Calendar of MRSEC Events

2022 Events

December, 2022
93rd New England Complex Fluids meeting
Harvard University
September, 2022
92nd New England Complex Fluids meeting
Brandeis University
June 10, 2022
91st New England Complex Fluids meeting
UMass Boston
May 24, 2022
Squishy Physics Seminar
Gwennou Coupier, Grenoble Alpes University, Laboratoire Interdisciplinaire de Physique
6 - 7:30pm | Pierce Hall 301, 29 Oxford Street

Flow generation by buckling instability

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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May 18, 2022
Squishy Physics Seminar
Dorothee Kern, Brandeis University
6 - 7:30pm | Pierce Hall 301, 29 Oxford Street

Evolution of Protein Dynamics - Time Travel to the Past and Future

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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May 4, 2022
Squishy Physics Seminar
Richard Henshaw, Tufts University
6 - 7:30pm | Pierce Hall 301, 29 Oxford Street

Lagrangian stretching, transport, and modal structure of active turbulence

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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April 30, 2021
Microbial Sciences 19th Annual Symposium
9am - 6pm at Northwest Building, 52 Oxford Street, Cambridge, MA
Registration required, is free, and is open to the public
Speakers: Libusha Kelly, John F. Brooks II, Otto X. Cordero, Sophie Helaine, Andrea Giometto, Robinson Fulweiler, Karla Fullner Satchell, and Karthik Anantharaman

About the MSI 198th Annual Symposium

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.

April 28, 2022
Active Matter Seminar, Center of Mathemetical Sciences and Applications
Guillaume Duclos, Department of Physics, Brandeis University
1:00pm – 2:30pm (EST) | Remote

Building active nematic and active polar liquids out of biological machines

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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April 20, 2022
Squishy Physics Seminar
Amélie Chardac, Department of Physics, Brandeis University
6 - 7:30pm | Pierce Hall 301, 29 Oxford Street

Life and death of topological defects in polar active matter

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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April 13, 2022
Squishy Physics Seminar
Guillermina Ramirez-San Juan, Brandeis University
6 - 7:30pm | Pierce Hall, room 301, 29 Oxford Street

Collective dynamics, waves and synchronization in arrays of cilia

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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April 7, 2022
Active Matter Seminar, Center of Mathemetical Sciences and Applications
Ben Simons, Cambridge University
1:00pm – 2:30pm (EST) | Remote

Theories of branching morphogenesis

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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April 6, 2022
Squishy Physics Seminar
John Berezney, Department of Physics, Brandeis University
6 - 7:30pm | Pierce Hall, room 301, 29 Oxford Street

Kinesin-driven reorganization of actin/microtubule composites

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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March 30, 2022
Squishy Physics Seminar
Colm Kelleher, Department of Molecular and Cellular Biology, Harvard University
6 - 7:30pm | Pierce Hall, room 301, 29 Oxford Street

The Mammalian Meiotic Spindle: A Living Material

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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March 24, 2022
MSI Thursday Seminar Series
Georg K. Gerber, MD, PhD, MPH; Associate Professor of Pathology, Harvard Medical School
4 - 5pm EST | Remote meeting

Novel machine learning methods for gaining insights into complex and dynamic host-microbial ecosystems

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.

Register for (remote only) MSI Thursday Seminar Series

March 23, 2022
Squishy Physics Seminar
Benjamin Freedman, Wyss Institute, Harvard University
6 - 7:30pm | Pierce Hall, room 301, 29 Oxford Street

Janus Tough Adhesives for Tendon Regeneration

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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March 24, 2022
Active Matter Seminar, Center of Mathemetical Sciences and Applications
Katherine Copenhagen, Princeton University
1:00pm – 2:30pm (EST) | Remote

Topological defects drive layer formation in gliding bacteria colonies

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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March 16, 2022
Squishy Physics Seminar
Qiaoling Huang, Department of Physics, Xiamen University
6 - 7:30pm | Pierce Hall, room 301, 29 Oxford Street

Structure-property relationships between TiO2-based materials and biological responses

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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March 11, 2022
90th New England Complex Fluids meeting
Northeastern University
March 11, 2022
Microbial Sciences Initiative Chalk Talk
Dr. Travis Gibson
12 - 1pm, 24 Oxford Street, Room 375, Cambridge, MA

Intrinsic instability of the dysbiotic microbiome

March 9, 2022
Squishy Physics Seminar
rescheduled to April 13th
March 2, 2022
Squishy Physics Seminar
Rafael Gomez-Bombareli, MIT
6 - 7:30pm | Pierce Hall, room 301, 29 Oxford Street

Generative machine learning for Coarse-Graining atomistic simulations

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.

February 24, 2022
Active Matter Seminar, Center of Mathemetical Sciences and Applications
Amin Doostmohammadi, Niels Bohr Institute, University of Copenhagen
1:00pm – 2:30pm (EST) | Remote

Taming Active Matter: from ordered topological defects to autonomous shells

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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February 23, 2022
Squishy Physics Seminar
Pepijn Moerman, Department of Chemical and Biomolecular Engineering, Johns Hopkins University
6 - 7:30pm | Pierce Hall, room 301, 29 Oxford Street

Chasing interactions between oil droplets driven by non-reciprocal oil exchange

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.

February 18, 2022
Microbial Sciences Initiative Chalk Talk
Dr. Ana Paula Guedes Frazzon
12 - 1pm, 24 Oxford Street, Room 375, Cambridge, MA

Microbiological view of anthropogenic impacts in nature: enterococci as sentinel organisms for monitoring antimicrobial resistance in wild animals in South Brazil

February 16, 2022
Squishy Physics Seminar
Alexandre Bisson, Department of Biology, Brandeis University
6 - 7:30pm | Pierce Hall, room 301, 29 Oxford Street

Life Under (Gentle) Pressure

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.

February 10, 2022
Active Matter Seminar, Center of Mathemetical Sciences and Applications
Margaret Gardel, University of Chicago
1:00pm – 2:30pm (EST) | Remote

Active Matter Controlling Epithelial Dynamics

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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February 9, 2022
Squishy Physics Seminar
Daniel Pearce, Department of Mathematics, MIT
6 - 7:30pm | Pierce Hall, room 301, 29 Oxford Street

Chasing interactions between oil droplets driven by non-reciprocal oil exchange

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.

February 2, 2022
Squishy Physics Seminar
Qiang Cui, Department of Chemistry, Boston University
6 - 7:30pm | Pierce Hall, room 301, 29 Oxford Street

Lipid membrane remodeling by proteins: development and application of coarse-grained computational models

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.

January 27, 2022
Active Matter Seminar, Center of Mathemetical Sciences and Applications
Petros Koumoutsakos, Harvard University
1:00pm – 2:30pm (EST) | Remote

Learning to School in the presence of hydrodynamic interactions

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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