Condensed Matter & Biological Physics Seminar Condensed Matter & Biological Physics Seminar| Date | Speaker | Affiliation | Title | Host |
|---|---|---|---|---|
| September 19th | Anatoly Kolomeisky | Rice University | Complex Dynamics of Polymer Translocation: Effect of folded configurations and charge distribution | Movileanu |
| We investigate the effect of folded configurations and charge distribution on polymer translocation dynamics using simple discrete-state stochastic models. For folded polymers the overall transport is viewed as a sequence of 2 events: motion of the folded segment through the channel followed by the linear part of the polymer. It is shown that there are two dynamic regimes depending on the strength of interaction between the polymer and the pore. Our theoretical calculations successfully applied for analysis of experimental translocations through solid-state nanopores. For translocation of inhomogenously charged polymers we consider a polymer with a single charged monomer. It is found that the position of the charged site that minimizes the translocation time is determined by entropic factors. The presence of polymer-pore interactions modify the optimal charge position. Our results provide insight into the effect of charge inhomogeneity on protein translocation through biological membranes. | ||||
| September 26th | Kristian Mueller-Nedebock | University of Stellenbosch, South Africa | Dealing with counter-ions in polyelectrolyte solutions | Marchetti |
| The watery environment of cells contains a number of charged macro-ions in an environment with salt that in the first instance contributes to screening of interactions between the macro-ions. In the past decade it has become evident that the small counter-ions play a more significant role than simply decreasing the range of interaction: the counter-ions can condense on the polyelectrolytes and fluctuate causing surprising effective interactions between the macro-ions. In order to understand the origins of these effective interactions and how the valence of the counter-ion influences such behaviour, carefully constructed models are useful. In this talk an overview of polyelectrolytes will be given, to be followed by a discussion of continuum and discrete theoretical treatments that reveal the roles of the counter-ions in such systems. In particular, a theory of network formation can be used in order to gain some insight into the phenomena associated with multi-valence and relevant polyelectrolyte chain conformational properties. | ||||
| October 3rd | Jay Tang | Brown University | Biomechanics and Micro-rheology of F-actin network | Marchetti |
| Protein filaments F-actin are the primary component of cytoskeleton, endowing eukaryotic cells their 3-D shape, mechanical strength and compliance. A dynamical actin network is also vital for force generation and migration of many types of cells. My laboratory of biological physics focuses on the biomechanics of actin networks reconstituted in test tubes or microscope slides, in order to capture the fundamental physics responsible for their similar properties in live cells. This talk will illustrate micro-rheological properties of F-actin dictated by thermodynamic phase transition, weak inter-filament association and depletion force. These aspects of fundamental physics contribute much to the biological functions of actin network, and in some cases, provide useful insights to certain physiological processes such as wound healing, leukocyte migration and phagocytosis. Our conviction is that researchers with sound training in soft condensed physics can make major contributions to biological research on cell motility and beyond. | ||||
| October 10th | Carolina Ilie | SUNY Oswego | Water Interactions with Crystalline Polymers with Large Dipoles | Schiff |
| We compare the interactions of water with the ferroelectric copolymer poly(vinylidene fluoride (PVDF)- trifluoroethylene (TrFE)) and poly(methylvinylidenecyanide) (PMCV) a strongly dipole ordered polymer. We propose that the microscopic scale, dipole interactions matter and affect the surface chemistry at these polymer surfaces, as does lattice strain caused by water absorption. Surface dipoles can affect the binding site of water species adsorbed at the surface and sterically hinder or enhance desorption of adsorbed and absorbed water. Perturbations of local surface dipoles can affect desorption of absorbed water. As we are dealing with polymers, the absorption of water is persistent, even with largely hydrophobic polymers, and with the absorption of water, polymer lattice strain plays an important role [1].
The electronic structure of the ferroelectric copolymer films of vinylidene fluoride with trifluoroethylene films is locally altered with incident UV radiation suggesting metastable excited states that may involve dipole reorientation [2]. Light polarization dependent photo-assisted thermal desorption helps demonstrate that water desorption from surface and bulk can be influenced by the formation of electronic metastable states [2]. Changes in local dipole orientation and the formation of long lived metastable states affect the strength of the coupling between the dipoles of water molecules and the dipoles of the copolymer poly(vinylidene fluoride - trifluoroethylene). These effects were not observed for water absorption and adsorption on poly(methylvinylidenecyanide). The water desorption from poly(methyl-vinylidenecyanide) is an intrinsically activated process by the strain in the polymer [1,3]. This tends to suggest that dipole rotation in the polymer substrate may play a key role.
References: [1] Carolina C. Ilie, P.A. Jacobson, I.N. Yakovkin, Luis G. Rosa, Matt Poulsen, D. Sahadeva Reddy, James M. Takacs, and P.A. Dowben , J. Phys. Chem. B 111 (2007) 7742-7746. [2] Luis G. Rosa, P.A. Jacobson, and P.A. Dowben, J. Phys. Chem. B 110 (2006) 7944-7950. [3] P. A. Dowben, Luis G. Rosa, C. C. Ilie, Zeitschrift für Physikalische Chemie 222 (2008) 755-778. |
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| October 17th | Gianfranco Durin | Istituto Nazionale di Ricerca Metrologica (I.N.Ri.M), Torino, Italy | Crackling noise and complexity in natural systems | Marchetti |
| Is there any relation between a devastating earthquake, a snow avalanche, some water drops in a sponge, or a ferromagnet under a magnetic field? Despite huge differences, all these natural systems respond to external perturbations by a burst of events on a broad range of sizes. This random response, known as "crackling noise", is common to many complex natural systems. In this talk, after a general excursion on the main features of these 'crackling' systems, we aim to present the most recent results on a particular crackling noise produced in soft magnetic materials, known as Barkhausen noise. Many of the theoretical and experimental results obtained in ferromagnets can in fact be applied with success to the study of other complex systems. This helps us to understand complexity within a more general theoretical framework, and focus the role of criticality and universality to understand the noise properties. | ||||
| October 24th | Britton Plourde | Syracuse University | Tailored superconducting channels for controlling vortex dynamics | Middleton |
| The dynamics of vortex flow in confined geometries can be explored with nanostructured weak-pinning channels of superconducting a-NbGe surrounded by strong-pinning NbN channel edges. The lack of pinning allows the vortices to move through the channels with the dominant interaction determined by the shape of the channel walls. We have fabricated such weak-pinning channels with asymmetric sawtooth edges for controlling the motion of vortices. This design results in substantial asymmetries in the vortex dynamics in the channels, thus forming a ratchet for producing net vortex motion in response to an oscillatory drive. Using these weak-pinning channels, we are able to explore the influence of vortex interactions on the ratchet response by fabricating strips with different channel spacings and measuring these over a range of vortex densities. We have also investigated vortices flowing in a single circular ratchet channel arranged in a Corbino disk geometry, where the asymmetric response is even more pronounced compared with our measurements of straight vortex ratchet channels. | ||||
| November 7th | William Irvine | Center for Soft Matter Research, New York University | 2-dimensional crystallography at an oil water interface | Bowick |
| Charged hydrophobic (PMMA) colloids in an oil phase (cyclohexyl bromide) are attracted, without wetting, to an oil-water interface by image charge effects. The micron size colloids form a monolayer on the interface and interact via screened coulomb potentials to form a crystalline or hexatic lattice, depending on the tunable ratio of lattice spacing to screening length. I will present experiments in which a stress is applied to such a lattice either by a tailored optical potential, using holographic techniques, or by curving the underlying interface. This model system provides unique opportunities to probe the statics and dynamics of frustrated two-dimensional solids. | ||||
| November 14th | Sriram Ramaswamy | Indian Institute of Science | Active Films and Filaments | Marchetti |
| I summarise our recent work on the collective properties of active matter. In the first part I present the hydrodynamic instabilities of the free surface of a thin fluid film containing polar active particles. In the second I discuss the dynamics of a single semiflexible filament suspended in an active medium. | ||||
| November 18th Tuesday |
Stefano Zapperi | INFM-CNR Italy | Dislocation avalanches, strain bursts, and the problem of plastic forming at the micron scale | Middleton |
| Under stress many crystalline materials exhibit irreversible plastic deformation caused by the motion of lattice dislocations. In plastically deformed microcrystals, internal dislocation avalanches lead to jumps in the stress-strain curves (strain bursts) whereas in macroscopic samples plasticity appears as a smooth process. By combining three-dimensional simulations of the dynamics of interacting dislocations with statistical analysis of the corresponding deformation behavior, it is possible to determine the distribution of strain changes during dislocation avalanches and establish its dependence on microcrystal size. Our results suggest that for sample dimensions on the micron and sub-micron scale large strain fluctuations may cause problems in controlling the resulting shape in a plastic forming process. | ||||
| November 28th | Thanksgiving | |||
| December 5th | Liviu Movileanu | Syracuse University | Interrogating single proteins with a nanopore: challenges and opportunities | Middleton |
| Advances in rational protein design and single-molecule technology allow for biochemical sampling at high temporal and spatial resolution and for the detection, manipulation, and exploration of individual molecules. We have developed a methodology for examining single biopolymer dynamics within a protein nanopore, a simple system that is highly pertinent to several more complex biological processes such as the translocation of DNA and proteins through transmembrane pores. The ionic current through a single protein nanopore was determined by single-channel electrical recordings in lipid bilayers. The results revealed the stochastic dynamics of biopolymers, such as their conformational fluctuations and interactions with other molecules, as well as the energetic requirements for their transition from one state to another. I will discuss various examples that demonstrate an accurate control of single proteins and protein pore-based nanostructures by using simple principles learned from physics and modern biology. | ||||
| December 19th 2 pm |
William D. Oliver | MIT, Lincoln Laboratory | Amplitude spectroscopy with a superconducting artificial atom | Plourde |
| Superconducting persistent-current qubits are quantum-coherent artificial atoms with multiple energy levels. In the presence of large-amplitude harmonic excitation, the qubit state can be driven through one or more of the energy-level avoided crossings. The resulting Landau-Zener-Stueckelberg (LZS) transitions mediate a rich array of quantum-coherent phenomena as a function of the driving amplitude and frequency.
In this talk, we present three demonstrations of LZS-mediated quantum coherence in a strongly-driven niobium persistent-current qubit. The first is Stueckelberg interferometry [1], with which we observed quantum interference fringes in the transition rates for n-photon transitions, with n = 1…50. The second is microwave-induced cooling [2], by which we achieved effective qubit temperatures < 3 mK, a factor 10x-100x lower than the dilution refrigerator ambient temperature. The third is amplitude spectroscopy [3], a spectroscopy approach that monitors the system response to amplitude rather than frequency. This allowed us to probe the energy spectra of our artificial atom from 0.01 – 120 GHz, while driving it at a fixed frequency 0.16 GHz.
These experiments exhibit a remarkable agreement with theory, and are extensible to other solid-state qubit modalities. In addition to our interest in these techniques for fundamental studies of quantum coherence in strongly-driven systems, we anticipate they will find application to qubit control and state-preparation methods for quantum information science and technology [4].
[1] W.D. Oliver et al., Science 310, 1653 (2005) [2] S.O. Valenzuela et al., Science (2006) [3] D.M. Berns et al., Nature 455, 51 (2008) [4] A.J. Kerman and W.D. Oliver, PRL 101, 070501 (2008) The work at Lincoln Laboratory was sponsored by the Air Force under Air Force Contract FA8721-05-C-0002. Opinions, interpretations, conclusions, and recommendations are those of the author(s) and are not necessarily endorsed by the United States Government. |
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| Date | Speaker | Affiliation | Title | Host |
|---|---|---|---|---|
| January 9th | ||||
| January 15th Thursday |
Matthew Bell | University of Buffalo | Topological Excitations in Superconducting Nanostripes | Plourde |
| We investigate the competition between one- and two-dimensional topological excitations, phase slips and vortices, in the formation of resistive states in quasi-two-dimensional superconductors in a wide temperature range below the mean-field transition temperature TC0. The widths w = 100 nm of our ultra-thin Niobium Nitride (NbN) samples studied are substantially larger than the Ginzburg-Landau coherence length ? ~ 4-8 nm, and the fluctuation resistivity observed above TC0 has a two-dimensional character. However, our results show that the resistivity below TC0 is produced by one-dimensional excitations, thermally activated phase slip strips (PSSs) overlapping the sample cross section. We determine the scaling phase diagram, which shows that even in wider samples the PSS contribution dominates over vortices in a substantial region of current and/or temperature variations. The above fluctuations generated by topological excitations provide a sensitivity limit to superconducting detectors operating in a resistive state, e.g. for dark counts in single-photon nanostripe-based detectors. Our universal phase diagram represents a whole picture of competition between electron heating, vortices, and PSSs within a broad range of temperatures and bias currents in nanostripe based devices. | ||||
| January 23rd | Helmut G. Katzgraber | Texas A & M University | Do spin glasses order in a field? | Middleton |
| Spin glasses are paradigmatic models that deliver concepts relevant for a variety of systems. However, despite ongoing research spanning several decades in the area of glassy systems, there remain many fundamental open questions. Rigorous analytical results are difficult to obtain for spin-glass models, in particular for realistic short-range systems. Therefore large-scale numerical simulations are the tool of choice. Concepts from the solution of the mean-field model, such as ergodicity breaking, aging, ultrametricity, and the existence of an instability line at finite magnetic fields known as the Almeida-Thouless line, have been applied to realistic short-range spin-glass models as well as to fields as diverse as structural biology, geology, computer science and even financial analysis. After presenting a brief overview of the properties of spin glasses, I discuss recent results on the existence of a spin-glass state in an external field. Our results show that the spin-glass state is not stable in a field for short-range systems below the upper critical dimension. | ||||
| January 30th | ||||
| February 6th | Xianglin Ke |
The Pennsylvania State University | Magnetothermodynamics of geometrically frustrated magnets - spin ice and related compounds | Schiff |
| Geometrically magnetic frustration, which results from the competition of spin-spin interactions of magnetic ions on a regular magnetic lattice, leads to a variety of exotic low temperature states including 'spin ice'. 'Spin ice' refers to a magnetic state wherein the two-in/two-out spin configurations of rare earth pyrochlore compounds mimic the proton positions in the water ice, characterized by the 'zero point entropy' of Rln(3/2). In this study, we examine how structural disorder affects spin dynamics and the magnetic 'zero point entropy'. By diluting the 'spin ice' materials with nonmagnetic ions on the rare earth sites, we have found that the entropy of the diluted species depends non-monotonically on the dilution concentration, and we explain this behavior using a generalized Pauling approximation. Nonmagnetic doping on B sites leads to only a small decrease of the 'zero point entropy', indicating the robust nature of 'spin-ice'. We have also studied Dy2Ge2O7, which has the same chemical formula as 'spin ice' materials and Ising-like spins but a tetragonal structure. Dy2Ge2O7 undergoes a long range antiferromagnetic ordering transition, but the spin dynamics at temperatures above the order transition is similar to that observed in the canonical 'spin ice' systems, suggesting that such dynamics are generic to a broader class of Ising-like rare earth systems. Reference: X. Ke et al., Phys. Rev. Lett. 99, 137203 (2007); Phys. Rev. B. 76, 214413 (2007); Phys. Rev. B. 78, 104411 (2008). | ||||
| February 9th | Jared Hertzberg | Cornell University | Back-action Cooling and Back-action Evading Measurements of Nanomechanical Motion Approaching Quantum Limits |
Plourde |
| It is a long-standing experimental goal to measure the motion of a mechanical simple harmonic oscillator at a precision limited only by Heisenberg uncertainty principle, and to cool theoscillator to its quantum ground state. [1] To do so, we must consider the perturbation of themotion by the measurement itself, so-called "back-action." Recently, we have performedexperiments with a 5.57 MHz nanomechanical resonator capacitively coupled to a 5 GHzsuperconducting microwave cavity and cooled to temperatures below 142mK. By driving thecavity with a microwave pump signal, we observe sidebands generated by the mechanicalmotion. Using this arrangement, we may exploit the back-action to cool the motion. [2] In thismanner we achieved effective mode temperatures of < 10 mK, corresponding to an occupationfactor of n ~ 20 quanta in the resonator. Application of two phase-coherent pumps at the properfrequencies also enables back-action evading (BAE) detection of one quadrature of theresonator’s motion. [3] Using this technique we achieved a measurement precision of ~100 fm,which is 4 times the Heisenberg limit on continuous position detection for this device. We alsoidentified a parametric instability in this system, which can enhance the position sensitivity butultimately limits the BAE effect. These results advance our the possibilities for truly quantumlimitedmeasurement and non-classical states of motion in an object containing >10^10 atoms. | ||||
| February 13th | Vernita Gordon | University of IL, Urbana-Champaign | Functional peptides in biomembranes: the roles of curvature and specific lipid interactions | Schiff |
| February 27th | Jacinta Conrad | University of IL, Urbana-Champaign | Colloids under flow: assembly and patterning | Schiff |
| March 3d | Pengpeng Zhang | Pennsylvania State University | Structure and Electronic Transport Properties of Nanometer-Scale Silicon-on-Insulator Membranes | Schiff |
| March 6th | Sergei Urazhdin | West Virginia University | Thermally activated reversal statistics in magnetic nanostructures: a sensitive tool for the studies of nanomagnets. |
Schiff |
| Applications of nanomagnets in information technology rely on the stability of their magnetic configuration for information storage. However, the magnetic configuration should be also easily reversed during the writing process by an external magnetic field or spin-polarized current via the spin transfer effect. The dominant mechanism for the loss of magnetic stability is the thermal fluctuation of the magnetic moments. Fluctuations also play a significant role in the current-induced magnetic reversal (CIMS), which at moderate currents occurs via a thermal activation process. I will describe our measurements of CIMS statistics in magnetic nanostructures, and demonstrate that such measurements provide significant information about the thermal fluctuations, the microscopic mechanisms of magnetic reversal, dynamical coupling between ferromagnets discussed in my Colloquium, and even the surface properties of nanomagnets. If time permits, I will also discuss the effects of temperature on spin transport in magnetic nanostructures, and its implications for CIMS. | ||||
| March 13th | Spring Break | |||
| March 20th | March Meeting | |||
| March 27th | ||||
| April 3rd | Patrick Underhill | Rensselaer Polytechnic Institute | Correlations in suspensions of swimming microorganisms: theory and simulation | Marchetti |
| he motion of single swimming microorganisms, including different methods of propulsion and responses to the environment such as chemical gradients, has been studied for many years. However, much less work has examined populations. Large collections of swimming microorganisms are able to produce collective motions on a scale much larger than the scale of a single organism. In particular, the collective behavior leads to velocities larger than that of an isolated organism, fluid structures larger than the size of an organism, enhanced transport in the fluid, and enhanced stress fluctuations which produce altered rheological properties. We show theoretically how these phenomena are linked to the interactions between the organisms and compare the predictions with the results from computer simulations. In this way we can understand how the behavior scales with concentration, the importance of the method of swimming used, the influence of run-and-tumble like motions of the organisms, and how the interactions can lead to large-scale fluid structures. In periodic geometries, the large-scale fluid structures lead to simulation results that depend on the simulation box size. This result is in stark contrast with results from confined systems. The additional length scale (screening length) introduced by the confinement seems to prevent these large-scale structures from forming. | ||||
| April 10th | Andre Marziali | University of British Columbia | Electrophoretic methods for nucleic acid manipulation and analysis | Movileanu |
| Nucleic acids are growing in importance as a diagnostic molecules for a variety of disease states and responses to treatment, both as indicators of genetic predisposition, and as biomarkers of disease. In many cases, nucleic acid biomarker diagnostic techniques have fallen short of their revolutionary potential, in part due to the difficulty associated with extraction of rare nucleic acids from contaminated samples, and due to the cost and complexity of extraction and analysis techniques. I will present two technologies we have developed to help address these issues. The first, SCODA, is a non-linear electrophoresis technology that uses a form of second-harmonic generation in DNA electrophoresis to generate unique velocity fields in a gel. These allow highly selective extraction of nucleic acids from samples, including sequence-specific extraction. The second is an implementation of force spectroscopy using nanometer scale pores. This technique allows us to detect DNA sequence with single nucleotide resolution, without labeling of the target molecule, and in some cases can be used to uncover heterogeneity of molecule populations by extracting information on individual molecules one at a time. A variety of applications will be presented, ranging from metagenomics of Alberta tar sands, to prion protein stability analysis using nanopore force spectroscopy. | ||||
| April 17th | John Clarke | University of California, Berkeley | Flux 1/f Noise in Qubits and SQUIDs: The Saga Continues | Plourde |
| At millikelvin temperatures, superconducting flux qubits (quantum bits) and SQUIDs (Superconducting QUantum Interference Devices) both suffer from intrinsic magnetic flux noise. The noise power spectrum scales as 1/fb, where f is frequency and b is approximately unity. Low-frequency flux noise enhances decoherence in qubits and reduces flux resolution in SQUIDs. Remarkably, all devices show approximately the same level of noise, a few mF0Hz-1/2 at 1 Hz; F0 is the flux quantum. Since the magnitude of the flux noise scales only weakly with the area of the device, external uniform magnetic field noise is ruled out as the source. A model based on the random flipping of surface electrons between up and down states is consistent with the observed weak dependence of the noise on area. This model requires an areal electron density of about 5 x 1017 m-2 to account for the observed magnitude of the noise. Recent experiments at Wisconsin and Stanford on the paramagnetic susceptibility of SQUIDs and normal metal rings yield the same areal density. Three different models for the origin of the random flipping of electron spins are briefly discussed. Arguments are given that the noise cannot be generated by nuclear spins. This intriguing problem–which is now a quarter of a century old–still remains to be solved. | ||||
| April 24th | ||||