Past Events

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