Condensed Matter & Biological Physics Seminar Condensed Matter & Biological Physics Seminar| Date | Speaker | Affiliation | Title | Host |
|---|---|---|---|---|
| August 31st | ||||
| September 7th | Tanniemola B. Liverpool | University of Leeds | Fluctuations, pauses and backtracking in transcription | Marchetti |
| September 14th |
Alex Travesset | Iowa State University and Ames Lab | Pluronics, functionalized pluronics and nanoparticles | |
| The phase diagram of soluble non-ionic polymers in aqueous solutions containing hydrophobic monomers is amazingly rich. A prototypical example is provided by Pluronic (or Poloxamers) polymers, consisting of symmetric triblocks of Polyethylene oxide (PEO) and Polypropilene oxyde (PPO), which have been intensively studied over the last decade and display a miriad of phases, both liquid crystalline (nematic, cubatic, etc..) or crystalline (bcc, fcc, hexagonal, etc..) as a function of concentration, block length and temperature. In this talk, I will first present a general approach to map the phase diagram of non-ionic multiblock polymers from coarse-grained molecular dynamics simulations. As a concrete example, I will discuss micellar crystals with cubic symmetry in pluronic systems. In the second part of the talk I will discuss the properties of functionalized pluronics, that is, pluronic block copolymers where particular functional groups are attached to their end groups. I will show how functionalized pluronics can be combined with inorganic components such as nanoparticles to create new composite materials where self-assembled inorganic crystals follow the mesoscopic order imposed by the polymeric phase, which serves as a template. I will conclude with some perspectives and outlook. | ||||
| September 21st Room B126 |
Daniel ben-Avraham | Clarkson University | On the Ordering of Random Walkers on the Line | Schwarz |
| The survival probability of various orderings of random walkers on the line is a problem that has attracted considerable interest among physicists and applied mathematicians. In this talk, I shall highlight connections between N walkers and the Poisson equation in N-1 dimensions, and to the eigenvalues of random matrices, including the recent discovery of Tracy and Widom concerning the edge of the distribution. Although new results will be presented, the talk will be especially accessible to non-experts (students). I will also discuss a couple challenging open problems that you may take home with you. | ||||
| September 28th | David Amberg | Upstate Medical University | Genetic Influences on Actin Function | Schwarz |
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The actin cytoskeleton of eukaryotic cells is a critical organizing structure that facilitates a diversity of functions. It is composed of helical filaments assembled from a globular protein; a typical cell maintains a balance between the monomeric and filamentous forms of the protein. These filaments are meta-stable/extremely dynamic and their assembly and organization is highly regulated both spatially and temporally through the cell division cycle. Perturbations in the regulation of actin dynamics lead to defects in many cellular processes. The work in our lab has focused on how actin associated proteins can locally alter actin dynamics and thereby the organization of the actin cytoskeleton. In this presentation I will discuss our findings on actin regulation by oxidation and the role of the protein Oye2p in reversing this oxidative damage. Accumulation of actin with an intra-molecular disulfide bond leads to elaboration of the actin cytoskeleton due to actin filament stabilization. This in turn triggers a feedback loop that drives levels of reactive oxygen species to such an extent that cell death is triggered. It is the normal job of Oye2p to keep actin reduced to maintain normal cytoskeleton dynamics/plasticity and thereby prolong cell viability. Secondly, I will discuss a systems level, genomics approach to identify bigenic interactions between actin and other genes in the eukaryotic genome. These studies are uncovering hundreds of genes that are required under conditions of limited actin concentration for cell health and viability. This network of genes is functionally enriched for activities related to known functions of the actin cytoskeleton as well as novel activities. We are currently mapping these interactions onto the structure of the actin protein to attribute defects to localized disturbances in actin activities. References
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| October 5th | Andrew N. Jordan | University of Rochester | Weak quantum measurements in the solid state | Plourde |
| Extensive research into controllable quantum systems and detectors has led to a reexamination of the very nature of quantum measurement in a condensed matter context. Quantum detectors used in recent experiments naturally give rise to weak quantum measurements, where the detector output is not perfectly correlated with the state of the measured system. I will show how to undo a weak quantum measurement (quantum undemolition) using quantum dot and superconducting quantum systems, showing that quantum information is written in pencil, not pen. A realization of weak values will also be discussed, and shown to be intimately related to the “temporal Bell inequality” of Leggett and Garg. | ||||
| October 12th | Ioan Andricioaei | University of Michigan | Conformational Kinetics of Nucleic Acids under External Forces | Movileanu |
| Two aspects concerning the effect of external forces on biomolecular conformational kinetics will be presented. Firstly, we shall address the structural transitions, thermodynamic equlibrium and the phase diagram of DNA and RNA under torque and tension. Secondly, we shall present a stochastic path integral formalism enabling the calculation of the force dependence of the kinetic rate constant for conformational transitions. | ||||
| October 19th | Douglas Durian | University of Pennsylvania | Truly effective temperatures and dynamical heterogeneities near jamming | |
| Grains remain at rest, and sandpiles maintain their shape, unless driven by sufficiently strong forces. While popular driving methods, like shaking and tumbling, lead to a wealth of beautiful and unexpected phenomena, they tend to inject energy at a boundary and hence lead to an intrinsically nonuniform response. In this talk, the focus will be on microscopic dynamics created by a fluidizing upflow of air - such that the upward drag helps cancel gravity and such that turbulence kicks the grains stochastically. I will present early experiments on bulk systems of small grains, as well as new experiments on quasi-two dimensional systems of large grains rolling on a plane. For the latter, we find that grain-scale fluctuations may be described by an effective temperature that has all the attributes of a true statistical-mechanical temperature. However, on approach to jamming, this description breaks down as dynamical heterogeneities become more prevalent. | ||||
| October 26th | ||||
| November 2nd | Dimitrios Vavylonis | Lehigh University | Actin polymerization kinetics: the role of formins in building cytoskeleton structures in fission yeast | Schwarz |
| Many basic biological processes such as cytokinesis during cell division and the motion of eukaryotic cells depend on the ability of actin proteins to rapidly polymerize and depolymerize into networks consisting of long actin filaments. I will review our understanding of the kinetics of pure actin polymerization and of how the hydrolysis of ATP bound to actin subunits can power steady state filament turnover (treadmilling). Actin filament turnover in the cell is accelerated and controlled by a large number of actin-binding proteins. I will describe recent work on how formin proteins help nucleate and accelerate actin polymerization by processively associating with the growing ends of filaments and by recruiting actin subunits near growing filament ends. In fission yeast, a model organism for the study of cytokinesis and actin dynamics, formin proteins nucleate actin filaments for the actomyosin contractile ring during cytokinesis and actin filament bundles (actin cables) for intracellular transport. I will present results of a collaborative work involving a combination of live cell imaging and modeling that addresses the mechanisms of formin-mediated formation of the contractile ring and of actin cables. | ||||
| November 9th | Corey O'Hern | Yale University | Reversible plasticity in amorphous materials | Schwarz/Xing |
| A fundamental assumption in our understanding of material rheology is that when microscopic deformations are reversible, the material responds elastically to external loads. Plasticity, i.e. dissipative and irreversible macroscopic changes in a material, is assumed to be the consequence of irreversible microscopic events. However, these microscopic failure events have not been identified and studied in amorphous materials. Here we show direct evidence for reversible plastic events at the microscopic scale in both experiments and simulations of two-dimensional foam. In the simulations, we demonstrate a link between reversible plastic rearrangement events and pathways in the potential energy landscape of the system. These findings represent a fundamental change in our understanding of materials: microscopic reversibility does not necessarily imply elasticity. Furthermore, foam is representative of a large class of amorphous systems, and thus these results are expected to apply generally to such materials. | ||||
| November 16th 10:00 A.M. |
Aleksei Aksimentiev | University of Illinois, Urbana-Champaign | Synthetic nanopores for sequencing DNA | Movileanu |
| Within just a decade from the pioneering work demonstrating the utility of nanopores for molecular sensing, nanopores have emerged as versatile systems for single molecule manipulation and analysis. In such systems, a gradient of the electrostatic potential captures charged solutes from the solution and forces them to move through the nanopores. The ionic current blockades resulting from the presence of a solute in a nanopore can reveal the type of the solute, for example, the nucleotide sequence of a DNA strand. Despite great successes, the microscopic mechanisms underlying the functionality of such stochastic sensors remain largely unknown, as it is not currently possible to characterize the microscopic conformations of single biomolecules directly in a nanopore and thereby unequivocally establish the causal relationship between the observables and the microscopic events. In this talk I will demonstrate how such relationship can be determined using large-scale molecular dynamics simulations. Methods for sequencing DNA using restriction enzymes and electric field pulses will be introduced. | ||||
| November 23rd | Thanksgiving | |||
| November 30th | ||||
| December 7th |
Leo Radzihovsky | University of Colorado Boulder | ||
| December 14th | 5th New York Complex Matter Workshop | |||
| Date | Speaker | Affiliation | Title | Host |
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| January 18th | ||||
| January 23rd Wednesday |
Cristian Staii | University of Wisconsin-Madison | Nanoscale Chemical and Biological Sensors: From Functionalized Carbon Nanotubes to Protein Microarrays | |
| Biosensors are simple, inexpensive measurement systems which fuse the exquisite sensitivity and specificity of living systems with the processing power of micro and nano electronics. In my presentation I will talk about two different types of biological and chemical sensors. First, I will show that singe-walled carbon nanotube field effect transistors decorated with single-stranded DNA act as high sensitivity gas sensors with conductivity changes in response to application of different chemical species (analytes). Second, I will demonstrate that both natural and genetically engineered proteins have a great potential for applications as nanoscale biosensors because they possess molecular recognition sites with high affinity and excellent selectivity for specified analytes. In particular, I will describe a new approach to protein based biosensor design, which uses the Atomic Force Microscope in a mode called nanografting to immobilize proteins at addressable locations on gold surfaces. This technique opens the possibility of preparing highly ordered, nanometer size protein arrays that can be patterned at different addressable locations on a metallic surface. I will also show that these arrays can be used to study interesting physical phenomena such as thermodynamic and conformational properties of proteins packed at high densities. | ||||
| January 25th | Ruchirej Yongsunthon | Corning Inc. | Native Protein Conformation and Binding Mechanisms on Living Cells | |
Atomic Force Microscopy (AFM) and Molecular Force Spectroscopy are promising techniques for the study of native protein conformation and binding mechanisms on living cells. I will discuss an experiment where these techniques were used in conjunction with confocal laser scanning microscopy to probe fundamental forces between a fluorescent chimeric protein on the outer membrane of a living Escherichia coli bacterium and a solid substrate. The chimera was composed of a portion of outer membrane protein A fused to the cyan-fluorescent protein AmCyan. The worm-like chain model was used to predict the “force-signature” of the chimera as it formed a bond with another surface. This observed force spectroscopy signatures were consistent with theoretical predictions for the mechanical extension of the chimeric segments in series. Additionally, I will discuss extension of these spectroscopy techniques to the study of surface sensing abilities and binding mechanisms in Staphylococcus aureus . |
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| February 1st | ||||
| February 8th | ||||
| February 15th | Martin Forstner | University of California, Berkeley | Bio-Membranes: Structured, Adaptive and Dynamic- New Insights from in vivo and in vitro Experiments | |
| Lipid membranes are an essential building block of all cellular life, separating the inside of a cell from the outside and compartmentalizing the cell interior. Once thought of as passive and featureless environments for membrane proteins, a new picture of bio-membranes has begun to emerge that paints them as structured, complex fluids that are organized on many time and length scales. Recent advances in optical microscopy and spectroscopy techniques have facilitated the study, on a single molecule level, of membrane structure, membrane interactions with proteins and their underlying physics. Recent results on both bio-mimetic model membranes and live cell membranes not only gives credence to the new membrane model, but also point towards a much more active role for membranes in the fascinating physicochemical machinery of cellular life. | ||||
| February 22nd | ||||
| February 29th | Kareem Elsayad | Indiana University | Coulomb drag: A novel way of distinguishing the insulating phases of disordered films. | Schiff |
| Over the last two decades the Coulomb drag effect has evolved as a useful experimental tool for studying the low energy dynamic properties of 2 dimensional electron and hole gas systems. Whilst theoretical studies on the Coulomb drag effect between various materials have appeared in the literature, there has been an absence of experimental work supporting such predictions. By performing measurements on insulating a-Si_{1-x}Nb_{x} bilayer systems, we show that Coulomb drag between two Anderson insulators can be used to distinguish the types of insulating states. Unlike conventional transport measurements, which yield qualitatively similar temperature and frequency dependences (with the same overall trend) of the low energy transport coefficients, Coulomb drag measurements offer a clear distinction to be made between materials where intra-layer Coulomb interactions are well screened (so called Fermi glasses or Mott -type Anderson insulators) and those where they are not (so-called Coulomb glasses or Efros-Shklovskii -type Anderson insulators). Having experimental means to separately measure the effects of disorder and long-range electron-electron interactions is crucial to furthering our understanding of the electrodynamics of disordered materials. | ||||
| March 7th | ||||
| March 14th | Spring Break | |||
| March 17th Monday |
Jean-Francois Joanny | Institut Curie, Paris | Mechanics of cells and tissues | Marchetti |
| I will discuss the mechanical properties of both isolated cells and tissues. The mechanical properties of isolated cells are controlled by the cytoskeleton which is composed of actin filaments and myosin molecular motors. We have formulated a continuum theory of the cytoskeleton by describing it as an active polar gel. I will describe the general theory and its application to the study of certain cellular oscillations. To describe the mechanical properties of tissues one must incorporate cell division and cell death. I will introduce the notion of homeostatic pressure and discuss the process of invasion of normal tissue by carcirogenic tissue. | ||||
| March 28th | Robin Selinger | Liquid Crystal Institute, Kent State University | Simulation studies of orientational order and topological defects in curved geometries | Bowick |
| Recent studies of orientation order on curved substrates have pointed to a close relationship between curvature and topological defects. To explore this relationship, we develop a new computational approach to simulate orientational order on surfaces of arbitrary shape. We place xy spins on the surface in a disordered mesh constructed via random sequential absorption. We apply this approach to a sphere, a torus, and an "egg-crate" surface. In each case we find that positive (negative) defects tend to localize in regions of positive (negative) Gaussian curvature. We also find some surprising defect properties, e.g. on the surface of a skinny torus, topological defects typically annihilate in groups of four. We further generalize this modeling approach to 3-d to examine defect configurations in thin liquid crystal nematic shells studied experimentally by Fernandez-Nieves et al. Lastly, we will discuss defect dynamics and shape evolution in giant unilamellar vesicles in the tilted "gel" phase. | ||||
| April 4th | Gijsje Koenderink | Institute of Atomic and Molecular Physics, Netherlands | Physics of active biopolymer networks in cells and tissues | Jointly with Biomedical and Chemical Eng. |
| Living cells are active soft materials in which non-equilibrium driving forces lead to shape changes, contractility, and migration. Tissues such as skin and cartilage, which are composed of 3D biopolymer networks with embedded cells, can likewise be viewed as active soft materials controlled by cell activity. To elucidate the physical origin of the self-organization and mechanical properties of these active materials, we reconstitute simple model systems from purified cytoskeletal or extracellular matrix proteins. I will focus on model systems of filamentous actin containing active myosin II motors. These networks exhibit active internal stress fluctuations and active stiffening. The myosin motors use chemical energy to generate directional forces on the actin filaments to slide filaments past one another. In un-crosslinked networks, this leads to transient contractile stresses. These are apparent when microtubules, cytoskeletal filaments with a persistence length of 1 mm, are embedded in the actin network. In the presence of processive myosin thick filaments, the microtubules display large, non-thermal bending fluctuations. These reveal transverse forces of 10-20 pN originating from local network contractions. Even though the myosin motors are processive, they generate random stress fluctuations because they transiently bind and then collectively release. When the actin filaments are cross-linked with an actin-binding protein such as filamin A, myosin contractile forces generate an internal stress that drives the network into a non-linear, stress-stiffened regime. These findings shed light on physical design principles of the living cytoskeleton. I will also briefly touch on biomimetic tissues composed of collagen with embedded fibroblast, where whole-cell contractility reorganizes and tenses the tissue. | ||||
| April 9th Wednesday 2 pm | Wolfgang Losert | University of Maryland | Decision making in D. discoideum | Marchetti |
| Cell motion is crucial for many biological processes, from wound healing to organ formation. To move, cells must first determine a preferred direction, and then mechanically move in that direction. In this talk I will first outline the outstanding ability of cells to detect small chemical gradients but adapt to strong variations in the chemical signal. Then I will describe how cells interact with each other and with the surface. In particular our experimental work focuses on characterizing group migration of cells, and decision making of cells faced with obstacles in surface topography. Work in collaboration with C. Parent and R. Nossal, NIH | ||||
| April 11th Time : TBA |
Stevenson Biomaterials Lecture : Lori Setton , Duke University | |||
| April 18th | Homin Shin | Syracuse University | Order, defects and dynamics on the sphere. | Bowick |
| April 25th | Carl Modes | University of Pennsylvania | Hard Discs on the Hyperbolic Plane: A Proposal for a New Model of Glassy Systems | Schwarz |
| We examine a simple hard disc fluid with no long range interactions on the two-dimensional space of constant negative Gaussian curvature, the hyperbolic plane. This geometry provides a natural mechanism by which global crystalline order is frustrated, allowing us to construct a tractable, one-parameter model of disordered monodisperse hard discs. We extend free area theory and the virial expansion to this regime, deriving the equation of state for the system, and compare both these analytical predictions and simulation results with the qualitative behavior of real hard-sphere systems in three dimensions. | ||||