Condensed Matter & Biological Physics Seminars

Series director: Alan Middleton, Yaouen Fily Administrative Questions: Penny Davis	Time: Friday, 11:00am Location: Room 202/204, Physics Building
Condensed Matter & Biological Physics Research Group
Physics Colloquia (Thursday 3:45pm) Previous years seminars: 2003/2004 2004/2005 2005/2006 2006/2007 2007/2008 2008/2009 2009/2010 2010/2011
Upcoming seminar	Scheduling page

Fall 2011

Date	Speaker	Affiliation	Title	Host
September 9	Zhenwei Yao	Syracuse University	Self-Propulsion of Droplets by Spatially-Varying Surface Topography	Bowick
	Under partial wetting conditions, making a substrate uniformly rougher enhances the wetting characteristics of the corresponding smooth substrate ‒ hydrophilic systems become even more hydrophilic and hydrophobic systems even more hydrophobic. Here we show theoretically that spatial texturing of the substrate topography may lead to spontaneous propulsion of droplets. Individual droplets tend to be driven toward regions of maximal roughness for intrinsically hydrophilic systems and toward regions of minimal roughness for intrinsically hydrophobic systems. Spatial texturing can be achieved by patterning the substrate with sinusoidal wrinkles whose wavelength varies in one direction (inhomogeneous wrinkling) or lithographically etching a radial pattern of fractal (Koch curve) grooves on the substrate. Richer energy landscapes for droplet trajectories can be designed by combining texturing of spatial topography with chemical or material patterning of the substrate.
September 16	Adil Mughal	Aberystwyth University	Topological defects in the crystalline state of one-component plasmas of non-uniform density	Bowick
	We study the ground state properties of classical Coulomb charges moving on a plane but confined by a circular hard wall boundary. The charge density in the continuum limit is determined analytically and is non-uniform. Because of the non-uniform density there are both disclinations and dislocations present and their distribution across the system is calculated and shown to be in agreement with numerical studies of systems of N charges, where values of N up to 5000 have been studied. We show quantitatively that a consequence of these defects is that although the charges locally form into a triangular lattice structure, the lattice lines acquire a marked curvature.
September 23	Shiladitya Banerjee	Syracuse University	Instabilities, oscillations and contractility in cross-linked active gels	Marchetti
	I will describe some recent theoretical efforts in understanding emergent phases of a permanently cross-linked active gel, in which molecular motors control the gel elasticity. The system may be realized in acto-myosin gels cross-linked by actin binding proteins such as filamin-A or alpha-actinin. Using a generic continuum formulation we describe the gel by a two-component model consisting of an elastic network coupled frictionally to a permeating fluid. Activity is induced by active cross-linkers that undergo an ATP-activated cycle and transmit forces to the network. Our analysis shows that the gel can be tuned through three classes of dynamical steady states by increasing motor activity: a constant unstrained state of homogeneous density, a state where the local density exhibits sustained oscillations, and a steady-state which is spontaneously contracted, with a uniform mean density. Our active gel model unifies spontaneous contractility and oscillations, as ubiquitously observed in cell cytoskeleton, and provides a minimal continuum model relevant to many biological systems with motor-filament assemblies that behave as solids at low frequencies.
September 30

October 7	Jay Gambetta	IBM Watson Research Center	Quantum information processing with superconducting qubits	Plourde
	Over the last decade, superconducting circuits have made considerable progress on all the requirements necessary for a solid-state quantum computer. In this talk I will present the latest results from IBM on quantum information processing with superconducting qubits. I will outline the architecture that we are investigating to build a quantum computer and the methods we are using to verify its performance. I will present recent results that show high fidelity single-qubit and two-qubit operations which only required microwave controls.
October 14	Frans Spaepen	SEAS Harvard	An Overview of the Deformation of Metallic Glasses	Bowick
	An overview of the basic phenomenology of the deformation of metallic glasses will be presented: elastic deformation, anelasticity, homogeneous plastic flow, strain softening, inhomogeneous plastic flow, structural relaxation and fracture. Much of this information can be summarized on a deformation mechanism map. The basic ingredients of continuum modeling of the deformation will be reviewed, followed by the basic atomistic mechanisms, such as the free volume model. Finally, it will be shown how the atomistic mechanisms can be observed directly by confocal microscopic tracking of the particles in colloidal glasses.
October 21	Ben Palmer	University of Maryland	Relaxation Effects in Cooper Pair Box Qubits	Lahaye
	I will describe and contrast two different sets of measurements we have made on the lifetime of the excited state of a charge qubit. In our case, the charge qubit is a superconducting Al/AlOx/Al single-Cooper-pair box that is cooled to 20 mK. Using a dissipative measurement and decoupling our qubit from charge noise, we were able to obtain lifetimes of a few microseconds. This measurement technique allowed us to use the Cooper-pair box as a “quantum spectrum analyzer” and showed that anomalous charge fluctuators in the Josephson tunnel junction can cause the lifetime of the qubit to decrease to a few hundred nanoseconds.† More recently, we have used a circuit QED scheme to dispersively measure the lifetime of a charge qubit. Using this scheme we have found a strong correlation between the lifetime of the qubit and the inverse of the coupling to the dissipative environment. At the smallest coupling, we have measured a maximum lifetime of 200 microseconds which represents an order of magnitude improvement from previous results. This long lifetime places a bound in the dielectric loss of the Josephson junction barrier less than tan d < 10^-7.
October 28	Sidney Redner	Boston University	Fate of the Kinetic Ising Model	Schwarz
	What is the fate of a homogeneous, finite-size Ising model that is prepared at infinite temperature and subsequently evolves by zero-temperature Glauber dynamics? Very different properties arise in one, two, and three dimensions. In one dimension, the ground state is always reached and the evolution can be solved exactly. In two dimensions, the ground state is reached in about 2/3 of all realizations, and the long-time evolution is characterized by two distinct time scales, the longer of which arises from topological defect states. In three dimensions, the evolution is much richer still: (i) Domains at long time are strongly interpenetrating and topologically complex, with their average genus growing algebraically with system size; (ii) The long-time state almost always contains "blinker" spins that can flip ad infinitum with no energy cost. (iii) The relaxation is characterized by multiple time scales, the longest of which grows exponentially with system size.
October 28 (1 PM, Shemin Auditorium, BMCE Distinguished Lecture Series)	Murugappan Muthukumar	University of Massachusetts	Packaging Biological Macromolecules and Delivery
	We will discuss how biological macromolecules are packaged in viruses and how they undergo translocation through narrow pores and protein channels. In the packaging problem, we will consider many RNA viruses and address the primary forces that control the assembly. A universal model, based on non-specific electrostatic interactions, is able to predict the essential aspects of genome packing in diversely different viruses, such as the genome size and its density distribution. In the second problem, we will address how single DNA/RNA molecules navigate through protein channels and synthetic nanopores, by implementing concepts from polymer physics. Resolution of several experimentally observed puzzles about polymer translocation will be presented. Implications of our findings on gene delivery and human genome sequencing will be addressed.
NOTE: Tuesday, November 1, 3:45 PM	Arthur Yelon	Ecole Polytechnique Montreal	High activation energies in physics, chemistry, and biology: What we should have known, but didn't ask	Schiff & Movileanu
	"nex
November 4 (2:30 PM, Stolkin Auditorium)	Charles Doering	University of Michigan	Ultimate state of two-dimensional Rayleigh-Benard convection between free-slip fixed-temperature boundaries	Glauser (MAE)
	[2:30 PM, Stolkin Auditorium] Rigorous upper limits on the vertical heat transport in two dimensional Rayleigh-B\'enard convection between stress-free isothermal boundaries are derived from the Boussinesq approximation of the Navier-Stokes equations. The Nusselt number $Nu$ is bounded in terms of the Rayleigh number $Ra$ according to $Nu \leq 0.2292 \, Ra^{5/12}$ uniformly in the Prandtl number $Pr$. This scaling challenges some theoretical arguments regarding the asymptotic high Rayleigh number heat transport by turbulent convection. This is joint work with Jared Whitehead.
November 11	David Weitz	Harvard	Stevenson Biomaterials Lecture - "Fluctuations and Dynamic Arrest in Cells" - 500 Hall of Languages, Noon for lunch (RSVP Karen Low), 1 PM lecture

November 18	Stefan Boettcher	Emory University	The Triviality of Aging	Middleton
	Confocal microscopy of relaxation in dense colloids is like watching the proverbial paint dry. Rarely does the in-situ jiggle of particles lead to any perceivable displacement, and density fluctuations much beyond the particle scale are non-existent. Particle tracking suggests strongly sub-diffusive behavior, which further slows down during the observation in a manner characteristic of many disordered systems, a process referred to as "aging". Yet, light-scattering experiments show that the dynamics is also very heterogeneous in time and space, marked by infrequent but comparatively large rearrangement of the position of groups of particles. Stipulating that this collective behavior can be described by a simple phenomenology of particle clustering, the data can be modeled successfully in terms of "record dynamics". The break-up probability of clusters serves as the only control that distinguishes between ordinary diffusion at low density and the characteristic aging behavior at high density of the colloidal suspension. Simulations and a mean-field equation for this phenomenology confirm the role of well-separated "quakes" in setting the clock by which high-density colloids relax. As any set of independent, record-sized events are produced at a rate of $1/t$, their probability is homogeneous in $\log t$, indicative of a $\log$-Poisson process. Hence, aging emerges \emph{generically} as ordinary diffusion but on a logarithmic time scale, as our novel analysis of experimental data shows. It may explain the prevalence of aging in a range of glassy systems with vastly different microscopic dynamics. (Joint work with Paolo Sibani)
November 25	Thanksgiving

December 2	Timon Idema	University of Pennsylvania	Mitotic wavefronts in the fruit fly embryo
	Mitosis in the early syncytial Drosophila embryo has a high degree of spatial and temporal correlations, visible as mitotic wavefronts that travel across the embryo. We analyze these wavefronts and their effects on the embryo as a whole, and develop models to explain their origin. Using confocal microscopy data, we observe two distinct wavefronts in each cycle: one corresponding to chromosome condensation, and one to the actual mitosis event. These two wavefronts are separated by a time interval that is independent of cell cycle and propagate at the same speed for a given embryo in a given cycle, consistent with the existence of a biochemical clock. We study wavefront propagation in excitable media theoretically, using a model with biochemical signaling and one with mechanical signaling. We find that the dependence of wavefront speed on cell cycle number is most naturally explained via a mechanical signaling, and that the entire process suggests a scenario in which biochemical and mechanical signaling are coupled.
December 9	New York Complex Matter Workshop		At Cornell University

Spring 2012

Date	Speaker	Affiliation	Title	Host
January 27	Jane Wang	Cornell University	How do Insects Fly and Turn?	Marchetti
	Insect's aerial acrobatics results from the concerted efforts of its brain, flight muscles, and flapping wings. To understand its flight, we started from the outer scale, analyzing the unsteady aerodynamics of flapping flight, and are gradually working toward the inner scale, deducing the control algorithms. We are particularly interested in seeking mechanistic explanations for their flight dynamics. In this talk, I will first describe the aerodynamics tricks that dragonfly employs to hover and fly efficiently. I will then describe how fruit flies recover from aerial stumbles, and how they make subtle wing movements to induce sharp turns in 40-80ms, or tens of wing beats. These work involves direction numerical simulations, reduced order models for unsteady fluid forces, and analyses of experimental data of insects in free flight.

February 3

February 10	Jon Machta	UMass, Amherst	The Three-Dimensional Ising Spin Glass at Low Temperatures	Middleton
	The Ising spin glass is among the simplest non-trivial disordered systems in statistical physics. Nonetheless, it is poorly understood and remains a subject of controversy. After reviewing the Ising spin glass and the arguments about its low temperature phase, I will report on our recent large-scale numerical study. I will describe parallel tempering, the algorithm used in the study and many other computational studies of glassy systems, and discuss the efficiency of parallel tempering. Finally, I will present data on the equilibrium properties of the 3D Ising spin glass and discuss its relevance to resolving the controversy about the low temperature phase.
February 17	Nadir Kaplan	Brandeis University	Phenomenological theory of colloidal monolayers assembled from chiral rod-like particles	Bowick
	Microscopic chirality can alter numerous macroscopic properties of materials. One particular ex- ample is monodisperse suspensions of the rod-like chiral fd viruses. These viruses are condensed into one rod length thick colloidal monolayers of aligned rods by depletion forces. The layer form- ing tendency of fd due to its monodisperse nature competes with the twist deformations arising from chirality, driving the formation of novel structures. In this talk, I will present our theoretical approach to some of the rich phenomena in these fd systems, in particular (1) simple flat monolayers, where the layer forming tendency dominates, (2) defects arising from the coalescence of two flat monolayers, dubbed π-walls, and (3) twisted ribbons, where the twist deformations are strong enough to replace flat monolayers and result in macroscopic chirality.
February 21 TUESDAY, 3:30 PM	Lena Lopatina	Kent State University	Statistical Mechanics of Nanoparticle Suspensions and Granular Materials	Marchetti
	In this talk we discuss topics united by the idea of using statistical mechanics to study systems in which the main component is an ensemble of particles. We study a distribution of particles either in an interacting ensemble by itself or in a host medium, and analyze connections between the internal properties of individual particles and the resulting macroscopic properties of the material with many particles. Recent experiments have reported that ferroelectric nanoparticles have drastic effects on nematic liquid crystals-increasing the isotropic-nematic transition temperature by about 5 K, and greatly increasing the sensitivity to applied electric fields. We modeled these effects through a Landau theory and Maier-Saupe-type model, based on coupled orientational order parameters for the liquid crystal and the nanoparticles. A Landau-like theory provides a simple approach to the statistical mechanics of the suspension, and a Maier-Saupe-type model gives more detailed predictions for full range of the parameters. Jamming has attracted growing attention as a possible unifying theme for granular materials, glasses and threshold behavior in materials. Recent results for frictionless granular systems suggest that jamming is a second order phase transition with critical properties. A question of paramount importance is whether this behavior is universal to more complex systems. To address this issue we have simulated the compression of granular polymers. The jamming density of the granular polymers decreases with increasing chain length due to formation of loops or voids, in agreement with recent experiments. We show that the nature of the jamming in granular polymer systems has pronounced differences from the jamming behavior observed for polydisperse two-dimensional disk systems. This result indicates that there is more than one type of jamming transition.
February 24	Cynthia Reinhart-King 1 PM, Link 369 [Crosslisted BMCE seminar]	Cornell University	Cell Contractility in Disease Progression	Henderson
	To adhere and migrate, cells exert traction stresses against their extracellular matrix. In addition to aiding cell movements and helping to maintain cell shape, cellular traction stresses also contribute to the ability of cells to probe and remodel their environment. In this talk, I will discuss my lab’s work investigating the role of cellular traction stresses in mediating cell health. Using both in vitro and in vivo models, we have shown that changes in cell contractility occur during the progression of two deadly diseases: atherosclerosis and cancer. Altered cellular mechanical forces can lead to changes cell-cell and cell-matrix interactions that contribute to disorganized tissue structures, a hallmark of both cancer and atherosclerosis. Our data reveal that changes in cell contractility are linked to both atherosclerosis progression and metastasis, and that therapeutically targeting changes in cellular contractility may be one potential pathway to preventing disease progression.
March 2	March Meeting

March 5	Ana Hocevar	Jozef Stefan Institute	Space-filling problems in simple animal tissues	Manning
	We theoretically investigate simple animal tissues and cell aggregates using the elastomechanical theory of phospholipid vesicles based on vesicle bending energy and a model intermembrane adhesion energy. We first study the one-cell-thick epithelium tissue whose en face view resembles a polygonal tiling. We show that the structure of simple epithelia can be explained by an equilibrium model where energy-degenerate polygons in an entropy-maximizing tiling are described by a single geometric parameter that encodes their roundedness . Both the ordered and the disordered tilings found numerically closely reproduce the patterns observed in Drosophila, Hydra, and Xenopus. This model is free of a specific cell self-energy, cell-cell interaction, and cell division kinetics, and thus provides an insight into the universality of living and inanimate two-dimensional cellular structures. We also study periodic three-dimensional assemblies of identical lipid vesicles as models of simple bulk tissues. In this theory, each vesicle is represented as a convex polyhedron with flat faces, rounded edges, and rounded vertices. In the limit of strong adhesion, the minimal- energy shape of cells minimizes the weighted total edge length. We compare several candidate space-filling polyhedra to find that the oblate shapes are preferred over prolate shapes for all volume-to-surface ratios. The model is then extended to aggregates of vesicles whose adhesion strength on lateral faces is different from that on basal and apical faces. In addition, we study gastrulation, a morphogenetic process that takes place during embryonic development of animals. We focus on gastrulation in Drosophila melanogaster and use a simple two-dimensional model based on undifferentiated cells of identical properties whose energy resides in their membrane. Numerical results reproduce the experimentally observed invagination.
March 9	Bryan Chen	U Penn	Seeing and Sculpting Nematic Liquid Crystal Textures with the Thom construction	Bowick
	Nematic liquid crystals are the foundation for modern display technology and also exhibit topological defects that can readily be seen under a microscope. Recently, experimentalists have been able to create and control several new families of interesting defect textures, including reconfigurably knotted defect lines around colloids (Ljubljana) and the ``toron,'' a pair of hedgehogs bound together with a ring of double-twist between them (CU Boulder). We apply the Thom construction from algebraic topology to visualize 3 dimensional molecular orientation fields as certain colored surfaces in the sample. These surfaces turn out to be a generalization to 3 dimensions of the dark brushes seen in Schlieren textures of two-dimensional samples of nematics. Manipulations of these surfaces correspond to deformations of the nematic orientation fields, giving a hands-on way to classify liquid crystal textures which is also easily computable from data and robust to noise.
March 16	Spring Break

March 23	Blake Johnson	Raytheon BBN Technologies	Benchmarking of high-fidelity control in simple quantum processors	Plourde
	Quantum computing with superconducting qubits has rapidly matured over the past decade, driven, in part, by borrowing concepts from atomic systems. After showing how to build a circuit analog to cavity electrodynamics, I will show how recent improvements in control and coherence times have enabled single-qubit and two-qubit gate fidelities of >99% and >95%, respectively. Given this high degree of control, I will present an outlook for scalable quantum computing that uses a lattice of qubits and cavities in order to implement a two-dimensional surface code. Finally, I will present methods for benchmarking qubit operations that rely on randomization to achieve favorable scaling in large systems.
March 30	Jay Tang	Brown University	Microbial Life at the Interface	Marchetti
	The microbes inhabit planet earth over billions of years, and have adapted to diverse physical environment of water, soil, and particularly at or near interfaces. Following recent studies on bacterial swimming and accumulation near solid surfaces, we turned our attention to the behavior of Caulobacter crescentus, a singly flagellated bacterium at the interface of water/air or water/oil. Our ongoing study suggests that, besides most properties caused by a boundary confinement like that of the water/solid interface, the Caulobacter swarmer cells tend to get physically trapped at either water/air or water/oil interface. They continue to move in tight circles, and with speed reduced by about half at the air surface compared with their bulk speed, and even slower at the water/oil interface. The experimental data call for analysis based on low Reynolds number hydrodynamics, the known surface tension and surface viscosity at the interface. The overall goal of our study is to describe interfacial microbial functions through detailed analysis of their motion based on classical fluid physics.
April 6	Cristian Staii	Tufts University	Application of Advanced Scanning Probe Microscopies in Biophysics and Condensed Matter Physics: from Neuronal Networks to Reduced Graphene Oxide Nanosensors	Movileanu
	Invented in 1986, the Atomic Force Microscope (AFM) is probably the single most important tool in nanotechnology. A whole host of AFM-based techniques called Scanning Probe Microscopies (SPMs) have been developed to study a wide range of systems from imaging surfaces with sub-nanometer (sometimes even atomic) resolution and manipulation of matter at the level of molecules (nanoscale level) to studies of physical properties of biomolecules such as proteins and nucleic acids. In this presentation I will exemplify the use of SPMs to study some fundamental biophysical processes as well as the electronic transport in low-dimensional systems. As a first example, I will show that the AFM can be used to immobilize proteins at well-defined locations directly onto gold substrates, and to control effectively the adhesion, growth and interconnectivity of cortical neurons on these surfaces. I will demonstrate that this method allows us to control geometric and chemical factors that can be used to influence the growth and development of neuronal assemblages in simple geometries. As a second example, I will describe the use of SPM to study the doping mechanism and the charge transport in reduced graphene oxide chemical sensors.

April 13

April 20	Jonathan Baugh	IQC at Waterloo University	Recent advances in magnetic resonance QIP	Plourde
	I will present results from several recent experiments performed on small nuclear and electron magnetic resonance quantum information processors. In liquid-state NMR, we demonstrate a new algorithm for digital quantum simulation of thermal states, providing a benchmark for state-of-the-art quantum control in a 4-qubit system [1]. This class of algorithms is expected to be useful for digital simulation of open quantum systems. In solid-state NMR, we demonstrate a two effective rounds of error correction using the three-bit code, again relying on high-fidelity gate operations [2]. We also explore a new type of nuclear spin control via the anisotropic hyperfine interaction with an electron spin; here an entangling gate is performed between two nuclei on a timescale of 100's of nanoseconds using only microwave irradiation on resonance with the electron spin [3]. This approach suggests interesting future work that might lead to scalable spin-based QIPs. 1. J. Zhang, M.-H. Yung, R. Laflamme, A. Aspuru-Guzik and J. Baugh. http://arxiv.org/abs/1108.3270 2. O. Moussa, J. Baugh, C. A. Ryan and R. Laflamme, Phys. Rev. Lett. 107, 160501 (2011). 3. Y. Zhang, C. A. Ryan, R. Laflamme and J. Baugh, Phys. Rev. Lett. 107, 170503 (2011).
April 27	Christian Santangelo	U. Mass. Amherst	Building shapes from sheets	Manning
	Despite their everyday familiarity, thin sheets (paper, plastic, fabric, etc.) display remarkable and complex behaviors that still challenge theoretical description. The intricate coupling between the geometry of surfaces and the elasticity of a thin sheet necessarily leads to the formation of singularities, nonlinear elasticity, and geometric frustration. Nevertheless, multicellular organisms - like you - develop their three dimensional structures in part by exploiting these elastic phenomena. These considerations have led us to develop theoretical and experimental tools to shape elastic sheets into prescribed 3D shapes using the principles of non-Euclidean geometry. I will describe our attempts to design sheets that fold controllably into 3D structures and some related problems in the mechanics of origami, where 3D structure is developed by folding a piece of paper. These techniques open up new avenues in "experimental mathematics", allowing us to explore geometry experimentally. So far, however, no mathematical theorems have been harmed in the production of this research.