Past Events

December 14, 2016

Event: IRG 2
Speaker: Mike Norton, Fraden Lab Postdoc
Title: The effect of hydrodynamic and topological constraints on a confined active nematic material
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

Event: IRG 1
Speaker: Guillermo Rodriguez Lazaro, Hagan Lab Postdoc
Title: Mechanisms of virus assembly on membranes 
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

Event: TacoCat Social
*Grad students and postdocs only*

December 1, 2016

Event: MRSEC Seminar
Speaker: Slaven Garaj, National University of Singapore
Title: Nanofluidics with graphene membranes
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

Event: IRG 2
Speaker: Camille Girabawe, Fraden Lab Grad Student
Title: Synchronization in a pair of chemical heterogeneous Belousov-Zhabontisky droplets
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

Event: MRSEC Retreat

November 11, 2016

Event: TacoCat Social
*Grad students and postdocs only*

November 8, 2016

Event: There's a Scientist in my Classroom - Waltham teachers outreach event

October 31, 2016

Event: MRSEC Executive Committee

October 28, 2016

Event: IRG 2
Speaker: Caleb Wagner, Baskaran/Hagan Labs Grad Student
Title: Statistical mechanics of ideal active Brownian particles in 1d confinement
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

Event: IRG 1
Speaker: Leroy Jia, Powers Lab Grad Student, Brown University
Title: Chiral Edge Fluctuations of Colloidal Membranes
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

Event: TacoCat Social
*Grad students and postdocs only*

September 30, 2016

Event: IRG 2
Speaker: Mat Chamberlain, Gelles Lab Grad Student
Title: Diversity of transcription elongation complexes from non-equilibrium binding of regulatory proteins
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

Event: MRSEC Executive Committee

September 23, 2016

Event: New England Complex Fluids Workshop

September 16, 2016

Event: IRG 1
Speaker: Andrew Balchunas, Dogic Lab Grad Student
Title: Using Microfluidics to Measure the Equation of State for a 2D Colloidal Membrane
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

Event: IRG 2
Speaker: Danny Goldstein, Chakraborty Lab Grad Student
Title: A Kinetic Model of Active Extensile Bundles
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

Event: MRSEC Summer Student Seminar
Speaker: Thomas Litschel, Fraden Lab / Mathew Chamberlain, Gelles Lab Grad student

August 22, 2016

Event: MRSEC Executive Committee

August 10, 2016

Event: MRSEC Summer Student Seminar
Speaker: Gabriel Bronk, Kondev Lab Grad student / David Waterman, Haber Lab Grad student

August 5, 2016

Event: IRG 1
Speaker: Gabriel Bronk, Kondev Lab Grad Student
Title: Chromosome Refolding Model of Mating-Type Switching in Yeast
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

Event: Knowing Yourself Workshop, 2016 Hiatt Summer Science Career Series
*Open to all Science Undergrads*
Speaker: Abigail Crine

July 27, 2016

Event: MRSEC Summer Student Seminar

Speaker: Ben Hancock, Baskaran Lab Grad student / Anna Kazatskaya, Sengupta Lab Grad student

July 19, 2016

Event: IRG 2
Speaker: Kunta Wu, Dogic Lab

Title: Scale-invariant transition from turbulent to coherent flows in confined 3D active fluids

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

Event: Incorporating Summer Research into Your STEM Resumes, 2016 Hiatt Summer Science Career Series
*Open to all Science Undergrads*
Speaker: Jane Pavese

July 13, 2016

Event: MRSEC Summer Student Seminar

Speaker: Rylie Walsh, Rodal Lab Grad student / Joanna Robaszewski, Dogic Lab Grad student

July 7, 2016

Event: IRG 1

Speaker: Huaimin Wang, Xu Lab

Title: Enzyme-Regulated Supramolecular Assemblies of Cholesterol Conjugates against Drug-Resistant Ovarian Cancer Cells

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
Event: Linked-in/Networking Workshop, 2016 Hiatt Summer Science Career Series
*Open to all Science Undergrads*

June 29, 2016

Event: MRSEC Summer Student Seminar

Speaker: Nate Tompkins, Andrew Balchunas

June 23, 2016

Room: Shapiro Science Library

Time: 2 pm

Event: IRG 2

Speaker: David Harbage, Kondev Lab

Title: Regulating the size of self-assembling filamentous structures by a finite pool of subunits

June 16, 2016

Event: MRSEC Seminar

Speaker:  Colm Patrick Kelleher, Ph.D. student at NYU

Title: Phase Behavior of Charged Interfacial Colloids in Flat and Curved Space
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

Event: MRSEC Seminar
Speaker: Marcos J. Guerrero-Munoz, PhD, Hampton University Research Assistant Professor and Hampton PREM Pathway to Professor Fellow
Title: A Common Trigger of Neurodegeneration
Abstract: 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

Event: MRSEC Executive Committee

June 9, 2016

Event: IRG 1
Speaker: Farri Mohajerani, Hagan Lab

Title: Many-molecule encapsulation by an icosahedral shell

June 6, 2016

Event: MRSEC Seminar

Speaker: Daniel J Beltran, Postdoc with Ronald Larson at University of Michigan

Title: Kinetics of anisotropic particle assembly processes

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

Event: MRSEC Seminar

Speaker: Prof. Debashish Chowdhury, Indian Institute of Technology, Kanpur, India
Title: TIP for grip, catch or slip: rupture force and lifetime of microtubule-"receptor" attachments

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

Event: IRG 2

Speaker: Yi Fan, Breuer Lab, Brown University
Title: Simultaneous 3D tracking of passive tracers and microtubules in active matter

May 19, 2016

Event: MRSEC Seminar

Speaker: Yoav Lahini, Research Associate Harvard
Title: Non-monotonic slow relaxations and memory effects in disordered mechanical systems

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

Event: Research2Innovation

May 13, 2016

Event: MRSEC Social Hour, TGITacos
*Grad students and postdocs only*

May 12, 2016

Event: MRSEC Seminar

Speaker: Prof. Scott Milner, Penn State
Title: "Mobility, correlation lengths, and structural entropy in glass-forming hard-sphere liquids:  

new simulation results for an old system"

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

Event: MRSEC Executive Committee

May 10, 2016

Event: IRG 1
Speaker: Charlotte Kelley, Rodal Lab, Brandeis University
Title: "Bending bubbles: using giant vesicles and water droplets to study membrane remodeling proteins"

May 5, 2016

Event: MRSEC Seminar

Speaker: Prof. Kinneret Keren, Technion Israel Institute of Technology
Title: Actin turnover in motile cells
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

Event: MRSEC Seminar

Speaker: Prof. Zhenkun Zhang, Nankai University

Title: What can Chemistry do in the self-assembly of rodlike colloidal particles

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

Event: MRSEC Seminar

Speaker: Prof Rene Van Roij, Utrecht University, The Netherlands

Title: Blue energy and (other) sustainable heat-to-power conversion

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

*Grad students and postdocs only*

April 7, 2016

Event: MRSEC Seminar

Speaker:  Alex Klotz, MIT

Title: DNA Polymer Physics with Complex Geometry (and Topology)

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

Event: MRSEC Seminar

Speaker: Lutz Maibaum, University of Washington

Title: Spatial organization of the plasma membrane
 and peripheral membrane proteins

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

Event: MRSEC Seminar

Speaker: Simon Merminod, Université Paris Diderot

Title: Order-disorder transitions in a driven magnetic granular monolayer

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

Speaker: Arvind Baskaran, Postdoc candidate

Title: Entropic Stabilization of Strain-Driven Morphological Instabilities in Thin Film Growth

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

Time: 9:30 am

March 11, 2016

MRSEC Social Hour, TGITacos

*Grad students and postdocs only*

March 10, 2016

MRSEC Seminar

Speaker: Mohamed Gharbi, McGill University, Canada
Title: Elasto-capillarity: A new toolkit for directed assembly of advanced materials

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

Room: Abelson 229

Time: 4 pm

Event: MRSEC Seminar

Speaker: Baptiste Blanc, Fraden Lab

Title: Electroosmosis at liquid interfaces

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

Time: 9:30 am

February 18, 2016

MRSEC Seminar

Speaker: Madison Krieger, Brown University

Title: Locomotion in liquid crystals

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

Event: MRSEC Social Hour, TGITacos

*Grad students and postdocs only*

Click here to view poster.

February 9, 2016

MRSEC Seminar

Speaker: Marilia Barros, Carnegie Mellon

Title: Revealing the Molecular and Structural Basis of Retroviral Assembly and Endolysin PlyC Membrane Translocation

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

Event: MRSEC IRG Progress Report

Speaker: Xuewen Du, Xu Lab

Title: Self-assembled Molecular Nanofibers Promiscuously Interact with Cell Surface Death Receptors

January 25, 2016

Event: MRSEC Executive Committee

January 21, 2016

Event: MRSEC Seminar

Speaker: Johannes Zwanniken, UMass Lowell

Title: Electrolytes at the interface: charge stabilization in colloids, emulsions and polymer blends

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.

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