Bulletin of the American Physical Society
APS March Meeting 2016
Volume 61, Number 2
Monday–Friday, March 14–18, 2016; Baltimore, Maryland
Session B37: Phase Transitions and Self-Assembly in Biological Systems IIFocus
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Sponsoring Units: GSOFT DBIO Chair: Michael Hagan, Brandeis University Room: 340 |
Monday, March 14, 2016 11:15AM - 11:27AM |
B37.00001: Imaging the Dynamics of Individual Viruses in Solution Aaron Goldfain, Rees Garmann, Yoav Lahini, Vinothan Manoharan We have developed optical microscopy techniques that can detect and track individual, unlabeled viruses at thousands of frames per second. We use these techniques to study fast, dynamic processes in the life cycles of bacteriophages (viruses that infect bacteria). I will describe experiments that capture the ejection of double stranded DNA from bacteriophage $\lambda$. During the 1-2 second ejection, the DNA genome transitions from a compact, highly ordered spool within the capsid into an extended random coil in solution. By quantifying the amount of light scattered from a single $\lambda$ phage as its DNA ejects, we measure the amount of DNA remaining in the virus capsid as a function of time. Measuring small fluctuations in the rate of ejection may uncover clues about the complex conformational rearrangements that the DNA undergoes while escaping the capsid. [Preview Abstract] |
Monday, March 14, 2016 11:27AM - 11:39AM |
B37.00002: Chirality of Viral Capsids Sanjay Dharmavaram, Fangming Xie, Robijn Bruinsma, William Klug, Joseph Rudnick Most icosahedral viruses are classified by their T-number which identifies their capsid in terms of the number of capsomers and their relative arrangement. Certain T-numbers ($T=7$ for instance) are inherently chiral (with no reflection planes) while others (e.g. $T=1$) are achiral. We present a Landau-Brazovskii (LB) theory for weak crystallization in which a scalar order parameter that measures density of capsid proteins successfully predicts the various observed T-numbers and their respective chiralities. We find that chiral capsids gain stability by spontaneously breaking symmetry from an unstable chiral state. The inherently achiral LB-free energy does not preferentially select a particular chiral state from its mirror reflection. Based on the physical observation that proteins are inherently chiral molecules with directional interactions, we propose a new chiral term to the LB energy as a possible selection mechanism for chirality. [Preview Abstract] |
Monday, March 14, 2016 11:39AM - 11:51AM |
B37.00003: A Simple Model for Immature Retrovirus Capsid Assembly Stefan Paquay, Paul van der Schoot, Bogdan Dragnea In this talk I will present simulations of a simple model for capsomeres in immature virus capsids, consisting of only point particles with a tunable range of attraction constrained to a spherical surface. We find that, at sufficiently low density, a short interaction range is sufficient for the suppression of five-fold defects in the packing and causes instead larger tears and scars in the capsid. These findings agree both qualitatively and quantitatively with experiments on immature retrovirus capsids, implying that the structure of the retroviral protein lattice can, for a large part, be explained simply by the effective interaction between the capsomeres. [Preview Abstract] |
Monday, March 14, 2016 11:51AM - 12:03PM |
B37.00004: Autophagy selectivity through receptor clustering Andrew Rutenberg, Aidan Brown Substrate selectivity in autophagy requires an all-or-none cellular response. We focus on peroxisomes, for which autophagy receptor proteins NBR1 and p62 are well characterized. Using computational models, we explore the hypothesis that physical clustering of autophagy receptor proteins on the peroxisome surface provides an appropriate all-or-none response. We find that larger peroxisomes nucleate NBR1 clusters first, and lose them due to competitive coarsening last, resulting in significant size-selectivity. We then consider a secondary hypothesis that p62 inhibits NBR1 cluster formation. We find that p62 inhibition enhances size-selectivity enough that, even if there is no change of the pexophagy rate, the volume of remaining peroxisomes can significantly decrease. We find that enhanced ubiquitin levels suppress size-selectivity, and that this effect is more pronounced for individual peroxisomes. Sufficient ubiquitin allows receptor clusters to form on even the smallest peroxisomes. We conclude that NBR1 cluster formation provides a viable physical mechanism for all-or-none substrate selectivity in pexophagy. We predict that cluster formation is associated with significant size-selectivity. [Preview Abstract] |
Monday, March 14, 2016 12:03PM - 12:15PM |
B37.00005: Statistical Mechanics and Thermodynamics of Viral Evolution Barbara Jones, James Kaufman Using methods drawn from physics we study the life cycle of viruses. We analyze a model of viral infection and evolution using the ``grand canonical ensemble'' and formalisms from statistical mechanics and thermodynamics. Using this approach we determine possible genetic states of a model virus and host as a function of two independent pressures--immune response and system temperature. We show the system has a real thermodynamic temperature, and discover a new phase transition between a positive temperature regime of normal replication and a negative temperature ``disordered'' phase of the virus. We distinguish this from previous observations of a phase transition that arises as a function of mutation rate. From an evolutionary biology point of view, at steady state the viruses naturally evolve to distinct quasispecies. The approach used here could be refined to apply to real biological systems, perhaps providing insight into immune escape, the emergence of novel pathogens and other results of viral evolution. [Preview Abstract] |
Monday, March 14, 2016 12:15PM - 12:27PM |
B37.00006: Metastable Amyloid Phases and their Conversion to Mature Fibrils Martin Muschol, Tatiana Miti, Mentor Mulaj, Jeremy Schmit Self-assembly of proteins into amyloid fibrils plays a key role in both functional biological responses and pathogenic disorders which include Alzheimer’s disease and type II diabetes. Amyloid fibril assembly frequently generates compact oligomeric and curvilinear polymeric intermediates which are implicated to be toxic to cells. Yet, the relation between these early-stage oligomeric aggregates and late-stage rigid fibrils, which are the hallmark structure of amyloid plaques, has remained unclear. Our measurements indicate that lysozyme amyloid oligomers and their curvilinear fibrils only form after crossing a salt and protein concentration dependent threshold. These oligomeric aggregates are structurally distinct from rigid fibrils and are metastable against nucleation and growth of rigid fibrils. Our experimental transition boundaries match well with colloidal model predictions accounting for salt-modulated charge repulsion. We also report our preliminary findings on the mechanism by which these metastable oligomeric phases are converted into stable amyloid fibrils. [Preview Abstract] |
Monday, March 14, 2016 12:27PM - 12:39PM |
B37.00007: Patterns for Fluid Management: The Mechanical Origins of Microarchitectures Asja Radja, Maxim Lavrentovich, Eric Horsley, Randall Kamien, Alison Sweeney Pollen grains are the vehicles for the male germ line in land plants and are famous for the intricate microarchitectures of their protective coverings. It is not known whether these sub-micron-scale patterns have a functional role. A given microarchitectural pattern is maintained over geological time within a single species, yet, despite similar mechanisms of pollen development in all species, different species have extremely variable patterns. Until recently, many proposed mechanisms of pollen pattern formation were attributed to top-down assembly processes directed by the pollen cytoskeleton. We propose a novel view in which bottom-up mechanical processes akin to thermodynamic phase transitions may cause the final pollen structure. Here, we present a temporal view of pattern formation using several microscopy techniques. Our data show a rapid appearance of surface microstructures. We test the hypothesis of bottom-up pattern formation by physically manipulating the pattern formation process with mechanical forces and chemical solvents. Our data are consistent with bottom-up formation of these patterns; we discuss a hypothesis of pattern formation in this system involving Brazovskii phase transitions templated on a spherical geometry. [Preview Abstract] |
Monday, March 14, 2016 12:39PM - 12:51PM |
B37.00008: Pollen Patterning as a Brazovskii Phase Transition on a Sphere Maxim Lavrentovich, Eric Horsley, Asja Radja, Alison Sweeney, Randall Kamien Pollen grains acquire intricate, varied surface patterns during development. The patterns are reproducible within a single plant species, and yet exhibit a wide variation among species, despite having similar developmental steps. We model this pattern formation on spherical grains as a phase transition to a spatially modulated phase, characterized by an unstable wavelength $\lambda_0$. On the infinite, flat plane, the patterned phase consists of uniform stripes, as shown by Brazovskii. We find that, by contrast, the patterns may be much more varied on a spherical surface because the topological defects which must be present in the pattern may be accommodated in a variety of ways. This variation may explain the wide range of observed pollen patterns. We also argue that the first-order character of the transition may be responsible for the robust reproducibility of the patterns in a single plant species. Finally, we compute the free energy difference between the unpatterned, smooth phase and various patterned phases on the sphere. These calculations point toward possible future experimental tests of our model. [Preview Abstract] |
(Author Not Attending)
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B37.00009: Non-deterministic self-assembly of two tile types on a lattice Salvatore Tesoro I will present a complex behaviour that is both interesting from a statistical and complex systems point of view and from a more abstract point of view on complexity and evolutionary theory. I will introduce simple a theoretical framework to predict and describe all possible growth behaviours that self-assembly of two tile types can produce on a 2D lattice, given binary interaction rules between the faces of the tiles in the system. Such simple set up can give rise to critical transitions between bound and unbound growth regimes and other non-critical behaviours. I will illustrate how this work completes efforts conducted by Ahnert et Al. in the field of Complexity and Evolution, whereby deterministic self-assembly pathways have been exploited as a useful tool in addressing questions on complexity and modularity in nature. I will further show how this theoretical framework can be experimentally verified using DNA-tiles as a building material and providing experimental validation of the theoretical predictions made. [Preview Abstract] |
Monday, March 14, 2016 1:03PM - 1:15PM |
B37.00010: Generic Phase Diagram of Binary Superlattices Alexei Tkachenko Emergence of a large variety of self-assembled superlattices is a dramatic recent trend in the fields of nanoparticle and colloidal sciences. Motivated by this development, we propose a model that combines simplicity with a remarkably rich phase behavior, applicable to a wide range of such self-assembled systems. Those include nanoparticle and colloidal assemblies driven by DNA-mediated interactions, electrostatics, and possibly, by controlled drying. In our model, a binary system of Large and Small hard sphere (L and S)interact via selective short-range ("sticky") attraction. In its simplest version, this Binary Sticky Sphere model features attraction only between 'S' and 'L' particles, respectively. We demonstrate that in the limit when this attraction is sufficiently strong compared to kT, the problem becomes purely geometrical: the thermodynamically preferred state should maximize the number of S-L contacts. A general procedure for constructing the phase diagram as a function of system composition f, and particle size ratio r, is outlined. In this way, the global phase behavior can be calculated very efficiently, for a given set of plausible candidate phases. Furthermore, the geometric nature of the problem enables us to generate those candidate phases through a well defined and intuitive construction. We calculate the phase diagrams both for 2D and 3D systems, and compare the results with existing experiments. Most of the 3D superlattices observed to date are featured in our phase diagram, while several more are yet to be discovered. [Preview Abstract] |
Monday, March 14, 2016 1:15PM - 1:27PM |
B37.00011: Geometric and Topological Transitions of Small Clusters of Liquid Particles James Giammona, Otger Campas The geometry and topology of small particle clusters has been studied in several disciplines due to the fundamental nature of the problem and its relevance to applications. Recent theoretical work can predict observed packings for small numbers of hard, spherical particles, but little is known about how using deformable particles changes the geometry and topology of these clusters. To study this problem, we simulate small clusters of liquid particles using a Langevin approach and obtain the geometrical and topological transitions for clusters of N particles (up to N=7) as the particles’ interfacial tension and adhesion energy are varied. As particles become more adhesive and increase their contact angle, we observe well-defined packing transitions in the clusters. For N=5, a topological transition occurs at a critical value of the contact angle. For N=6, we obtain two stable cluster geometries for a given value of the contact angle, namely an 8-faced deltahedron and an octahedron. For N=7, there appears to be a complex landscape of cluster geometries and topologies, with transitions occurring at well-defined values of the contact angle. Our findings can help in the controlled assembly of particular arrangements of small clusters of bubbles or adherent droplets. [Preview Abstract] |
Monday, March 14, 2016 1:27PM - 1:39PM |
B37.00012: Helices Of Helices Mahsa Siavashpouri, Mark Zakhary, Christian Wachauf, Hendrik Dietz, Zvonimir Dogic Twisted ribbons are characteristic structural motifs that are prevalent in nature. However correlation between the macroscopic properties of the final self-assemblages and the microscopic features of the constituent molecules remain unknown. We describe a new class of supramolecular 1D assemblages with tunable mechanical properties. Using DNA origami technique, we design and structure rod-like colloidal particles that have excluded volume interactions and self-assemble into twisted ribbons in presence of attractive interactions mediated by non-absorbing polymers. By comparing behavior of DNA origami filaments and rodlike viruses we demonstrate that self-assembly into 1D twisted ribbons is universal and independent of the system materials. Tuning the molecular properties of the DNA origami particles, determines the physical properties of the entire self-assembled structures. Furthermore, to understand the connection between the chirality at the molecular scale and the macroscopic chiral structures, we measured twist periodicity (pitch) of cholesteric phase associated to various DNA origami designs which can develop a new framework in understanding microscopic origin of chirality in liquid crystals. [Preview Abstract] |
Monday, March 14, 2016 1:39PM - 1:51PM |
B37.00013: Theory of Microphase separation in bidisperse Chiral membranes Raunak Sakhardande, Stefan Stanojeviea, Arvind Baskaran, Michael Hagan, Aparna Baskaran, Bulbul Chakraborty We discuss the phase behavior of bidisperse chiral colloidal membranes, which are monolayers of rodlike molecules containing two species of rods, each with opposite handedness. Using a Ginzburg Landau theory, we show that the system exists in three stable states, separated by first-order phase transitions: a compositionally homogeneous state, macrophase separation between the two rod species, and a micro-phase separated state in which the minority rod species forms circular domains with a well-defined, narrow size distribution. We find that the phase behavior can be controlled by tuning two parameters, one associated with the driving force for membrane assembly, and the other related to the difference in chirality between the two rod species. We discuss implications of the calculated phase diagram for a recently developed experimental system in which bidisperse colloidal membranes comprised of two species of rodlike viruses exhibit micro-phase separation. [Preview Abstract] |
Monday, March 14, 2016 1:51PM - 2:03PM |
B37.00014: Measuring the equation of state for a 2D colloidal membrane: A microfluidic approach to buffer exchange Andrew Balchunas, Rafael Cabanas, Seth Fraden, Zvonimir Dogic 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 bi-layers, 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. k$_{\mathrm{on\thinspace }}$and k$_{\mathrm{off}}$ rates of rod to membrane binding were measured by lowering the osmotic pressure until membrane evaporation occurred. [Preview Abstract] |
Monday, March 14, 2016 2:03PM - 2:15PM |
B37.00015: Tuning Raft Interactions in Colloidal Membranes using Component Chirality Joia Miller, Prerna Sharma, Zvonimir Dogic Two-dimensional colloidal membranes composed of rods of different lengths display rich phase behavior. In particular, the chirality of constituent rods stabilizes assembly of colloidal rafts, micron-sized droplets enriched in one type of rod floating in a membrane background with a different rod composition. Raft interactions are mediated by local rod twisting due to their rods' inherent chirality, leading to long-range repulsive interactions. We explore the behavior of rafts while reducing the net chirality of the membrane background. Even in the achiral limit, stable or metastable rafts form. However, in the achiral case the long-range interactions between rafts are attractive but not pairwise additive, resulting in the assembly of clusters of individual rafts. The membrane background has large-scale density fluctuations which we correlate to the raft interactions. Our work demonstrates a new method for assembly of well-defined clusters, one that does not rely on complex colloidal synthesis, but rather on the unique anisotropic environment of the colloidal membranes. [Preview Abstract] |
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