaFold2 and evolutionary ML pipelines. Current single sequence models. Protein language models (LM): single sequence + LM embeddings. Combining LM models with Frenet-Serret construction for protein structure prediction. Applying AlphaFold2 and OpenFold for language models.

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12-1pm EST | 24 Oxford Street, classroom #375, Cambridge, MA

Is there an item that's been languishing on your to-do list? Do you have an assignment to do and just can't harness the motivation to take the first step? Register and join the Microbial Sciences Initiative for a Micro-Goal Lunch Hour! Open to all Harvard students and postdocs, especially those with an interest in the microbial world.

Amin Doostmohammadi, Niels Bohr Institute, University of Copenhagen
1:00pm – 2:30pm (EST) | VIRTUAL or 20 Garden St, seminar room G-10

Abstract: I will focus on the interaction between different active matter systems. In particular, I will describe recent experimental and modeling results that reveal how interaction forces between adhesive cells generate activity in the cell layer and lead to a potentially new mode of phase segregation. I will then discuss mechanics of how cells use finger-like protrusions, known as filopodia, to interact with their surrounding medium. First, I will present experimental and theoretical results of active mirror-symmetry breaking in subcellular skeleton of filopodia that allows for rotation, helicity, and buckling of these cellular fingers in a wide variety of cells ranging from epithelial, mesenchymal, cancerous and stem cells. I will then describe in-vivo experiments together with theoretical modeling showing how during embryo development specialized active cells probe and modify other cell layers and integrate within an active epithelium.

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Douglas H. Bartlett, PhD, UC San Diego
4 - 5pm EST | William James Hall, Room 105, 33 Kirkland Street, Cambridge, MA

A major portion of microbial life on Earth is present in low-temperature/deep-sea environments, and yet much remains to be learned of their diversity, adaptations and activities. Studies of these microbes in situ and ex situ is providing fundamental and biotechnological insights, and will be critical to many possible ocean-based decarbonization processes. In this presentation I will first discuss what we have learned about proteomes and cell envelopes of piezophilic (high pressure-adapted) isolates. Then I will transition to investigations of deep-sea microbial activities using pressure-retaining seawater sampling to collect microbes with minimal temperature/pressure alteration, followed by the sorting and identification of cells active under in situ deep-sea conditions. One aspect of this work is the indication that certain microbial groups (e.g., members of the Thaumarchaeota) are highly sensitive to decompression/incubation effects, reducing their perceived significance when collected using standard methods.
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Sascha Feldmann, Rowland Institute, Harvard University
6 - 7:30pm | Pierce Hall 301, 29 Oxford Street

Abstract: Halide perovskites are an emerging class of low-cost solution-processable semiconductors that have recently demonstrated exceptional performance when employed in optoelectronic devices like solar cells or light-emitting diodes (LEDs) for displays. Yet, we don't understand how these materials can work so very efficiently, given the presence of structural disorder and electronic traps, compared to highly crystalline silicon currently produced at scale under energy-extensive conditions. I will discuss our latest mechanistic insights from spectroscopy on both 3D (bulk) halide-perovskite thin-films as well as quantum-confined and doped 0D colloidal nanocrystals, enabling highly efficient flexible solar cells and ultra-bright displays. We find that energetic disorder and local structural symmetry breaking are key for explaining our observations.

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Dr. Jackie Y. Ying, Department of Biomedical Engineering,
A*STAR Senior Fellow and Director of NanoBio Lab, Institute of Materials Research and Engineering and A*STAR Infectious Diseases Labs
4 - 5:30pm | Pierce Hall 209, 29 Oxford Street

Abstract: Nanostructured materials can be designed with sophisticated features to fulfill the complex requirements of advanced material applications. Our laboratory has developed organic and inorganic nanoparticles and nanocomposites for advanced drug delivery, antimicrobial, stem cell culture, and tissue engineering applications. In addition, we have nanofabricated microfluidic systems for drug screening, in vitro toxicology, and diagnostic applications. The nanosystems allow for the rapid and automated processing of drug candidates and clinical samples in tiny volumes, greatly facilitating drug testing, genotyping assays, infectious disease detection, point-of-care monitoring, as well as cancer diagnosis and prognosis.

We have also synthesized metallic, metal oxide, and semiconducting nanoclusters, nanocrystals and nanosheets of controlled dimensions and morphology. The nano-sized building blocks are used to create multifunctional systems with excellent dispersion and unique properties. Nanoporous materials of a variety of metal oxide and organic backbone have also been created with high surface areas and well-defined porosities. These nanostructured materials are successfully tailored towards energy and sustainability applications.

Speaker Bio:
Jackie Y. Ying received her Ph.D. from Princeton University. She was Professor of Chemical Engineering at MIT (1992-2005), and Founding Executive Director of Institute of Bioengineering and Nanotechnology, Singapore (2003-2018). She is currently A*STAR Senior Fellow and Director of NanoBio Lab, Institute of Materials Research and Engineering and A*STAR Infectious Diseases Labs.

For her research on nanomaterials and bioengineering, Prof. Ying has been recognized with the American Ceramic Society Purdy Award, David and Lucile Packard Fellowship, ONR Young Investigator Award, NSF Young Investigator Award, Camille Dreyfus Teacher-Scholar Award, ACS Faculty Fellowship Award in Solid-State Chemistry, Technology Review's Inaugural TR100 Young Innovator Award, AIChE Colburn Award, International Union of Biochemistry and Molecular Biology Jubilee Medal, Mustafa Prize "Top Scientific Achievement Award," Turkish Academy of Sciences Academy Prize in Science and Engineering Sciences, and Journal of Drug Targeting's Lifetime Achievement Award.

Prof. Ying is an elected Member of the German National Academy of Sciences-Leopoldina, and U.S. National Academy of Engineering. She is a Fellow of MRS, RSC, AIMBE, AAAS, and U.S. National Academy of Inventors. She was the Founding Editor-in-Chief of Nano Today.

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Kimia Witte, Department of Biomedical Engineering, University of Strathclyde
6 - 7:30pm | Pierce Hall 301, 29 Oxford Street

Abstract: The underlying molecular mechanism of autism, a known example of neurodiversity, remains largely unknown, with cognitive differences providing the main means of diagnosis. I would like to make an argument for the connection between neurodiversity and the emergence of aberrant viscoelastic properties of the extracellular matrix in the central nervous system. A mechanical interplay like this can enable us with a diagnosis based on a measurable physiological feature: the mechanical fingerprint of our tissues.

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Presenters:
Pia Leon (@pialeonkjolle) Chef and Co-owner of Kjolle, Central (Lima, Perú), MIL (Cusco, Perú), World's Best Female Chef of 2021

Malena Martinez (@malenamater) Co-Director of Mater Iniciativa, Central

Roland Hatzenpichler, PhD, Montana State University
4 - 5pm EST | William James Hall, Room 105, 33 Kirkland Street, Cambridge, MA

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Max Prigozhin, Harvard University
1pm (EST) | CMSA, 20 Garden St, Seminar room G-10

Abstract: My lab is developing biophysical methods to achieve multicolor and dynamic biological imaging at the molecular scale. Our approach to capturing the dynamics of cellular processes involves cryo-vitrifying samples after known time delays following stimulation using custom cryo- plunging and high-pressure freezing instruments. To achieve multicolor electron imaging, we are exploring the property of cathodoluminescence—optical emission induced by the electron beam. We are developing nanoprobes ("cathodophores") that will be used as luminescent protein tags in electron microscopy. We are applying these new methods to study G-protein - coupled receptor signaling and to visualize the formation of biomolecular condensates.

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M. Cristina Marchetti, Distinguished Professor of Physics, University of California Santa Barbara
4:30pm (EST) | Jefferson 250 (17 Oxford Street)

Abstract: Over the last decade there has been growing evidence demonstrating that dense biological tissue can spontaneously undergo transitions between a solid-like (jammed) state and a fluid-like (unjammed) state. The rheological state of the tissue in turn influences the transmission of mechanical deformations, which plays a central role in driving developmental processes, such as wound healing and morphogenesis, and tumor progression. Using computational models and analytical approaches, we have investigated the linear and nonlinear constitutive equations of confluent tissue, with no gaps between cells, under shear deformations. We find that an initially undeformed fluid-like tissue acquires finite rigidity above a critical applied strain and that solid-like tissue quickly exhibit nonlinear stress-strain response. We formulate a continuum model that couples cell shape to flow and captures both the tissue solid-liquid transition and its rich linear and nonlinear rheology.

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M. Cristina Marchetti, Distinguished Professor of Physics, University of California Santa Barbara
4:30pm (EST) | Jefferson 250 (17 Oxford Street)

Abstract: There are many situations where active fluids coexist with passive ones. In bacterial swarms internal boundaries form separating cells of different type or separating live and dead cells. In cell biology the evidence for the formation of membraneless organelles has fueled interest in the role of active processes in liquid-liquid phase separation. Inspired by recent experiments that combine a microtubule-based active fluid with an immiscible binary polymer mixture, we have used numerical and analytical methods to explore how active stresses and associated flows modify the properties of the soft interfaces in a phase separating mixture. Experiments and theory have revealed a wealth of intriguing phenomena, including giant interfacial fluctuation, traveling interfacial waves, activity suppressed phase separation, and activity controlled wetting transitions.

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Presenter: Tracy Chang (@gopagu) Pagu Restaurant (Cambridge, MA)

M. Cristina Marchetti, Distinguished Professor of Physics, University of California Santa Barbara
4:30pm (EST) | Jefferson 250 (17 Oxford Street)

Abstract: Birds flock, bees swarm and fish school. These are just some of the remarkable examples of collective behavior found in nature. Physicists have been able to capture some of this behavior by modeling organisms as "flying spins'' that align with their neighbors according to simple but noisy rules. Successes like these have spawned a field devoted to the physics of active matter - matter made not of atom and molecules but of entities that consume energy to generate their own motion and forces. Through interactions, collectives of such active particles organize in emergent structures on scales much larger than that of the individuals. There are many examples of this spontaneous organization in both the living and non-living worlds: motor proteins orchestrate the organization of genetic material inside cells, swarming bacteria self-organize into biofilms, epithelial cells migrate collectively to fill in wounds, engineered microswimmers self-assemble to form smart materials. In this lecture I will introduce the field of active matter and highlight ongoing efforts by physicists, biologists, engineers and mathematicians to model the complex behavior of these systems, with the goal of identifying universal principles.

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Farzan Vafa, Harvard University
6 - 7:30pm | Pierce Hall 301, 29 Oxford Street

Abstract: We investigate the ground-state configurations of two-dimensional liquid crystals with p-fold rotational symmetry (p-atics) on cones. The cone apex develops an effective topological charge, which in analogy to electrostatics, leads to defect absorption and emission at the cone apex as the deficit angle of the cone is varied. We find three types of ground-state configurations as a function of cone angle, which is determined by charged defects screening the effective apex charge: (i) for sharp cones, all of the +1/p defects are absorbed by the apex; (ii) at intermediate cone angles, some of the +1/p defects are absorbed by the apex and the rest lie equally spaced along a concentric ring on the flank; and (iii) for nearly flat cones, all of the +1/p defects lie equally spaced along a concentric ring on the flank. We check these results with numerical simulations for a set of commensurate cone angles and find excellent agreement.

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Minwoo Bae
12 - 1pm, 24 Oxford Street, Room 375, Cambridge, MA

Is there an item that's been languishing on your to-do list? Do you have an assignment to do and just can't harness the motivation to take the first step? Join the Microbial Sciences Initiative for a Micro-Goal Lunch Hour! Come with a task that is reachable in about 45 minutes - like answering an email or two, writing a paragraph, reading a chapter, or organizing a dataset. It doesn't have to be Microbiology-related, but if it is, we can help!
Register for the Micro-Goal Hour

Thomas Videbaek, Brandeis University
6 - 7:30pm | Pierce Hall 301, 29 Oxford Street

Abstract: Biological systems can create complex self-limited structures, such as viral capsids and microtubules, by controlling the valence and binding angles of biomolecular interactions. Inspired by this strategy, we create DNA origami subunits with specific interactions and prescribed binding angles that assemble into tubules whose self-limited width is much larger than the subunit size. Although we target a single tubule geometry, we find that thermal fluctuations can produce a variety of assemblies close to the target structure. This challenge is compounded by the fact that specific, valence-limited interactions localize subunit binding and limit their mobility within an assembly. Therefore, the tubule structures are unable to relax to equilibrium even as they continue to grow. To circumvent this challenge, we consider two routes for reducing polymorphism in the final assemblies: (i) increasing the assembly complexity to remove states close to the target and (ii) designing soft directions in the assembly that allow the tubules to anneal towards their equilibrium structure. I will show some recent experimental results highlighting the potential for both of these strategies. These results show how including degrees of freedom for assemblies to avoid or anneal out of kinetics traps can help reduce polymorphism as we strive to make more complex structures.

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Presenter:
Eduard Xatruch (@disfrutarbcn) Disfrutar and Compartir Barcelona

Minwoo Bae
12 - 1pm, 24 Oxford Street, Room 375, Cambridge, MA

Karla Ðurđić, Harvard University
6 - 7:30pm | Pierce Hall 301, 29 Oxford Street

Abstract: Enzymes are highly specific catalysts delivering improved drugs and greener industrial processes. Naturally occurring enzymes must typically be optimized which is often accomplished through directed evolution based on error prone PCR; however, this method limits exploration of fitness landscape to only evolutionary favored amino acid substitutions and results in high number of silent mutations. We develop a new library preparation method based on overlapping oligo pools and gene recombination to enable introduction of all possible substitutions at each position with highly controllable mutation rates. While conventional highest throughput methods for screening of enzyme libraries are limited by throughput of microfluidic devices and E. coli transformation efficiency to 107-8 variants, we leverage in vitro transcription and translation in a combination with multiple consecutive microfluidics-based sorting to screen libraries with more than 1012 variants. We combine new library preparation and screening methods to convert lipase into a protease in a single mutagenesis step.

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Presenter:
Sean Sherman (@the_sioux_chef), Chef, Founder of The Sioux Chef, Co-Founder of NĀTIFS (North American Traditional Indigenous Food Systems), Co-Owner of Owamni by The Sioux Chef

Matthew B. Sullivan, Ohio State University
4 - 5pm EST | William James Hall, Room 105, 33 Kirkland Street, Cambridge, MA

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Presenter:
Bryan Furman (@bs_pitmaster), Pitmaster, Bryan Furman BBQ, B's Cracklin Barbecue, Chef in Residence at Stone Barns Center for Food & Agriculture

Andrew Van Camp
12 - 1pm, 24 Oxford Street, Room 375, Cambridge, MA

Avinoam Rabinovich, School of Mechanical Engineering, Tel Aviv University
6 - 7:30pm | Pierce Hall 301, 29 Oxford Street

Abstract: Modeling multiphase flow in subsurface formations such as aquifers and hydrocarbon reservoirs is a challenging task with many open questions. An important tool for investigating these flows on the laboratory scale are coreflooding exeriments conducted on rock samples (cores) extracted from reservoirs. Coreflooding experiments with computed tomography (CT) imaging are becoming common practice. They allow to investigate the sub-core scale properties such as relative permeability and capillary pressure, and to construct multiphase flow models that not only capture the core average flow, but also the flow on the sub-core (millimeter) scale. These core flow models are important for a number of reasons. First, they allow to evaluate the applicability of mathematical models and numerical simulators. Second, coreflooding models can be applied towards forecasting, therefore replacing experiments. Finally, models can be used for relating between sub-core scale properties and core effective properties, which can provide insight on upscaling and used in developing upscaling methods for larger scales. In this presentation, we will discuss results of recent work on modelling both drainage and imbibition coreflooding experiments and methods for estimating properties on both core and sub-core scales. Experimental data of three-dimensional saturation distribution, capillary pressure measurements and core pressure drop will be presented. The core properties will be estimated using various different models and simulation results will be compared to the data.

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Presenter:
Kate Strangfeld (@kate_cooks, @bitescizededucation), Founder of Bite Scized Education, Former Middle School Science and Chemistry Teacher, Washington International School
*This is a special session for teachers, educators, or anyone who is interested in using food to teach science

Jeffrey Cameron, PhD, University of Colorado
4 - 5pm EST | Biolabs Lecture Hall, Room 1080, 16 Divinity Avenue, Cambridge, MA

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Nikhil Gupta, Mechanical and Aerospace Engineering Department, New York University
6 - 7:30pm | Pierce Hall 301, 29 Oxford Street

Abstract: The viscoelastic nature of soft materials, such as polymers and biomaterials, is a significant challenge in their mechanical characterization due to the strong dependence of their properties on strain rate. Young's modulus is a well understood elastic constant for metals but less so for many soft materials. Especially, the long chain molecules may deform by triggering mechanisms such as chain bending, sliding, and rotation rather than loading of primary bonds at small strains. This talk will discuss the applicability of the existing time and frequency domain characterization methods to soft materials with the aim of developing a correspondence between the elastic and viscoelastic properties. Many assumptions such as small deformation, constant Poisson's ratio and large aspect ratio of the specimens, inherent to the conventional test method, are violated in soft materials and need to be compensated for. The effect of these parameters is examined as well as a transform is developed to convert the frequency domain measurements to time domain to account for the strain rate sensitivity.

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Dr. Jacinta Conrad, Associate Professor, University of Houston
Abstract: The dispersity, or breadth in the molecular weight distribution, is an inherent feature of synthetic polymer systems. Typically treated as an unfortunate consequence of polymer synthesis, here I will discuss how polymer dispersity can be tuned to generate novel function in bulk and interfacial properties. In bulk systems, I will show that both the shear and extensional rheology of mixtures of colloids and non-adsorbing polymers, a common model system for feedstocks for 3-D printing and coating, depend on the polymer dispersity. In interfacial systems, I will show how shaping the molecular weight distribution of surface-grafted polymer brushes can modulate both brush structure and stimulus response. Thus, molecular weight distributions represent an intriguing route for tailoring polymer properties.

Presenter:
Fatmata Binta (@chef_binta) Chef of "Dine on a Mat" and Founder of Fulani Kitchen Projects

12 - 1pm, 24 Oxford Street, Room 375, Cambridge, MA

Abdullah Bannan
CRISPR detection of circulating cell-free Mycobacterium tuberculosis DNA

Jimena Luque
Assessment of possible concerted chromosome loss in yeast

Llinca Mazureac
Growth rate regulation in rod shaped bacteria

Register for the Chalk Talk

Leila Deravi, Northeastern University
6 - 7:30pm | Pierce Hall 301, 29 Oxford Street

Abstract: We are developing systems, structures, and machines that can perform complex tasks or exhibit intelligence in response to external stimuli all using bio-inspired materials. Inspired by systems spanning from how tissues build themselves to how animals camouflage, I will discuss our molecular-level approach to building new materials that can produce controllable transformations in response to specific chemical inputs for applications ranging from colorimetric sensors to implantable electronics.

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Presenter:
Chintan Pandya (@chefchintan) Chef and Partner of Unapologetic foods including Dhamaka, Adda, and Semma

Presenter:
Arielle Johnson, Ph.D. (@arielle_johnson) Flavor Scientist, Gastronomy and Innovation Researcher, Co-founder of the Noma Fermentation Lab

Fiorenzo Omenetto, Tufts University
6 - 7:30pm | Pierce Hall 301, 29 Oxford Street

Abstract: Natural materials offer new avenues for innovation across fields, bringing together, like never before, natural sciences and high technology. Significant opportunity exists in reinventing naturally-derived materials, such as structural proteins, and applying advanced material processing, prototyping, and manufacturing techniques to these ubiquitously present substances. This approach help us imagine and realize sustainable, carbon-neutral strategies that operate seamlessly at the interface between the biological and the technological worlds. Some of these opportunities include biomaterials-based applications in edible and implantable electronics, food preservation, energy harvesting, wearable sensors, compostable technology, distributed environmental sensing, medical devices and therapeutics, biospecimen stabilization, advanced medical diagnostics, and will be outlined in this talk.

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Presenter:
Joanne Chang '91 (@jbchang), Flour Bakery and Café, Myers + Chang, author of "Flour", "Flour Too", "Myers + Chang at Home", and "Baking With Less Sugar"

Dragana Rogulja, Harvard University Medical School
6 - 7:30pm | Pierce Hall 301, 29 Oxford Street

Abstract: Sleep emerged in early animals and is ubiquitous today. No explanation could be found for why this behavior is essential for survival. We recently discovered that when sleep is prevented, the organ most critically injured is the gut - gut dysfunction can even explain why severe sleep loss can be lethal. More recently we found that the relationship between sleep and the gut is bidirectional, with a gut-derived signal regulating sleep depth. I will discuss these and related results which argue that sleep should not be studied only from a brain-centric perspective.

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Josef Käs, Leipzig University
1:00pm - 2:00pm (EST) | Remote

Abstract: Based on cell unjamming we derive a cell motility marker for static histological images. This enables us to sample huge numbers of breast cancer patient data to derive a comprehensive state diagram of unjamming as a collective transition in cell clusters of solid tumors. As recently discovered, cell unjamming transitions occur in embryonic development and as pathological changes in diseases such as cancer. No consensus has been achieved on the variables and the parameter space that describe this transition. Cell shapes or densities based on different unjamming models have been separately used to describe the unjamming transition under different experimental conditions. Moreover, the role of the nucleus is not considered in the current unjamming models. Mechanical stress propagating through the tissue mechanically couples the cell nuclei mediated by the cell's cytoplasm, which strongly impacts jamming.

Based on our exploratory retrospective clinical study with N=1,380 breast cancer patients and vital cell tracking in patient-derived tumor explants, we find that the unjamming state diagram depends on cell and nucleus shapes as one variable and the nucleus number density as the other that measures the cytoplasmic spacing between the nuclei. Our approach unifies previously controversial results into one state diagram. It spans a broad range of states that cancer cell clusters can assume in a solid tumor. We can use an empirical decision boundary to show that the unjammed regions in the diagram correlate with the patient's risk for metastasis.

We conclude that unjamming within primary tumors is part of the metastatic cascade, which significantly advances the understanding of the early metastatic events. With the histological slides of two independent breast cancer patients' collectives, we train (N=688) and validate (N=692) our quantitative prognostic index based on unjamming regarding metastatic risk. Our index corrects for false high- and low-risk predictions based on the invasion of nearby lymph nodes, the current gold standard. Combining information derived from the nodal status with unjamming may reduce over- and under-treatment.

More about the Active Matter Seminar

Presenters:
Dave Arnold (@CookingIssues), Booker and Dax, author of "Liquid Intelligence", host of "Cooking Issues," founder of the Museum of Food and Drink
Harold McGee (@Harold_McGee), author of "On Food and Cooking", "Curious Cook", "Nose Dive: A Field Guide to the World's Smells"

Zhenwei Ma, Harvard University
6 - 7:30pm | Pierce Hall 301, 29 Oxford Street

Abstract: Bandages, glues, and stickers are commonly seen bioadhesives that are used extensively in the clinics and our daily lives. However, they usually have weak adhesion on wet biological tissues, and are challenging to control precisely the location, strength and duration of the formed adhesion. We report an ultrasound (US)–mediated strategy to achieve tough bioadhesion with controllability and fatigue resistance. Without chemical reaction, the US can amplify the adhesion energy and interfacial fatigue threshold between hydrogels and porcine skin by up to 100 and 10 times. Combined experiments and theoretical modeling suggest that the key mechanism is US-induced cavitation, which propels and immobilizes anchoring primers into tissues with mitigated barrier effects. Our strategy achieves spatial patterning of tough bioadhesion, on-demand detachment, and transdermal drug delivery. This work expands the material repertoire (polymers, nanoparticles and proteins) for tough bioadhesion and enables bioadhesive technologies with high-level controllability. The universal applicability of our strategy promises impacts in broad areas ranging from wearable devices to drug delivery.

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2nd Fluids & Health Conference
Mt. Holyoke College (50 College Street, South Hadley, MA)

About: As COVID-19 continues to remind us, significant gaps and exceedingly difficult scientific and translational challenges must be addressed to better prepare, mitigate, and face epidemics and global pandemics, that are bound to continue to occur with all the associated global economic and human life costs. These challenges cannot be left to be solved in a few months once a pandemic starts. Solid and deep scientific foundations, built over continued and sustained efforts, are required; and such challenges simply cannot be tackled by isolated, traditional fields of research.

This 2022 Gordon Research Conference brings together experts from a range of synergistic and complementary disciplines (mathematics/physics, engineering, microbiology/virology, epidemiology) to exchange on frontier research in health, including respiratory/nosocomial infectious diseases transmission and public health, where bio- and fluid physics are at the core.

The fantastic line-up of participants covers a wide range of fields to continue our 2019 effort to build a sustained and solid intellectual foundation and connected community. Thought and program leaders come together with young researchers to address the subtle and complex challenges of the growing intersection between fluid physics, biophysics, soft matter, infectious diseases and contamination across scales.

Note that applicants for posters or attendance can be in areas that are much broader than "infectious disease transmission." Similarly to the F&H 2019 conference, this GRC 2022 iteration will involve discussions on technical, theoretical, methodological, and translational challenges relevant for a range of open scientific questions at the intersection of virology/microbiology/physiology/mechanics/fluid mechanics, biophysics/soft matter, mixing/soft matter/applied math/modelling and health broadly defined. So those in these areas should also consider applying for the posters and attendance!

Please apply before attending

John Zimmermann, Harvard University
6 - 7:30pm | Pierce Hall 301, 29 Oxford Street

Abstract: The human heart is made up of helically aligned myofibers, with the left ventricle transitioning from a left- to right-handed helix across the septal wall. For more than half a century, it has been argued that this helical arrangement is critical for achieving physiologically relevant ejection fractions, however testing this fundamental assumption has been difficult. While surgical corrections can affect slight changes over these tissue alignments in animal studies, these are often characterized by concomitant changes in protein expression and metabolism. This makes it difficult to delineate their biophysical and biochemical effects on cardiac health. Conversely, in vitro studies have difficulty reproducing these complex architectures, including helical cardiomyocyte alignment. To address these challenges, here we introduce a novel additive textile manufacturing approach, Focused Rotary Jet Spinning (FRJS), which allows for the rapid manufacturing of micro/nanofibers scaffolds with controlled alignments and helical architectures. Using these scaffolds to control tissue morphogenesis and alignment, we demonstrate the biofabrication of in vitro cardiac ventricle models with controlled helical and circumferential alignments. With their aligned tissue structures, these models can preserve some clinically relevant features of ventricle performance, including ventricle twist, and increased apical to base conduction velocities. Using these models, we show that helically aligned ventricles display increased, axial shortening, cardiac output, and ejection fractions when compared to circumferential alignments. This shows that cardiac tissue alignment is an important regulator of ventricular performance in three-dimensional (3D) tissue-scaffolds, and confirms fundamental theoretical predictions regarding cardiac physiology made over fifty years prior. Overall, this work suggests that FRJS may serve as a valuable tool for future biofabrication, and may be used as a potential alternative, or in conjunction with more traditional approaches such as 3D bioprinting.

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Harvard University
Wednesday, August 3rd: 10am - 3pm | Maxwell Dworkin 119, 33 Oxford Street
Thursday & Friday, August 4 & 5: 10am - 3pm, Allston SEC 1.321

Sponsored by the Harvard MRSEC
11:00 AM to 1:00 PM | Pierce Hall 209 (29 Oxford St, Cambridge)

About: Have you ever found yourself renaming files as script.py, script_mod.py, script_final.py, and then script_final2.py, script_really_final.py? If so, this course is for you! By the end of this interactive workshop, you will know how to harness the power of version control to keep track of file changes and data in a safe and consistent way. The tools for the job will be Git and GitHub allowing you to organize both simple and complex code projects as well to make teamwork and collaborations easy and effective.

• Setting up a (local) repository
• Adding, committing, stashing, reverting, resetting...
• Branching, merging
• Example of best practices (e.g. tracking code vs ignoring large output data)
• Remote vs local branches
• Pull requests and merging
• Forking
• Issues
• Project planning
• Wiki

Instructors: Giovanni Bordiga, Eder Medina, Louis-Justin Tallot and Florent Pollet
The meeting will have two sessions, each will last 50 minutes.
Session 1: 11:00 - 11:50 AM
Session 2: 12:00 - 12:50 PM
Lunch: 1:00 PM

Hyoungsoo Kim, Korea Advanced Institute of Science and Technology, Korea
10 am to 2 pm | Pierce Hall 209 (29 Oxford St, Cambridge)

About: The short course is designed for the quick introduction for flow visualization techniques including shadowgraphy, Schlieren, and particle image velocimetry. The course is organized in three sessions over 3 hours.

For the first lecture, we will talk about shadowgraphy and Schlieren methods that are the method to detect the difference of the refractive index in fluid media. By using the distortion of the light ray through a different fluid, we can observe the motion of fluid.

Secondly, the most conventional flow visualization technique will be introduced, so-called particle image velocimetry (PIV). In this lecture, to perform PIV, three main aspects are discussed, particle, light source, and optics. Furthermore, the optimal conditions for achieving a good vector field are summarized and explained.

Lastly, we will shortly discuss micro-PIV, which is for microfluidics applications. Some distinct features compared to conventional PIV are treated during the lecture.

The meeting will have three sessions, each will last 50 minutes.
Session 1: 10:00 - 10:50 AM
Session 2: 11:00 - 11:50 AM
Lunch: 12:00 - 1:00 PM
Session 3: 1:00 - 1:50 PM

Please register before attending

Max Bi, Department of Physics, Northeastern University
Dr. Dave Weitz's Lab, 9 Oxford St - LISE 424

About: Learn about the latest in confocal microscopy from Leica Instruments during this demonstration of the Stellaris 8 by Leica Instruments.

About the Leica Stellaris 8 Confocal Demonstration

Max Bi, Department of Physics, Northeastern University
6 - 7:30pm | Pierce Hall 301, 29 Oxford Street

Abstract: Biological processes, from morphogenesis to tumor invasion, spontaneously generate shear stresses inside living tissue. The mechanisms that govern the transmission of mechanical forces in epithelia and the collective response of the tissue to bulk shear deformations remain, however, poorly understood. Using a minimal cell-based computational model, we investigate the constitutive relation of confluent tissues under simple shear deformation. We show that an initially undeformed fluidlike tissue acquires finite rigidity above a critical applied strain. This is akin to the shear-driven rigidity observed in other soft matter systems. Interestingly, shear-driven rigidity can be understood by a critical scaling analysis in the vicinity of the second order critical point that governs the liquid-solid transition of the undeformed system. We further show that a solidlike tissue responds linearly only to small strains and then switches to a nonlinear response at larger stains, with substantial stiffening. Finally, we propose a mean-field formulation for cells under shear that offers a simple physical explanation of shear-driven rigidity and nonlinear response in a tissue.

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Benny Davidovitch, UMass Amherst
6 - 7:30pm | Pierce Hall 301, 29 Oxford Street

Abstract: Large floating viscous bubbles whose interior gas is rapidly depressurized exhibit a remarkable dynamics, characterized by a periodic pattern of radial wrinkles that permeate the liquid film in the course of its flattening. This instability was discovered in 1998 by Debregeas et al. [1] and has been attributed to the joint effect of gravity and the expansion of a circular rupture [2]. However, a recent experiment by Oratis et al. [3] demonstrated that the instability appears even in the absence of gravity or rupture, indicating a mechanism dominated solely by viscous and capillary forces.

Motivated by these experiments we address Stokes flow in a curved film of a non-inertial incompressible liquid with free surfaces, generated by temporal variation of the Gaussian curvature R [4]. Notwithstanding the close analogy between the Newtonian hydrodynamics of viscous liquids and the Hooeakn elasticity of solids, often called “Stokes-Rayleigh analogy”, the fact that stress in viscous films is generated by the rate-of-change ∂tR, rather than by R itself as is the case for elastic sheets, reflects a profound difference between these two branches of non-inertial, yet geometrically-nonlinear continuum mechanics. Whereas the rigidity of elastic sheets derives from the existence of a “target” metric, their viscous counterparts are not endowed with a preferred metric. We reveal the experimental observations of Ref. [3] as a dramatic ramification of this distinction - a universal, curvature-driven & momentum-conserving surface dynamics, imparted by viscous resistance to ∂tR ̸= 0. Specifically, rapidly-depressurized viscous bubbles flatten by forming a radially moving front of highly localized ∂tR that separate a flat core and a spherically-shapes periphery, and become wrinkled due to a hoop-compressive stress field at the wake of the propagating front [5].

This novel surface dynamics has close ties to "Jelium physics", where topological defects spontaneously emerge to screen elastic stress, similarly to dipoles-mediated screening of electrostatic field in conducting media, thereby extending the classic analogy between Wigner crystals, Abrikosov lattice in type-II superconductors, and 2D elasticity of curved crystals, to non-equilibrium 2D viscous hydrodynamics. A particularly exciting possibility is the emergence of such a universal geometrically-noninear 2D viscous hyrodynamics in strongly-correlated electronic liquids in 2D crystals.

[1] G. Debregeas, P.G. de Gennes, F. Brochard-Wyart, "The life and death of 'bare' viscous bubbles," Science 279, 1704-1707 (2000).
[2] R. da Silviera, S.Chaieb, L.Mahadevan, "Rippling instability of a collapsing bubble," Science 287, 1468-1471 (2000).
[3] A.T. Oratis, J.W.M. Bush, H.A. Stone, J. Bird, "A new wrinkle on liquid sheets: Turning the mechanism of viscous bubble collapse upside down," Science 369, 685 (2020).
[4] P.D. Howell, "Models for thin viscous sheets," Eur. J. App. Math. 7, 321-343 (1996).
[5] B. Davidovitch and A. Klein, "How viscous bubbles collapse: topological and symmetry- breaking instabilities in curvature-driven hydrodynamics" (2022).

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Gwennou Coupier, Grenoble Alpes University, Laboratoire Interdisciplinaire de Physique
6 - 7:30pm | Pierce Hall 301, 29 Oxford Street

Abstract: Buckling of elastic structures is an effective way to produce rapid motion in a fluid at any scale. Encapsulated microbubbles, which are currently used as ultrasound contrast agents, can deform and collapse under an external load from an acoustic wave. They reinflate when the pressure decreases. The shape hysteresis associated with this deformation cycle makes this simple object a good candidate to become an ultrasound controlled micro-swimmer.

I will explore this possibility through experiments at macro and micro scales and numerical simulations. The coupling between the acoustic wave and the self-oscillation of the deformed shell leads to complex - sometimes chaotic - dynamics with direct consequences on the direction and efficiency of the swimming.

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Dorothee Kern, Brandeis University
6 - 7:30pm | Pierce Hall 301, 29 Oxford Street

Abstract: The essential role of protein dynamics for enzyme catalysis has become more generally accepted. Since evolution is driven by organismal fitness hence the function of proteins, we are asking the question of how enzymatic efficiency has evolved. First, I will address the evolution of enzyme catalysis in response to one of the most fundamental evolutionary drivers, temperature. Using Ancestral Sequence Reconstruction (ASR), we answer the question of how enzymes coped with an inherent drop in catalytic speed caused as the earth cooled down over 3.5 billion years. Tracing the evolution of enzyme activity and stability from the hot-start towards modern hyperthermophilic, mesophilic and psychrophilic organisms illustrates active pressure versus passive drift in evolution on a molecular level (1). Second, I will share a novel approach to visualize the structures of transition-state ensembles (TSEs), that has been stymied due to their fleeting nature despite their crucial role in dictating the speed of biological processes. We determined the transition-state ensemble in the enzyme adenylate kinase by a synergistic approach between experimental high-pressure NMR relaxation during catalysis and molecular dynamics simulations (2). Third, a novel general method to determine high resolution structures of high-energy states that are often the biologically reactive species will be described (3). With the ultimate goal to apply this new knowledge about energy landscapes in enzyme catalysis for designing better biocatalysts, in “forward evolution” experiments, we discovered how directed evolution reshapes energy landscapes in enzymes to boost catalysis by nine orders of magnitude relative to the best computationally designed biocatalysts. The underlying molecular mechanisms for directed evolution, despite its success, had been illusive, and the general principles discovered here (dynamic properties) open the door for large improvements in rational enzyme design (4). Finally, visions (and success) for putting protein dynamics at the heart of drug design are discussed.

1. V. Nguyen et. al., Evolutionary Drivers of Thermoadaptation in Enzyme Catalysis” Science 2017, 355(6322):289-294
2. J. B. Stiller et. al., Probing the Transition State in Enzyme Catalysis by High-Pressure NMR Dynamics 2019, Nature Catalysis (2019) 2, 726–734
3. J. B. Stiller et. al., Structure Determination of High-Energy States in a Dynamic Protein Ensemble Nature 2022, in press
4. R. Otten et. al., How directed evolution reshapes energy landscapes in enzymes to boost catalysis Science 2020, 2020 Dec 18;370(6523):1442-1446

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Richard Henshaw, Tufts University
6 - 7:30pm | Pierce Hall 301, 29 Oxford Street

Abstract: The collective motion of dense suspensions of swimming bacteria is typical of a broad class of active materials, ranging from flocking birds and schooling fish down to the sub-cellular movement of actin filaments. Descriptions of the dy- namics of these systems have predominately focused on the characterization of spatio-temporal correlations of the velocity field, but whilst the importance of active turbulence is widely recognized, their structure, transport properties and mixing kinematics still remain largely unknown.

Here, we use Lagrangian analysis techniques to study the chaotic flow fields gen- erated by bacterial turbulence in dense suspensions of Bacillus subtilis. High- resolution velocity fields are measured using PIV across a range of bacterial swimming speeds, where the computed Lagrangian stretching visualizes the induced stretching and folding, characteristic of mixing. Close inspection of the finite-time Lyapunov exponent (FTLE) field reveals time and swimming speed dependent FTLE statistics reminiscent of intermittent dynamics in clas- sical chaotic dynamical systems. At moderate P ́eclet numbers, experiments and Langevin simulations reveal that manifolds of the FTLE field guide scalar mix- ing and regulate transport in these active suspensions, ecologically relevant to the dispersal of chemical resources and particulates in dense bacterial colonies.

Secondly, we apply proper orthogonal decomposition (POD) analysis to quantify the dynamical flow structure of active turbulence under a variety of conditions. In isotropic bulk turbulence, the modal representation shows that the most en- ergetic flow structures dictate the spatio-temporal dynamics across a range of suspension activity levels. In confined geometries, POD analysis illustrates the role of boundary interactions for the transition to bacterial turbulence, and it quantifies the evolution of coherent active structures in externally applied flows. Beyond establishing the physical flow structures underpinning the complex dy- namics of bacterial turbulence, the low-dimensional representation afforded by this modal analysis will facilitate data-driven modeling of active turbulence.

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Since its inception in 2004, the Microbial Science Initiative has sponsored and hosted an annual symposium for those in the Harvard and greater Boston communities. The spring event showcases magnificent research across a breadth of microbe-centric topics spanning environmental and biomedical sciences. The MSI Symposium is free and open to the public. Welcome to the microbial world! Mid-morning and mid-afternoon breaks with refreshments will be provided, and there will be a 75 minute break for lunch mid-day.

Guillaume Duclos, Department of Physics, Brandeis University
1:00pm - 2:30pm (EST) | Remote

Abstract: Active matter describes out-of-equilibrium materials composed of motile building blocks that convert free energy into mechanical work. The continuous input of energy at the particle scale liberates these systems from the constraints of thermodynamic equilibrium, leading to emergent collective behaviors not found in passive materials. In this talk, I will describe our recent efforts to build simple active systems composed of purified proteins and identify generic emergent behaviors in active systems. I will first discuss two distinct activity-driven instabilities in suspensions of microtubules and molecular motors. Second, I will describe a new model system for polar fluid whose collective dynamics are driven by the non-equilibrium turnover of actin filaments. Our results illustrate how biomimetic materials can serve as a platform for studying non-equilibrium statistical mechanics, as well as shine light on the physical mechanisms that regulate self-organization in living matter.

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Amélie Chardac, Department of Physics, Brandeis University
6 - 7:30pm | Pierce Hall 301, 29 Oxford Street

Abstract: Active-matter physics describes the mesmerizing dynamics of interacting motile bodies : from bird flocks and cell colonies, to collections of synthetic units independently driven far from equilibrium. When motile units self-assemble into flocks where all particles propel along the same direction, they realize one of the most robust ordered phase observed in Nature. But, after twenty five years of intense research the very mechanism controlling the ordering dynamics of both living and artificial flocks has remained unsettled.

In this talk, building on model experiments based on Quincke rollers, I will first explain how a flock suppresses its singularities to form an ordered spontaneous flow. Combining experiments, simulations and theory I will show how to elucidate the elementary excitations of 2D polar active matter and explain their phase ordering dynamics as a self-similar process emerging from the annihilation of ±1 defects along a filamentous network of domain walls with no counterparts in passive systems.

In a second part, I will address the robustness of long range order and discuss the stabilization of topological defects in a polar active fluid through disordered media. Combining experiments and theory, I will show that colloidal flocks collectively cruise through disorder without relaxing the topological singularities of their flows, unlike in pure systems. Introducing colloidal flocks in micro patterned circular chambers, we reveal a state of strongly disordered active matter with no counterparts in equilibrium : a dynamical vortex glass. The resulting state is highly dynamical but the flow patterns, shaped by a finite density of frozen vortices, are stationary and exponentially degenerated.

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Guillermina Ramirez-San Juan, Brandeis University
6 - 7:30pm | Pierce Hall, room 301, 29 Oxford Street

Abstract: Living organisms rely on flows to perform essential functions that range from swimming and feeding in unicellular organisms to mucus clearance in humans. These flows are generated by the inte­grated activity of thousands of microscopic beating filaments attached to cell surfaces (cilia). In cells, collections of cilia exhibit highly complex temporal patterns known as metachronal waves. The lack of measurements of the geometric and dynamic properties of cilia arrays has limited our ability to understand the mechanisms of pattern formation. In my talk I will discuss the advantages of ciliated swimmers as experimental model systems where such measurements can be readily performed. Performing precise measurements and perturbations of temporal patterning in cilia arrays will enable the identification of the physical mechanisms underlying collective behaviors of cilia. This integrated view that seeks to link cilia patterning with flow structure will significantly increase our understanding of the physiology of cilia arrays in vivo.

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Ben Simons, Cambridge University
1:00pm - 2:30pm (EST) | Remote

Abstract: The morphogenesis of branched tissues has been a subject of long-standing debate. Although much is known about the molecular pathways that control cell fate decisions, it remains unclear how macroscopic features of branched organs, including their size, network topology and spatial pattern are encoded. Based on large-scale reconstructions of the mouse mammary gland and kidney, we begin by showing that statistical features of the developing branched epithelium can be explained quantitatively by a local self-organizing principle based on a branching and annihilating random walk (BARW). In this model, renewing tip-localized progenitors drive a serial process of ductal elongation and stochastic tip bifurcation that terminates when active tips encounter maturing ducts. Then, based on reconstructions of the developing mouse salivary gland, we propose a generalisation of BARW model in which tips arrested through steric interaction with proximate ducts reactivate their branching programme as constraints become alleviated through the expansion of the underlying mesenchyme. This inflationary branching-arresting random walk model offers a more general paradigm for branching morphogenesis when the ductal epithelium grows cooperatively with the tissue into which it expands.

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John Berezney, Department of Physics, Brandeis University
6 - 7:30pm | Pierce Hall, room 301, 29 Oxford Street

Abstract: The out-of-equilibrium active reorganization of cytoskeletal networks by molecular motors is necessary for fundamental life processes, such as cell division, cell motility, and environmental sensing. While the passive structure and mechanics of such materials have been well documented, the effects of their steady-state out-of-equilibrium reorganization is a site of current research. In this work, we introduce an active cytoskeletal composite material whose viscoelasticity is controlled by the actin filament concentration. Three qualitatively different states are observed: (1) an extensile fluid phase, (2) localized aster-like contractile structures in coexistence with an extensile fluid, and (3) a bulk contractile gel. The aster-like state consists of locally contracted heterogeneous structures that maintain their complex layered structure over a range of sizes. While the actin concentration triggers a contractile state in coexistence with the active fluid, the resultant filament-rich structures are transient and their lifetimes increase with actin concentration. These results demonstrate that self-organized dynamical states and patterns, evocative of those observed in the cytoskeleton, do not require precise biochemical regulation but can arise due to purely mechanical interactions of actively driven filamentous materials.

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Colm Kelleher, Department of Molecular and Cellular Biology, Harvard University
6 - 7:30pm | Pierce Hall, room 301, 29 Oxford Street

Abstract: Meiosis is the specialized form of cell division in which gametes are created. In meiosis, a mother cell must ensure that the daughter gamete inherits exactly one copy of each chromosome. This, in turn, necessitates physical organization and motion of DNA over length scales of tens of microns. To create the forces required to move chromosomes, the cell builds an organelle called the meiotic spindle. Like the analogous structure in mitotic cells, the meiotic spindle is composed primarily of microtubules -- long, rigid protein polymers -- as well as a variety of other proteins. Some of these associated proteins create (active or passive) forces between microtubules; another class allows microtubules to exert forces on chromosomes.

Despite our detailed knowledge of the spindle's molecular composition, as mechanical objects, both meiotic and mitotic spindles are very poorly understood. It is not known, for instance, which specific molecular or structural components of the spindle are responsible for generating the forces that actually move chromosomes, or which components transfer those forces to chromosomes. Likewise, from a materials physics perspective, it is unclear how we should think about self-organized, biochemically complex, fuel-consuming structures like the spindle.

In this talk, I will discuss how we can adapt a variety of tools from materials physics to characterize various aspects of the spindle's microscopic structure and organelle-scale physical properties, like elastic stiffness and surface tension. I will discuss our attempts to understand these measurements within the context of a quantitative, coarse-grained theory in which spindles from mouse and human eggs are modeled as active liquid crystal droplets.

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Georg K. Gerber, MD, PhD, MPH; Associate Professor of Pathology, Harvard Medical School
4 - 5pm EST | Remote meeting

Abstract: The human gut microbiome is highly temporally dynamic. Some of the most profound changes over time occur during infancy and early childhood when the microbiome is first becoming established. Although the gut microbiome is more stable in adulthood, it continues to undergo significant changes over time due to diet, travel, antibiotic use, infection, gut inflammation, and a variety of other factors. Microbial dynamics, particularly early in life, have been linked to many human diseases including necrotizing enterocolitis, diabetes, food allergies, obesity, and inflammatory bowel diseases. Given the complexity of complex and dynamic host-microbial ecosystems, sophisticated computational methods are essential for analyzing data from these systems and ultimately deriving experimentally testable hypotheses. In this talk, I will first introduce the challenges of analyzing dynamic microbiomes. Then, I will present intuitive descriptions of some of the novel machine learning methods we have developed to address different problems, including: (a) forecasting microbiome dynamics and quantitating the “keystoneness” of individual microbes or groups of microbes, (b) finding groups of microbes that respond consistently to introduced perturbations, and (c) predicting the status of the human host (e.g., disease onset) given past changes in the microbiome. Throughout, I will give examples of biomedical applications of our work, including developing microbial consortia to treat or prevent Clostridioides difficile infection or food allergies. I will gear the talk to a broad audience, focusing on the intuition behind machine learning approaches rather than technical details.

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Benjamin Freedman, Wyss Institute, Harvard University
6 - 7:30pm | Pierce Hall, room 301, 29 Oxford Street

Abstract: Hydrogels that provide mechanical support and sustainably release therapeutics have been used to treat tendon injuries. However, most hydrogels are insufficiently tough, release drugs in bursts, and require cell infiltration or suturing to integrate with surrounding tissue. Here we report that a hydrogel serving as a high-capacity drug depot and combining a dissipative tough matrix on one side and a chitosan adhesive surface on the other side supports tendon gliding and strong adhesion (larger than 1,000 J m-2) to tendon on opposite surfaces of the hydrogel, as we show with porcine and human tendon preparations during cyclic-friction loadings. The hydrogel is biocompatible, strongly adheres to patellar, supraspinatus and Achilles tendons of live rats, boosted healing and reduced scar formation in a rat model of Achilles-tendon rupture, and sustainably released the corticosteroid triamcinolone acetonide in a rat model of patellar tendon injury, reducing inflammation, modulating chemokine secretion, recruiting tendon stem and progenitor cells, and promoting macrophage polarization to the M2 phenotype. Hydrogels with 'Janus' surfaces and sustained-drug-release functionality could be designed for a range of biomedical applications.

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Katherine Copenhagen, Princeton University
1:00pm - 2:30pm (EST) | Remote

Abstract: The developmental cycle of Myxococcus xanthus involves the coordination of many hundreds of thousands of cells aggregating to form mounds known as fruiting bodies. This aggregation process begins with the sequential formation of more and more cell layers. Using three-dimensional confocal imaging we study this layer formation process by observing the formation of holes and second layers within a base monolayer of M xanthus cells. We find that cells align with each other over the majority of the monolayer forming an active nematic liquid crystal with defect point where cell alignment is undefined. We find that new layers and holes form at positive and negative topological defects respectively. We model the cell layer using hydrodynamic modeling and find that this layer and hole formation process is driven by active nematic forces through cell motility and anisotropic substrate friction.

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Qiaoling Huang, Department of Physics, Xiamen University
6 - 7:30pm | Pierce Hall, room 301, 29 Oxford Street

Abstract: Biological responses to biomaterials are a complex topic as they not only involve diverse bio-components (such as proteins, cells, blood, etc.) but also sophisticated materials with a large array of relevant properties. As our understanding of structure-property–function relationships grows, it is becoming clear that a slight change of a single material property can heavily affect biological responses and many factors remain unknown about these relationships. For example, TiO2 nanotubes (TNTs) have a similar structure to the natural compact bone, and studies have confirmed TNTs can improve osteogenic differentiation. However, the structural properties of titanium dioxide nanotubes are diverse, and the optimal TNTs for bone repair remain to be determined. In this talk, I will discuss how the surface properties of TiO2 nanomaterials affect the biological response, including protein adsorption, cell behaviors and platelet adhesion. Our results show that the various structural properties of these material surfaces do not vary individually and will synergistically affect biological responses. On the other hand, we can obtain different or even opposite results by tuning experimental details.

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Dr. Travis Gibson
12 - 1pm, 24 Oxford Street, Room 375, Cambridge, MA

Rafael Gomez-Bombareli, MIT
6 - 7:30pm | Pierce Hall, room 301, 29 Oxford Street

Abstract: Coarse-Graining (CG) is a simulation strategy that simplifies all-atom molecular systems by grouping selected atoms into pseudo-beads and propagating their motion collectively. CG drastically accelerates simulations for two reasons: first there are fewer particles to simulate and second the dynamics can be integrated with larger time steps.

Coarse-graining involves two coupled learning problems: defining the mapping from an all-atom representation to a reduced representation, and parameterizing a Hamiltonian over coarse-grained coordinates. We have recently proposed a generative modeling framework based on variational auto-encoders to unify the tasks of learning discrete coarse-grained variables and parameterizing coarse-grained force fields. Furthermore, CG approaches result in irreversible information loss, which makes accurate backmapping, i.e., restoring fine-grained (FG) coordinates from CG coordinates, a long-standing challenge. We propose a model that rigorously embeds the probabilistic nature and geometric consistency requirements of the backmapping transformation. The model encodes the distribution of FG expansions of the beads into an invariant latent space and decodes them back to FG geometries via equivariant convolutions.

Amin Doostmohammadi, Niels Bohr Institute, University of Copenhagen
1:00pm - 2:30pm (EST) | Remote

Abstract: The spontaneous emergence of collective flows is a generic property of active fluids and often leads to chaotic flow patterns characterized by swirls, jets, and topological disclinations in their orientation field. I will first discuss two examples of these collective features helping us understand biological processes: (i) to explain the tortoise & hare story in bacterial competition: how motility of Pseudomonas aeruginosa bacteria leads to a slower invasion of bacteria colonies, which are individually faster, and (ii) how self-propelled defects lead to finding an unanticipated mechanism for cell death.

I will then discuss various strategies to tame, otherwise chaotic, active flows, showing how hydrodynamic screening of active flows can act as a robust way of controlling and guiding active particles into dynamically ordered coherent structures. I will also explain how combining hydrodynamics with topological constraints can lead to further control of exotic morphologies of active shells.

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Pepijn Moerman, Department of Chemical and Biomolecular Engineering, Johns Hopkins University
6 - 7:30pm | Pierce Hall, room 301, 29 Oxford Street

Abstract: Suspensions of microscopic particles, such as reaction mixtures with catalyst particles and nutrient solutions with bacteria, often contain heterogeneous distributions of solute. The concentration gradients that result from these inhomogeneities can put the particles in motion through a process called phoresis, or chemotaxis in the case of living systems. Through this process bacteria manage to find places with higher nutrient concentrations and white blood cells can chase after bacteria. In this work, we employed a model system of oil droplets that exchange oil with each other in an aqueous surfactant solution to study the forces that particles exert on each other through the formation of local concentration gradients. We found that the solute-mediated interactions can be repulsive or attractive depending on the rate of oil exchange. When the type of oil droplets and surfactant are chosen correctly, one type of droplet chases after the other.

Dr. Ana Paula Guedes Frazzon
12 - 1pm, 24 Oxford Street, Room 375, Cambridge, MA

Alexandre Bisson, Department of Biology, Brandeis University
6 - 7:30pm | Pierce Hall, room 301, 29 Oxford Street

Abstract: Cells sense and respond to their physical surroundings using organized molecular machinery that is tightly regulated in space and time. Although each of us feels like an individual we are, in fact, consortia. This becomes clear when we observe tissues under the microscope, but very little is known how the material properties of these tissues emerged from a vast majority of life forms that employ rigid cell walls to withhold their turgor pressure. Here, I will discuss how multicellularity first emerged in archaeal cells - the closest prokaryotes to animals. We observed that not only multiple lineages of archaea create multicellular colonies, but also that physical compression triggers a developmental program in some species cells that leads to a multicellular physiological state. We show this new mechanosensing mechanism is independent of the stiffness or rugosity of the surfaces around cells and there are specific molecular sensors that allow cells to sense the viscoelasticity state of their envelope. Altogether, our data suggest archaea should be an interesting model for the development of bioinspired material and the study of how physical constraints shape evolution.

Margaret Gardel, University of Chicago
1:00pm - 2:30pm (EST) | Remote

Abstract: My lab is interested in the active and adaptive materials that underlie control of cell shape. This has centered around understanding force transmission and sensing within the actin cytoskeleton. I will first review our current understanding of the types of active matter that can be constructed by actin polymers. I will then turn to our recent experiments to understand how Cell shape changes in epithelial tissue. I will describe the two sources of active stresses within these tissues, one driven by the cell cycle and controlling cell-cell stresses and the other controlled by cell-matrix signaling controlling motility. I will then briefly describe how we are using optogenetics to locally control active stresses to reveal adaptive and force-sensitive mechanics of the cytoskeletal machinery. Hopefully, I will convince you that recent experimental and theoretical advances make this a very promising time to study this quite complicated form of active matter.

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Daniel Pearce, Department of Mathematics, MIT
6 - 7:30pm | Pierce Hall, room 301, 29 Oxford Street

Abstract: Collectively migrating cells in living organisms often take advantage of barriers and internal interfaces to achieve directed motion, although the physical origin of this behavior is still debated. Here we demonstrate that human fibrosarcoma cells (HT1080) plated on narrow stripe-shaped channel undergo collective migration by virtue of a novel type of topological edge currents, resulting from the interplay between liquid crystalline (nematic) order, microscopic chirality and topological defects. Thanks to a combination of in vitro experiments and theoretical active hydrodynamics, we show that, while heterogeneous and chaotic in the bulk of the channel, the spontaneous flow arising in confined populations of HT1080 cells is rectified along the edges, leading to directed motion, with broken parity symmetry. These edge currents are fueled by layers of +1/2 topological defects, anchored at approximately 74 degrees with respect to the channel's edge and acting as local sources of chiral active stress. This shows how multicellular systems can take advantage of topology to achieve collective migration, even in the absence of hard-wall confinement. Finally, it demonstrates the importance of chirality in these systems and suggests a possible mechanism for the emergence of chiral cellular flows in vivo.

Qiang Cui, Department of Chemistry, Boston University
6 - 7:30pm | Pierce Hall, room 301, 29 Oxford Street

Abstract: Cell membrane remodeling is involved in many important cellular events such as cell division and virus infection. Multiple possible mechanisms for membrane remodeling have been proposed over the years, ranging from intuitive factors such as shallow insertion of protein motifs to more recent discovery of contributions from collective processes such as liquid-liquid phase separation of prepheral proteins. To help establish the relative importance of various factors to the specific system of interest, including the effect of disease-causing mutations, it is desirable to develop multi-scale models that are sensitive to molecular details, such as protein sequence and membrane composition, yet computationally efficient for studying the process of membrane remodeling. Using several examples from our recent studies, which involve protein and nanoparticle regulated membrane remodeling, we highlight both challenges and progress made in developing such multi-scale computational models, and initial mechanistic insights into ESCRTIII driven membrane fission. Finally, we will also briefly discuss the potential involvement of pre-wetting transitions at membrane surface as a mechanism that disordered proteins drive membrane remodeling, including the impact of membrane obstacles (e.g., proteins anchored to cytoskeletons) on the sensitivity of such a mechanism.

Petros Koumoutsakos, Harvard University
1:00pm - 2:30pm (EST) | Remote

Abstract: Fluids pervade complex systems, ranging from fish schools, to bacterial colonies and nanoparticles in drug delivery. Despite its importance, little is known about the role of fluid mechanics in such applications. Is schooling the result of vortex dynamics synthesized by individual fish wakes or the result of behavioral traits? Is fish schooling energetically favorable? I will present multifidelity computational studies of collective swimming in 2D and 3D flows. Our studies demonstrate that classical models of collective swimming (like the Reynolds model) fail to maintain coherence in the presence of long-range hydrodynamic interactions. We demonstrate in turn that collective swimming can be achieved through reinforcement learning. We extend these studies to 2D and 3D viscous flows governed by the Navier Stokes equations. We examine various hydrodynamic benefits with a progressive increase of the school size and demonstrate the importance of controlling the vorticity field generated by up to 300 synchronized swimmers.

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Abstract: Water is essential for all forms of life. However, some organisms survive severe desiccation by undergoing cryptobiosis, during which most metabolic processes are suspended and the host organism enters a dormant, protective state until a favorable environment is restored. Recent studies have demonstrated that intrinsically disordered proteins (IDPs) are often expressed at high levels in extremotolerant tardigrades, suggesting that this class of unstructured protein is critical to maintaining cell survival under adverse conditions. We focus on specific class of tardigrade-specific IDPs that are secreted extracellularly, characterize their structures and phase separation behaviors, and investigate protective phenotypes both in vitro and in vivo. Ultimately, we hope to explore applications of these proteins in engineering drought tolerance in mammalian cells, or stabilizing biomedical products for long-term storage.

Abstract: Integrating synthetic circuitry into larger transcriptional networks to mediate predictable cellular behaviors remains a challenge within synthetic biology. While significant efforts have been devoted to the design of enhanced synthetic circuitry, less is understood regarding how cellular hardware may impose fundamental performance limitations on integrated circuits. Within the mammalian context, cellular reprogramming continues to generate new cell types, increasingly expanding our perspective of cellular plasticity. Despite improved genetic tools and epigenetic modulations, reprogramming remains a rare cellular event. In this talk, I will describe how we identified molecular roadblocks in reprogramming that arise from tradeoffs between transcription and proliferation rates. Our discovery suggests that topological stress impacts the function of gene networks and constrains cellular transitions. To test this hypothesis, my lab constructs synthetic gene circuits that transmit topological stress into changes in expression to identify plastic cells in cell-fate transitions through the model of cellular reprogramming. I will discuss how this work and recent findings from my lab open completely new questions about how the structure of the genome stabilizes cellular identity and suggests strategies to improve the design of synthetic gene circuits.

Abstract: Experiments with fire-ant columns reveal similarities and differences with granular columns. There are force chains, but these are always supportive (not compressive) and fluctuate due to activity. In 2D columns, we observe the propagation of waves along the vertical direction; these are density, activity and alignment waves, ultimately reflecting the existence of activity cycles whereby the fire-ant collective changes “state” from “active”, where all the ants move, to “inactive”, where a large fraction of the ants cluster and remain stationary. Our findings indicate that while the “active” states correspond to collective motion, in the “inactive” states there is clustering reminiscent of a motility-induced attraction resulting from the social interactions between the ants.

Abstract: The mammalian sensory nervous system densely innervates barrier tissues including the skin and gut that are exposed to microbes. Nociceptors are specialized neurons that mediate pain and itch. These unpleasant sensations are critical to protect organisms from danger. We find that nociceptors actively participate in host defense by detecting bacterial pathogens and signaling to the immune system. We will explore how bacteria interact with neurons to drive pain and itch, and how this crosstalk could regulate host defense.

Watch "Bacterial Interactions with Pain and Itch" on YouTube

Abstract: If a sessile droplet containing suspended particulates evaporates on a substrate, it eventually leaves a ring pattern due to non-uniform evaporative flux profiles. To control and suppress coffee-ring effects, it is important to understand how the flow structures evolve and what kind of solvent and solute components are. We use solutal Marangoni stresses and geometrical effects to control the dried pattern. In this talk, I will present a series of representative examples of how to control or suppress the coffee-ring pattern and furthermore new features will be identified and exploited. The examples include that (1) whisky dried patterns, (2) DNA droplet, (3) coffee-ring-less QD-LED polygonal patterns, and (4) liquid metal coating and its applications. These problems characterize my approach of using optical measurement techniques to explore new questions in multiphase flows and physicochemical hydrodynamics.

Wylie Dufresne (@WylieDufresne), Du's Donuts & Coffee, BK, Stretch Pizza (formerly wd~50)
Ted Russin (@CIACulinarySci) School of Culinary Science and Nutrition, Culinary Institute of America

Abstract: Generating neutralizing antibodies (Abs) is one of the key functions of vaccines. These high affinity Abs bind to active sites of proteins on pathogens' surfaces, prevent their entry into host cells, and mark them for elimination via innate immune cells. While vaccines are intended to elicit such protection, some fail to induce neutralizing Abs against diseases such as HIV. To understand this variability, we must look to the germinal centers (GCs) within follicles, where B-cells interact with both the vaccine antigen (Ag) and T-cells as they mutate their receptors during affinity maturation. Recent studies illustrate that large proportions of GC B-cells do not recognize intact vaccine Ags and lead to formation of plasma cells that secrete Abs incapable of neutralizing the actual virus. This prompted us to evaluate the stability of Ags in vivo and examine the protease activity within LNs after immunization; areas that are both severely understudied in vaccinology. By developing dye labeled HIV Ags that show a loss in fluorescence resonance energy transfer (FRET) with degradation, we discovered regions of intact and degraded Ags within the LNs. This was caused by a class of functionally active proteases that are upregulated in a spatially dependent manner and are expressed within cells that come into direct contact with the lymph-borne Ags. To examine the impact of Ag proteolysis, we used different vaccination conditions that show spatially distinct localization of Ag within LNs and investigated the capacity of the corresponding GC and Ab responses to recognize intact Ags or degraded Ag by-products. Our work here illuminates the role of protease activity within LNs shortly after vaccination and its role in modulating downstream humoral response.

Abstract: Understanding how organs transform into their target shapes during development is a challenge at the interface between physics and biology. In visceral organs, multiple tissue layers interact to orchestrate complex shape changes. While there has been significant progress in identifying genetic and anatomical ingredients underlying organogenesis, tracing the dynamics of cell behavior and tissue deformation that drive organ shape change remains an outstanding and essential challenge. Here, leveraging the Drosophila midgut as a model system, we use light-sheet microscopy, optogenetics, computer vision, and tissue cartography to reconstruct in toto shape dynamics of a developing organ in vivo. We identify the kinematic and biological mechanisms driving shape change by linking out-of-plane motion to active contraction patterns cell behaviors, and genetic patterning. Our multi-scale analysis traces how biology controls a physical process generating whole-organ shape change in heterologous tissue layers.

Abstract: Control over the fate of excited states at the nanoscale is the holy grail of excitonic devices, including light-emitting diodes and photovoltaic devices. Photosynthesis provides the master blueprint on how we can move energy efficiently through molecules. However, dissecting the salient parts that underlie this efficient steering of energy is encumbered by challenges in re-engineering natural machines without losing function. Alternative to re-engineering photosynthetic machinery, we have recently developed a bottom-up approach using DNA to emulate the chromophore organization in nature light-harvesting systems. DNA provides a rich molecular toolbox to control the spatial relationships of multiple synthetic pigments enabling us to recapitulate emergent quantum behavior of molecular aggregates found in photosynthetic machines. In this talk, I'll discuss our recent work on DNA templated aggregates, how we can use DNA to form aggregates with defined electronic structures, and the function of these aggregates in the context of energy transport. Finally, I'll show some ongoing work in the lab that seeks to understand the complex interplay between long-range, Coulombic, and short-range, charge-transfer interactions.

Dr. Maya Warren (@maya.warren), Ice Cream Scientist

Watch "The Science of Ice Cream" on YouTube

Abstract: Innovation in food science and technology is the alternative to overcome the current challenges of the food industry. In my talk, I will discuss some food model systems that we are currently exploring through knowledge/tools from chemistry, biology, and physics. For example, despite goat milk having benefits for human health over cow's milk, goat milk yogurt (GY) has a delicate texture, a more rupture-susceptible gel structure, low consistency, and viscosity, which reduces its overall acceptability by the consumer. Thus, new innovative methods such as ultrasound and high hydrostatic pressure can be alternatives to improve the quality of GY. Furthermore, the addition of inulin, maltodextrin, whey protein, and cupuassu pulp can improve the taste and rheological characteristics of goat milk yogurts. Recent advances on kefiran, an exopolysaccharide derived from kefir grain microflora, have shown its electrospinning ability to be transformed in nanofiber, potentially useful for encapsulating bioactive ingredients for food, probiotic/ drug delivery, and scaffolds to tissue engineering. On the other hand, conventional food preservation methods have demonstrated several disadvantages and limitations in the efficiency of microbial load reduction and maintaining food quality. Hence, non-thermal preservation technologies (NTPT) and alternative chemical compounds (ACC) have been considered a high promising replacer for decontamination, increasing the shelf life and promoting low levels of physicochemical, nutritional, and sensorial alterations in meat and fish. However, NTPT promotes the connections between the oxidative process (lipids and proteins) and the impact of color and rheology characteristics. The demand for more environment-friendly technologies has gained worldwide attention to food processing and preservation. Brazil has over 40,000 varied plant species rich in phytochemicals, which have great potential as a source of ACC that can be replacer for synthetic compounds currently applied in the meat industry. Nevertheless, natural antioxidant compounds are not stable. In this way, nanocomposites based on biodegradable polymer/graphene-based nanomaterials with antioxidant activity can be combined with natural antioxidants and applied in the meat industry. I will also share some of our recent data that shows how the science behind food processing and preservation can be interesting and beneficial to the food industry, consumers and government.

Alexandra Whisnant (@gatecommedesfilles), chocolatier, gâté comme des filles, Somerville, MA

Abstract: Innovation in food science and technology is the alternative to overcome the current challenges of the food industry. In my talk, I will discuss some food model systems that we are currently exploring through knowledge/tools from chemistry, biology, and physics. For example, despite goat milk having benefits for human health over cow's milk, goat milk yogurt (GY) has a delicate texture, a more rupture-susceptible gel structure, low consistency, and viscosity, which reduces its overall acceptability by the consumer. Thus, new innovative methods such as ultrasound and high hydrostatic pressure can be alternatives to improve the quality of GY. Furthermore, the addition of inulin, maltodextrin, whey protein, and cupuassu pulp can improve the taste and rheological characteristics of goat milk yogurts. Recent advances on kefiran, an exopolysaccharide derived from kefir grain microflora, have shown its electrospinning ability to be transformed in nanofiber, potentially useful for encapsulating bioactive ingredients for food, probiotic/ drug delivery, and scaffolds to tissue engineering. On the other hand, conventional food preservation methods have demonstrated several disadvantages and limitations in the efficiency of microbial load reduction and maintaining food quality. Hence, non-thermal preservation technologies (NTPT) and alternative chemical compounds (ACC) have been considered a high promising replacer for decontamination, increasing the shelf life and promoting low levels of physicochemical, nutritional, and sensorial alterations in meat and fish. However, NTPT promotes the connections between the oxidative process (lipids and proteins) and the impact of color and rheology characteristics. The demand for more environment-friendly technologies has gained worldwide attention to food processing and preservation. Brazil has over 40,000 varied plant species rich in phytochemicals, which have great potential as a source of ACC that can be replacer for synthetic compounds currently applied in the meat industry. Nevertheless, natural antioxidant compounds are not stable. In this way, nanocomposites based on biodegradable polymer/graphene-based nanomaterials with antioxidant activity can be combined with natural antioxidants and applied in the meat industry. I will also share some of our recent data that shows how the science behind food processing and preservation can be interesting and beneficial to the food industry, consumers and government.

Abstract: Living matter relies on the self organization of its components into higher order structures, on the molecular as well as on the cellular, organ or even organism scale. Collective motion due to active transport processes has been shown to be a promising route for attributing fascinating order formation processes on these different length scales. Here I will present recent results on structure formation on actively transported actin filaments on lipid membranes and vesicles, as well as the cell migration induced structure formation in the developmental phase of pancreas organoids.

Bryan Furman (@bs_pitmaster), Pitmaster, Bryan Furman BBQ, B's Cracklin Barbecue, Chef in Residence at Stone Barns Center for Food & Agriculture

Amanda Cohen (@dirtcandynyc), Dirt Candy, New York, NY

Tracy Chang (@gopagu), Pagu Restaurant, Cambridge, MA

Watch "The Science of Hand Pulled Noodles" on YouTube

Jason White (@teamsilent), Director of Fermentation at NOMA, Copenhagen, Denmark

Watch "Fermentation: A Springboard for Modern Gastronomy" on YouTube

Joanne Chang '91 (@jbchang), Flour Bakery and Café, Myers + Chang, author of "Flour", "Flour Too", "Myers + Chang at Home", and "Baking With Less Sugar"

Watch "The Science of Sugar" on YouTube

Dave Arnold (@cookingissues), Booker and Dax, author of "Liquid Intelligence," host of "Cooking Issues," founder of the Museum of Food and Drink

Harold McGee (@mcgee.onfood.onsmells), author of "On Food and Cooking," "Curious Cook," "Nose Dive: A Field Guide to the World's Smells"

Guillaume Duclos, Brandeis University
  Instabilities and liquid to solid transition in a three-dimensional active network
Margaret Gardel, University of Chicago
  Building soft, living materials
Mathias Kolle, MIT
  Optical emulsions, focused and in color
Chinedum Osuji, University of Pennsylvania
  Block Copolymer Assembly Nematic Solvents

I present a new mechanism whereby spatially varying order in a thin liquid crystal film, induced by chemical or topographic patterning on a substrate, can lead to spontaneous topography on an opposing free interface. Analytical and numerical results will be shown to elucidate this mechanism, together with recent experimental evidence and connections to other free interface problems.

Abstract: Open any biology textbook and you are likely to learn that, in contrast to eukaryotes, bacteria do not contain organelles to compartmentalize and facilitate cellular functions. However, numerous protein- and lipid-bounded organelles are known to exist within a diverse array of bacterial species. In my group, we look at the process of compartmentalization at a molecular level in order to understand the origins and functions of bacterial organelles and exploit them for future applications. I will discuss our work on the biogenesis and subcellular organization of the magnetic magnetosome organelles of magnetotactic bacteria and our recent discovery of ferrosomes—iron-accumulating compartments that define a novel class of bacterial organelles.

Watch "The ins and outs of bacterial organelles" on YouTube

Self-assembly of simple subunits into multi-subunit structures with increased complexity and functionality underlies many biological processes and is becoming an important route to bottom-up materials design. In this talk I will consider a special class of self-assembly processes --- self-limiting assembly --- defined as an assembly process that autonomously terminates at an equilibrium structure with a well-defined, finite size that is much larger than the size of individual subunits. I will begin with an overview of the basic statistical mechanical framework that describes the thermodynamics of self-assembly. With this framework, I will introduce the physical ingredients that are required to achieve self-limited assembly. I will then discuss three (time permitting) examples of self-limiting assembly, with results from theoretical and computational modeling as well as from experiments by collaborators: (1) Bacterial microcompartments, which are ‘organelles' inside of bacteria, consisting of large icosahedral protein shells that assemble around collections of enzymes; (2) Synthetic capsids (icosahedral shells) formed by self-assembling DNA origami subunits; and (3) Tubules whose self-assembly terminates at a well-defined length due to geometric frustration.

First, I'll present triaxial weaving, a craft technique used to generate surfaces using tri-directional arrays of initially straight elastic ribbons. We achieve smooth, three-dimensional weaved structures by prescribing in-plane curvatures to the flat ribbons. The potential of this novel design scheme is demonstrated with a few canonical target shapes.

Second, I'll present the mechanics of two elastic rods in a crossing contact, whose geometric counterpart is often referred to in the mathematics community as a ‘clasp.' We compare our experimental and computational results to a well-established description for ideal clasps of geometrically rigid strings, finding that the latter acts as an underlying ‘backbone' for the full elasticity solution.

Abstract: Biological systems can self-organize in complex structures, able to evolve and adapt to widely varying environmental conditions. Despite the importance of fluid flow for transporting and organizing populations, few laboratory systems exist to systematically investigate the impact of advection on their spatial evolutionary dynamics. In this talk, I will show how we can address this problem by studying the morphology and genetic spatial structure of microbial colonies growing on the surface of a viscous substrate. I will illustrate how the interplay between microbial growth geometry, metabolic activity and fluid flows can generate positive feedback with the environment and lead to accelerated propagation, fragmentation of the initial colony and the formation of growing microbial jets.

Bio: Dr. Severine Atis is a postdoctoral fellow in the physics department at the University of Chicago where she studies self-organization in active fluids in Professor William Irvine's group. She received her PhD from Sorbonne University in Physics where she worked with reaction wave propagation in disordered flows. She joined Professor David Nelson's group at Harvard University as a postdoctoral scholar where she worked on evolutionary dynamics coupled with hydrodynamic flows in collaboration with Professor Andrew Murray in the department of Molecular and Cellular Biology.


Watch "Growing in flows" on YouTube

Abstract: The spreading dynamics of genetic information plays a key role in evolution of spatially structured populations. Diffusive populations (which experience short-ranged migration or dispersal behaviour) exhibit spatiotemporal patterns of genetic variation which differ markedly from well-mixed populations (where each individual interacts with all others over the population range). Between these two extremes lies the situation of populations experiencing long-range dispersal, with migration events drawn at random from a broad probability distribution (akin to Lévy flights). Although long-range dispersal is ubiquitous in nature (plants whose seeds and pollen are spread wide by wind, water, or animals; pathogens riding on jetsetting humans), its evolutionary consequences are still being uncovered. I'll talk about recent work that uses simulations and theory to elucidate the patterns left behind by multiple genetic variants during range expansions driven by stochastic long-range dispersal. By studying a class of models in which the dispersal distribution is systematically broadened, I'll show how stochastic effects accumulate to give rise to qualitatively different phases and counterintuitive effects on both local and population-wide genetic diversity.

Garima Arora (@arorgarima), first Indian woman to win a Michelin Star, Asia's Best Female Chef 2019 by World's 50 best, Restaurant Gaa, Bangkok, Thailand

Watch "The Science of Indian Culinary Traditions" on YouTube

Marike van Beurden (@marikevanbeurden), Pastry Chef and Master Chocolatier, Dutch Chocolate Master 2013, 2nd World Chocolate Master 2013

Watch "Viscosity, Pastry and Chocolate" on YouTube

Jose Andrés (@chefjoseandres), Think Food Group, minibar, Jaleo

Watch "Honorary Book Celebration Lecture" on YouTube

Abstract: Phase separation is a common theme in physical and biological contexts, including the demixing of unlike lipids in cell membranes, the formation of membraneless compartments in the cytoplasm of cells, and the separation of cooled metal alloys. Although the equilibrium nature of such phase separations is now well-established, textbook material, new and surprising phenomena occur when such systems are driven out of equilibrium. I will describe the formation of striped phases in models of phase separating, binary mixtures under an applied field which drives the mixture in one direction. The drive induces a stripe order with the stripe size decreasing with increasing drive. Signatures of this stripe order persist in the disordered (mixed) phase and generate characteristic peaks in the structure factor of the mixture, reminiscent of an equilibrium microemulsion phase. I will then discuss the prospects of understanding this phenomenon more generally by deriving a coarse-grained field theory for the driven mixture.

Lois Ellen Frank (@lois_ellen_frank), New Mexico-based chef, author, Native food historian, "Native American with a modern twist," Red Mesa Cuisine, Santa Fe, New Mexico

Watch "Culinary Ash in Contemporary Native American Cuisine" on YouTube

Nina Compton (@ninacompton), James Beard winning Saint Lucian chef, chef/owner of Compére Lapin and Bywater Bistro in New Orleans, Louisiana

Watch "The Equation for Gnocchi" on YouTube

Andoni Luis Aduriz (@andoniluisaduriz), chef/owner of the two Michelin star restaurant Mugaritz, top 10 of The World's 50 Best Restaurants.
Ramon Perisé, Director of Fermentation and R&D at Mugaritz, Spain

Watch "Fermenting Brains. A Journey to Mugaritz microworld" on YouTube

Joanne Chang '91 (@jbchang), Flour Bakery and Café, Myers + Chang, author of "Flour," "Flour Too," "Myers + Chang at Home," and "Baking With Less Sugar"

Abstract: Topological defects are fundamental to the chaotic self-stirring dynamics of active nematics: materials with liquid crystal-like order but also a continual generation of non-equilibrium internal forces. In 2D active nematic monolayers, point-like disclination defects continually unbind, self-propel, and annihilate in pairs of opposite winding number. This generic behavior has recently been identified in a broad range of biophysical systems including growing bacterial colonies and epithelial tissues. However, bulk active materials cannot behave in the same way, because nematic defects are much more complex in 3D. Here, I'll show that the predominant topological excitations of 3D active nematics are closed-loop disclination lines that change type along their length and are topologically neutral as a whole—that is, they arise individually and self-annihilate. I'll also explore other uniquely 3D phenomena seen in active nematics, including twist distortions, defect reconnections, and a self-reconfiguring network of extended disclination lines.

Abstract: The ability of a material to undergo limited deformation is a critical aspect of conferring toughness as this feature enables the local dissipation of high stresses, which would otherwise cause fracture. The mechanisms of such deformation can be widely diverse. Although plasticity from dislocation motion in crystalline materials is most documented, inelastic deformation can also occur via in situ phase transformations in certain metals and ceramics, sliding of mineralized collagen fibrils in rooth dentin and bone, rotation of such fibrils in skin, frictional motion between mineral "platelets" in seashells, and even by mechanisms that also lead to fracture such as shear banding in glasses and microcracking in geological materials and bone. Resistance to francture (toughness) is thus a compromise—a combination of two, often mutually exclusive, properties of strength and deformability. It can also be considered as a mutual competition between intrinsic damage processes that operate ahead of the tip of a crack to promote its advance and extrinsic crack-tip shielding mechanisms that act mostly behind the crack tip to locally diminish crack-tip stresses and strains. Here we examine the interplay between strength and ductility and between intrinsic and extrinsic mechanisms in developing toughness in a range of biological and natural materials, including bone, skin and fish scales, and in new advance metallic alloys, notably high-entropy alloys.
YouTube recorded Webinar

Dave Arnold (@CookingIssues), Existing Conditions, author of "Liquid Intelligence," host of "Cooking Issues," founder of the Museum of Food and Drink
Harold McGee, (@Harold_McGee), author of "On Food and Cooking," "Curious Cook," and the forthcoming book "Nose Dive: A Field Guide to the World's Smells."

Watch "A Nose Dive into Kitchen Pyrolysis" on YouTube

Abstract: The interplay between fluid flows and living organisms plays a major role in the competition and organization of microbial populations in liquid environments. Hydrodynamic transport leads to the dispersion, segregation or clustering of biological organisms in a wide variety of settings. To explore such questions, we have created microbial range expansions in a laboratory setting by inoculating two identical strains of S. cerevisiae (Baker's yeast) with different fluorescent labels on a nutrient-rich fluid 10^4 to10^5 times more viscous than water. The yeast metabolism generates intense flow in the underlying fluid substrate several times larger than the unperturbed colony expansion speed. These flows dramatically impact colony morphology and genetic demixing, triggering in some circumstances a fingering instability that allows these organism to spread across an entire Petri dish in roughly 24 hours. We argue that yeast colonies create fluid flow by consuming nutrients from the surrounding fluid, decreasing the fluid's density, and ultimately triggering a baroclinic instability when the fluid's pressure and density contours are no longer parallel. Our results suggest that microbial range expansions on viscous fluids will provide rich opportunities to study the interplay between advection and spatial population genetics.

Watch YouTube presentation

Abstract: We re-examine a classic question in liquid-crystal physics: What are the elastic modes of a nematic liquid crystal? The analysis uses a recent mathematical construction, which breaks the director gradient tensor into four distinct types of mathematical objects, representing splay, twist, bend, and a fourth deformation mode. With this construction, the Oseen-Frank free energy can be written as the sum of squares of the four modes, and saddle-splay can be regarded as bulk rather than surface elasticity. This interpretation leads to an alternative way to think about several previous results in liquid-crystal physics. It also leads to a generalized concept of flexoelectricity, and to ideal liquid-crystal deformations in non-Euclidean geometry.

Abstract: Multivalent biopolymers phase separate into membrane-less organelles (MLOs) which exhibit liquid-like behavior. Here, we explore formation of prototypical MOs from multivalent proteins on various time and length scales and show that the kinetically arrested metastable multidroplet state is a dynamic outcome of the interplay between two competing processes: a diffusion limited encounter between proteins, and the exhaustion of available valencies within smaller clusters. Clusters with satisfied valencies cannot coalesce readily, resulting in metastable, longliving droplets. In the regime of dense clusters akin to phase-separation, we observe co-existing assemblies, in contrast to the single, large equilibrium-like cluster. A system-spanning network encompassing all multivalent proteins was only observed at high concentrations and large interaction valencies. In the regime favoring large clusters, we observe a slow-down in the dynamics of the condensed phase, potentially resulting in loss of function. Therefore, metastability could be a hallmark of dynamic functional droplets formed by sticker-spacer proteins.

Abstract: Over the past few years, mounting interests have been attracted in topics involving intrinsically disordered proteins (IDP). Particularly in the fields of protein engineering, supramolecular self-assembly, functional hydrogels and biomechanics, sophisticated design and manufacturing are realized through amalgamating the IDPs with bioactive components. As one type of the most important IDPs, elastin presents multiple extraordinary properties, including good biomechanical characteristics, biopolymeric phase separation behavior, biodegradability and low immunogenicity. These promising features allow elastin-like proteins to be developed as a new generation of functional biomaterials in the context of cross-disciplinary studies. However, it is challenging to supercharge elastin variants for macroscopic assembly of advanced materials. This talk will highlight recent technical advances and practical applications employing Supercharged elastin-like Proteins (SUPs). First, I will introduce the interplay between SUPs and surfactants and soft matter ensembles generated through the two-component complexation. Second, an artificial tongue consisting of SUPs and polyelectrolyte elements for whiskey discrimination will be underscored. Lastly, a recent finding on etiology of Alzheimer's disease and elastin would be presented.

Abstract: Gelation of colloidal suspensions plays a crucial role in the formation of numerous solids. Examples range from cement to yogurt, which results respectively from the aggregation of CSH nanoparticles and casein micelles. In both systems, short-range attractive interactions between the particles lead to the formation of a percolated network that is responsible for the solid-like behavior of the material. Generated by a kinetic arrest, these solids are out-of-equilibrium structures, whose properties are sensitive to the route followed during gelation. Indeed, external shear often comes to compete with the attractive interactions that drive the gelation, affecting the gel's microstructure, which encodes the gel's shear history. Such a "memory effect" is, for instance, easily visualized in the various morphologies of crack patterns that form when the gel is left to dry.

Abstract: Self-organization phenomena that lead to pattern formation and synchronization play an important role in biology, chemistry, physics and technological applications. They manifest for example in electrical waves on the heart muscle, fireflies flashing in unison, power-grid blackouts and neurological functions as well as disorders. I will present a versatile experimental setup based on optically coupled catalytic micro-particles, that allows studying synchronization patterns in very large networks of relaxation oscillators under well-controlled laboratory conditions. In particular I will show the experimental verification of the elusive spiral wave chimera state, whose existence was predicted more than 15 years ago. This pattern features a wave rotating around a spatially extended core that consists of phase-randomized oscillators. The spiral wave chimera is likely to play a role in cortical cell ensembles, arrays of SQUIDS and carpets of cilia. Furthermore, these experimental capabilities facilitate the free choice of network topology, coupling function as well as its strength, range and time delay, which can even be chosen as time-dependent. This opens the door to a broad range of future experimental inquiries into pattern formation and synchronization on large networks, which were previously out of reach.

Abstract: Optical techniques can enable non-invasive, in situ measurements of the properties of biologically or industrially relevant colloidal particles. One such property is the fractal dimension of fractal-like aggregates, which can be formed by some proteins when heated. Here, we consider recent experiments that used holographic microscopy, a technique based on optical interference, and an optical scattering model based on an effective-medium theory to determine the fractal dimension of colloidal aggregates. We numerically generate fractal aggregates with a known structure, simulate the images that would be experimentally obtained from those aggregates, and analyze the simulated images using the proposed scattering model. Our results show that holographic microscopy accurately determines the fractal dimension (to within ~10%) when multiple scattering within the aggregates is negligible. They also suggest that holographic microscopy is useful because it probes the extinction cross section of the aggregates.

José Andrés (@chefjoseandres), Think Food Group, minibar, Jaleo
Harold McGee, (@Harold_McGee), author of "On Food and Cooking", "Curious Cook"

Joan Roca (@CanRocaCeller), El Celler de Can Roca, Girona, Spain, best restaurant in the world 2013 and 2015
Heloise Vilaseca, (@heloislois), director of R&D, El Celler de Can Roca, Girona, Spain
Ahmoy Panagiotis, El Celler de Can Roca, Girona, Spain

Animals fly, run, swim, and crawl by self-deforming, changing the shape of their bodies using internally generated forces, to interact with their surroundings. While traditionally viewed as obstacles to locomotion, limbless animals like snakes must self-deform to take advantage of environmental heterogeneities and overcome drag on the elongate body. While progress has been made in understanding undulatory locomotion in fluids, little is known about how snakes ably traverse terrestrial terrains ranging from desert to forest. In this talk I will present our studies of the motion of live snakes in laboratory models of terrestrial terrain. I will discuss how a permanently deformable substrate, granular matter, was found to help or hinder snakes depending on how the waveform remodeled the material. Surprisingly, locomotion was non-inertial despite the surface slithering speed, and resistive force theory accurately predicted performance of a desert specialist snake moving in a frictional-fluid-like regime. We next studied the neuromechanical control strategy of this desert specialist by observing it traversing a simple multi-component terrain—a single row of posts in a uniform substrate. Combining trajectories from many trials revealed a pattern of trajectory reorientations reminiscent of the diffraction of, e.g., light. Using this mechanical diffraction phenomenon, we show that the desert specialist could rapidly transit the sparse obstacles without additional neural input by relying on passive body buckling. Lastly, I will discuss the role of control specialization by comparing the waveform of the desert specialist with that of a habitat generalist snake as they move through a 2D array of rigid posts embedded in a slippery whiteboard. We used persistent homology to search for periodic cycles in the kinematics and found that the sand snake, adapted to use the omnipresent GM in its natural habitat, targeted desired kinematics while those of the generalist, which encounters a range of materials and obstacle densities, were aperiodic. Force measurements in a simplified terrain, a single post in the whiteboard, suggested that the generalist is instead targeting an advantageous force pattern. Studying the interplay between animal and environment furthered our understanding of the terrain itself as well as the animals' goals and their strategies for achieving them.

In this talk I will show several examples of an interesting and surprising competition between buoyancy and Marangoni forces.

First, I will introduce the audience to the jumping oil droplet—and its sudden death—in a density stratified liquid consisting of water in the bottom and ethanol in the top : After sinking for about a minute, before reaching the equilibrium the droplet suddenly jumps up thanks to the Marangoni forces. This phenomenon repeats about 30-50 times, before the droplet falls dead all the sudden. We explain this phenomenon and explore the phase space where it occurs.

Next, I will focus on the evaporation of multicomponent droplets, for which the richness of phenomena keeps surprising us. I will show and explain several of such phenomena, namely evaporation-triggered segregation thanks to either weak solutal Marangoni flow or thanks to gravitational effects. The dominance of the latter implies that sessile droplets and pending droplets show very different evaporation behavior, even for Bond number << 1. I will also explain the full phase diagram in the Marangoni number vs Rayleigh number phase space, and show where Rayleigh convections rolls prevail, where Marangoni convection rolls prevail, and where they compete.

The research work shown in this talks combines experiments, numerical simulations, and theory. It has been done by and in collaboration with Yanshen Li, Yaxing Li, and Christian Diddens, and many others.

Enric Rovira (@enrovira), Master Chocolatier, Barcelona, Spain
Ramon Morató, (@ramonmorato_), Master Chocolatier, author of "Chocolate" and "Four in One"

How do we move when walking alone or inside dense crowds? Is it possible to develop mathematical models capable of accurately describing the statistical properties of pedestrian dynamics? These challenging and fascinating scientific questions can also directly impact on our daily comfort, and even safety, when visiting crowded urban areas.

In recent years we^[1] have been conducting a number of real-life experiments aimed at providing some answers. We employ 3d depth-sensor cameras to observe the dynamics of millions of pedestrians in a variety of real-life settings: from a small University corridor, to a museum entrance, city festivals, crowded train stations, etc. Our 3d depth-map cameras have allowed us to record pedestrian trajectories with high space and time accuracies while preserving the privacy of single individuals. Thanks to the large acquired datasets we could study fluctuations and not just average behaviours.

To describe our observations, we borrowed and extended mathematical tools ordinarily used in physics. In this talk we will present some of them and we will discuss how the dynamics of single individuals can be modeled in terms of path integrals or stochastic differential equations. We will discuss how to model collisions between individuals, in low density crowds, and how to learn generic space-time patterns. We will also show how machine learning algorithms can be used to accurately extract orientational data from depth-map images and, finally, we will discuss experiments that we conducted in order to investigate the possibility to nudge human crowds via light stimuli.

Alessandro Corbetta, Jasper Meeusen, Chung-min Lee, Roberto Benzi, Federico Toschi
Physics-based modeling and data representation of pairwise interactions among pedestrians Journal Article
Physical Review E, 98 , pp. 062310, 2018.

Alessandro Corbetta; Chung-min Lee; Roberto Benzi; Adrian Muntean; Federico Toschi
Fluctuations around mean walking behaviours in diluted pedestrian flows
Physical Review E, 95 , pp. 032316, 2017.

Untangling structure-function relationships on the nanoscale is critical to understanding biological molecular machinery and to engineering human-made nano-devices. In this talk I will give an overview of my lab's approaches to probing and controlling sub-nanometer atomic arrangements in biological and synthetic systems. First, I will introduce our single molecule conductance measurements which show that molecular conductance signatures can serve as Angstrom-scale rulers and demonstrate how we apply these techniques to probe the conductance of DNA building blocks. Next I will discuss our approaches to single molecule absorption spectroscopy using an optical tweezer and outline some future research directions.

Spontaneous collective motion or flocking of a large collection of self-propelled entities, is seen on many scales in nature, ranging from bird flocks to the coherent migration of cells during development, along with several synthetic realizations in granular and colloidal systems. Understanding the distinct nonequilibrium phenomena in such active fluids remains crucial to developing insight into the organizational principles of living matter, while still posing a serious challenge to conventional statistical mechanics. On the other hand, condensed matter now uses a wider range of tools, particularly topology, that is not rooted in equilibrium physics. In this talk I will present two examples of topological phenomena that acquire unique realizations in polar active fluids. In the first half, I will show how broken time-reversal symmetry due to spontaneous motion allows polar flocks on a curved surface to support topologically protected sound modes, analogous to edge states in a quantum Hall system. Later I will switch to discuss flocks flowing through a disordered environment, where the ordered flock undergoes a two-step melting transition through an intriguing intermediate state - a vortex glass with frozen topological defects. I will end with a brief outlook on the broader role of topology in active matter.

Carles Tejedor (@CarlesTejedor), Oilmotion and Sofia Be So Restaurant, Manresa, Spain
Pere Planagumà, ROM and Mas de Torrent restaurants, Spain

The invasion of one fluid into another of higher viscosity is unstable in a quasi-two dimensional geometry. In isotropic systems, this viscous-fingering instability typically produces complex patterns that are characterized by repeated branching of the evolving structure, which leads to the common morphologies of fractal or dense-branching growth. In anisotropic systems, by contrast, the growth morphology changes to a highly ordered dendritic growth characterized by stable needle-like protrusions decorated with regular side-branches. We investigate such morphology transitions between dendritic growth and dense-branching growth in an intrinsically anisotropic liquid; a lyotropic chromonic liquid crystal in the nematic phase. We show that the transition is remarkably sensitive to the interface velocity and the viscosity ratio between the less-viscous inner fluid and the more-viscous outer liquid crystal. We discuss the importance of a stable shear alignment of the liquid crystal in governing the morphology transition to dendritic growth.

Expanding our work to more complex fluids, dense suspensions, that exhibit both shear-thickening and shear-jamming behavior as a response to an applied stress allows us to probe transitions from flow instabilities to fracture instabilities. Displacing a cornstarch suspension by a pressure-controlled injection of air, we observe a variety of patterns: smooth fingering in the fluid regime and different modes of fractures, ranging from slow branched cracks to single fast fractures. We discuss strategies to predict and control these different failure modes in dense suspensions.

Marsia Taha (@marsia_taha_gustu), Gustu, La Paz, Bolivia
Natalie Del Carpio, Gustu, La Paz, Bolivia

Plant matter is being used increasingly in construction and in various other applications thanks to its remarkable porous and mechanical properties, but water transfers play a critical role on these properties and their possible alteration. Water in plants may be either in a “free” liquid state in capillaries, or in a “bound” state after adsorption in cell-walls, associated with significant deformation of the structure. Here we show that the coexistence of these two effects strongly affect the transport properties.

We demonstrate this from Synchrotron and MRI observation in hardwoods, which exhibit a relatively simple hydraulic structure. Capillary imbibition dynamics appears to be dramatically damped (velocity decreased by several orders of magnitude), but the liquid can still climb over significant heights (in contradiction with its dynamics) as soon as sufficient bound water has been adsorbed. This contradiction is confirmed by 3D Synchrotron images of the internal structure obtained during imbibition, which show that the liquid-air interfaces in the capillary vessels remain planar, which implies negligible Laplace pressure, but significantly advance along the vessels, again unexpectedly.

From MRI measurements allowing to distinguish bound and free water, but also direct measurements of the induced macroscopic deformation distribution in time, we then show that this contradiction is explained by the adsorption of a slight amount of bound water in the capillary walls. This adsorption governs the process: it momentarily damps wetting and then allows further advance later when the walls are saturated with bound water. The generality of the process for hygroscopic systems is demonstrated with a model material, i.e. hydrogel, from which both the position and shape evolution of liquid-air interface and the adsorption and propagation of bound water may be directly observed (see below). This suggests the development of bio-inspired porous materials able to absorb liquid with a tunable timing, for pharmaceutical or chemical engineering applications.

We finally discuss the opposite process, i.e. liquid transfers in hardwood structures during drying, as observed from MRI and Synchrotron imaging, and in particular show the essential role of bound water.

Affinity maturation (AM) is the process through which the immune system evolves antibodies (Abs) which efficiently bind to antigens (Ags), e.g. to spikes on the surface of a virus. This process involves competition between B-cells: those that ingest more Ags receive signals (from T helper cells) to replicate and mutate for another round of competition. Modeling this process, we find that the affinity of the resulting Abs is a non-monotonic function of the target (e.g. viral spike) density, with the strongest binding at an intermediate density (set by the two-arm structure of the antibody). We argue that, to evade the immune system, most viruses evolve high spike densities (SDs). This is indeed the case, except for HIV whose SD is two orders of magnitude lower than other viruses. However, HIV also interferes with AM by depleting T helper cells, a key component of Ab evolution. We find that T helper cell depletion results in high affinity antibodies when SD is high, but not if SD is low. This special feature of HIV infection may have led to the evolution of a low SD to avoid potent immune responses early on in infection.

Advances in optical stepper lithography have opened the door to high-throughput on-chip parallel fabrication and assembly of addressable complex nanoscale structures, including processors and memory, that have amazingly low defects. By combining these advances with an enabling particle fabrication-release protocol, which involves roughness controlled depletion attractions, we make idealized two-dimensional monolayers of differently shaped mobile colloidal tiles that can be pre-assembled at high densities in interesting new ways without the need for patchy programmable interactions. The size and volume fraction of the depletion agent are tuned so that the face of each tile remains near the flat smooth substrate, yet the edges of the tiles have nearly hard interactions. As a first demonstration of lithographically pre-assembled monolayers (litho-PAMs), we produce a Brownian Penrose P2 quasi-crystal (QC) of dense microscale kite and dart tiles with low defects over large areas, and we study this fluctuating five-fold P2 QC using time-lapse optical video microscopy. Beyond measuring the equilibrium fluctuations and structure of this multi-scale form of soft matter, we examine motif dynamics of sets of tiles and calculate motif superstructural pair correlation functions. Moreover, by removing a confining wall, we melt this P2 QC and deduce the tile area fraction associated with its melting. Since a wide range of shape-designed tiles can be fabricated and pre-configured lithographically, litho-PAMs represents a major advance over prior work that merely fabricated different colloidal shapes using lithography, and it opens the door to a wide range of new experimental soft-matter systems. The related paper is: Nature 561: 94–99 (2018)

An odor is not composed of a single molecule but a mixture of various molecules in most cases. These molecules are so-called ‘odorous molecules', and it is known that the number of odorous molecules amounts to approximately 400,000 or more. As hundreds of, or sometimes thousands of the odorous molecules mix together to form an odor, there are a vast number of odors existing in the world. Such versatility is one of the reasons why odor analysis takes time and requires special analytical instruments which are usually bulky and very expensive. On the other hand, the complex and versatile nature of odors indicates that they obviously contain detailed information on their origin which we have not been fully understood and exploited so far. In this talk, I will introduce our olfactory sensor project and share with you some of the recent results including fundamental physical/chemical studies and several examples of applications. By using a newly developed sensing platform—Membrane-type Surface stress Sensor (MSS)—with high sensitivity and tunable selectivity, we are trying to overcome various barriers to a practically useful mobile olfactory sensing system which has never been achieved.

David Zilber (@David_Zilber), Director of Fermentation at Noma in Copenhagen, Co-author with René Redzepi of "The Noma Guide to Fermentation"
Jason White

The best understood crystal ordering transition is that of 2D freezing, which proceeds by the rapid eradication of lattice defects as the temperature is lowered below a critical threshold. This behavior is described by the Kosterlitz-Thouless-Halperin-Nelson-Young (KTHNY) model, which assumes that the system in question is confined to an infinite flat plane. However, many natural and man-made 2D systems possess finite curvature and/or non-trivial topology. Crystals that assemble on such surfaces may be required by topology to have a minimum number of lattice defects, called disclinations, that act as conserved topological charges—consider the 12 pentagons on a soccer ball or the 12 pentamers on a viral capsid. Moreover, crystals assembled on curved surfaces can spontaneously develop additional lattice defects to alleviate the stress imposed by the curvature. A priori, it is unclear how—or even if—crystallization can proceed in such a system. In this talk, I will discuss the results of experiments and simulations that address the phase behavior of repulsive particles on the surface of a sphere, the simplest surface on which it is impossible to eliminate lattice defects. Our work shows that freezing on a sphere proceeds by the formation of a single, encompassing crystalline 'continent', which sequesters remaining defects into 12 isolated 'seas' with the same icosahedral symmetry as soccer balls and viruses. By aligning the vertices of an icosahedron with the defect seas and unfolding the faces onto a plane, we can use this broken symmetry to construct a new order parameter that reveals the underlying long-range orientational order of the lattice.

Joanne Chang '91 (@jbchang), Flour Bakery and Café, Myers + Chang, author of "Flour", "Flour Too", "Myers + Chang at Home", and "Baking With Less Sugar"

Dave Arnold (@CookingIssues), Booker and Dax, author of "Liquid Intelligence", host of "Cooking Issues", founder of the Museum of Food and Drink
Harold McGee (@Harold_McGee), author of "On Food and Cooking", "Curious Cook"

Many cellular and developmental processes rely on self-organization of protein patterns in space and time for proper functioning. These proteins can couple to molecular force generators and pattern mechanical stresses, leading to cell shape deformation. But how does cell shape information get transmitted to these upstream regulatory proteins? In this talk, I will present a robust mechanism that couples cell shape to biochemical regulators in starfish oocytes. When the oocytes are confined in different geometries, we find that the meiotic Rho pulse adapts to cell shape. Through mathematical modeling, we show that the excitable Rho pulse is tightly regulated by a bistable front of the Rho regulator Ect2. In turn, the Ect2 front decodes the cell shape information encoded in the Cdk1 (cell cycle regulator) cytosolic gradient, allowing cell shape to provide feedback on biochemical processes. We posit that the hierarchical coupling between a biochemical gradient and self-organization is a robust mechanism for cell shape sensing and mechanochemical feedback.

Many cellular and developmental processes rely on self-organization of protein patterns in space and time for proper functioning. These proteins can couple to molecular force generators and pattern mechanical stresses, leading to cell shape deformation. But how does cell shape information get transmitted to these upstream regulatory proteins? In this talk, I will present a robust mechanism that couples cell shape to biochemical regulators in starfish oocytes. When the oocytes are confined in different geometries, we find that the meiotic Rho pulse adapts to cell shape. Through mathematical modeling, we show that the excitable Rho pulse is tightly regulated by a bistable front of the Rho regulator Ect2. In turn, the Ect2 front decodes the cell shape information encoded in the Cdk1 (cell cycle regulator) cytosolic gradient, allowing cell shape to provide feedback on biochemical processes. We posit that the hierarchical coupling between a biochemical gradient and self-organization is a robust mechanism for cell shape sensing and mechanochemical feedback.

Infection with Human Immunodeficiency Virus (HIV) is incurable, despite the existence of antiretroviral therapy (ART) that effectively targets the viral life cycle. The lack of a cure for HIV infection has been linked to an extremely rare population of replication-competent HIV proviruses that persists during ART even when viremia is undetectable. To study the latent population requires a system that can 1) process millions of cells at ultra-high throughput, 2) detect one infected cell within a background of a thousand uninfected cells, and 3) single cell sort and sequence the rare cell population. This talk will discuss the development of a microfluidic workflow that can single cell RNA-sequence infected cells containing a single HIV proviral sequence. Although the system was design to understand the genomic mechanisms that control HIV latency in vivo, it can be applied to find and sequence any cell based on the presence of DNA or RNA biomarkers.

Living systems are out of equilibrium and nearly all cellular processes require a continual supply of energy. The realization of the importance of non-equilibrium processes for subcellular organization helped to inspire the field of active matter, which seeks to understand the behaviors of system in which energy is input at the microscale. Despite intensive work on the dynamics and mechanics of active matter, there is very little known about the thermodynamic flows in these systems which are ultimately responsible for their non-equilibrium nature. Such thermodynamic flows are also extremely important (and extremely poorly understood) in biological systems, because the breakdown of metabolic processes responsible for energy transduction has diverse cellular and developmental consequences, and underlies a variety of diseases. In this talk, I will describe quantitative experiments on: 1) the non-equilibrium thermodynamics of mixtures of microtubules and molecular motors; 2) the metabolism of mammalian oocytes.

From power grids to neurons, oscillator networks represent a broad class of human-made and naturally occurring dynamical systems. Behaviors of multicellular organisms are organized by specialized neural tissues, underscoring the rich spatiotemporal patterns such networks exhibit. Towards developing synthetic analogs, we build and study a rudimentary model oscillator network system composed of Belousov-Zhabotinsky chemical oscillators housed in microfluidic wells and diffusively-coupled through PDMS membranes. In this talk, I will highlight recent work on two different network topologies with inhibitory coupling: stars or "hub and spoke" networks and a ring of three oscillators. For the former, I will discuss how the phase relationship between the hub and arm nodes is altered by the number of arms. For the latter, I will show how optimal control theory can be used to generate spatiotemporal patterns of photochemical perturbations that drive the network between its two attractors: wave states that propagate around the network with opposite sense. Such switching can leverage the system's inherent bistability to robustly generate different gaits at will or store information.

Colloidal suspensions are ubiquitous in our daily life. Micrometric particles dispersed in a solvent are indeed present in common liquids such as paints, inks or even food products. We will discuss the properties of those colloidal suspensions from their liquid phase to special properties of their solid deposits after drying. First, colloidal suspensions exhibit a wide range of rheological behaviors from shear-thinning to yield stress fluids. We will focus on the shear-thickening transition when dense suspensions experience a dramatic increase in viscosity above a critical shear-stress. By changing the physico-chemistry of the particles, we can tune this rheological transition and thus understand the interactions involved in this behavior. Increasing concentration can also be noticed during drying when solvent evaporates: particles finally form a solid deposit. After drying, a drop of a colloidal suspension leads to a variety of patterns from coffee-stain to more homogeneous coatings in paintings. We will discuss the effect of the initial concentration of particles on the drying pattern and on the subsequent mechanical instabilities. Finally, after the whole drying of the colloidal suspension, coatings are achieved. Depending of the nature of the particles, we can tune the wettability of the substrate up to superhydrophobic solid. We will briefly discuss how such a water-repellent substrate can allow levitation of liquids.

Metabolism is fundamental to all living systems. It drives cell growth, fuels ion pumps, powers cell migration, and much more. In the absence of cell metabolism, active processes that define life would cease to exist. Despite great leaps in understanding metabolism's role in maintaining cell homeostasis and contributing to pathological disorders, connections between cell mechanical events and energy metabolism remain poorly understood. In this talk, I present work focused on measuring the metabolic state of cells during collective cell migration achieved through unjamming of the confluent epithelial layer.

Professor David (Dave) Weitz is the Mallinckrodt Professor of Physics and Applied Physics at Harvard University He is the director of the NSF Materials Research Science Engineering Center at Harvard, as well as the co director of the BASF Advanced Research Initiative His research group at Harvard investigates the behavior of soft materials, studies a variety of biological systems from a soft matter perspective, and is well known for pioneering work in the area of microfluidics, including the physics of microfluidics, the engineering of microfluidic devices, and the application of microfluidics to biology, materials science, and two phase flow in porous media Weitz and his research group have extensive interactions with industry, with some of their work motivated by science that addresses technologically important problems Research in the group has led to several start up companies In addition to his research, Professor Weitz teaches courses in innovation and entrepreneurship, and is one of the founding faculty of the highly popular Harvard and EdX course Science Cooking From Haute Cuisine to Soft Matter Science.

Professor Weitz will talk about the relationship between scientific innovation and commercialization, and will describe different routes to entrepreneurship based on his experience in creating and advising biotech and materials startup companies He will also answer student questions on when and how to create or work for a start up company.

Professor Weitz received his B Sc In Physics from the University of Waterloo and his PhD from Harvard University He worked as research physicist for 18 years at Exxon, leading the Interfaces and Inhomogeneous Materials group and Complex Fluids area Prior to joining Harvard, he was Professor of Physics at University of Pennsylvania.

Microswimmers, and among them aspirant microrobots, generally have to cope with flows where viscous forces are dominant, characterized by a low Reynolds number (Re). This implies constraints on the possible sequences of body motion, which have to be nonreciprocal. Furthermore, the presence of a strong drag limits the range of resulting velocities. In this presentation, I will propose a swimming mechanism which uses the buckling instability triggered by pressure waves to propel a spherical, hollow shell. With a macroscopic experimental model, I'll show that a net displacement is produced at all Re regimes. An optimal displacement caused by nontrivial history effects is reached at intermediate Re. I'll show that, due to the fast activation induced by the instability, this regime is reachable by microscopic shells. The rapid dynamics would also allow high-frequency excitation with standard traveling ultrasonic waves. Scale considerations predict a swimming velocity of order 1  cm/s for a remote-controlled microrobot, a suitable value for biological applications such as drug delivery.

Droplet-based microfluidics, a method to produce emulsion drops in a controlled way and at high-throughputs, enables the miniaturization and automation of biological and chemical experiments. Each emulsion drop is used as a closed reaction vessel, enabling the performance of thousands of experiments per second, at throughputs traditional technologies cannot meet. To prevent emulsion drops from coalescing, they can be stabilized with surfactants. They adsorb at the liquid-liquid interface, lower the interfacial tension, and add steric stability. For most drop-based biological assays, aqueous drops are dispersed in fluorinated oils. These drops are stabilized with fluorinated surfactants, composed of two perfluoropolyether blocks linked to a polyethylene glycol (PEG) block. We studied how the composition of fluorinated surfactants influences the stability of emulsion drops and how the surfactant can contribute to the transport of encapsulants between drops leading to cross-contamination. We show that the mechanical and thermal stability of single emulsion drops strongly depends on the composition of the surfactants. We studied the leakage from double emulsions, resulting in cross-contamination, and show that it is mainly caused by tiny emulsion drops with sizes around 100 nm that spontaneously form at the water-oil interface. We show that the leakage can be reduced by an order of magnitude if surfactants that only moderately lower the interfacial tension or double emulsions with shell thickness similar to the diameter of the spontaneously forming drops are used. Lastly, I will present novel types of surfactants containing a catechol group in the hydrophilic block, that can be ionically cross-linked at the interface of a drop, creating a viscoelastic shell. We demonstrate that by cross-linking the surfactant at the drop interface, we create capsules that show high mechanical stability, and are impermeable to encapsulants. Leveraging their stickiness, we demonstrate that these capsules, if densely packed, can be printed into 3D structures.

Surface acoustic wave (SAW) technology integration into microfluidics has gained significant attention over the past years and has great potential to support and advance flow cytometry, cell sorting, and sample handling. SAW-based microfluidics provides many advantages such as versatile fluid handling, biocompatibility, easy integration into various channel designs, rapid prototyping, and is compact while maintaining all the benefits of using a microfluidic device. One of the more notable advantages that has been shown are the abilities to actively sort or provide spatial control of particles. We discuss this technology and its various applications with an emphasis on cell sorting. I report a fully enclosed microfluidic fluorescence activated cell-sorting (µFACS) device that employs a single transducer to generate traveling surface acoustic waves (TSAW) to sort cells upon fluorescence detection at rates comparable to conventional jet-in-air FACS machines, with sort purity and cell viability in excess of 90%. The device operates in continuous flow without encapsulating cells in droplets or labeling them with responsive beads prior to sorting. By studying SAW's fast fluidic actuation and forces in microchannels, we can engineer a variety of biocompatible SAW-based microfluidic devices for the field of flow cytometry and cell sorting.

Cartographers have early realized that it is impossible to draw a flat map of the Earth without deforming continents. Gauss later generalized this geometrical constrain in his Theorema Egregium. Can we invert the problem and obtain a 3D shape by changing the local distances in an initially flat plate? This strategy in widely used in Nature: leaves or petals may develop into very complex shapes by differential growth. From an engineering point of view, similar shape changes can be obtained when a network of channels embedded in a flat patch of elastomer is inflated. Can we program the final inflated shape?

Understanding the forces on small bodies at a fluid interface has significant relevance to a range of natural and artificial systems. In this talk, I will discuss two recent investigations in my lab where we've developed custom experiments to explore different forces on “capillary disks”: centimeter-scale hydrophobic disks trapped at an air-water interface.

In the first part, we investigate the friction experienced by a capillary disk sliding along the interface. We demonstrate that the motion is dominated by skin friction due to the viscous boundary layer that forms in the fluid beneath the moving body. We develop a simple model that considers the boundary layer as quasi-steady, and that is able to capture the experimental behavior for a range of disk radii, masses, and fluid viscosities.

In the second part, we present direct measurements of the attractive force between capillary disks. It is well known that objects at a fluid interface may interact due to the mutual deformation they induce on the free surface, however very few direct measurements of such forces have been reported. In the present work, we characterize how the attraction force depends on the disk radius, mass, and relative spacing. The magnitudes of the measured forces are rationalized with a simple scaling argument and compared directly to numerical predictions.

Future directions in this area will also be discussed, in particular, we are beginning to investigate the motion and interactions of "active" capillary disks at the interface.

Controlled and programmable fabrication of functional materials at the nano to micro scales under mild aqueous conditions is an unmet challenge. Our approach to addressing these challenges is biofabrication, that is to understand and utilize the programmable functionalities of biologically derived materials and interactions. Viral assemblies have attracted substantial attention as templates for materials synthesis due to their precisely controlled dimensions, chemical functionalities and the ability to impart additional modalities through genetic modification. We harness several unique properties of tobacco mosaic virus (TMV) for facile synthesis of catalytically active palladium (Pd) nanoparticles. Unique advantages of TMV templates include robust nanotubular structure providing large surface area, high stability in a wide range of conditions, easy mass production and biological safety. We have demonstrated size-controlled synthesis of small palladium nanoparticles under mild aqueous conditions via spontaneous reduction of precursors. High catalytic activity and stability of TMV-templated Pd nanoparticles are examined via dichromate reduction reaction. The results show that the TMV-templated Pd nanoparticle synthesis offers attractive routes to highly active, controlled and stable catalyst systems.

Polymeric hydrogels offer attractive platforms for a large range of applications including bioassays, separation and catalysis. We exploit simple photo-induced radical polymerization of poly(ethylene glycol) diacrylate and related materials to capture the as-prepared viral-nanoparticle complexes for facile catalytic reaction applications via replica molding and interfacially initiated hydrogel layer synthesis. This simple, robust and readily tunable scheme allows the large nanocomplexes to be captured and utilized without aggregation or leakage in a stable fashion while small molecule reactants and products can access the catalytic sites with minimal mass transfer limitation. Combined, our facile synthesis-capture strategy integrates potent viral nanotemplates, high catalytic activity and stability of the small nanocatalysts, and robust polymerization schemes. We thus believe that our strategy can be readily extended to programmable manufacturing of a large array of multifunctional materials.

In this presentation, our recent progress on the fabrication of multifunctional membranes via interfacially initiated radical polymerization offering controlled macroporous structures for size-selective protein purification as well as catalytic remediation of toxic compounds will be highlighted.

Early in embryonic development the blastocyst consists of a mix of two different cell populations, one primed towards the epiblast which will later develop into the fetus, and one primed for the endoderm, which will develop into the amniotic sac. Initially, those two populations are mixed and later they segregate into the fetus and amniotic sac. Using embryonic stem cells as a relevant model system, we use optical tweezers to quantify the physical properties of those two populations and demonstrate that their viscoelastic properties are significantly different. By modeling, we also show that this relatively small but significant difference in viscoelasticity in those two cell populations is enough to cause a segregation of the two populations, hence, the biomechanical properties alone can drive the process.

Mechanical forces and biophysical properties of cells are also vital for the morphogenesis of organs and embryos. However, how mechanical force and biophysical properties specifically contribute to tissue formation is poorly understood, predominantly due to a lack of tools to measure and quantify biomechanical parameters deep within living developing organisms without causing severe physiological damage. Using an adapted version of optical tweezers we quantify cellular viscoelasticity as deep as 100-150 µm within living embryos and demonstrate that liver and foregut morphogenesis in zebrafish entails progenitor populations with varying mechanical properties. Gut progenitors exhibit are more elastic compared to the more viscous neighboring cell populations, indicating that viscoelastic properties influence specific morphogenetic behaviors. The higher elasticity of gut progenitors correlates with an increased cellular concentration of microtubules and may be decisive for organ positioning. This approach opens new possibilities for quantitative in vivo investigation of cell mechanics in biological systems with complex 3D organization, such as embryos, explants or organoids.

Controlled and programmable fabrication of functional materials at the nano to micro scales under mild aqueous conditions is an unmet challenge. Our approach to addressing these challenges is biofabrication, that is to understand and utilize the programmable functionalities of biologically derived materials and interactions. Viral assemblies have attracted substantial attention as templates for materials synthesis due to their precisely controlled dimensions, chemical functionalities and the ability to impart additional modalities through genetic modification. We harness several unique properties of tobacco mosaic virus (TMV) for facile synthesis of catalytically active palladium (Pd) nanoparticles. Unique advantages of TMV templates include robust nanotubular structure providing large surface area, high stability in a wide range of conditions, easy mass production and biological safety. We have demonstrated size-controlled synthesis of small palladium nanoparticles under mild aqueous conditions via spontaneous reduction of precursors. High catalytic activity and stability of TMV-templated Pd nanoparticles are examined via dichromate reduction reaction. The results show that the TMV-templated Pd nanoparticle synthesis offers attractive routes to highly active, controlled and stable catalyst systems.

Polymeric hydrogels offer attractive platforms for a large range of applications including bioassays, separation and catalysis. We exploit simple photo-induced radical polymerization of poly(ethylene glycol) diacrylate and related materials to capture the as-prepared viral-nanoparticle complexes for facile catalytic reaction applications via replica molding and interfacially initiated hydrogel layer synthesis. This simple, robust and readily tunable scheme allows the large nanocomplexes to be captured and utilized without aggregation or leakage in a stable fashion while small molecule reactants and products can access the catalytic sites with minimal mass transfer limitation. Combined, our facile synthesis-capture strategy integrates potent viral nanotemplates, high catalytic activity and stability of the small nanocatalysts, and robust polymerization schemes. We thus believe that our strategy can be readily extended to programmable manufacturing of a large array of multifunctional materials.

In this presentation, our recent progress on the fabrication of multifunctional membranes via interfacially initiated radical polymerization offering controlled macroporous structures for size-selective protein purification as well as catalytic remediation of toxic compounds will be highlighted.

Bubbles are commonly found in the world around us, from industrial processes to carbonated beverages. In this talk I will present two studies about bubbles, from an applied use to a fundamental phenomenon. First, I will discuss the use of bubbles to prevent the growth of marine biofouling. Bubbles rising along a submerged surface have been shown to inhibit biofouling growth, but little work has been done to determine the primary mechanisms responsible for their antifouling behavior. Here I will present a combination of field and laboratory experiments used to gain insight into the mechanisms at play, thus laying a foundation for optimization of this antifouling technique.

For the second half of the talk, I will discuss the fundamental stability of bubbles in volatile liquids. When a bubble arrives at a free surface, we typically expect the film of the bubble cap to thin over some period of time until it ruptures. Traditionally, the drainage of this film has been considered inevitable with evaporation only hastening the film rupture. Here I will present air bubbles at the free surface of liquids which appear to defy traditional drainage rules and can avoid rupture, persisting for hours until dissolution. Using pure, volatile liquids free of any surfactants, we highlight and model a thermocapillary phenomenon in which liquid surrounding the bubble is continuously drawn into the bubble cap, effectively overpowering the drainage effects.

The symposium will feature interactive discussion sessions with faculty and is catered toward early-career researchers.

Hagfish slime is a unique predator defense material containing a network of long fibrous threads each 10-15 cm in length. Hagfish releases the threads in a condensed coiled state known as skeins (~100 μm), which must unravel within a fraction of a second and form a soft hydrogel to thwart a predator attack. The mechanisms of how the hagfish controls the unraveling rates, and the properties of the resulting gel are not well understood. I will present results from our recent experiments and modeling that will address these questions. First, the hypothesis that the viscous hydrodynamics may be responsible for the rapid unravelling rates is considered, and the scenario of a single skein unspooling as the fiber peels away due to viscous drag is discussed. As a result, I will show that under reasonable physiological conditions viscous-drag-induced unravelling can occur within a few hundred milliseconds, comparable with the physiological time scales. Subsequently, I will show that key rheological and structural features of hagfish slime are insensitive to its concentration, in spite of the uncontrolled gelation process, and this peculiar characteristic may be vital for its physiological use.

Asatekin lab focuses on new polymeric materials designed to self-assemble to impart improved and/or new functionality to separation membranes by controlling nano-scale morphology and surface functionality. Our work aims to develop new membranes for generating fresh water, treating wastewater, and process separations. We focus on preventing membrane fouling and controlling membrane selectivity while maintaining high flux and simple, scalable manufacturing methods.

In one research direction, we aim to understand how zwitterion-containing copolymers self-assemble, and utilize their behavior to develop membranes with improved capabilities. Zwitterions, functional groups with equal numbers of positive and negative charges, strongly resist fouling, defined as performance loss due to the adsorption and adhesion of feed components onto the membrane. They also easily self-assemble due to strong intermolecular interactions. We have developed high flux, fouling resistant, size-selective membranes utilizing the self-assembly of random copolymers of zwitterionic and hydrophobic monomers. The effective membrane pore size or ~1 nm closely matches the size of self-assembled zwitterionic nanodomains. These membranes are exceptionally fouling resistant, showing little to no flux decline during the filtration of a wide range foulants and complete flux recovery with a water rinse.

We also aim to develop membranes that can separate small molecules of similar size based on their chemical properties. For this purpose, we prepared membranes by depositing micelles formed by random copolymers of a highly hydrophobic fluorinated monomer with methacrylic acid on a porous support. The gaps between the micelles act as 1-5 nm nanochannels functionalized with carboxylic acid groups. These membranes show charge-based selectivity between organic molecules. Furthermore, the carboxyl groups can be functionalized to alter the selectivity of the membrane. We used this method to prepare membranes that exhibit aromaticity-based selectivity. We believe these approaches will eventually lead to novel membranes that are capable of new separations and can replace more energy intensive methods such as distillation or extraction.

taste of science is an annual festival in cities across the United States. This year, the physics event focuses on soft and active matter. Aditi Chakrabarti (postdoc in Mahadevan's group) and John Berezney (postdoc from Brandeis on active nematics) will be speaking at Sissy K's.

Cells must move through tissues in many important biological processes, including embryonic development, cancer metastasis, and wound healing. Often these tissues are dense and a cell's motion is strongly constrained by its neighbors, leading to glassy dynamics. Although there is a density-driven glass transition in particle-based models for active matter, these cannot explain liquid-to-solid transitions in confluent tissues, where there are no gaps between cells and the packing fraction remains fixed and equal to unity. I will demonstrate the existence of a new type of rigidity transition that occurs in confluent tissue monolayers at constant density. The onset of rigidity is governed by a model parameter that encodes single-cell properties such as cell-cell adhesion and cortical tension. I will also introduce a new model that simultaneously captures polarized cell motility and multicellular interactions in a confluent tissue and identify a glassy transition line that originates at the critical point of the rigidity transition. This work suggests an experimentally accessible structural order parameter that specifies the entire transition surface separating fluid tissues and solid tissues. Finally, I will discuss recent work using a culture of human lung epithelial tissue to compare a newly discovered mode of fluidization of jammed cells—the unjamming transition (UJT)—with the canonical epithelial-to-mesenchymal transition (EMT).

The extracellular matrix (ECM) is a complex assembly of structural proteins that provides physical support and biochemical signaling to cells in tissues. Over the last two decades, studies have revealed the important role that ECM elasticity plays in regulating a variety of biological processes in cells, including stem cell differentiation and cancer progression. However, tissues and ECM are often viscoelastic, displaying stress relaxation over time in response to a deformation, and can exhibit mechanical plasticity. My group has been focused on elucidating the impact of ECM viscoelasticity and plasticity on cells. Our approach involves the use engineered biomaterials for 3D culture, in which the mechanical properties can be independently modulated. In this talk, I will discuss our recent findings on how cells sense ECM viscoelasticity through stretch activated ion channels, how cancer cells generate extracellular force in order to divide in confining ECMs, and on how matrix mechanical plasticity regulates cancer cell migration.

Liquid crystalline materials are pervasive, enabling devices in our homes, purses, and pockets.

It has been long-known that liquid crystallinity in polymers enables exceptional characteristics in high performance applications such as transparent armor or bulletproof vests.

This talk will generally focus on a specific class of liquid crystalline polymeric materials: liquid crystalline elastomers. These materials were predicted by de Gennes to have exceptional promise as artificial muscles, owing to the unique assimilation of anisotropy and elasticity.

Subsequent experimental studies have confirmed the salient features of these materials, with respect to other forms of stimuli-responsive soft matter, are large stroke actuation up to 400% as well "soft elasticity" (stretch at minimal stress).

This presentation will survey our efforts in directing the self-assembly of these materials to realize distinctive functional behavior with implications to soft robotics, flexible electronics, and biology. Most notably, enabled by the chemistries and processing methods developed in my laboratories, we have prepared liquid crystal elastomers with distinctive actuation and mechanical properties realizing nearly 20 J/kg work capacities in homogenous material compositions.

Local control of orientation dictates nonuniformity in the elastic properties, which we recently have shown could be a powerful means of ruggedizing flexible electronic devices. Facile preparation of optical films, prepared with the cholesteric phase, capable of concurrent shape and color change will also be discussed.

In addition, there will be an Industrial Forum Luncheon hosted by Sigma-Aldrich in Pierce 209 at noon, sandwiches and refreshments from Flour Bakery will be provided. This lecture will be a wonderful opportunity to hear more about industrial career opportunities.

Representatives from Sigma-Aldrich will include:

Beth Rosenberg is the Manager of Research Technology Specialist (RTS)-North America. She leads a team of Chemistry, Materials Science and Life Science RTS whose mission is deepen scientific relationship.

Na Li is the Global Product Manager for Electronic Materials at MilliporeSigma.

Tyler Gravelle is the Harvard MilliporeSigma representative and his been working with campus researchers for the past two years.

Until very recently, most cancer biologists operated with the assumption that the most common route to metastasis involved cells of the primary tumor transforming to a motile single-cell phenotype via complete EMT (the epithelial-mesenchymal transition). This change allowed them to migrate individually to distant organs, eventually leading to clonal growths in other locations. But, a new more nuanced picture has been emerging, based on advanced measurements, and on computational systems biology approaches. It has now been realized that cells can readily adopt states with hybrid properties, use these properties to move collectively and cooperatively, and reach distant niches as highly metastatic clusters.

This talk will focus on the accumulating evidence for this revised perspective, the role of biological physics theory in instigating this whole line of investigation, and on open questions currently under investigation.

Abstract: Smart fluids - or a fluid with suspended particles in which an applied field produces a substantial change in properties - are a fascinating class of soft materials that are widely used in applications ranging from automotive suspension to high performance speakers. However, predicting their performance from first principles remains challenging. Our underlying hypothesis is that a deeper understanding can be gained by studying highly controlled model particles and connecting these to emergent behavior of the system. Here, we explore two model systems, (1) the electric-field directed assembly of nanoparticles and (2) the mechanical properties of particle-laden interfaces. In the first section, we introduce a novel method to measure the polarizability of nanoparticles based upon modest trapping fields and fluorescence microscopy. By using this assay, we determine that nanoparticles can exhibit polarizabilities that are >30 times larger than would be expected based upon simple models, corroborating early theoretical work that includes contributions from space charge in the Debye layer. In the second section, we discuss the mechanical properties of liquid marbles, or drops of liquid coated with a layer of hydrophobic particles that render the entire structure non-wetting. By developing a novel method to study the deformation of liquid marbles, we find that while the elastic mechanics of liquid marbles are invariant of the particle coating, the failure properties of marbles depend strongly on the particle identity, suggesting that more weakly interacting particles constitute tougher marbles. These observations are further explored using a series of macroscopic experiments studying the break-up of particle rafts based on a funnel method. While there remain open questions about the behavior of smart fluids, these lessons illustrate that important insights can be gained by combining novel multi-scale characterization strategies and well-characterized particles.

Abstract: In many biological phenomena, cells migrate through confining environments. To study such confined migration, we place migrating cells in two-state micropatterns, in which the cells stochastically migrate back and forth between two square adhesion sites connected by a thin bridge. We adopt a data-driven approach where we learn an equation of motion directly from the experimentally determined short time-scale dynamics, decomposing the migration into deterministic and stochastic contributions. This equation captures the dynamics of the confined cell and accurately predicts the transition rates between the sites. We thereby derive the emergent non-linear dynamics that governs the migration directly from experimental data. In particular, we find that the deterministic dynamics is poised near a bifurcation between a limit cycle and bistable behaviour. As a result, we find that cells are deterministically driven into the thin constriction; a process that is sped up by noise. Our approach yields a conceptual framework that may be extended to describe cell migration in more complex confining environments.

Abstract: Like mixtures of oil and water, artificial lipid membranes undergo liquid-liquid phase separation. Unraveling the physical mechanisms behind the organization of these liquid phases in membranes is a central goal in biophysics, while the ability to reproduce them in synthetic structures holds great potential for applications in self-assembly and drug delivery. Previous studies on vesicles and supported lipid bilayers have unveiled a fundamental interplay between the membrane geometry and position of different lipid domains. However, the detailed mechanisms behind this coupling remain incompletely understood, because of the difficulty of independently controlling the membrane geometry and composition. In this talk, I will show how we overcome this limitation by fabricating multicomponent lipid bilayers supported by colloidal scaffolds of prescribed shape. Thanks to a combination of experiments and theoretical modeling, we demonstrate that the substrate local curvature and the global chemical composition of the bilayer determine both the spatial arrangement and the amount of mixing of the lipid domains.

Abstract: Packing problems occur in numerous applications, such as granular media under confinement, Pickering emulsions, viral structure, etc. When identical particles are packed occurs on a curved geometry, crystalline order is necessarily disrupted by the curvature, necessitating introduction of defects: a paradigmatic example is the “scars” or grain boundaries found in the packing of spherical particles on a spherical shell. Conversely, for very polydispersed or heterogeneous systems, packings are amorphous. We connect these two regimes by investigating packings as a parameter of particle shape, finding that the spherical crystallography and amorphous regimes are linked by growth and percolation of the scar network. Prospects for experimental realizations of such systems will also be presented.

Abstract: A mixture of particles suspended in a fluid is ubiquitous around us, in nature and applications. When a suspension is sheared, it exhibits a complex, rich and varied behavior such as shear thinning, shear thickening, shrinking or dilating, and so on. Despite extensive available data on mixture reactions to shearing, determination of macroscopic properties of a suspension has remained a challenge, as such mixture properties are dependent on particle systems and sizes, shearing magnitude, experimental duration and experimental methods, even when hydro-clustering is avoided, and the suspension is composed of uniform rotationally-neutral monodispersed spherical particles. At the same time, microstructural ordered states of sheared suspensions have been detected and reported for numerous spherical mixtures. In this presentation, relationships between dynamic and effective ordered states and two components of stress tensor will be explored, the first linear viscosity coefficient and the second normal stress. A proper relationship between these two components will also be developed.

We consider solid spherical particles that are interacting both locally and globally, and form a single effective ordered or unordered structure in the mixture when viscosity is the dominant dissipation mechanism. It is demonstrated that this assumption is sufficient to predicting stress components of the mixture response to an applied shear stress under different conditions, for both colloidal and non-colloidal suspensions, up to but not including the jamming limit. We'll show that our analysis is consistent with the light-scattering observations of Ackerson group in the past decades. For non-colloidal mixtures, both viscosity and the 2nd-particle pressure data confirm the first Ackerson transition at particle volume fractions 45-50%. For colloidal suspensions, the observed non-Newtonian effects such as shear thinning at higher volume fractions or at higher shear-rates coincide with emergence of the second Ackerson transition to a higher-order crystalline state by the shear flow.

Through the REU program, we provide a coordinated, educational and dynamic research community to inspire and encourage young scientists to continue on to graduate school. We emphasize professional development workshops and seminars for a career in science and engineering. Weekly faculty seminars highlight research and community activities are integrated into the program. Undergraduate students research in world-class laboratories, and focusing on an in-depth research project while exploring multidisciplinary research topics to hone your science communication skills. We are seeking undergraduates from chemistry, physics, biology, computer science, mathematics (applied and pure), statistics, and engineering. Students without prior research experience, including freshman and sophomore students, are especially encouraged to apply.