Past Events

Thursday, June 18, 2020
MRSEC Seminar: Carving non-equilibrium pathways to control self-assembly
Jérémie Palacci, UCSD
Abstract: Active particles are microscopic particles, which can inject energy locally and were made available by recent progress in colloidal science. They are ideal "pump-probes" to explore the emergent properties in soft systems powered from within or control and direct self-assembly at the microscale.
 In this talk, I will first show how active particles added to a material can regulate its activity internally and boost the annealing of a colloidal monolayer. It opens a broad range of novel opportunities to thermal treatments, where the properties of matter are not controlled macroscopically but microscopically and in real time by active dopants. Next, I will introduce a new type of self-assembly through a novel approach to devise spinning microrotors that self-assemble and synchronize, from a single type of building block — a colloid that self-propels. Using photo-active particles and light patterns, I will demonstrate the potential of non-equilibrium(phoretic) interactions to program self-assembly and control dynamical colloidal architectures. It shows that, as in living systems, non-equilibrium processes hold the key to the realization of synthetic machines from machines.
Recording of seminar

Thursday, June 11, 2020
MRSEC Seminar: Growing Droplets in Cells and Gels
Eric Dufresne, ETH Zurich
Abstract: To function effectively, living cells compartmentalize myriad chemical reactions.  In the classic view, distinct functional volumes are separated by thin oily-barriers called membranes.  Recently, the spontaneous sorting of cellular components into membraneless liquid-like domains has been appreciated as an alternate route to compartmentalization.
I will review the essential physical concepts thought to underlie these biological phenomena, and outline some fundamental questions in soft matter physics that they inspire.  Then, I will focus on the coupling of phase separation to elastic stresses in polymer networks.   Using a series of experiments spanning living cells and synthetic materials, I will demonstrate that bulk mechanical stresses dramatically impact every stage in the life of a droplet, from nucleation and growth to ripening and dissolution.
These physical phenomena suggest new mechanisms that cells could exploit to regulate phase separation, and open new routes to the assembly of functional materials.

Thursday, June 4, 2020
MRSEC Seminar: Building Order and Adaptiveness in Protein Materials by Chemical Design
Akif Tezcan, UCSD
Abstract: Proteins represent the most versatile building blocks available to living organisms or the laboratory scientist for constructing functional materials and devices. Underlying this versatility is an immense structural and chemical heterogeneity that renders the programmable self-assembly of proteins a highly challenging design task. To circumvent the challenge of designing extensive non-covalent interfaces for controlling protein self-assembly, we have endeavored to develop strategies that combine elements of inorganic, supramolecular and polymer chemistry. These strategies have led to the construction of 1-, 2- and 3D protein assemblies that couple structural order over many length scales with adaptiveness and stimuli-responsiveness, thus providing an example for the control of bulk-scale properties of biological materials with molecular-scale design.

Thursday, May 28, 2020
MRSEC Seminar: The mechanics of robust tissue folding
Hannah Yevick, Massachusetts Institute of Technology
Abstract: Tissue folding is a ubiquitous shape change event during development whereby a cell sheet bends into a curved 3D structure. In this talk, I will show that this mechanical process is remarkably robust, and the correct final form is almost always achieved despite internal fluctuations and external perturbations inherent in living systems. While many genetic and molecular strategies that lead to robust development have been established, much less is known about how mechanical patterns and movements are ensured at the population level. I will describe how quantitative imaging, physical modeling and concepts from network science can uncover collective interactions that govern tissue patterning and shape change.
Actin and myosin are two important cytoskeletal proteins involved in the force generation and movement of cells. Both parts of this talk will be about the spontaneous organization of actomyosin networks. First, I will present how out-of-plane curvature can trigger the global alignment of actin fibers and a novel transition from collective to individual cell migration in culture. I will then describe how tissue-scale cytoskeletal patterns can guide tissue folding in the early fruit fly embryo. I will show that actin and myosin organize into a network that spans a large region of the embryo. Redundancy in this supracellular network encodes the tissue’s intrinsic robustness to mechanical and molecular perturbations during folding. Moving forward, deciphering the physical basis of robustness in living systems will inspire new ways to engineer and control biological tissues and bioinspired active materials that can spontaneously fold into predetermined complex 3D shape.
Recording of seminar

Thursday, May 21, 2020
MRSEC Seminar: Collective behavior underlying the mechanobiology of tissues
Moumita Das, Rochester Institute of Technology
Abstract: Living cells and tissues are highly mechanically sensitive and active. Mechanical forces and stimuli influence the shape, motility, and functions of cells, modulate the behavior of tissues, and play a key role in diseases as different as osteoarthritis and cancer metastasis. In this talk, I will discuss how collective biophysical properties of tissues emerge from the interplay between different mechanical properties and statistical physics of underlying components. I will use examples of two complementary tissue types to illustrate how the emergent mechanobiology of tissues is facilitated by their heterogeneous and composite nature, and proximity to phase transitions. I will start with mechanical structure-function relationships in articular cartilage (AC), a soft tissue that has very few cells, and its mechanical response is primarily due to its network like extra-cellular matrix. AC is a remarkable tissue: it can support loads exceeding ten times our body weight and bear 60+ years of daily mechanical loading and resist fracture, despite having minimal regenerative capacity. I will discuss the biophysical principles underlying this exceptional mechanical response using the framework of rigidity percolation theory, and compare our predictions with experiments done by our collaborators. Next, I will discuss how differences in cell mechanics, adhesion, and proliferation in a co-culture of breast cancer cells and healthy breast epithelial cells may modulate experimentally observed phase separation and transport properties. Our results may provide insights into the mechanobiology of tissues with cell populations with different physical properties present together, such as during the formation of embryos or the initiation of tumors. By obtaining a mechanistic understanding of the biophysical properties of these two systems, we hope to elucidate principles underlying the robustness and tunability of tissue properties and gain insights into design principles for soft robotics.
Recording of seminar

Thursday, May 14, 2020
MRSEC Seminar: Fascinating flows and emergent mechanics in living animals
Vivek Prakash, University of Miami
Abstract: Organismal behavior results from emergent properties of a large number of physical and biological processes occurring across multiple scales. My overarching research goal is to reveal how biomechanical phenomena at small-scales determine emergent behavior at large-scales in different animal systems. In the first part of my talk, I will show examples of how tissues exhibit liquid-like ‘cellular flows’ while maintaining their integrity, during morphogenesis and development. I will present our surprising discovery of physiological tissue fractures and healing in a simple, early divergent animal - the Trichoplax adhaerens, and demonstrate how fracture mechanics govern extreme plastic shape changes. Next, I will show fascinating bilateral cellular flows during early chick embryo development, and reveal their key role in establishing the embryonic symmetry axis. In the last part of my talk, I will focus on the role of fluid mechanics in marine invertebrates. I will elucidate how a beautiful array of vortex structures around starfish larvae creates a physical tradeoff between feeding and swimming. My research exemplifies the promise of leveraging physics to unearth the general organizing principles underlying fundamental form-function relationships in organismal biology.

Thursday, May 7, 2020
MRSEC Seminar: Cytoskeleton dynamics and function across domains of life
Alexandre Bisson, Brandeis University Biology
Abstract: Cytoskeletal polymers control the assembly of cellular structures and transport cargo in virtually all known living organisms. Despite their ubiquitous function, these self-assembled powerhouses come in a variety of flavors in terms of sizes, structures, and kinetic properties. In this talk, I will walk through my past and present work on the relationship between the dynamics and cellular function of cytoskeletal systems throughout evolution. Using single-molecule tracking in live cells, I will discuss the mechanisms in which tubulin-like polymers control cell division in bacteria. To further understand how these bacterial filaments evolved to eukaryotic microtubules, my group studies the functions and properties of multiple tubulins in archaea, the last prokaryotic common ancestor of eukaryotes. Interestingly, we see the presence of both eukaryotic-like and bacterial-like tubulin systems, suggesting the first eukaryotes likely comprised prokaryotic traits. We anticipate our results will unveil unprecedented information about self-assembly regimes and the emergency of new biophysical features in cells.
Recording of seminar

Thursday, April 23, 2020
MRSEC Seminar: Building the cellular skeleton, one molecule at a time
Shashank Shekhar, Brandeis University Postdoc
Abstract: Living cells employ self-assembly to build intracellular structures orders of magnitude larger than their individual constituent units. One such example is the actin cytoskeleton, formed from polymerization of actin monomers into linear filaments. Cells use actin polymerization to generate forces required for cell movement and to sense their mechanical environment. Although the key proteins required for actin remodeling have been identified, how they act in concert to produce complex cellular actin dynamics still remains a mystery. The overarching goal of my work is to investigate and reconstitute multicomponent molecular mechanisms underlying physiological actin dynamics. I employ a range of quantitative experimental biophysical approaches such as microfluidics, multispectral single-molecule and single-filament imaging. First, I will show how a dynamic interplay between enhancers (formin) and inhibitors (capping protein) of actin polymerization leads to tunable control of actin assembly. Second, I will present a novel multicomponent mechanism comprising of two actin disassembly factors resulting in over 300‑fold enhancement of actin depolymerization. These results illustrate how the interplay between molecular components and mechanical forces leads to complex cytoskeleton dynamics. My research exemplifies the power of synthetic biological approaches to dissect fundamental molecular mechanisms governing living cells.

Thursday, April 16, 2020
MRSEC Seminar: From Cytoskeletal Assemblies to Living Machines
Peter Foster, MIT
Abstract: The cytoskeleton has the remarkable ability to self-organize into living machines which underlie diverse cellular processes. These nonequilibrium machines are driven by molecular motor proteins which shape cytoskeletal components into soft active materials. How the properties of these materials emerge from protein-level interactions and energetics is an open question. Here, I’ll present work on the dynamics, mechanics, and energetics of microtubule/motor protein networks. In cell extracts, we’ve found that microtubule networks undergo a spontaneous bulk contraction driven by the motor protein dynein, which can be quantitatively understood using an active fluid model coarse-grained from motor-scale interactions. Additionally, we’ve used picowatt calorimetry to measure the heat dissipated by an active cytoskeletal material composed of purified components and found that the efficiency for generating large-scale flows is remarkably low. Taken together, these results uncover design principles for building active materials and represent a step towards building a thermodynamic understanding of active matter.

Thursday, April 9, 2020
MRSEC Seminar: Nucleation and growth of DNA-programmed crystallization
Ben Rogers, Brandeis University
Abstract: Grafting DNA onto microscopic colloidal particles can `program' them with information that tells them exactly how to self-assemble. Recent advances in our understanding of the specific interactions that emerge due to DNA hybridization have enabled the assembly of a wide variety of crystal structures. However, the dynamic pathways by which these crystals self-assemble are largely unknown. In this talk I will present an experimental study of the nucleation and growth kinetics of colloidal crystallization due to DNA hybridization. Specifically, I will describe a microfluidics-based approach in which we produce hundreds of monodisperse, isolated droplets filled with colloidal particles and then track the formation of crystals within each drop as a function of time. We find that the initial nucleation of crystals from a supersaturated solution involves overcoming a free-energy barrier, whose height depends strongly on temperature and can be described using classical nucleation theory. We also find that once nucleated, colloidal crystals grow at a rate that is limited by the diffusive flux of colloidal particles to the growing crystal surface. Taken together, these two findings quantitatively describe the full dynamic pathway leading from the initial disordered fluid to the final ordered solid. We anticipate that our results will yield new protocols for making higher quality or more complex self-assembled structures by controlling the dynamics of their assembly.
Recording of seminar

Thursday, April 2, 2020
MRSEC Seminar: Bi-phase emulsion droplets as dynamic fluid optical systems
Mathias Kolle, MIT 
Abstract: Micro-scale optical components play a critical role in many applications, in particular when these components are capable of dynamically responding to different stimuli with a controlled variation of their optical behavior. Here, we will discuss the potential of easily reconfigurable, micro-scale, bi-phase emulsion droplets as a material platform for dynamic, fluid optical components. Such droplets can act as liquid compound micro-lenses with tunable focal lengths. They can display stunning iridescent structural colors with a rich structure-dependent variation in angular and spectral distribution of reflected coloration. The droplet morphology can be controlled with optical stimuli, chemical perturbations in their environment, and they are also very responsive to minute thermal gradients. Finally, we provide evidence of the droplet’s utility as a fluidic optical element in potential application scenarios.
Recording of seminar

Tuesday, March 31, 2020
MRSEC Community Forum
The MRSEC hosted a facilitated community forum to address your concerns and give advice. We don't pretend to have answers, but we believe the path forward is for us to articulate our concerns and using our collective wisdom to forge a plan to improve our futures. The panel will include three recent MRSEC alumni, Camille Girabawe (Adobe), Rylie Walsh (Harvard Medical School) and Gabe Redner (Google). They describe how they leveraged their Brandeis education to transition to industry and give advice on how to use the opportunity of the covid disruption to prepare for an industrial career once the economy recovers.
Recording of forum

Thursday, March 5, 2020
MRSEC Seminar (two presentations)
Spatiotemporal Optimal Control of an Extensile Active Nematic Suspension
Michael Norton, Center for Neural Engineering, Pennsylvania State University
Abstract: Active nematic suspensions are self-driven fluids that exhibit rich spatiotemporal dynamics characterized by director field buckling, defect nucleation/annihilation and chaotic trajectories of those defects. Towards developing experimental methods for controlling these dynamics, we consider an optimal control problem which seeks to find the spatiotemporal pattern of active stress strength required to drive the system towards a desired director field configuration. As an exemplar, we consider an extensile active nematic fluid confined to a disk. In the absence of control, the system produces two topological defects that perpetually circulate. Optimal control identifies a time-varying active stress field that drives the defects to orbit in the opposite direction.
Active Composites of Actin and Kinesin-driven Microtubules
John Berezney, Postdoctoral Fellow, Brandeis University
Two major structural proteins, actin and microtubules, form multiple co-existing and interpenetrating filamentous protein networks within the cell cytoplasm. The out-of-equilibrium active reorganization of these structures by molecular motors is necessary for basic physiological 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. To demonstrate some of the mechanics governing the active reorganization of these materials, we have built a polymer blend of kinesin-driven microtubule networks which reorganize a passive entangled actin network. We find both the mechanics of the actin network as well as its initial structure can have dramatic effects on the steady-state behavior of the system. To capture the range of behaviors, we build a state diagram which captures the non-equilibrium phenomena we observe.

Thursday, February 27, 2020
MRSEC Seminar: The density and 3D arrangement of actin filaments in the cytoskeleton dictate how myosin Va molecular motors transport their cargo
Sam Walcott, WPI
Abstract: Inside a cell, material must be transported large distances to specific targets.  Passive diffusion is too slow and imprecise, so eukaryotic cells employ molecular motors (like myosin Va), which use chemical energy to "walk" along the 3D network of protein filaments (like actin) of the cytoskeleton.  Despite a wealth of experimental and theoretical work at the single molecule level, it is unclear how molecular motors work together to navigate their cargoes through the apparent random tangle of the cytoskeleton.  I will discuss a series of experiments performed by collaborators at the University of Vermont aimed at unraveling this process, and a mathematical model that makes sense of the experimental results.  The central results of this work are that: 1) measurements in 3D can differ fundamentally from similar 2D measurements; 2) the local geometry of an actin intersection dictates if and how long teams of myosin Va motors become stationary; 3) parameters like actin mesh density and cargo size can determine whether motors act as transporters or tethers.  This work suggests mechanisms by which cells can regulate intracellular transport.

Thursday, December 5, 2019
Joint MRSEC/Mathemathematics Colloquium
Title: Traveling waves in actin dynamics from reaction-diffusion and non-reaction-diffusion systems
Jun Allard, University of California, Irvine
Abstract: Living cells exhibit many forms of spatial-temporal dynamics, including recently-discovered traveling waves. There is evidence that cells use these traveling waves to organize their interiors, improve cell-cell communication, and tune their motility. Some of these traveling waves arise from excitability (positive feedback) and non-local coupling (dynamics that spread spatially on timescales much faster than the timescale of wave motion). My research has studied two traveling waves involving the mechanics of the cytoskeletal protein actin: one that is approximately equivalent to a reaction-diffusion system [Barnhart et al., 2017, Current Biology], and one that is not [Manakova et al., 2016, Biophysical Journal]. For the non-reaction-diffusion wave, we demonstrate conditions for wave travel analogous to ones previously derived for reaction-diffusion waves. We also demonstrate the existence of a "pinned" regime of parameter space absent in the equivalent reaction-diffusion system.

Thursday, November 21, 2019
Coherent force transmission in disordered particle media, and its relation to macroscopic mechanics
Prabhu Nott, Indian Institute of Science
Abstract: Static and flowing granular materials are ubiquitous in nature and industry, but our understanding of their mechanics lags far behind that of fluids. In a densely packed state, granular materials (and other athermal particle aggregates) transmit stress in a manner that belies their microstructural disorder – a subset of the particle contact network is strikingly coherent, wherein contacts are aligned nearly linearly and transmit large forces. The origin of these “force chains” has long been a puzzle. In this talk I will attempt to convey the findings of recent studies in my group, wherein we have used cluster linearity as a network connectivity measure to classify subnetworks of connected contacts. In static granular assemblies and in steady shear, we find a percolation transition at a critical linearity at which the network is sparse, coherent, and contains the force chains. The subnetwork at critical linearity explains some important experimentally observed features of granular materials: the orientation of the clusters strongly reflects the imposed macroscopic stress, and explains distinctive, even anomalous, features of the stress in granular columns. I will end by connecting our findings to some current questions on constitutive models for granular flow, and the statistics of granular packings.

Thursday, November 14, 2019
Title: Biologically fabricated materials from engineered microbes

Neel Joshi, Wyss Institute at Harvard University
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 to engineered therapeutic probiotics. Another project in the group focuses on interfacing yeast cells with light harvesting nanoparticles to create inorganic-biohybrids with light-driven enhanced metabolic output.

Thursday, November 7, 2019
Title: Hydrodynamics of Active Defects: from chaos to defect ordering and patterning
Suraj Shankar, Harvard Society of Fellows
Abstract: Topological defects play a prominent role in the physics of two-dimensional materials. In active nematics, which are orientationally ordered fluids composed of self-driven elongated particles, disclinations can acquire spontaneous self-propulsion and drive self-sustained flows upon proliferation. Here, I present a comprehensive theory of active nematics by recognizing that defects are the relevant excitations in the system. Upon extending the well-known Coulomb gas mapping of equilibrium defects to the active realm, we develop an effective particle like description of interacting active defects. Using this, we demonstrate that activity drives a nonequilibrium defect unbinding transition to active turbulence, which can further transition to a novel defect ordered flock at high activity. Furthermore, within a hydrodynamic approach, we also show that spatially inhomogeneous activity can be used to pattern and segregate defects, demonstrating the versatility and relevance of our framework to control and design transport in active metamaterials and devices.

Thursday, October 24, 2019
Title: Biomechanical imaging of cancer cells and tumor development in 3D

Ming Guo, MIT Mechanical Engineering
Abstract: Sculpting of structure and function of three-dimensional multicellular tissues depend critically on the spatial and temporal coordination of cellular physical properties. Yet the organizational principles that govern these events, and their disruption in disease, remain poorly understood. Here, I will introduce our recent progress performing biomechanical imaging to quantify cell and extracellular matrix (ECM) mechanics, as well as their mechanical interaction. By integrating confocal microscopy with optical tweezers, we have developed a platform to map in three dimensions the spatial and temporal evolution of positions, motions, and physical characteristics of individual cells throughout a growing mammary cancer organoid model. Compared with cells in the organoid core, cells at the organoid periphery and the invasive front are found to be systematically softer, larger and more dynamic. These mechanical changes are shown to arise from supracellular fluid flow through gap junctions, suppression of which delays transition to an invasive phenotype. Together, these findings highlight the role of spatiotemporal coordination of cellular physical properties in tissue organization and disease progression. Furthermore, I will introduce our recent progress on experimentally characterizing the local matrix stiffening induced by contraction of individual living cells inside a 3D biopolymer matrix, and will also introduce a method, called Nonlinear Stress Inference Microscopy, with which we can determine the cell-induced local matrix stress from nonlinear microrheology measurements inside various types of extracellular matrix in 3D.

Thursday, September 26, 2019
Ashwin Gopinath, MIT
Title: DNA origami: The bridge to the bottom
Abstract: Conventional top-down nanofabrication, over the last six decades, has enabled almost all the complex electronic, optical and micro-fluidic devices that form the foundation of our society. Parallel efforts, exploring bottom-up self-assembly processes, have also enabled design and synthesis of structures like quantum dots, carbon nanotubes and unique bio-molecules that possess technologically relevant proper- ties unachievable top-down. While both these approaches have independently matured, ongoing efforts to create “hybrid nanostructures” combining both strategies, has been fraught with technical challenges. The main roadblock is the absence of a scalable method to deterministically organize components built bottom-up within top-down nanofabricated structures.
In this talk, I will first introduce a directed self-assembly technique that utilizes DNA origami as a molecular adaptor to modularly position, and orient, bottom-up nano-components (like quantum dots, light emitters and proteins) within top-down nanofabricated devices. I will then present experimental results demonstrating the utility of the technique to achieved absolute, arbitrarily scalable, control over the integration of discrete emitters inside optical devices. Finally, I conclude by presenting my vision of how a DNA origami based bridge between top-down and bottom-up nanofabrication can enable a range of highly transformative, and functional, devices. Specifically, I will present data demonstrating arrays of single-photon sources, method for extremely economical nanotexturing as well as a modular molecular interface between biology and solid-state.

Thursday, September 19, 2019
Douglas Holmes, Boston University
Title: Functional Kirigami Mechanical Metamaterials for Actuators, Muscles, and Grippers
Abstract: It is far easier to bend an object than it is to stretch it, and so how does one design thin structures capable of stretching and adopting complex shapes? In recent years, scientists have used cuts in thin sheets to provide local regions that can easily deform. Termed kirigami, in reference to the ancient Japanese art of folding and cutting paper, kirigami-based mechanical metamaterials have provided a simple way to to endow a generic material with extraordinary properties. Lattice cuts, in which cuts are oriented perpendicular to the stretching direction, provide a simple way to enhance the stretchability of a thin sheet. We show that certain lattice configurations are more stretchable than others, while certain configurations produce an array of bistable unit cells. The bistability provides a means to tune the stiffness of the structure in situ, while also providing a means for mechanical memory. We demonstrate the how to switch between stable states using magnetic actuation. Lattice cuts on a curved sheets, i.e. kirigami shells, enable additional functionality. The natural curvature of the sheet causes the bistable lattices to curve together and close around an object, which enables the kirigami shells to act as soft robotic grippers. Finally, non-lattice cuts open up a range of actuation possibilities. Coupling these soft rotation modes with stiff lift modes enables us to generate kirigami linear actuators, that exhibit pitch, yaw, roll, and lift in response to uniaxial stretching. The underlying buckling mechanism is independent of thickness to a first order approximation, and thus these results translate down to 2D materials such as graphene and MoS2, as we demonstrate with MD simulations.

Thursday, September 12, 2019
Per Sebastian Skardal, Trinity College
Title: Practical Questions in Network Synchronization: Control and Optimization
Abstract: Collective behavior in large ensembles of network-coupled dynamical systems remains an active area of research in the nonlinear dynamics and networks science communities. Applications stem from both natural and man-made systems, e.g., cardiac pacemaker cells, synthetic cell circuits, and power grids. Researchers’ efforts have illuminated rich nonlinear phenomena in heterogeneous oscillator systems, including the onset of synchronization, effects of community structure, and effects of time delay. However, important practical questions remain, including: (i) How can heterogeneous oscillator networks be optimized for synchronization? and (ii) What is the most efficient protocol for controlling heterogeneous oscillator networks? In this talk I will present a body of work that explores and answers these important questions. Central to this work is the development of several theoretical tools, including the Synchrony Alignment Function, which quantifies the interplay between a complex network structure and the heterogeneous internal dynamics of each oscillator. Using these new developments I will show how to implement solutions to practically constrained problems and explore the structural and dynamical properties that are critical in controlling and optimizing oscillator networks.

Thursday, September 5, 2019
Robert Macfarlane, MIT
Title: Systems-Level Control of Structural Hierarchy
Abstract: Structural hierarchy is a powerful design concept where specific geometric motifs are used to influence material structure across multiple size regimes. These complex levels of organization are typically achieved in the laboratory by conceptually breaking a material down into the smallest components that can be manipulated (e.g. individual molecules, macromolecules, or nanoparticles), and manipulating the thermodynamics of chemical bonding between those components to control how they build up into larger length scale patterns. Conversely, complex assemblies in natural systems are commonly achieved through a more holistic approach where assembly behaviors at the molecular, nano, and macroscopic scales are interlinked. This means that not only does structural information contained in molecular building blocks filter upwards to dictate material form at the nano to macroscopic levels, but also that the environment created by the larger length scale features can affect the behavior of individual components. Here, we will discuss two different methods to synthesize materials in a systems-focused approach that mimics nature's ability to general complex structural motifs across a wide range of size regimes. The first uses nanoscale design handles to deliberately control the multivalent assembly of particle-grafted supramolecular binding moieties, where control over both molecular and nanostructure of material building blocks is then used to manipulate the mesoscale structure of the resulting materials. The second uses macroscopic interfaces to dictate the assembly behavior of DNA-grafted nanoparticles, generating superlattice architectures with controlled sizes, shapes, and orientations. Together, these techniques allow for systems-level approaches to materials design, expanding our ability to program hierarchical ordering at the molecular, nano, and macroscale simultaneously.  

Thursday, August 29, 2019
Navish Wadhwa, Harvard University
Title: Environmentally regulated self-assembly of the bacterial flagellar motor
Abstract: Macromolecular protein complexes perform essential biological functions across life forms. The assembly of such complexes is known to be regulated at the level of gene transcription, but little is known about the factors that control their assembly once the mature protein subunits enter their target space (cytoplasm, membrane, or cell wall). Even less is known about how their assembly is regulated by extracellular signals from the environment. The bacterial flagellar motor is a large macromolecular machine that powers motility in bacteria. The torque-generating stator units of the motor assemble and disassemble in response to changes in external load. We used electrorotation (applying high frequency rotating electric fields) to drive tethered cells forward, which decreases motor load, and measured the resulting stator dynamics. No disassembly occurred while the torque remained high, but all of the stator units were released when the motor was spun forward at high speed. When the electrorotation was turned off, so that the load was again high, stator units were recruited, increasing motor speed in a stepwise fashion. A model in which speed affects the binding rate and torque affects the free energy of bound stator units captures the observed stator assembly and disassembly dynamics, providing a quantitative framework for the environmentally regulated self-assembly of a major macromolecular machine.

Monday, August 19, 2019
Yael Roichman, Tel Aviv University
Title: Seeing and manipulating the microscopic world to study soft matter
Abstract: Holographic optical tweezers combined with optical microscopy and single particle tracking allow us to reach into the microscopic world, see it, manipulate it, and characterize its behavior. Applying these techniques to model driven colloidal suspensions, to biomimetic gels, and to living matter allows us to study the material properties of these systems as well as their dynamics and fluctuations. In the talk I will give two examples of such studies, the first studying the material properties of the plasma membrane of cells, and the second focusing on stochastic thermodynamics of systems far from thermal equilibrium.

Thursday, July 25, 2019
Kinneret Keren, Technion
Title: Hydra Regeneration and the Physics of Morphogenesis
Abstract: Morphogenesis, the emergence of form and function in a developing organism, is one of the most remarkable examples of pattern formation in nature. Despite substantial progress, we still do not understand the organizational principles underlying the convergence of this process, across scales, to form viable organisms under variable conditions. We focus on the mechanical aspects of morphogenesis using Hydra, a small multicellular fresh-water animal, as a model system. Hydra has a simple body plan and is famous for its ability to regenerate an entire animal from small tissue pieces, providing a flexible platform to explore how mechanical forces and feedback contribute to the formation and stabilization of the body plan during morphogenesis. I will present our recent results showing that the supra-cellular actin fibers, which exhibit nematic order, direct body-axis formation during regeneration. I will further describe our efforts to develop a framework that relates the dynamics of the actin nematic to the development of the animal’s body plan, in which topological defects in the nematic order act as organizers of the morphogenesis process. Finally, we aim to directly demonstrate that mechanical constraints can pattern the body plan during morphogenesis via mechanical feedback and I will describe our progress in this direction.

Thursday, July 11, 2019
Spencer Smith, Mt. Holyoke College
Title: Chaotic Advection, Topology, and Active Nematics
Abstract: For a large class of fluids, those undergoing chaotic advection, mixing arises from the stretching and folding of material lines and not from the usual mechanisms of turbulence.   In order to characterize the complexity of these flows we consider the topological entropy, a fundamental quantity associated with the topology of braided trajectories formed from the motion of an ensemble of tracer particles.  Certain braiding patterns topologically force a minimal amount of stretching and therefore mixing.  In the usual narrative, mixing is enforced at the global scale through mixing rods or boundary conditions, and fluid element stretching on the small scale necessarily follows.  In this talk, we will apply novel topological advection algorithms to the analysis of mixing in an active nematic system.  Active nematics are out-of-equilibrium fluids composed of rod-like subunits, which can generate large-scale, self-driven flows. We examine a microtubule-kinesin-based active nematic confined to two-dimensions, exhibiting chaotic flows with moving topological defects.  Here, in contrast to the usual narrative, we have uniform stretching enforced on the small scale, and the pattern of mixing observed in topological defects at the global scale is an emergent, necessary phenomenon.

Thursday, June 20, 2019
Tim Fessenden, MIT Biology
Title: Focal Adhesion Stability Controls Tissue Shape Changes
Abstract: Developing tissues change shape and tumors initiate spreading through collective cell motility. Despite a wealth of knowledge on individual cell migration in 3D matrices, conserved mechanisms by which tissues initiate motility into their surroundings are not known. We investigated cytoskeletal regulators during collective invasion by tumor organoids and epithelial Madin–Darby canine kidney (MDCK) spheroids undergoing branching morphogenesis in collagen. Inhibiting formins, but not the Arp2/3 complex, prevented the formation of migrating cell fronts in both cell types. Depleting the formin Dia1 in MDCK cells did not alter planar cell motility either within spheroids or in 2D scattering assays. However, Dia1 was required to stabilize protrusions extending into the collagen matrix. Live imaging of actin, myosin, and collagen in wild type spheroids revealed myosin-rich adhesions that deformed individual collagen fibrils and generated large traction forces, whereas Dia1-depleted spheroids exhibited unstable adhesions and lower force generation. This work delineates focal adhesions that drive planar cell motility from those required for tissue shape changes, and describes the cytoskeletal architecture on which these adhesions rely.

Thursday, June 6, 2019
Ethan Levien, Postdoc Brandeis/Harvard
Title: Untangling stochasticity in microbial population growth
Abstract: A central problem in microbial population dynamics is understanding how measurable phenotypic traits such as a cell's size, growth rate, or expression of a gene affect fitness. To answer this question, we need to understand how fitness is affected by variability of phenotypic traits throughout clonal populations, as there is rarely a well-defined mapping from genotype to phenotype.  Variability in phenotypic traits can be generated at the cellular level due to intrinsic factors, such as the stochasticity of biochemical reactions, or due to environmental fluctuations that induce distinct responses throughout the population.  How do these different factors shape the population dynamics of microbial systems involving multiple species? How do the fitness affects of phenotypic variability depend on the environment?  In this talk, a mathematical framework for exploring these questions will be presented. It will be shown that whether variability in a phenotypic trait is beneficial or detrimental to the population’s fitness depends heavily on the model details, such as the environmental conditions and the dynamics of the trait over a cell’s lifetime.

Thursday, May 23, 2019
Nathan Derr, Smith College
Title: Investigating cytoskeletal motor mechanisms and (bio)physical force integration using DNA origami
Abstract: Cytoplasmic dynein and kinesin-1 are opposite polarity microtubule-based motor proteins that contribute to essential aspects of eukaryotic cell biology, including mitosis and intracellular cargo transport. In vivo studies indicate that these motors often team-up in small ensembles to achieve their diverse tasks. Yet, how the myriad biochemical and biophysical properties of individual motors, and their cargos, contribute to the emergent motile properties of ensemble transport remains elusive. To investigate these aspects of multiple-motor driven cargo transport, we employ the molecular construction techniques of DNA origami to create well-defined systems of motor ensembles on customizable cargos. This approach enables us to both control and investigate how individual aspects of the motors and their cargo affect the ensemble’s motility. Our work focuses on how cargo shape, size, and rigidity interact with motor type and copy number to determine overall motility.  Our research trajectory has led us recently to design 1) spherical DNA origami structures for investigating the role of cargo geometry in ensemble transport, and 2) modular DNA origami structures for studying the (bio)physics of nano-scale force integration among teams of dynein motors.

Thursday, May 16, 2019
Rebecca Menapace and Bozhanka Vitanova, Brandeis Innovation Center
Title: An Introduction to the I-Corps Program for the MRSEC
The Brandeis Innovation Center will present an overview of the NSF-funded i-Corps Program and showcase how MRSEC research could have applications beyond campus. Attendees will get a sense of what it takes to connect their academic insights to industry applications and even create a new enterprise. If you've ever wondered how Bio-Inspired research could lead to innovation, this session is for you!

Thursday, May 9, 2019
Renato Mirollo, Boston College
MRSEC Seminar: Coupled Oscillator Networks:  What’s Hyperbolic Geometry Got To Do With It?
In the study of coupled oscillator systems, special focus is often given to the class of Kuramoto oscillators, in which the individual oscillators are driven by a simple first-order trig function.  For example, simplified models of Josephson junction arrays have this form.  It has been known since the early nineties that Kuramoto oscillator networks are almost completely integrable, in the sense that a network of N oscillators has N-3 constants of motion, thus limiting the evolution of an initial configuration to a 3D subspace. We take this one step further, and show that the space of possible phase configurations is equivalent to a 2D disc, which has a natural hyperbolic geometry.  Using this geometry, we can give a complete description of the long-term network dynamics.  In particular, we exhibit examples when the dynamics are gradient, Hamiltonian, or even both simultaneously.  In addition to stable synchronized states, the network can have stable (N-1,1) states, in which all but one of the oscillators are in sync, as well as families of neutrally stable fixed states or closed orbits, in which none of the oscillators are in sync. And in special cases, the dynamics are equivalent to the 2D electric field given by a collection of point charges on the boundary of the disc.  We will conclude with some suggestions for extending these techniques to more general oscillator networks.

Thursday, May 2, 2019
Kirill Korolev, Boston University
MRSEC Seminar: Universality classes in the evolutionary dynamics of expanding populations
Abstract: Reaction-diffusion waves describe diverse natural phenomena from crystal growth in physics to range expansions in biology. Two classes of waves are known: pulled, driven by the leading edge, and pushed, driven by the bulk of the wave. Recently, we examined how demographic fluctuations change as the density-dependence of growth or dispersal dynamics is tuned to transition from pulled to pushed waves. We found three regimes with the variance of the fluctuations decreasing inversely with the population size, as a power law, or logarithmically. These scalings reflect distinct genealogical structures of the expanding population, which change from the Kingman coalescent in pushed waves to the Bolthausen-Sznitman coalescent in pulled waves. The genealogies and the scaling exponents are model-independent and are fully determined by the ratio of the wave velocity to the geometric mean of dispersal and growth rates at the leading edge. Our theory predicts that positive density-dependence in growth or dispersal could dramatically alter evolution in expanding populations even when its contribution to the expansion velocity is small. On a technical side, our work highlights potential pitfalls in the commonly-used method to approximate stochastic dynamics and shows how to avoid them.

Thursday, April 11, 2019
Thomas Fai, Brandeis Applied Mathematics
MRSEC Seminar: Fluid dynamics of vesicle transport in dendritic spines
Abstract: We model the fluid dynamics of vesicle transport into dendritic spines, micron-sized structures located at the postsynapses of neurons. Dendritic spines are characterized by their thin necks and bulbous heads, and recent high-resolution 3D images show a fascinating variety of spine morphologies. Our model reduces the fluid dynamics of vesicle motion to two essential parameters representing the system geometry and elasticity and allows us to thoroughly explore phase space. Upon including competing molecular motor species that push and pull on vesicles, we observe multiple stable solutions reminiscent of the observed behavior. We discuss whether it would be feasible that neurons could exploit such a switch to control the strength of synapses.

Thursday, April 4, 2019
John Biddle, Harvard Medical School
MRSEC Seminar: Negative Reciprocity underlies the interactions of Sox2 and Oct4 on DNA: Implications for energy expenditure in gene regulation
Abstract: Single-molecule tracking data on the transcription factors Sox2 and Oct4 were cited at the time of their publication five years ago as evidence of ordered assembly of Sox2 and Oct4 on murine DNA.  The quantity cited in support of this conclusion, however, does not pertain to ordered assembly.  Moreover, these single-molecule tracking experiments aim to infer what takes place at DNA binding loci by following transcription factors, and this inference requires a more in-depth biophysical analysis than had been carried out.  We performed such an analysis and found that the data were inconclusive with respect to the hypothesis of ordered assembly, but we also found something novel: that the expression of Sox2 in these cells increased genomic binding by Oct4, while the expression of Oct4 decreased genomic binding by Sox2.  We call this surprising phenomenon “negative reciprocity”, and show that it cannot be accounted for at thermodynamic equilibrium with only one kind of Sox2-Oct4 binding locus.  Either the cell must expend energy so as to maintain the system away from thermodynamic equilibrium, or Sox2 and Oct4 must bind at diverse genomic loci in such a way that at some of these loci they assist each other in binding, while at others they hinder each other. The analytical techniques used to derive these results are of general interest, and increasingly so as single-molecule tracking techniques continue to develop.

Thursday, March 28, 2019
Alexander Petroff, Clark University
MRSEC Seminar: Fast-moving bacteria self-organize into active two-dimensional crystals of rotating cells
Abstract: We investigate a new form of collective dynamics displayed by Thiovulum majus, one of the fastest-swimming bacteria known. Cells spontaneously organize on a surface into a visually striking two-dimensional hexagonal lattice of rotating cells. As each constituent cell rotates its flagella, it creates a tornado like flow that pulls neighboring cells towards and around it. In the first part of the talk, we describe the earliest stage of crystallization, the attraction of two bacteria into a hydrodynamically-bound dimer. In the second part of the talk, we present the dynamics of bacterial crystals, which are composed of 5–200 hydrodynamically bound cells. As cells rotate against their neighbors, they exert forces on one another, causing the crystal to rotate and cells to reorganize. We show how these dynamics arise from hydrodynamic and steric interactions between cells. We derive the equations of motion for a crystal, show that this model explains several aspects of the observed dynamics, and discuss the stability of these active crystals.

Thursday, March 21, 2019
Johannes Zwanikken, UMass Lowell
MRSEC Seminar: The emergence of multiple time scales in active matter: creating memory by tuning the direction of self-propulsion
Abstract: Active materials, where the components dissipate energy into directed motion, display unique phases and functional properties that are not available to their ‘passive’, thermal counterparts, which are extensively used in nature and hold great promise for the design of new functional materials with unique structural and dynamic properties. However, the powerful predictive tools that have been designed for passive matter do not translate to active systems. Despite many recent contributions and advances, the connection between the microscopic properties of the components and the behavior of the ensemble is still difficult to predict.

To interrogate that connection further we study ensembles of active polygons with Newtonian dynamics,  focusing on how clustering and collective motion is affected by the direction of self-propulsion. We observe that both the structural and dynamic properties of the clusters are strongly dependent on the direction of self-propulsion, enabling a switch between effective Markovian behavior and periodic behavior with long characteristic time scales. We design a reaction network model for the dynamic evolution of the clusters in a ‘state space’, and find that the topology of this network is strongly influenced by the typical collision dynamics of the particles. Certain topologies enable loops in state space that have characteristic time scales and connect to the emergence of periodic behavior. We conclude that if a Boltzmann-type distribution could be formulated for active matter, it would need to incorporate not only the interaction potential, but also the character of the microscopic motion. Furthermore, we demonstrate that relatively simple active systems can harness a complex dynamic behavior with a hierarchy of characteristic time scales.

Thursday, March 14, 2019
Shuang Zhou, UMass Amherst
MRSEC Seminar: Living liquid crystals
Abstract: Active matter formed by self-propelled particles exhibits fascinating patterns and dynamics, shaped by the interactions of the active particles among themselves and with the environment. Many studies deal with self-propelled particles in an isotropic Newtonian fluid, where the interactions are mainly hydrodynamic or steric. Spontaneous orientational order only emerges at high particle density. The situation is different when the fluid itself is a nematic liquid crystal. In this talk, I will introduce an active matter system called living liquid crystal, which combines lyotropic chromonic liquid crystals with living bacteria Bacillus Subtilis. I will show a wealth of interesting phenomena in this system, including 1) controlling bacteria trajectories through liquid crystal director field, 2) optical visualization of the motion of nanometer-thick bacteria flagella, 3) local melting of the liquid crystal by bacteria flow, 3) cargo particle transportation, 4) bend instability, 5) low Reynolds number turbulence with topological defects, and 6) modified tumbling behavior of bacteria, among others. I will explain them by the long range interactions, both elastic and hydrodynamic, mediated by the nematic media, and make connections to the very remarkable viscoelastic properties of the chromonic liquid crystals themselves.

Friday, March 1, 2019
Melissa Rinaldin, Leiden University (Kraft and Giomi groups)
Special Seminar: Demixing on curved surfaces
Abstract: Like oil in water in vinaigrette or lava lamps, 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, bio-sensing, 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 impossibility 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.

Thursday, February 28, 2019
Timothy Atherton, Tufts University
MRSEC Seminar: Shape Sculpting and Shapeshifting with Soft Matter
Abstract: Soft materials are ideal candidates for advanced engineering applications including soft, biomimetic robots, self-building machines, shape-shifters, artificial muscles, and chemical delivery packages. In many of these, the material must make a dramatic change in shape with an accompanying re-ordering of the material; in others changes in the ordering can be used to drive or even interrupt shape change. To optimize the materials and structures, it is necessary to have a detailed understanding of how the microstructure and macroscopic shape co-evolve. In this talk, I will therefore discuss the interactions between order and shape evolution, as well as the role of the kinetics in determining the final state, with examples primarily drawn from my group’s work on emulsions and liquid crystals. To develop the description, we draw upon differential geometry, topology, optimization theory and computer simulations, and connect our results to other work on jamming and crystallography on curved surfaces.

Thursday, February 14, 2019
Dan Nguyen, Harvard Medical School
MRSEC Seminar: Self-assembling DNA complexes: an in vitro platform to probe the relation between transcription and condensed DNA phases
Abstract: DNA organization within a cell is multifaceted and dynamic. Not only does chromatin structure vary with position, as there is significant heterogeneity in the degree of local compaction within the global DNA complex, but it also changes with time, showing dependence on, e.g., the growth stage of a cell. The condensation state of DNA is intimately coupled to gene accessibility and expression: changes to DNA organization can modulate transcription and, in turn, transcribed RNA can re-organize chromatin structure. We sought to develop a more tractable, in vitro platform to probe this complex relationship and utilized a self-assembling DNA nanostar (NS) as the principal component of a chromatin mimic. In this talk, I will discuss our research with condensed phases of self-assembled NSs, highlighting key structural properties of the system's two phases (i.e. NS-networks & NS-liquids), features of NS-liquids that enable application as a model of membraneless organelles, and initial work examining the transcription of genes integrated within NS-liquids.

Thursday, January 24, 2019
Jonathan Touboul, Brandeis Mathematics
MRSEC Seminar: Some Topics in Mathematical Modeling of Embryonic Development
Abstract: Embryonic development is one of the main historical examples of biological problems where mathematical modeling was successfully applied. From the seminal works of D’Arcy Thompson and Alan Turing, a number of models were proposed to account for embryonic differentiation, increasingly supported by experimental data. In this talk, I will review some recent developments in mathematical modeling of embryonic development. 
I will start by discussing the mechanisms that control the mammalian brain development. First, we will explore the hypothesis that the non-conventional non-cell autonomous action of homeoproteins, a class of transcription factors highly expressed during, could play a role in the localization and regularity of boundaries between brain areas. At a finer scale, we will investigate the mechanisms that may control the number of neurons in the different neocortical layers. With data collected by our collaborators on various mutant mice models of microcephaly or neural cell death, we will highlight a few key mechanisms that could support homeostasis in brain’s basic architecture. If time allows, we will conclude on a recent work aimed at deciphering the mechanisms supporting skin patterning in birds, with new data on five bird species and a unified model, valid across all species, and reproducing not only the final phenotype of feather patterning but also the dynamics of the establishment of the pattern.

Thursday, December 6, 2018
Nabuan Naufer, Northeastern University
MRSEC Seminar: Single molecule mechanochemical characterization of the replicative DNA polymerase from E. coli
Abstract: Replicative DNA polymerases are responsible for duplicating chromosomal DNA, which carries a large amount of information during cell division, and hence must be replicated with high fidelity to sustain life.  The required fidelity is achieved not only by high selectivity during nucleotide incorporation (polymerization) but also through proofreading by excision (exonucleolysis) during misincorporation.  To elucidate the mechanism by which these two complementary functions are regulated we use optical tweezers to probe the three-subunit subassembly of the E. colireplicative DNA polymerase III holoenzyme (pol III core). pol III core contains the catalytic polymerase subunit α, the 3′ → 5′ proofreading exonuclease ε, and a subunit of unknown function, θ. Because polymerization or exonucleolysis alters the length of the substrate DNA, mechanical manipulation of the template tension allows us to probe the catalytic trajectory of a single pol III core molecule. By analyzing the template tension and protein concentration dependence of polymerization and exonucleolysis, we demonstrate that the process of switching between polymerase and exonuclease substrates is governed solely by primer stability, which changes with temperature, force, and the presence of mismatches.

Thursday, November 29, 2018
Philip Pearce, MIT
MRSEC Seminar: Physical determinants of bacterial biofilm architectures
Abstract: In many situations bacteria aggregate to form biofilms: dense, surface-associated, three-dimensional structures populated by cells embedded in matrix. Biofilm architectures are sculpted by mechanical processes including cell growth, cell-cell interactions and external forces. Using single-cell live imaging in combination with simulations we characterize the cell-cell interactions that generate Vibrio cholerae biofilm morphologies. Fluid shear is shown to affect biofilm shape through the growth rate and orientation of cells, despite spatial differences in shear stress being balanced by cell-cell adhesion. Our results demonstrate the importance of cell dynamics mediated by adhesion proteins and matrix generation in determining the global architecture of biofilm structures.

Thursday, November 15, 2018
Gonen Ashkenasy, Ben-Gurion University of the Negev
MRSEC Seminar: Emergence of Function in Primitive Chemical Networks Out of Equilibrium
Abstract: Like many other open systems in nature, living organisms are replete with rhythmic and oscillatory behaviour at all levels, to the extent that oscillations have been termed as a defining attribute of life. Recently, we have started to investigate a chief challenge in contemporary Systems Chemistry research, that is, to synthetically construct "bottom-up" peptide-based networks that display bistable behaviour and oscillations. Towards this aim, we utilize replicating coiled coil peptides, which have already served to study emergent phenomena in complex mixtures. In the first part of this talk, we describe the kinetic behaviour of small networks of coupled oscillators, producing various functions such as logic gates, integrators, counters, triggers and detectors. These networks are also utilized to simulate the connectivity and network topology observed for the Kai-proteins circadian clocks, producing rhythms whose constant frequency is independent of the input intake rate and robust towards concentration fluctuations. Then, in the second part, we disclose our experimental results, showing for that the peptide replication process can also lead to bistability in product equilibrium distribution. We believe that these recent studies may help further reveal the underlying principles of complex enzymatic processes in cells and may provide clues into the emergence of biological clocks.

Thursday, November 8, 2018
Arthur Michaut, Harvard Medical School
MRSEC Seminar: Biomechanics of anteroposterior axis elongation in the chicken embryo
Abstract: In vertebrates, the elongation of the anteroposterior axis is a crucial step during embryonic development as it results in the establishment of the basic body plan. A previous study highlighted the importance of the presomitic mesoderm (PSM) in elongation and showed that a gradient of random cell motility along the anteroposterior axis is necessary for proper elongation of the chicken embryo (Bénazéraf et al., 2010). It was proposed that a gradient of random cell motility, downstream of a morphogen gradient, results in a biased posterior movement of PSM cells and drives axis extension. To date, the potential interaction between well-established molecular signaling and physical mechanisms involved in axis elongation remains largely unexplored. In particular, several mechanical questions need to be addressed. First, can the cell motility gradient lead to PSM extension? Second, is the force generated by PSM extension capable of promoting axis elongation? Third, how is PSM extension mechanically coupled with the elongation of other embryonic tissues?
In order to tackle these questions, a better description of the mechanical properties of embryonic tissues is required. Moreover, to assess specific tissues’ contribution to elongation, a quantitative analysis of their force production is needed. Therefore, we report an experimental investigation of the chicken embryo mechanics. In particular, we measure how the viscoelastic properties of both the PSM and the neural tube vary along the anteroposterior axis. We also demonstrate that isolated PSM explants are capable of autonomous elongation and we measure their contribution to the total force production in the embryo.

Thursday, November 1, 2018
Anastasios Matzavinos, Brown University
MRSEC Seminar: Bayesian uncertainty quantification for particle-based simulation of lipid bilayer membranes
Abstract: A number of problems of interest in applied mathematics and material science involve the quantification of uncertainty in computational and real-world models. A recent approach to Bayesian uncertainty quantification using transitional Markov chain Monte Carlo (TMCMC) is extremely parallelizable and has opened the door to a variety of applications which were previously too computationally intensive to be practical. In this talk, we first explore the machinery required to understand and implement Bayesian uncertainty quantification using TMCMC. We then describe dissipative particle dynamics, a computational particle simulation method which is suitable for modeling biological structures on the sub-cellular level, and develop an example simulation of a lipid membrane in fluid. Finally, we apply the algorithm to a basic model of uncertainty in our lipid simulation, effectively recovering a target set of parameters (along with distributions corresponding to the uncertainty) and demonstrating the practicality of Bayesian uncertainty quantification for complex particle simulations. This work was supported in part by the NSF through grants DMS-1521266 and DMS-1552903.

Thursday, October 25, 2018
Katja Taute, Rowland Institute at Harvard
MRSEC Seminar: "Physics and ecology of bacterial motility strategies"
Most motile bacteria move by rotating helical flagella, but species differ widely in the number, shape and arrangement of these flagella. The natural habitats of motile bacteria are similarly diverse, ranging from aqueous solutions such as oceans and lakes to complex environments such as mucus or soil. What motility behaviors are enabled by different flagellar architectures? Which behaviors are advantageous in which environments? Our lab strives to learn how physics and ecology interplay in shaping the natural selection of bacterial motility strategies. 
I will show how a recently developed high-throughput 3D tracking method facilitates the rapid and label-free behavioral phenotyping of large bacterial populations at unprecedented efficiency and ease. By combining 3D tracking with microfluidically generated gradients, we can directly determine chemotactic drift velocities in different types of environments, such as hydrogels, while simultaneously resolving 3D motility patterns and their modification in response to the gradient. The combination of substantial statistical power for precisely discerning population averages of traits with simultaneous knowledge of each individual’s behavior enables a multi-scale analysis connecting the two levels and provides unprecedented access to a mechanistic understanding of diverse chemotactic mechanisms. I will discuss recent applications and insights into the motility behavior of bacterial pathogens in complex environments.

Thursday, October 18, 2018
IRG Talk: Microphase Separation and Stability of Rafts in Colloidal Membranes
Chaitanya Joshi, Baskaran/Hagan Lab
Abstract: Despite being different in structure and thousands of times larger than lipid bilayers, colloidal membranes can be described by the same continuum theory. Their large size enables the study of behaviors that cannot be visualized in lipid bilayers. Colloidal membranes are an experimental system composed of rod-like chiral particles. A tunable depletion interaction drives the self-assembly of these rods into one-rod-length thick monolayers. Membranes formed from a mixture of short right-handed rods and long left-handed rods exhibit a microphase separation regime, wherein one rod species forms finite-sized domains, or rafts, floating in a background membrane of the other rod species. The short rods form right-handed rafts which have interactions mediated through the background membrane. We have a Ginzburg-Landau theory explaining the formation and interactions of these rafts. 
Recent experiments have studied how these rafts are affected upon tuning the background membrane chirality. This tuning can be achieved by having a mixture of two kinds of long rods that are of equal length but opposite handedness. It is found that lowering the background chirality this way allows the short rods to form both right-handed and metastable left-handed rafts. We are working towards a theory of microphase separation which accounts for the existence of these metastable rafts.

Thursday, October 4, 2018
MRSC Seminar: Deadly parasites, whirligig toys and droplet computers: do the math!

Georgios Katsikis, MIT
Abstract: I will present three problems on biophysics, low-cost diagnostic devices, and microfluidics. First, I will talk about a mathematical “T-swimmer” model, based on slender-body theory, that we developed to study how submillimeter-scale parasites swim in freshwaters to infect humans causing schistosomiasis, a disease comparable to malaria in global socio-economic impact. Juxtaposing this model with biological experiments and robotic prototypes, I will show how these parasites break time-reversal symmetry and propagate at an optimal regime for efficient swimming. Second, I will describe an ultralow-cost (20 cents), lightweight (2 g), human-powered paper centrifuge designed on the  basis of a mathematical model of a nonlinear, non-conservative oscillator inspired by the ancient whirligig toy. Our centrifuge achieves speeds of 125,000 r.p.m., separates pure plasma from whole blood in less than 1.5 min and isolates malaria parasites in 15 min. Finally, I will talk about a microfluidic platform that performs universal logic operations with droplets. Through a reduced-order model and scaling laws for understanding the underlying physics, I will demonstrate droplet-based AND, OR, XOR, NOT and NAND logic gates, fanouts, a full adder, a flip-flop and a finite-state machine

Thursday, September 20, 2018
MRSEC Seminar: Tales of Emerging Complexity: from Self-Assembly to Evolution
Alexei Tkachenko, Brookhaven National Laboratory
Abstract: Self-assembly is a key phenomenon in living matter, and at the same time, a booming field of modern material science and engineering. In my talk I will review emerging trends and ideas in this field, and give theorist's perspective on its conceptual challenges. I will discuss the strategy of programmable self-assembly that uses molecular recognition properties of DNA to build nano- and micro-scale building blocks with designed pairwise interactions. This approach opens an entirely new class of theoretical problems in statistical physics. Instead of studying phenomenology of a large system of particles with given properties, we must solve the inverse problem: finding the interactions that would result in a self-assembly of a desired macroscopic or mesoscopic morphology. I will start with a discussion of self-assembly in a very simple binary system of spherical particles, and gradually move towards a greater complexity of both the building blocks and the resulting structures.
Eventually, from the problem of programmable self assembly we will shift to a pursue of the simplest system potentially capable of self-replication. Namely, we will look at a model system of information-storing heteropolymers that are capable of self-templating, and subjected to a non-equilibrium driving force, such as day-night cycle. This system undergoes a transition from a primitive pre-biotic soup of monomers to relatively long chains. What is especially remarkable, it also exhibits a spontaneous reduction of information entropy due to competition of chains for constituent monomers. This natural-selection-like process ultimately results in a survival of a limited subset of polymer sequences. Importantly, the number of surviving sequences remains exponentially large, thus opening up the possibility of further increase in complexity due to Darwinian evolution.

Thursday, July 19, 2018
MRSEC Seminar: Inverting the Swelling Trends in Modular Self-Oscillating Gels Crosslinked by Redox-Active Metal Bipyridine Complexes

Michael Aizenberg, Wyss Institute - Harvard University
Abstract: The developing field of active, stimuli-responsive materials is in need for new dynamic architectures that may offer unprecedented chemomechanical switching mechanisms. Toward this goal, syntheses of polymerizable bipyridine ligands, bis(4-vinylbenzyl)[2,2′-bipyridine]-4,4′-dicarboxylate and N4,N4′-bis(4-vinylphenyl)-2,2′-bipyridine-4,4′-dicarboxamide, and a number of redox-active Ruthenium(II) and Iron(II) complexes with them are reported. Detailed characterizations by NMR, Fourier transform infrared spectroscopy, high-resolution mass-spectrometry, X-ray, and cyclic voltammetry show that the topology of these molecules allows them to serve as both comonomers and crosslinkers in polymerization reactions. Electronic properties of the ligands are tunable by choosing carboxylate- or carboxamido-linkages between the core and the vinylaryl moieties, leading to a library of Ru and Fe complexes with the M(III)/M(II) standard redox potentials suitable for catalyzing self-oscillating Belousov–Zhabotinskii (BZ) reaction. New poly(N-isopropylacrylamide)-based redox-responsive functional gels containing hydrophilic comonomers, which have been prepared using representative Ru bpy complexes as both a crosslinker and redox-active catalyst, exhibit a unique feature: their swelling/contraction mode switches its dependence on the oxidation state of the Ru center, upon changing the ratio of comonomers in the hybrid gel network. The BZ self-oscillations of such crosslinked hydrogels have been observed and quantified for both supported film and freestanding gel samples, demonstrating their potential as chemomechanically active modules for new functional materials.

Tuesday, July 17, 2018
Special Seminar: Colloidal Self Assembly - Structure to Function
Matan Yah Ben Zion, NYU
Abstract: Although stereochemistry has been a central focus of the molecular sciences since Pasteur, its province has previously been restricted to the nanometric scale. I will present our approach of combining DNA nanotechnology with colloidal science to program precision self-assembly of micron-sized clusters with structural information stemming from a nanometric arrangement. We bridged the functional flexibility of DNA origami on the molecular scale, with the structural rigidity of colloidal particles on the micron scale, by tuning the mechanical properties of a DNA origami complex. We demonstrate the parallel self-assembly of three-dimensional micro-constructs, evincing highly specific geometry that includes control over position, dihedral angles, and cluster chirality. We used the techniques developed to synthesize and study active systems: light driven fluid micro-particles, and sedimenting irregular clusters.

June 25-29, 2018
Microfluidics Course, Summer 2018

Thursday, May 31, 2018
MRSEC Seminar: Slimming down through frustration

Martin Lenz, Université Paris-Sud
Abstract: Controlling the self-assembly of supramolecular structures is vital for living cells, and a central challenge for engineering at the nano- and microscales. Nevertheless, even particles without optimized shapes can robustly form well-defined morphologies. This is the case in numerous medical conditions where normally soluble proteins aggregate into fibers. Beyond the diversity of molecular mechanisms involved, we propose that fibers generically arise from the aggregation of irregular particles with short-range interactions. Using minimal models of frustrated aggregating particles, we demonstrate robust fiber formation for a variety of particle shapes and aggregation conditions. Geometrical frustration plays a crucial role in this process, and accounts for the range of parameters in which fibers form as well as for their metastable, yet long-lived character.

Thursday, May 24, 2018
MRSEC Seminar: Amoeba-like Living Crystallites in Active Colloids

Paddy Royall, University of Bristol
Abstract: Many kinds of swimmers and self-propelled particles constitute physical models to describe collective behaviour and motility of a wide variety of living systems, such as the cytoskeleton, bacteria colonies. bird flocks and fish schools. Here study colloidal particles in an external DC electric field. Our experimental model system consists of quasi-two-dimensional arrays of electrically- driven particles and exhibits a rich phase behaviour. At low field strength, the particles undergo Brownian motion, yet electrohydrodynamic flows lead to long-ranged non-reciprocal? attractions and self-organisation into hexagonal crystallites. With an increase in field strength, we observe self-propulsion of the particles due to the electrohydrodynamic phenomenon known as Quincke rotation, i.e. the particles behave as active matter. This activity leads to surface melting resulting in an ordered phase of active matter where crystallites move and constantly change shape and collide with one another in a manner reminiscent of ameobae. At higher field strengths, we reveal an activity-mediated gas-solid transition, with an intermediate phase possessing orientational order. We combine our experiments with computer simulations, which reproduce the phase behaviour and moreover at higher field strengths than we reach in the experiments exhibit an activity-driven demixing to form a banded structure.

May 14-15, 2018
NSF Site Visit

Thursday, April 26, 2018
IRG Talk: A Novel Actin Filament Sliding and Compaction Mechanism Jointly Catalyzed by Srv2/CAP and its Interacting Partner Abp1

Sean Guo, Goode Lab
Abstract: Dynamic remodeling of filamentous actin networks is a critical step in cell migration, cell adhesion, and many other actin-based processes. However, we are only beginning to understand the mechanisms used by cells to reorganize actin network architecture. Here, we describe a new remodeling activity, jointly catalyzed by two conserved actin binding proteins that interact: Abp1 (Actin binding protein 1) and Srv2/CAP (Cyclase-associated protein). In TIRF microscopy assays, these two proteins together induce dynamic crosslinking and sliding of filaments, resulting in filament coalescence and compaction into thick bundles as well as overall coarsening of the actin network. Remodeling depended on direct interactions between Abp1 and Srv2/CAP, and on interactions between Abp1 and F-actin. Structurally, Srv2/CAP self-assembles into a hexameric wheel-shaped hub with six Abp1-binding sites, making the combination of the two proteins a robust actin crosslinker. Using multi-wavelength TIRF microscopy with labeled Abp1 and Srv2/CAP molecules, we directly visualized Abp1-Srv2/CAP complexes gliding diffusively along filaments and accumulating in regions of highest filament overlap, in turn leading to further coalescence. These observations define a new mode of actin network reorganization, driven by the unique molecular architecture of Srv2/CAP hexamers and their interactions with Abp1. We further recapitulated this ATP-free, contractile system into oil-water interface and 3D emulsion system. The prospect of combining a contractile polymer system with an extensile system (microtubule and kinesin) raises exciting new possibilities for observing emergent properties.

Thursday, March 29, 2018
MRSEC Seminar: Some studies on self-assembly of colloids and peptoids
John Edison, Lawrence Berkeley National Laboratory
Abstract: I will present three self-assembly problems I have recently worked on, beginning with theoretical and simulation studies on the phase behavior of colloids, suspended in a near-critical binary solvent. The results show how interactions between the colloids mediated by the solvent, could potentially enable control of colloidal self-assembly in a reversible and in-situ manner. Next, I will discuss a simulation study on the phase behavior of a mixture of hard spheres (colloids) and freely-jointed hard chains (polymers). The results show that the polymers can stabilize the hexagonally close packed (HCP) structure of colloids over the face-centered cubic (FCC) structure by exploiting the difference in distribution of void space between the two polymorphs. Finally, I will present a novel secondary structure displayed by biomimetic sequence-specific peptoid polymers that is unseen in nature. This structure enables strands to densely pack into macroscopically large (millimeter-sized) bilayer nanosheets.

February 27 - March 1, 2018
MRSEC Winter School

The first Brandeis MRSEC Winter School was held at the Highland Center in Crawford Notch, NH. There were workshops, training sessions, and discussion of research, as well as an opportunity to hike and explore the beautiful White Mountains with fellow MRSEC participants. See MRSEC Winter School for the schedule and a gallery of images.

Thursday, December 7, 2017
MRSEC Seminar: Quantifying the Energy Landscapes of Ribosome Function
Paul Whitford, Northeastern University
Abstract: The breadth of information available on ribosome structure and dynamics makes it the ideal system for systematically investigating the physical-chemical properties that enable large-scale biological processes. Through the use of simplified models (40,000-150,000 atoms) and explicit-solvent simulations, we are identifying the balance between structural flexibility and energetics during large-scale (20-100Å) conformational transitions. In recent applications of these models, we have identified specific structural features that give rise to free-energy barriers during tRNA accommodation, hybrid-state formation and translocation. These simulations also allow us to identify kinetically relevant reaction coordinates, which provides a quantitative bridge between experimental kinetics, single-molecule measurements, structural/mutational data and theoretical calculations. With this knowledge, it is now possible to interpret findings from these unique approaches within a consistent framework, which is allowing a unified description of the dynamics to emerge.

Thursday, November 30, 2017
IRG Talk: Active Plasticity
Danny Goldstein, Chakraborty Lab
Abstract: Active nematics - systems made of biological filaments and motors - show a wide variety of interesting behaviors. These system transition from a passive gel to flowing states when supplied with ATP. To capture this change in rheological properties we propose a minimal model of the stress organization in these system where the activity is captured by self-extending force dipoles that are part of a cross linked network. This network can reorganize itself through buckling of extending filaments and cross linking events that alter the topology of the network. Mean field calculations and simulations of this network reveal that these force dipoles build up stress with time, coupled with an average dissociation time of these force dipoles this give a typical yield stress similar to a yielded plastic solid. 

Thursday, November 16, 2017
MRSEC Seminar: Super-resolution imaging of transcription in living mammalian cells
Ibrahim Cissé, MIT
Abstract: Protein clustering is a hallmark of genome regulation in mammalian cells. However, the dynamic molecular processes involved make it difficult to correlate clustering with functional consequences in vivo. We developed a live-cell super-resolution approach to uncover the correlation between mRNA synthesis and the dynamics of RNA Polymerase II (Pol II) clusters at a gene locus. For endogenous β-actin genes in mouse embryonic fibroblasts, we observe that short-lived (~8 s) Pol II clusters correlate with basal mRNA output. During serum stimulation, a stereotyped increase in Pol II cluster lifetime correlates with a proportionate increase in the number of mRNAs synthesized. Our findings suggest that transient clustering of Pol II may constitute a re-transcriptional regulatory event that predictably modulates nascent mRNA output.

Thursday, November 9, 2017
IRG Talk:
Characterizing DNA-mediated interactions between colloidal particles and fluid membranes
Simon Merminod, Rogers Lab
Abstract: Binding of small particles (e.g. proteins, viruses, or colloids) to fluid membranes via ligand-receptor interactions can drive selective translocation across them or direct the self-organization of two-dimensional assemblies, as in the 'purple membrane' in Halobacteria. In this talk, I will present a model system for exploring the physical mechanisms leading to self-assembly of colloidal particles bound to interfaces. To start, we characterize the interactions between colloidal particles and a solid surface. Specifically, we graft single-stranded DNA onto colloidal particles and a glass coverslip, so that hybridization of complementary DNA molecules generates an attractive, specific force between them. Using a custom-made total internal reflection microscope, we measure particle-surface attractions with kT-scale precision and the associated binding kinetics with high temporal resolution. We aim to explore how the strength, specificity, and dynamics of the interactions that emerge depend on the molecular attributes of the ligands and receptors. These experiments may help shed light on the self-assembly of small particles bound to membranes, and possibly the formation of complex membrane structures, such as the 'microribs' in Morpho butterfly wings, which give them their brilliant coloration and iridescence.

Thursday, November 2, 2017
MRSEC Seminar: Giant Acceleration of DNA Diffusion in an Array of Entropic Barriers
Derek Stein, Brown University
Abstract: Statistical mechanics away from thermodynamic equilibrium is an important frontier of physics. The subject is challenging because there is no clear way to generalize the state variables and concepts, like entropy, that are so useful for understanding systems at equilibrium. Relatively few nonequilibrium phenomena have been solved analytically. Giant acceleration of diffusion (GAD) is one of the few. GAD is a dynamical phenomenon exhibited by a Brownian particle in a tilted periodic potential. The hallmark of GAD is that the effective diffusivity of the particle peaks at a critical value of the tilt, where it can exceed the diffusivity in a uniform potential by orders of magnitude. It was theoretically predicted that Brownian particles conveyed across entropic barriers could also exhibit GAD, but this had not been shown experimentally. The entropic case is remarkable because entropy is not well defined out of equilibrium; entropic barriers can change or even vanish as the system is driven away from equilibrium. In this seminar, I will describe experiments and computer simulations which investigate giant acceleration of diffusion of DNA polymers in nanofluidic channels with nanotopographic features that create a periodic entropic array barriers.

Thursday, October 26, 2017
MRSEC Seminar: On Growth and Form of Range Expansions at Liquid Interfaces
Séverine Atis, Harvard University
Abstract: Transport phenomena shape and constantly reorganize materials at every scale. In presence of hydrodynamical flows, the Lagrangian advection of individual particles strongly influences their dispersion, segregation and clustering. Range expansions of living cells resting on liquid substrates is of great importance in understanding the organization of microorganism populations. However, combining growth dynamics of an expanding assembly of cells with hydrodynamics leads to challenging problems, which involve the coupling of nonlinear dynamics, stochasticity and transport. In this talk, I will present laboratory experiments, combined with numerical modelling, focused on the collective dynamics of genetically labelled microorganisms undergoing division and competition in the presence of a variety of flows. We have created an extremely viscous medium that allows us to grow cells on a controlled liquid interface over macroscopic scales. I will show that an expanding population of microorganisms can itself generate a radial flow, leading to an accelerated propagation and fragmentation of the initial colony. I will show how the dynamics and morphology of these microbial populations is affected by the fluid dynamics triggered by this metabolically generated flow. I will conclude by discussing the potential influence of transport and mixing on evolutionary dynamics, and how the control of cell assemblies on liquid interfaces can lead to a wide range of phenomena at the intersection between cellular biology and physics.

Thursday, October 12, 2017
MRSEC Seminar: Polymers under tension: single-molecule elasticity measurements of a model brush polymer reveal scale-dependent stiffness

John Berezney, Dogic Lab
Abstract: Brush polymers are characterized by closely spaced side chains which exhibit steric repulsion. The interactions of these side chains can control the conformation and physical properties of the brush polymers, resulting in extension of the polymer backbone and effective stiffening of the molecule. We quantify this stiffening using single molecule elasticity measurements. Similar to results in flexible polyelectrolyte behavior, these measurements show the side chain induced stiffening is manifested only at long length scales while, at shorter length scales, the flexibility of the backbone is maintained. From the elasticity data, we are able to extract an estimate for the internal tension generated by the steric repulsion of side chains which is consistent with blob-based estimates of this parameter.

Thursday, September 28, 2017
MRSEC Seminar: Beyond 2D: Self-Organizing Patterns in Nanomaterials and Cancer
Ian Wong, Brown University
Abstract: Living cells exhibit collective, self-organizing behaviors during 3D tumor progression and tissue morphogenesis. These emergent phenomena have inspired the patterning of artificial nanomaterials into higher dimensional architectures from the "bottom-up." In this seminar, I will present recent results from my group based on these two research themes: First, we explore cancer biology inspired by soft materials. In particular, we investigate tumor cell invasion and heterogeneity using a combination of single cell tracking and engineered microstructures. We are particularly interested in the scattering and dissemination of individual cells from a collective multicellular front, which has been associated with the epithelial-mesenchymal transition (EMT). We show that these complex behaviors have analogies with a phase transition that occurs during the solidification of binary mixtures. Second, we explore the patterning of 2D nanomaterials inspired by biological morphogenesis. We show that graphene oxide films deposited on polystyrene "shrink films" can be shaped into hierarchically wrinkled and crumpled architectures that span multiple length scales. Remarkably, distinct sequences of mechanical deformations generate unique structural features, suggestive of a mechanically encoded memory. We further demonstrate that these graphene oxide structures can be exactly replicated into metal oxides through metal ion intercalation. Overall, our biological research beyond 2D monolayer culture may enable fundamental insights into the tumor microenvironment, as well as physiologically relevant invasion assays for precision medicine. Moreover, we envision that large area patterning of 2D nanomaterials can be used for curved and stretchable multifunctional devices beyond wafer scale.

Thursday, August 3, 2107
MRSEC Seminar: Vibrated Granular Squares as Equilibrium and Active Matter

Lee Walsh, UMass Amherst
Abstract: Within a fluid of hard grains, the interactions among grains, and between grains and the system boundaries, are largely determined by the shape of each grain. Thus, collective static or dynamic properties of the material can be controlled by anisotropy in shape. In this talk, I will describe an experimental system of vibrated hard square grains, which I have used to study the collective effects of shape and of dynamical asymmetry on two-dimensional granular fluids. The first study concerns the fragile phase diagram of a fluid of square particles, which exhibits an orientationally ordered phase that balances molecular orientational order and bond-orientational order. Using the same experimental setup with self-propelled particles, the second study demonstrated that athermal vibrated grains can be well described by an active Brownian particle model. Finally, different melting behaviors may be induced in crystals composed of these particles by manipulating the self-propulsion independently from the crystalline structure.

Thursday, July 27, 2017
IRG2 Talk (two presentations):  
Title:  Bacterial Ratchet Motors
Mikael Garabedian, Brandeis
Abstract:  Self-propelling bacteria are a nanotechnology dream. These unicel- lular organisms are not just capable of living and reproducing, but they can swim very efficiently, sense the environment, and look for food, all packaged in a body measuring a few microns. Before such perfect machines can be artificially assembled, researchers are beginning to explore new ways to harness bacteria as propelling units for microdevices. Proposed strategies require the careful task of aligning and binding bacterial cells on synthetic surfaces in order to have them work cooperatively. Here we show that asymmetric environments can produce a spontaneous and unidirectional rota- tion of nanofabricated objects immersed in an active bacterial bath. The propulsion mechanism is provided by the self-assembly of motile Escherichia coli cells along the rotor boundaries. Our results highlight the technological implications of active matter’s ability to overcome the restrictions imposed by the second law of thermo-dynamics on equilibrium passive fluids
Title: Topological Defects in a Living Nematic Ensnare Swimming Bacteria 
Mohamed Gharbi, Brandeis
Abstract:  Active matter exemplified by suspensions of motile bacteria or synthetic self-propelled particles exhibits a remarkable propensity to self-organization and collective motion. The local input of energy and simple particle interactions often lead to complex emergent behavior manifested by the formation of macroscopic vortices and coherent structures with long-range order. A realization of an active system has been conceived by combining swimming bacteria and a lyotropic liquid crystal. Here, by coupling the well-established and validated model of nematic liquid crystals with the bacterial dynamics, we develop a computational model describing intricate properties of such a living nematic. In faithful agreement with the experiment, the model reproduces the onset of periodic undulation of the director and consequent proliferation of topological defects with the increase in bacterial concentration. It yields a testable prediction on the accumulation of bacteria in the cores of þ1=2 topological defects and depletion of bacteria in the cores of −1=2 defects. Our dedicated experiment on motile bacteria suspended in a freestanding liquid crystalline film fully confirms this prediction. Our findings suggest novel approaches for trapping and transport of bacteria and synthetic swimmers in anisotropic liquids and extend a scope of tools to control and manipulate microscopic objects in active matter.

Thursday, July 20, 2017
IRG1 Talk Title: Friction Mediates Scission of Tubular Membranes Scaffolded by BAR Proteins
ShiYu Wang and Zhaoqianqi Feng, Brandeis
Abstract:  Membrane scission is essential for intracellular trafficking. While BAR domain proteins such as endophilin have been reported in dynamin-independent scission of tubular membrane necks, the cutting mechanism has yet to be deciphered. Here, we combine a theoretical model, in vitro, and in vivo experiments revealing how protein scaffolds may cut tubular membranes. We demonstrate that the protein scaffold bound to the underlying tube creates a frictional barrier for lipid diffusion; tube elongation thus builds local membrane tension until the membrane undergoes scission through lysis. We call this mechanism friction-driven scission (FDS). In cells, motors pull tubes, particularly during endocytosis. Through reconstitution, we show that motors not only can pull out and extend protein-scaffolded tubes but also can cut them by FDS. FDS is generic, operating even in the absence of amphipathic helices in the BAR domain, and could in principle apply to any high-friction protein and membrane assembly.

Thursday, June 29, 2017
From Molecules to Fruiting Bodies: Bridging Scales in Biological Collective Behavior

Allyson Sgro, Boston University
Abstract: Coordinated collective behavior is a common feature of a diverse range ofbiological systems, including multicellular systems such as bacterial biofilms, cancertumors, and healing wounds. These population-wide behaviors are controlled by cell-to-cell communication, which is coordinated by complex molecular networks residingwithin individual cells. One of the most striking examples of these behaviors is the tran-sition from an independent, single-celled state to a multicellular aggregate fruitingbody in the eukaryotic social amoeba Dictyostelium discoideum. This talk will focus onnew experimental approaches for directly observing and using light to spatially controlthe production of the key signaling molecule used for cell-to-cell communication thatmediates this transition. Combining these experimental approaches with mathemat-ical models permits us to connect the dynamics of signaling molecules inside singlecells to the population-wide phenomena they control, laying the groundwork for iden-tifying common principles of how collective cellular behavior arises in nature.

June 15, 2017
MRSEC Seminar: Confinement of Graphene Oxide Sheets
Rafael Leite Rubim, Centre de Recherche Paul Pascal, Bordeaux, France
Abstract: Since the discovery of graphene oxide (GO), this material has been widely studied for applications in science and technology. We developed a procedure to obtain GO dispersions in water at high concentrations, that allows the investigation of the structure of hydrated GO sheets in a previously unexplored range of concentrations. The GO dispersion are then mixed to surfactant molecules to form a complex system, where the sheets are inserted into the surfactant matrix. Tentatively applying models designed for describing the small-angle scattering curve in the Smectic A phase of lyotropic systems, it is possible to extract structural and elastic parameters characterising the system. 

June 8, 2017
MRSEC Seminar: Fabrication, reconfiguration, and assembly of shape-programmed polymer sheets
Ryan Hayward, University of Massachusetts Amherst
Abstract: Coordinated collective behavior is a common feature of a diverse range of biological systems, including multicellular systems such as bacterial biofilms, cancer tumors, and healing wounds. These population-wide behaviors are controlled by cell-to-cell communication, which is coordinated by complex molecular networks residing within individual cells. One of the most striking examples of these behaviors is the transition from an independent, single-celled state to a multicellular aggregate fruiting body in the eukaryotic social amoeba Dictyostelium discoideum. This talk will focus on new experimental approaches for directly observing and using light to spatially control the production of the key signaling molecule used for cell-to-cell communication that mediates this transition. Combining these experimental approaches with mathematical models permits us to connect the dynamics of signaling molecules inside single cells to the population-wide phenomena they control, laying the groundwork for identifying common principles of how collective cellular behavior arises in nature.

May 25, 2017
IRG1 Talk: Effects of Chirality on Microstructures in Colloidal Membranes
Joia Miller and Raunak Sakhardande, Brandeis University
Abstract: Colloidal membranes composed of micron-long rods are a rich system for studying membrane properties. Specifically, we study membrane-mediated interactions between self-assembled rafts of shorter rods suspended in the membrane. These rafts are made up of chiral rods and display strongly repulsive interactions when in a background membrane of the opposite chirality. However, lowering the net chirality of the membrane allows rafts to bind together into groups by stabilizing an alternate raft state with unfavorable internal twist. Experimental results along with a Ginzburg-Landau theoretical description of the system show how these interactions depend on rod chirality and the strength of the attraction between rods.

May 18, 2017
MRSEC Seminar: How does a virus capsid grow? Monitoring the process one capsid at a time
Rees Garmann, Harvard University 
Abstract: Viruses are the most numerous pathogens on the planet: they infect humans andthe vast majority of other organisms. Often they overwhelm their host simply byhow fast they replicate. Toward this end, many viruses have evolved streamlinedstructures which consist entirely of a single-molecule-thick protein shell (capsid) thatsurrounds the genome. The capsids form by self-assembly from a disordered soupof freshly synthesized viral proteins and genome molecules within the host cell. Wewant to understand this self-assembly process. There are many methods for monitor-ing the bulk kinetics of viral capsid assembly in vitro, but these methods have failedto completely resolve the underlying mechanisms. A single-molecule technique ca-pable of monitoring the growth of individual capsids could help clarify the key steps,but the small size of viral capsids makes this a major experimental challenge. We aredeveloping methods to measure the growth of single capsids using a recent opticalmicroscopy technique termed interferometric scattering microscopy. In this talk, Iwill describe the basic ideas behind the technique and I will show some of our pre-liminary results measuring the kinetics of capsid assembly in a few model systems.

May 1, 2017
MRSEC Seminar: DNA Origami: Building at the Nanoscale
Tom Gerling, Technische Universität München
Abstract: One of the great quests of contemporary science is to establish a nanotechnology that would allow the rational design and manufacturing of artificial molecular machines mimicking the complex functionalities seen in biological machines. One possible and promising approach represents molecular self-assembly using DNA. Structural DNA nanotechnology is a rapidly developing field that utilizes DNA molecules as a programmable molecular building material for the bottom-up self-assembly of discrete custom-shaped objects at the nanoscale. Within the last decade, the field has seen substantial progress towards significantly increasing structural as well as functional complexity demonstrating its potential, versatility, and applicability. In my talk, I will give an introduction to the field in general and of the DNA origami methodology in particular. Furthermore, I will give an overview of a selection of projects we have been working on recently. This would include synthetic lipid membrane channels, measuring weak interactions between nucleosomes, rotary mechanisms, higher-order assemblies and DNA-protein hybrid origami.

April 27, 2017
MRSEC Seminar: Optimizing self-assembly kinetics for biomolecules and complex nanostructures
William Jacobs, Harvard University
Abstract: In a heterogeneous self-assembling system, such as a large biomolecule or nanostructure, there is no guarantee that the lowest-free-energy state will form. Defects and mis-interactions among subunits often arise during a self-assembly reaction, particularly in systems comprising many distinct components. As a result, if we wish to assemble complex nanostructures reliably, we need to design robust kinetic pathways to the target structures, and not focus solely on their thermodynamic stabilities. In this talk, I shall describe a theoretical approach to predicting self-assembly pathways, with applications to both engineered nanostructures and natural biomolecules. First, I shall discuss design principles that can be used to tune the nucleation and growth rates of DNA ‘bricks’. These principles have crucial implications for low-defect self-assembly and the design of time-dependent experimental protocols. Then, to highlight the biological importance of self-assembly kinetics, I shall present evidence that evolutionary selection has tuned ribosome translation rates to optimize the folding of globular proteins.

April 6, 2017
MRSEC Seminar: Tubular crystals: Plastic deformation by helical motion of defects
Daniel Beller, Harvard University
Abstract: Two-dimensional crystalline order on surfaces with cylindrical topology gives rise to helical lattices. This type of packing occurs in biology at many scales, from biofilaments to viral capsids to botany, as well as in carbon nanotubes and in colloidal crystals. Changes in the shape of the tube generally require changes in the crystalline tessellation of the surface. This evolution can be undertaken step-by-step via the motion of elementary defect pairs through the tubular crystal. I will discuss the physics of plastic deformation in tubular crystals by the unbinding and glide separation of pairs of dislocation defects along helical trajectories through the lattice. Through theory and simulation, this work examines how the tubular crystal’s radius and helicity affect, and are in turn altered by, the mechanics of dislocation glide. 

March 30, 2017
 Amphipathic DNA origami nanoparticles to scaffold and deform lipid membrane vesicles
Joanna Robaszewski, Rylie Walsh, Brandeis University
Abstract: [The authors: Aleksander Czogalla, Dominik J. Kauert, Henri G. Franquelim, Veska Uzunova, Yixin Zhang, Ralf Seidel, and Petra Schwille] report a synthetic biology-inspired approach for the engineering of amphipathic DNA origami structures as membrane-scaffolding tools. The structures have a flat membrane-binding interface decorated with cholesterol-derived anchors. Sticky oligonucleotide overhangs on their side facets enable lateral interactions leading to the formation of ordered arrays on the membrane. Such a tight and regular arrangement makes [their] DNA origami capable of deforming free-standing lipid membranes, mimicking the biological activity of coat-forming proteins, for example, from the I-/F-BAR family.

March 23, 2017
IRG2: Disordered actomyosin networks are sufficient to produce cooperative and telescopic contractility
Greg Hoeprich and Guillaume Duclos, Brandeis University
Abstract: While the molecular interactions between individual myosin motors and F-actin are well established, the relationship between F-actin organization and actomyosin forces remains poorly understood. Here we explore the accumulation of myosin-induced stresses within a two-dimensional biomimetic model of the disordered actomyosin cytoskeleton, where myosin activity is controlled spatiotemporally using light. By controlling the geometry and the duration of myosin activation, we show that contraction of disordered actin networks is highly cooperative, telescopic with the activation size, and capable of generating non-uniform patterns of mechanical stress. We quantitatively reproduce these collective biomimetic properties using an isotropic active gel model of the actomyosin cytoskeleton, and explore the physical origins of telescopic contractility in disordered networks using agent-based simulations.

March 17, 2017
TacoCat Social

March 9, 2017
MRSEC Seminar: DNA Origami 101
Seth Fraden, Brandeis University
Abstract: An introduction to DNA origami. Description of the assembly of hollow capsids inspired by the self assembly of icosahedral viruses based on the principle of quasi-equivalance.

February 16, 2017
IRG1: Relaxation of Loaded ESCRT-III Spiral Springs Drives Membrane Deformation
Avital Rodal, Michael Hagan, Brandeis University
Abstract: ESCRT-III is required for lipid membrane remodeling in many cellular processes, from abscission to viral budding and multi-vesicular body biogenesis. However, how ESCRT-III polymerization generates membrane curvature remains debated. Here, we show that Snf7, the main component of ESCRT-III, polymerizes into spirals at the surface of lipid bilayers. When covering the entire membrane surface, these spirals stopped growing when densely packed: they had a polygonal shape, suggesting that lateral compression could deform them. We reasoned that Snf7 spirals could function as spiral springs. By measuring the polymerization energy and the rigidity of Snf7 filaments, we showed that they were deformed while growing in a confined area. Furthermore, we observed that the elastic expansion of compressed Snf7 spirals generated an area difference between the two sides of the membrane and thus curvature. This spring-like activity underlies the driving force by which ESCRT-III could mediate membrane deformation and fission.

February 9, 2017
IRG2: Microtubule sliding & cytoplasmic streaming: why would a physicist or a biologist care?
Bruce Goode, Zvonimir Dogic, Brandeis University
Cytoplasmic streaming in Drosophila oocytes is a microtubule-based bulk cytoplasmic movement. Streaming efficiently circulates and localizes mRNAs and proteins deposited by the nurse cells across the oocyte. This movement is driven by kinesin-1, a major microtubule motor. Recently, we have shown that kinesin-1 heavy chain (KHC) can transport one microtubule on another microtubule, thus driving microtubule–microtubule sliding in multiple cell types. To study the role of microtubule sliding in oocyte cytoplasmic streaming, we used a Khc mutant that is deficient in microtubule sliding but able to transport a majority of cargoes. We demonstrated that streaming is reduced by genomic replacement of wild-type Khc with this sliding-deficient mu¬tant. Streaming can be fully rescued by wild-type KHC and partially rescued by a chimeric motor that cannot move organelles but is active in microtubule sliding. Consistent with these data, we identified two populations of microtubules in fast streaming oocytes: a net¬work of stable microtubules anchored to the actin cortex and free cytoplasmic microtubules that moved in the ooplasm. We further demonstrated that the reduced streaming in sliding-deficient oocytes resulted in posterior determination defects. Together, we propose that kinesin-1 slides free cytoplasmic microtubules against cortically immobilized microtubules, generating forces that contribute to cyto¬plasmic streaming and are essential for the refinement of posterior determinants.

February 10, 2017
TacoCat Social

January 13, 2017
TacoCat Social

December 19, 2016
MRSEC Seminar: Localized Stress Fluctuations in Shear Thickening Suspensions
Jeffrey Urbach, Professor at Georgetown University
Abstract: The mechanical response of solid particles dispersed in a Newtonian fluid exhibits a wide range of nonlinear phenomena including a dramatic increase in viscosity with increasing applied stress. While the bulk rheological response of concentrated suspensions is well documented, there are many open questions about microscopic origins of shear thickening and the role of spatio-temporal fluctuations. We report direct measurements of spatially resolved surface stresses for shear thickening suspensions. Surprisingly, we do not observe a smoothly increasing uniform local stress during continuous shear thickening, a regime where the average viscosity increases smoothly with applied stress.  Instead we find that above a critical stress, there are clearly defined regions of substantially increased local stresses. The high stress regions appear intermittently and are highly dynamic. As the applied stress is increased further, these high stress regions become a larger fraction of the total surface area, and that increase accounts quantitatively for the observed shear thickening. The high stress regions are indicative of high viscosity fluid phases with a viscosity that is nearly independent of shear rate but that increases rapidly with concentration. The characteristic size of the high stress regions is approximately equal to the gap between the rheometer plates, with no observable stress variations on the particle scale. These observations suggest that continuous shear thickening arises from increasingly frequent localized discontinuous transitions from a low viscosity state to a high viscosity state, with the viscosities of the two states only weakly non-Newtonian, but separated by more than an order of magnitude.

December 14, 2016
IRG 2: The effect of hydrodynamic and topological constraints on a confined active nematic material
Mike Norton, Fraden Lab Postdoc
Abstract: Understanding the role of boundary conditions on non-equilibrium materials is key to creating systems with designed behaviors. In this talk I will discuss ongoing numerical work investigating the behavior of a 2D active nematic material confined to a circular container inspired by the experimental results of several researchers from the Dogic lab. In the model used, the evolution of the nematic order tensor is governed by Landau-deGennes free energy descent with convective and flow-alignment terms; the hydrodynamics are driven by the active, extensile stress and balanced by viscous dissipation in the Stokes limit.  The circular boundary plays a dual role, enforcing both no-slip & impermeable condition at the walls, and setting the total topological charge of the system. I will discuss the dynamics of +/- 1/2 defects, which spontaneously form, as a function of activity. In particular, I will focus on a state consisting of two +1/2 co-rotating defects that appear to coarsen the system, preventing other defects from nucleating.  An interesting interplay between hydrodynamics and topology is observed when finite patches of perpendicular (rather than parallel) anchoring is introduced. Strong activity and flow alignment "comb" over the boundary feature and the system prefers a net topological charge of +1; however, when the active flow is weak, the sign of the defects near the perpendicular/parallel junction change, creating a system with a total charge of +3/2. I will conclude with a critique of the model's ability to replicate the behavior of the experimental system.

December 9, 2016
IRG 1: Mechanisms of virus assembly on membranes 
Guillermo Rodriguez Lazaro, Hagan Lab Postdoc
Abstract: Many viruses have an envelope covering and protecting the nucleocapsid, a protein shell that contains the viral genome. Some enveloped viruses assemble directly on the cell membrane, including alphavirus and flavirus (eg Chikunguya and Zika viruses, respectively). These viruses typically consist of the nucleocapsid, and an outer layer consisting of lipid membrane and viral transmembrane glycoproteins. Despite extensive experimental efforts to understand the lifecycle of enveloped viruses, their assembly pathways and the factors which control budding remain poorly understood. For example, it remains an open question whether the nucleocapsid assembles on the cell membrane concomitant with budding, or whether the nucleocapsid first assembles in the cytoplasm and then subsequently buds through the cell membrane. Resolving this question has been challenging due to the lack of controllability within cells and the transient nature of assembly intermediates. Therefore, we have developed a coarse-grained model for viral proteins and the cell membrane, with which we aim to compare these two possible budding pathways.  In particular, we plan to characterize how membrane properties such as rigidity and domain structure affect assembly timescales and particle morphologies for each case, to identify the main barriers which need to be overcome on either pathway, and to determine if one mechanism is more robust to variations in parameters than the other. In this talk, I will describe our current progress toward this goal.

December 9, 2016
TacoCat Social

December 1, 2016
MRSEC Seminar: Nanofluidics with graphene membranes
Slaven Garaj, National University of Singapore
Abstract: Graphene’s unique interaction with water, ions and molecules implies its superior performance in diverse application such as next-generation DNA sequencing or filtration. Water flows unhindered over sp-derived surfaces of carbon nanotubes and graphene nanochannels, similar to some biological membrane pores. Another model system revealing such behavior is the graphene-oxide (GO) membrane, consisting of stacked layers of graphene sheets, sporting a percolated network of pristine graphene channels delimited by chemical functional groups. We investigated – within nanometer-high graphenic channels of GO – mobility of a wide selection of aqueous salts ions. Two general trends were revealed: (a) cation permeability decreases exponentially with increased hydration radius; and (b) permeability of negatively charged ions is suppressed by order of magnitude compared to positive ions of similar radius. We conclude that the dominant mechanisms for the ion rejection in GO membranes are size exclusion due to compression of the ionic hydration shell in narrow channels, and electrostatic repulsion due to membrane surface charge. Armed with the insight into the physical mechanism governing the ionic flow, we were able to engineer new membranes with decreased the ionic cut-off size and increased charge selectivity; all leading to promising applications in desalination and electrodialysis.

November 22, 2016
IRG 2: Synchronization in a pair of chemical heterogeneous Belousov-Zhabontisky droplets
Camille Girabawe, Fraden Lab Grad Student
Abstract: Emulsion microfluidics is used to produce aqueous droplets containing the oscillatory Belousov-Zhabotinsky reaction immersed in a continuous oil phase. Each drop can be thought of as a clock whose intrinsic frequency is set by its chemical composition. The reaction inside each drop produces byproducts than can diffuse from one drop to another through the oil. An ensemble of such diffusively coupled drops will synchronize if their interaction is strong enough. This talk will focus on the smallest network of two BZ droplets to describe techniques to used measure the coupling strength and further steps taken to characterize synchronization between drops with different intrinsic frequencies set by a chemical heterogeneity.

November 18, 2016
MRSEC Retreat

November 11, 2016
TacoCat Social

November 8, 2016
There's a Scientist in my Classroom - Waltham teachers outreach event

October 31, 2016
MRSEC Executive Committee

October 28, 2016
IRG 2: Statistical mechanics of ideal active Brownian particles in 1d confinement
Caleb Wagner, Baskaran/Hagan Labs Grad Student
Abstract: The statistical mechanics of ideal active Brownian particles in 1d confinement is studied by obtaining the exact solution of the steady-state Smoluchowski equation for the 1-particle distribution function. The solution is derived using results from the theory of two-way diffusion equations, combined with an iterative procedure that is justified by numerical results and plausibility arguments. The spatial distribution and orientational order of the ensemble are discussed, and scaling relations for the bulk density and the fraction of particles on the confining wall are rigorously derived. By considering a constant-flux steady state, an effective diffusivity for ABPs is obtained which shows signatures of the persistent motion that characterizes ABP trajectories. Finally, we discuss how the techniques used here generalize to other active models, including systems whose activity is modeled in terms of an Ornstein-Uhlenbeck process.

October 14, 2016
IRG 1: Chiral Edge Fluctuations of Colloidal Membranes
Leroy Jia, Powers Lab Grad Student, Brown University
Abstract: We study chiral fluctuations of the edge of a mostly flat colloidal membrane, consisting of rod-like viruses held together by the depletion interaction. Describing the liquid-crystalline degrees of freedom by the edge tension, curvature, and geodesic torsion, we calculate the power spectrum of edge fluctuations. The spectrum depends on the elastic moduli, including the Gaussian curvature modulus, which we argue is positive due to the entropy of the polymer depletants. Our measurements of the spectrum agree with our predictions and show how the chirality and edge tension depend on temperature.

October 14, 2016
TacoCat Social

September 30, 2016
IRG 2: Diversity of transcription elongation complexes from non-equilibrium binding of regulatory proteins
Mat Chamberlain, Gelles Lab Grad Student
Abstract: In all organisms, the multi-subunit RNA polymerases (RNAPs) that synthesize messenger RNAs bind multiple accessory proteins to regulate elongation rate, transcriptional pausing, and termination.  However, the dynamics of regulatory protein association/dissociation and how different regulators influence one another’s function is unclear.  We used multi-wavelength single-molecule co-localization techniques to directly observe the association dynamics of the elongation regulators NusA and σ70 with E. coli RNAP in vitro. Contrary to previous proposals, NusA could repeatedly bind to and release from elongation complexes (EC) during synthesis of a single RNA.  However, elongation complexes that retained bound σ70 did not bind NusA and the RNAP-bound σ70 could be retained even in the presence of physiological (micromolar) concentrations of competing elongation factors NusA and/or NusG.  Factor occupancy of elongation complexes was non-equilibrium, with significant amounts of σ70ECs even in the absence of free σ70 because dynamics were dominated by slow σ70 dissociation from EC.  The data further demonstrate that same gene is transcribed by at least two different types of complexes with different elongation rates, pausing and termination propensity. These observations suggest that during cellular transcription different non-equilibrium dynamics dictates the composition of ECs whose different functional properties can cause traffic jams, altered pausing, and population shifting at intergenic transcriptional attenuators, all of which potentially allow fine-tuning of gene expression in bacterial cells.

September 26, 2016
MRSEC Executive Committee

September 23, 2016
New England Complex Fluids Workshop

September 16, 2016
IRG 1: Using Microfluidics to Measure the Equation of State for a 2D Colloidal Membrane
Andrew Balchunas, Dogic Lab Grad Student
Abstract: Previous work has shown that monodisperse rod-like colloidal particles, such as a filamentous bacteriophage, self assemble into a 2D monolayer smectic in the presence of a non-adsorbing depleting polymer. These structures have the same functional form of bending rigidity and lateral compressibility as conventional lipid bilayers, so we name the monolayer smectic a colloidal membrane. We have developed a microfluidic device such that the osmotic pressure acting on a colloidal membrane may be controlled via a full in situ buffer exchange. Rod density within individual colloidal membranes was measured as a function of osmotic pressure and a first order phase transition, from 2D fluid to 2D solid, was observed. Constituent rod diffusion speed as a function of membrane density will be discussed if time permits.

August 26, 2016
IRG 2: A Kinetic Model of Active Extensile Bundles
Danny Goldstein, Chakraborty Lab Grad Student
Abstract: Recent experiments in active filament networks reveal interesting rheological properties. This system consumes ATP to produce an extensile motion in bundles of microtubules. This extension then leads to self generated stresses and spontaneous flows. We propose a minimal model where the activity is modeled by self-extending bundles that are part of a cross linked network. This network can reorganize itself through buckling of extending filaments and merging events that alter the topology of the network. We numerically simulate this minimal kinetic model and examine the emergent rheological properties and determine how stresses are generated by the extensile activity. We will present results that focus on the effects of confinement and network connectivity of the bundles on stress fluctuations and response of an active gel.

August 24, 2016
MRSEC Summer Student Seminar
Thomas Litschel, Fraden Lab / Mathew Chamberlain, Gelles Lab Grad student

August 22, 2016
MRSEC Executive Committee

August 10, 2016
MRSEC Summer Student Seminar
Gabriel Bronk, Kondev Lab Grad student / David Waterman, Haber Lab Grad student

August 5, 2016
IRG 1: Chromosome Refolding Model of Mating-Type Switching in Yeast
Gabriel Bronk, Kondev Lab Grad Student
Abstract: Recent studies show that distant chromosomal regions become attached together by protein-chromatin interactions. For example, in mammalian cells there are tens of thousands of such attachments mediated by the protein CTCF. In this study, we quantitatively demonstrate that the function of a particular intrachromosomal attachment in yeast is to cause recombination between two particular genetic loci (MATa and HMLα) and inhibit recombination with another locus (HMRa). The control of this recombination allows the yeast to change its mating type (the sex of a yeast). During the process of mating-type switching, yeast turn on the attachment, bringing MATa and HMLα into close proximity and making them more likely to come into contact and recombine. We show that the observed recombination frequencies can be quantitatively understood by modeling yeast chromosome III as a random walk polymer and incorporating this chromosome “refolding” (i.e. attachment) into the model.

August 2, 2016
Knowing Yourself Workshop, 2016 Hiatt Summer Science Career Series
Abigail Crine

July 27, 2016
MRSEC Summer Student Seminar
Ben Hancock, Baskaran Lab Grad student / Anna Kazatskaya, Sengupta Lab Grad student

July 19, 2016
IRG 2: Scale-invariant transition from turbulent to coherent flows in confined 3D active fluids
Kunta Wu, Dogic Lab
Abstract: Fish schools. Bacteria swirl. Animate matters swarm. Each individuals match their motion with neighbors, align heads and tails, and migrate. These migrations are based on polar particle alignments. However it remains unclear if non-polar particles with no nematic order can migrate. To explore such a counter regime we synthesize micron-sized microtubules and associated nano-sized molecular motors. The motors drive microtubules, causing extensile bundles. These bundles constitute 3D active gels whose motions drive fluid flows, revealing an intrinsic vortex size of 100 um. When these gels are confined in a pipe loop, they migrate while remaining isotropic structure. They drive background fluids flowing coherently on meter lengthscale without suppressing their intrinsic bulk vortices. The criterion supporting such coherent flows is aspect ratio of pipe cross-section, rather than its absolute size. Such self-pumping active gels reveal non-conventional active matter migrations and the need for theoretical complement on collective 3D dynamics of confined non-polar active particles.

July 14, 2016
Incorporating Summer Research into Your STEM Resumes, 2016 Hiatt Summer Science Career Series
Jane Pavese

July 13, 2016
MRSEC Summer Student Seminar
Rylie Walsh, Rodal Lab Grad student / Joanna Robaszewski, Dogic Lab Grad student

July 7, 2016
IRG 1: Enzyme-Regulated Supramolecular Assemblies of Cholesterol Conjugates against Drug-Resistant Ovarian Cancer Cells
Huaimin Wang, Xu Lab
Abstract: Here we present phosphotyrosine cholesterol conjugates for selectively killing cancer cells, including platinum-resistant ovarian cancer cells. Remarkably, the tyrosine-cholesterol conjugates exhibits higher potency and higher selectivity than cisplatin against drug resistant human ovarian carcinoma cell lines (e.g., A2780cis) in cell assay. The conjugate increases the degree of non-covalent oligomerization upon enzymatic dephosphorylation in aqueous buffer. This enzymatic conversion of cholesterol conjugates also results in the assemblies of the cholesterol conjugates inside and outside cells and leads to cell death. Moreover, preliminary mechanistic study suggests that the formed assemblies of the conjugates not only interact with actin filaments and microtubules, but also affect lipid rafts. As the first report of multifaceted supramolecular assemblies of cholesterol conjugate against cancer cell, this work illustrates the integration of enzyme catalysis and self-assembly of essential biological small molecules on and inside cancer cells as a promising strategy for developing multifunctional therapeutics to treat drug-resistant cancers.

July 7, 2016
Linked-in/Networking Workshop, 2016 Hiatt Summer Science Career Series
Nate Tompkins, Andrew Balchunas

June 23, 2016
IRG 2: Regulating the size of self-assembling filamentous structures by a finite pool of subunits
David Harbage, Kondev Lab

June 16, 2016
MRSEC Seminar: Phase Behavior of Charged Interfacial Colloids in Flat and Curved Space
Colm Patrick Kelleher, Ph.D. student at NYU
Abstract: Hydrophobic PMMA colloidal particles, when dispersed in oil, can become highly charged. In the presence of an interface with a conducting aqueous phase, image charge effects lead to strong binding of colloidal particles to the interface, even though the particles are wetted very little by the aqueous phase. The fact that the forces in this system are purely electrostatic means that interparticle interactions are homogenous and time-independent, and so can be described by a simple yet quantitative model. In addition, the PMMA particles are large enough to be imaged in real space with optical microscopy, yet small enough that they can reach thermal equilibrium in experimental time scales. Thus, our system provides an ideal playground for studying a diverse array of many-body phenomena in classical 2D condensed matter physics. In this talk, I will first discuss the results of experiments my collaborators and I have performed to explore the nature of the interaction between colloidal particles which are bound to the oil-aqueous phase interface. I will then describe how we can use our system to study the phase behavior of repulsive particles in two dimensions, in both flat and curved space.

June 15, 2016
MRSEC Seminar: A Common Trigger of Neurodegeneration
Marcos J. Guerrero-Munoz, PhD, Hampton University Research Assistant Professor and Hampton PREM Pathway to Professor Fellow
Abstract: : A Common Trigger of Neurodegeneration Impaired proteostasis is one of the main features of neurodegenerative diseases, which are associated with the formation of insoluble protein aggregates. The aggregation process can be caused by overproduction or poor clearance of these proteins. However, numerous reports suggest that soluble aggregates are the most toxic species, rather than insoluble fibrillar material, in Alzheimer’s, Parkinson’s, and Prion diseases, among others. Although the exact protein that aggregates varies between neurological disorders, they all share common structural features that can be used as therapeutic targets.

June 13, 2016
MRSEC Executive Committee

June 9, 2016
IRG 1: Many-molecule encapsulation by an icosahedral shell
Farri Mohajerani, Hagan Lab

June 6, 2016
MRSEC Seminar: Kinetics of anisotropic particle assembly processes
Daniel J Beltran, Postdoc with Ronald Larson at University of Michigan
Abstract: Colloidal particles can assemble into a myriad of structures by virtue of the many interaction forces available to them. Variable range attraction and repulsion and the recently explored non-isotropic character, exemplified by Janus and Lock-and-Key particles, are examples of the versatility of colloidal particles as building blocks. In this work I aim to study two kinds of anisotropic colloidal building blocks in terms of their assembly kinetics. 

Firstly, I study Janus colloids, as examples of particles with simple patchy interactions, where the particle has a patch, or face, that interacts differently than the rest of the particle. A systematic approach to understand the assembly of Janus colloids, as a function of Janus balance and particle concentration is not yet available. In this work I assess the re-configurability of structures formed by Janus colloids by (1) determining equilibrium structures, (2) identifying possible traps in the structure switching process, and (3) assessing the speed of structure switching. My results show conditions for stability of several structures, including a fluid, a lamellar, and a rotator-close packed phase. I also find conditions for fast and reliable structure switching conditions between the rotator close-packed and the lamellar phase. These findings enable the understanding of the assembly process of Janus building blocks and provide a framework with which to study the kinetics of structure change. 
Secondly, a first-passage-time theory is developed for the binding kinetics of pairs of colloidal particles, one of which (the Lock particle) has an axisymmetric patch where strong “specific” binding occurs with the other particle (the Key particle), which has isotropic attractive interactions. When the key particle contacts the lock particle away from this strong-binding patch, “non-specifically"-bound particle pairs can form, but these pairs are weakly, and reversibly, bound. Starting from lock-key pairs that are non-specifically bound, predictions are made for the rates of formation of both specific lock-key binding, and of breakage of non-specifically-bound particle pairs to form free, non-interacting, spheres.  In these first-passage-time calculations, hydrodynamic interactions appear as combinations of normal modes of motion which combine rotation, sliding-translation and rotation-translation correlations. These are combined into an effective diffusion coefficient controlling the rate of variation in the angle between the line separating particle centers and the director describing the orientation of the attractive patch of the key particle. The first-passage-time predictions of the binding kinetics for ideal Lock-Key colloids are compared with Stokesian Dynamics simulations to validate the model. First-passage-time predictions are used to study the effect of the interaction potential on kinetics of non-specific to specific binding and of non-specific binding to free particles, and results are compared with experiments from the Solomon group. Knowledge of binding kinetics is important for novel hierarchical self-assembly applications where intermediate assemblies are required to build desired structures, and as models for predicting protein association and dissociation kinetics.

May 24, 2016
MRSEC Seminar: TIP for grip, catch or slip: rupture force and lifetime of microtubule-"receptor" attachments
Prof. Debashish Chowdhury, Indian Institute of Technology, Kanpur, India
Abstract: A microtubule (MT) is nature's nano-tube. Because of the unusual kinetics of its polymerization and depolymerization, a MT can "search" for various types of "receptors". In a mitotic spindle, the machinery for chromosome segregation, the searching plus end of MT gets "captured" by a special receptor complex called kinetochore that is bound to one of sister chromatids. In contrast, the plus end of the astral MTs get captured by the cell cortex with the participation of +TIPs like EB1. Using simple theoretical models of (a) the MT-kinetochore attachments, and (b) MT-cortex attachments,  we study the nature of the grip of a MT on these two distinct types of receptors. More specifically, we calculate (i) the mean lifetime of the attachments under force clamp conditions, and (ii) the mean rupture force under force-ramp conditions. The MT-kinetochore attachments exhibit a catch-bond-like behavior that arises from force-dependence of the depolymerization kinetics whereas the MT-cortex attachment is like a slip bond.

May 23, 2016
IRG 2: Simultaneous 3D tracking of passive tracers and microtubules in active matter
Yi Fan, Breuer Lab, Brown University

May 19, 2016
MRSEC Seminar: Non-monotonic slow relaxations and memory effects in disordered mechanical systems
Yoav Lahini, Research Associate Harvard
Abstract: Many disordered systems that are far from equilibrium exhibit a range of similar physical phenomena, such as logarithmic relaxations, aging, and memory effects. Yet, in spite of many studies that have been conducted on these recurring motifs across a broad range of systems, identifying the mechanisms underlying the unusual out-of-equilibrium dynamics of disordered systems remains an outstanding problem in condensed matter physics. Here, I will describe several disordered soft-matter systems that exhibit a similar repertoire of far-from-equilibrium behavior, including non-monotonic relaxation towards equilibrium and the ability to hold a memory of previous external conditions that can last hours. At the same time, each one of these systems offers a way to track the evolution of its internal structure, presenting an opportunity to reveal and compare the underlying mechanisms across different systems.

May 17, 2016

May 13, 2016
MRSEC Social Hour, TGITacos

May 12, 2016
MRSEC Seminar: Mobility, correlation lengths, and structural entropy in glass-forming hard-sphere liquids: new simulation results for an old system
Prof. Scott Milner, Penn State
Abstract: We can relate geometry and mobility in a glass-forming hard-sphere liquid by a purely geometric criterion:  “T1-active” particles, which can gain or lose a Voronoi neighbor by moving within their free volume with other particles fixed.  We use a “crystal-avoiding” MD method, which suppresses crystallization without altering the dynamics, to obtain geometrical and dynamical properties for monodisperse hard-sphere fluids with 0.40 < \phi < 0.64 .  We find the percolation threshold of T1-inactive particles is essentially identical to the commonly identified hard-sphere glass transition, \phi_g = 0.585.  

We can obtain correlation lengths in glass-forming hard-sphere liquids, from the response of dynamical properties (diffusion coefficient D and structural relaxation time \tau_\alpha) to a regular array of pinned particles. Dynamics slow dramatically as the correlation length becomes comparable to the spacing of the pinned array.  By assuming a scaling form, our results collapse onto a master curve, from which relative correlation lengths can be extracted.  The length obtained from dynamical property Q scales as log Q ~ \xi^\psi, with \psi \approx 1.
When a fluid glassifies, ergodicity is lost; configuration space is partitioned into many disconnected basins.  Each basin is a structurally distinct configuration of the glass; the structural entropy of a glass is the log of the number of such configurations.  We measure this entropy for glassy hard disks, by using the neighbor graph to identify configurations, and counting topologically distinct graphs for subsystems of increasing size.  We find the number of basins for N disks grows as e^{sN}, with s of order unity.

May 10, 2016
MRSEC Executive Committee

May 10, 2016
IRG 1: Bending bubbles: using giant vesicles and water droplets to study membrane remodeling proteins
Charlotte Kelley, Rodal Lab, Brandeis University

May 5, 2016
MRSEC Seminar: Actin turnover in motile cells
Prof. Kinneret Keren, Technion Israel Institute of Technology
Abstract: Actin turnover is the central driving force underlying cell motility. The molecular components involved are largely known, and their properties have been studied extensively in vitro. However, a comprehensive quantitative picture of actin turnover in vivo is still missing. We focus on lamellipodial fragments from fish epithelial keratocytes, which lack the cell body but retain the ability to crawl with speed and persistence similar to whole cells. The geometric simplicity of fragments and the absence of additional actin structures allow us to characterize the spatio-temporal actin organization in their lamellipodium with unprecedented detail. These experimental measurements serve to guide the development of a predictive quantitative model of actin turnover in motile lamellipodia. Our results indicate that the bulk of the cytoplasmic actin pool is not available for polymerization, allowing diffusion to recycle actin effectively and facilitate steady cell migration, while maintaining the cell’s ability to generate rapid focused acceleration when needed.

April 21, 2016
MRSEC Seminar: What can Chemistry do in the self-assembly of rodlike colloidal particles
Prof. Zhenkun Zhang, Nankai University
Abstract: Non-covalent interactions between building blocks ranging from molecules to colloidal particles are normally responsive for the assembling such units. Physics often play dominant roles in determining the hierarchical structure of the end assemblies. Chemistry, in most of cases, is only responsible for construction of the building blocks. However, chemistry sometimes can be explored to fine tune the non-covalent interactions such that reconfigurable assembly can be realized. In this talk, we shall summarize some of our works in the past five years to demonstrate how we have applied simple chemistry to influence the self-assembly of rodlike colloidal particles. We focus on two systems: the cholesteric liquid crystal (CLC) phase of rodlike viruses and side-by-side assembly of polymeric ellipsoids at fluid interfaces. In the former case, we shall show that chemical modifications of the virus building blocks can be exploited to fine-tune the ordering of the virus in the LC phases. The CLC phase of the re-functioned viruses can be responsive to external chemical information via in situ dynamic bond formation, which might be used as sensors. Several kinds of end-functionalized polymers have been designed in our groups and grafted to the rodlike virus which can further control the intervirus interactions, leads to stimuli- responsive LC phase and hydrogels with inherent internal chiral structure. In the case of ellipsoidal particles at 2D fluids, we shall show how chemistry is used to craft the surface properties and make the surface-deformation induced capillary attractions stand out and drive the ellipsoids assembly into well-defined ellipsoidal worms. 

April 14, 2016
MRSEC Seminar: Blue energy and (other) sustainable heat-to-power conversion
Prof Rene Van Roij, Utrecht University, The Netherlands
Abstract: More than 2 kJ of (free) energy is getting dissipated with every liter of river water that flows into the sea. This energy, which is equivalent to a waterfall of 200 meter, can nowadays be efficiently harvested with devices based on modern nanomaterials such nanoporous electrodes and ion-selective membranes. For instance, a water-immersed supercapacitor composed of nanoporous carbon electrodes (with a km2/kg surface area) has recently been used to harvest this so-called “blue energy” through a fourfold charging-desalination-discharging-resalination cycle [1] that bears astrong resemblance to the expansion-cooling-compression-heating cycle of a classical Stirling heat engine [2]. We will discuss this analogy and present calculations to show that the harvested blue energy per liter can be doubled if the fresh water is warm (50C) rather than cold (10C), where the elevated temperature should stem from waste heat [3]. We will also briefly discuss another recent heat-to-power converter that is based on a supercapacitor filled with an ionic liquid [4], and a device that converts small mechanical vibrations into electricity using deformable water droplets between a vibrating parallel-plate capacitor [5]. In all these cases ubiquitous gradients and sources are used to sustainably harvest electric energy using a variable capacitance.

[1] D. Brogioli, Phys. Rev. Lett. 103, 058501 (2009).
[2] N. Boon and R. van Roij, Mol. Phys. 109, 1229 (2011).
[3] M. Janssen, A. Härtel, and R. van Roij, Phys. Rev. Lett. 113, 268501 (2014).
[4] A Härtel, M Janssen, D Weingarth, V Presser, R van Roij, Energy & Envir. Science 8, 2396 (2015).
[5] M. Janssen, B. Werkhoven, and R. van Roij, RSC Advances 6, 20485 (2016)

April 11, 2016
MRSEC Executive Committee

April 8, 2016
MRSEC Social Hour, TGITacos

April 7, 2016
MRSEC Seminar: DNA Polymer Physics with Complex Geometry (and Topology)
Alex Klotz, MIT
Abstract: Single DNA molecules are used as model polymers due to their mesoscopic length scales, their monodispersity, and the availability of single-molecule imaging techniques. Nanofluidic confinement is a powerful tool to study single-molecule dynamics with DNA, both as a tool to probe the underlying physics governing polymer confinement and as stepping-stone to the development of genomics technologies. Here, I discuss my work studying DNA confined in a complex nanofluidic device featuring a nanofluidic slit embedded with an array of cavities, that causes molecules to partition contour between regions of varying confinement, such that they look like pieces from the video game Tetris. By examining the equilibrium DNA partitioning under different geometric conditions, I can investigate the competing effects of entropy, self-exclusion, and semi-flexibility on a single-molecule basis. I will also discuss recent work examining the behavior of knotted DNA molecules under extensional flow.

March 31, 2016
MRSEC Seminar: Spatial organization of the plasma membrane
 and peripheral membrane proteins
Lutz Maibaum, University of Washington
Abstract: Cellular membranes are complex organelles composed of phospholipids, sterols and proteins, among others. The spatial organization of these components affects its biological function. Our work uses computer simulations and modeling to study two mechanisms that lead to the emergence of spatial order: the phase behavior of multicomponent lipid bilayers and the effect of membrane-induced interactions on membrane-bound proteins.  Lipid composition heterogeneities have attracted much attention recently as they might form the basis for lipid rafts, small domains rich in sterols that corral membrane proteins. We study the phase behavior of multicomponent bilayers using simulations of coarse-grained molecular and general field-theory based models. We find a wide range of membrane systems that exhibit composition correlations over nanometer length scales. A different type of lateral structure can be induced by proteins binding to the membrane, which restricts the latter’s intrinsic fluctuations. This gives rise to an interaction between proteins that is transmitted by the membrane’s elastic properties. We develop a hybrid model that combines a continuum description of the membrane with a particle representation of the proteins, and show that the membrane-induced interaction gives rise to an effective attraction between proteins that can act on length scales much larger than typical intermolecular forces.

March 29, 2016
MRSEC Seminar: Order-disorder transitions in a driven magnetic granular monolayer
Simon Merminod, Université Paris Diderot
Abstract: In an experiment at the human scale, we can observe with the naked eye phenomena involved in the shaping of matter at the molecular scale, resulting from the competition between thermal disordered motion and non-contact interactions between particles. Soft ferromagnetic particles are placed inside a horizontal, quasi-two-dimensional cell and are vertically vibrated, so that they perform a horizontal quasi-Brownian motion. When immersed in a transverse magnetic field, the particles become magnetized and thus interact according to a dipolar repulsive law. Ordered and disordered phases are observed depending on the particle area fraction, the ratio of the magnetic energy to the kinetic energy, and the processing pathway. At low particle area fraction, we show that, prior to the complete solidification of the disordered granular gas into a crystalline state, the typical properties of this dissipative out-of-equilibrium granular gas are progressively lost, to approach those expected for a usual gas at thermodynamic equilibrium. Surprisingly, at a higher area fraction, the system solidifies into a large-scale disordered labyrinthine phase mostly constituted of randomly oriented chains of particles in contact, despite the magnetic repulsion. We characterize quantitatively this transition and explain the formation of these chains using a simple model. Moreover, by studying the aging properties of the labyrinthine phase, we show that it exhibits slow dynamics, which occurs typically in out-of-equilibrium disordered systems such as structural glasses.

March 28, 2016
MRSEC Seminar: Entropic Stabilization of Strain-Driven Morphological Instabilities in Thin Film Growth
Arvind Baskaran, Postdoc candidate
Abstract: Heteroepitaxial growth is the layer-by-layer growth of one crystalline material on a substrate of another. Popular film/substrate combinations include semiconductors such as Ge/Si and InGaAs/GaAs. When the film and substrate species are lattice mismatched the film introduces a strain in the substrate. This leads to a morphological instability where the film undergoes a transition from layer by layer growth to island formation known as the Stranski-Krastanov transition. These self-assembled islands can serve as quantum dots and are of great practical importance in construction of optoelectronic devices. The morphological characteristics of the islands determine the electronic properties of the quantum dots.  One key morphological feature is that this transition occurs after the deposition of a certain critical thickness of the film. Further the islands are observed to sit on top of a wetting layer of film atoms of a certain thickness. This talk will discuss the mechanisms that lead to the various features of the morphological transition. The talk will outline an atomistic kinetic Monte Carlo approach to model this system. Then through systematic numerical exploration a theory based on entropic stabilization mechanisms for this growth mode will be detailed. The relationship between growth conditions and the morphology will also be discussed. This work was done in collaboration with Peter Smereka.

March 21, 2016
MRSEC Executive Committee

March 11, 2016
MRSEC Social Hour, TGITacos

March 10, 2016
MRSEC Seminar: Elasto-capillarity: A new toolkit for directed assembly of advanced materials
Mohamed Gharbi, McGill University, Canada
Abstract: The opportunities for guiding assembly using elastic energy stored in soft matter are wide open. The emerging scientific frontiers in this field show an exceptional promise for significant new applications. Since soft materials can be readily reconfigured, there are unplumbed opportunities to make responsive devices including smart windows for energy efficiency, and responsive optical structures. In the other hand, the trapping of colloidal objects at interfaces between immiscible fluids has proven to exhibit incredible abilities to template the arrangement of particles into rich ordered structures. These structures are controlled by lateral forces that compete with capillary forces. However, these interactions are still unexplored when particles are trapped at the interface of an ordered fluid. In this talk, I will present recent progress in understanding the mechanisms that govern interactions between particles at liquid crystal interfaces. I will report how the resulting potential induced by the interplay between elasticity and capillarity could lead to new opportunities for genuine spontaneous self-assembly and create new strategies for making new generation of advanced materials that may find relevance in many applications in the field of energy technology.

March 3, 2016
MRSEC Seminar: Electroosmosis at liquid interfaces
Baptiste Blanc, Fraden Lab
Abstract: Electrokinetic (EK) transport couples hydrodynamics and electrostatics at liquid interfaces. In particular, it is possible to generate a flow near a charged interface in a liquid by applying an electric field, due to the drag force exerted on counter ions near the interface, a phenomenon referred to as electro-osmosis (EO). We propose here to use EO in the context of liquid foams, the charges being carried by the surfactants used to stabilize the foam. The main challenge of the project is to achieve a complete understanding of EK transport in a 3D liquid foam. To do so, we used a multiscale approach combining experimental and theoretical (molecular dynamics (MD) simulation) tools. In this article, we present our newest results on this general project.

February 22, 2016
MRSEC Executive Committee

February 18, 2016
MRSEC Seminar: Locomotion in liquid crystals
Madison Krieger, Brown University
Abstract: Swimming at the micron scale is a topic that is nearly a century old, yet has seen renewed interest as novel swimming mechanisms, fluid backgrounds, fluid-structure- and collective-effects have been discovered. Recent theoretical attention has been payed to swimming in rotationally-isotropic viscoelastic fluids and gels, and also to active nematics, which are inherently anisotropic. A phenomenon that lies between these two extremes is that of a single motile microorganism immersed in a nematic liquid crystal, where the nematogens are not active but the viscous and elastic anisotropy gives rise to several interesting swimming behaviors. We discuss some aspects of this locomotion problem in its own right and also seat it between these existing literatures as an active phase known as a "living liquid crystal." 

February 12, 2016
MRSEC Social Hour, TGITacos

February 9, 2016
MRSEC Seminar: Revealing the Molecular and Structural Basis of Retroviral Assembly and Endolysin PlyC Membrane Translocation
Marilia Barros, Carnegie Mellon
Abstract: Numerous biological processes are either triggered by or result in the formation of protein-lipid complexes at the membrane.  The study on the interactions between lipids and proteins is fundamental to gaining insights into the physical aspects of biological processes. We investigated molecular-scale aspects of such membrane interactions using sparsely-tethered lipid bilayer membranes (stBLMs). Applying complementary surface-sensitive techniques such as surface plasmon resonance (SPR) and neutron reflectometry, we  examined  the  details  of  two-stage interaction - surface adsorption and bilayer insertion - and demonstrate the first steps towards a mechanistic understanding of how the endolysin PlyC binding domain, PlyCB, initiates membrane translocation. We also assessed the specific roles of electrostatic, hydrophobic and lipid-specific contributions to HIV-1 matrix (MA) membrane coupling aiming to understand the mechanisms that lead to the recruitment of specific lipids into the viral shell. The impact of MA myristoylation was evaluated and the role of cholesterol was assessed in promoting protein affinity to the bilayer. The molecular level details reported here provide a better understanding of the lipid interactions of MA and their implications for proper Gag membrane association and retroviral particle assembly.

January 28, 2016
MRSEC IRG Progress Report: Self-assembled Molecular Nanofibers Promiscuously Interact with Cell Surface Death Receptors
Xuewen Du, Xu Lab

January 25, 2016
MRSEC Executive Committee

January 21, 2016
MRSEC Seminar: Electrolytes at the interface: charge stabilization in colloids, emulsions and polymer blends
Johannes Zwanniken, UMass Lowell
Abstract: Electrolytes play a vital role in numerous biological processes, and are key to the stability of many systems in Soft Condensed Matter, such as colloids, emulsions, and solutions of charged macromolecules. Since the work of Gouy, Chapman, Debye, Kirkwood et al., it is well known that ions 'screen' the interactions between charged solutes, and that elevated salt concentrations can induce aggregation, an effect also known as 'salting-out'. About three decades ago, however, it became clear that this picture is too simplistic after simulations and experiments had indicated that ions can also induce attractions between like-charged solutes.

I will discuss that ion-ion correlations are an important missing factor in the classical picture, and that the ignored 'cohesion' of the ion cloud can induce effects opposite to basic screening. We study ions in a narrow confinement with simulations (Car-Parrinello Molecular Dynamics), and with liquid state theory (Ornstein-Zernike with the anisotropic HNC closure), and find strong density oscillations and a liquid-like structure of ions for parameters that correspond to aqueous solutions of ~ 0.1 M concentrations [1]. Ion-induced interactions between colloidal particles are calculated, and are found to be repulsive or attractive, depending on the specific ion parameters and dielectric properties of the colloids.
In a similar fashion, one can shift the phase diagram of polyelectrolyte blends and block-copolymers in multiple directions by changing the ionic properties, as concluded from a hybrid Liquid-State Self-Consistent Field Theory (LS-SCFT) [2,3].
These correlational effects can be interpreted as the consequence of two 'thermal forces' that originate from direct interaction and the brownian motion of the ions. A generalization of these concepts to driven systems, and solutions with 'memory' could be most relevant for the development of soft ionic materials. Inspiration can be gleaned from recent developments in the field of Active Matter.

Past Events 2008-2015