Rate processes are ubiquitous in physics, chemistry, and biology. Theoretical description of a rate process is a central topic in chemical physics (Hanggi, et al., Rev. Mod. Phys. 62:251, 1990). I will discuss several problems from biology that require description beyond the rate equation formalism generally used in biochemistry and systems biology studies.

Protein motors are proteins that can use electro-chemical energy to perform mechanical work, and are essential for almost every biological process. Bacteria like E. Coli use a rotary motor to propel cell body motion utilizing transmembrane ion motive force. The Berg's lab (and followed by others) observed strange motor torque-speed relations. I will discuss how theoretical analysis gives a simple explanation to this long-standing puzzle (PNAS 103:1260, 2006).

Biochemists are used to use rate equations like the Michaelis-Menten equation to describe an enzymatic reaction. A central assumption in most rate theories is that one can identify a reaction coordinate which connects the reactant and the product regions, and is the slowest degree of freedom in the system. Recent single molecule experiments and (old) biochemistry/biophysics studies reveal that the assumption is in general not true for enzyme reactions. This is called dynamic disorder. I will discuss a general theoretical formalism and its implication on allosteric regulation (PRE 74:061911, 2006; PRL 99:168103, 2007). The latter refers to the property that binding of a regulator at one site of an allosteric protein affects the protein's activity at a distant site. The allosteric effect is largely analyzed by thermodynamics, but I suggest that it can be a nonequilibrium problem.

Last I will discuss some recent efforts in my lab on how the existence of dynamic disorder may modify our understanding of dynamics of protein interaction networks (PLOS ONE 3:e2140, 2008, and unpublished results).

A list of my publications can be found at http://www.biol.vt.edu/faculty/xing/xing_pub.html

Hosted by Michel Pleimling.

Since 1984, electric cell-substrate impedance sensing (ECIS) has been used to monitor cell behavior in culture and has proven sensitive to morphological changes and cell mobility. Several authors have associated fluctuations in the measured impedance with cellular micromotion; however we are unaware of any previous work applying statistical techniques in order to distinguish two different cell types. We have now demonstrated a method for distinguishing cancerous from non-cancerous cultures of human ovarian surface epithelial cells [1]. Applying similar ideas, we have also determined the presence and concentration of the toxin cytochalisin B in cultures of 3T3 fibroblasts at levels lower than the detection thresholds of other techniques. Measures indicative of both short-time (autocorrelation) and long-time (1/f^α noise in the power spectrum and Hurst and detrended-fluctuation-analysis exponents) show statistically significant differences between the populations. Our measures confirm that the noise from non-cancerous cultures has a higher degree of temporal order, order which we argue must arise from greater coordination of motion between healthy cells than between cancerous ones.

[1] D.C. Lovelady et al. Phys. Rev. E 76, 041908 (2007)

Hosted by Royce Zia.

Time-resolved magneto-optical imaging, recently developed at the College of William and Mary, offers the possibility to study the superconducting thin films dynamic response in presence of both external magnetic field and applied transport current. Instant maps of the magnetic flux distribution in broad areas of the sample are particularly effective to study how structural characteristics of superconducting thin films, such as homogeneity, granularity, defects, and cracks affect the behavior of the superconducting vortex matter. I will present and discuss interesting dynamic effects revealed by TRMOI in type II superconductors such as the ac current driven dynamic vortex states and the flux-antiflux boundary currents in YBCO thin films, the magnetic flux and current evolution in coupled multifilamentary YBCO thin film samples and the kinetic roughening of magnetic flux penetration in MgB₂.

Hosted by Uwe Täuber.

It is widely appreciated that population waves have played a crucial role in the evolutionary history of many species. In parallel with Fokker-Planck descriptions of stochastic processes in physics, population geneticists have independently developed methods for understanding mutations, genetic drift and selective advantage in such situations. Genetic footprints of many pioneer species are still recognizable today, and neutral genetic markers can be used to infer information about growth, ancestral population size and colonization pathways. Neutral mutations optimally positioned at the front of a growing population wave can increase their abundance via a "surfing" phenomenon. Experimental and theoretical studies of this effect will be presented, using bacteria and yeast as model systems.

Hosted by Uwe Täuber.

Accurate description of interactions between solvent and biomolecules is essential in biosimulation. Explicit treatment of solvent is, however, computationally demanding since the solvent usually greatly outnumbers the solute. In ab initio biosimulations explicit representation of solvent is prohibitively expensive and thus implicit solvent models are often used. While useful, the implicit treatment of solvent is known to yield incorrect results in certain cases. We have recently developed a hybrid method, which allows for efficient inclusion of explicit solvent in DFT calculations and provides seamless integration between regions treated by different methods. In this method, Kohn-Sham (KS) density functional theory (DFT) is combined with an orbital-free (OF) DFT. Solvent molecules not directly in contact with the biomolecule of interest are described by the OF DFT, in which they have have rigid geometries and frozen densities. The KS DFT is used to describe the biomolecule and the first solvation shells around it. The compatibility between the KS and OF DFT methods enables seamless integration between the two methods. In particular, the flow of solvent molecules across the KS/OF interface is allowed and the total energy is conserved for this process.

Applications of this method to study copper binding to proteins involved in prion and Parkinson's diseases will also be presented. The prion protein (PrP) study focused on two unknown aspects of Cu-PrP interaction: PrP's normal function and the role of Cu ions in prion diseases. Our calculations reveal that PrP favors bonding increasing amounts of Cu as its concentration increases, validating the buffering function hypothesis, according to which PrP's function is to store excess amount of copper ions, protecting other molecules from effect of free copper. Furthermore, our calculations on full-length PrP show that copper stabilizes the unfolded part of the PrP, suggesting a protective role of copper ions in prion diseases. In a second application we studied Cu binding to alpha-synuclein, a Parkinson's disease(PD) protein, and determined a molecular mechanism of the onset of PD. The link between Cu and PD was made before, but the molecular mechanism of Cu action was unknown. Our study shows that the Cu binding modifies the protein structurally, making it more susceptible to misfolding, an initial step in PD pathogenesis. The knowledge of the mechanism is a first step for finding an effective therapy for PD.

Hosted by Kyungwha Park.

The simulation, testing and prediction of different behaviors of multi-disciplinary systems are extremely difficult due to competing phenomena and mechanisms which result in the coexistence of different responses. Advances in computational methodologies and augmentation of available computational resources will enable the development of high-fidelity computer simulations of such systems. Yet, it will still be extremely difficult to choose initial conditions that would produce all possible solutions. For the same reasons, generic simulation or testing procedures that are based on blind or wide variations of input parameters would be extremely ineffective and, to a certain extent, precarious. Furthermore, most linear and nonlinear systems possess global invariants that depend in complicated ways on different parameters. Hence, it would be very difficult to determine the important parameters that affect these invariants with brute-force computations. These observations point to the need for the development of reduced-order models that embody proper physics and response characteristics and that (a) reproduce results of high-fidelity simulations and (b) show explicitly the dependence of theses invariants on the different parameters. In this presentation, we address the issue of how interrogative simulation or testing procedures can be implemented to develop mathematical models that embody the proper physics and response characteristics of multi-disciplinary systems. Particularly, we exploit specific system behaviors that can be represented by mathematical models. Then, we combine quantities developed from higher-order spectral analysis of simulated or measured data with approximate solutions of the representative mathematical models to characterize and identify the respective parameters.

Hosted by Beate Schmittmann.

In this talk I summarize my work on non-equilibrium processes in quantum chains, starting with a study on the non-equilibrium behavior of isolated spin chains.

I will then consider an initial thermal kink-like state where half of the chain is initially thermalized at a very high temperature T_b while the remaining half, called the system, is put at a lower temperature T_s. For this initial state I will derive analytically the Green function associated to the dynamical behavior of the transverse magnetization.

In the second part of the talk I will consider an open quantum chain where the interactions between the system and the environment are described by the repeated interaction process. In this case I will focus my attention on the properties of the stationary state.

Nanoscale resonators offer great potential as sensing devices due to their high sensitivity to added masses or external forces. The sensitivity of mechanical resonators scales favorably as their dimensions are reduced, offering a compelling path for the development of sensors with exceptional mass sensitivities. Nanomachining now allows the fabrication of mechanical objects with lateral dimensions of about 100 nm and resonant frequencies in the ultra-high frequency range. Given their small volumes and high surface-to-volume ratios, these nanoelectromechanical systems (NEMS) are of great interest for the detection of mass with high sensitivity.

The National Institute of Nanotechnology (NINT) is engaged in a series of state-of the art research programs related to the development and applications of nanomechanical resonators. Suspended resonators as narrow as 30 nm, the narrowest structures ever produced by any machining method, have been produced using a novel combination of surface nanomachining and bulk etching. Alternatively a partnership with Hewlett-Packard laboratories has recently enabled the production of clamped resonant nanowires with diameters as narrow as 20 nm. We will present an overview of those novel nanofabrication technologies, and discuss our efforts towards their applications for the analysis of molecular mixtures.

Hosted by Randy Heflin.

The theory of electric circuits was formulated by Kirchhoff in 1847 who introduced what is now known as the Kirchhoff tree matrix. The Kirchhoff tree matrix plays an important role in the theory of electric circuits and in graph theory. But it does not offer a simply way of computing resistances. The computation of effective resistances has remained a lingering unsettled problem in electric circuit theory.

This talk reports a new formulation of the Kirchhoff law expressing two-point resistances in a resistor network in terms of eigenvalues and eigenfunctions of the tree matrix. The formulation is applied to regular lattices and non-orientable surfaces, leading to results otherwise difficult to obtain. The formulation is further extended to impedance networks for which elements of the tree matrix are complex entities. An interesting prediction of the theory is the occurrence of multiple resonances in networks consisting of pure inductances and capacitances.

Hosted by Royce Zia.

We analyze dynamic local interaction in population games where the local interaction structure (modeled as an undirected graph) can change over time: A stochastic process generates a random sequence of graphs. This contrasts with models where the initial interaction structure (represented by a deterministic graph or the realization of a random graph) cannot change over time. Each time each player makes a binary choice. The underlying game for pairwise interaction is a coordination game. Our analysis is focused on models with two kinds of random graphs. In the first type of models, the support of the random graph consists of regular graphs, where all players have the same number of neighbors. In the second type of models, the underlying random graph is binomial.

Circular graphs are the two-regular graphs where the players can be arranged in a circle so that each player has one neighbor to the left and one neighbor to the right. Circular graphs are frequently used in economics. We find that if the support of the underlying random graph consists of all circular graphs, at least one player chose the risk dominant action initially, and updating is simultaneous, then contagion with respect to the risk dominant action occurs. In contrast, with simultaneous updating, an even number of players, and a fixed circular graph, convergence to a two-cycle can occur. We obtain less conclusive results for arbitrary regular graphs where each player has more than two neighbors.

In a binomial random graph, each possible edge is included independently of others with a given probability, which is the same for all edges. This is the random graph model most commonly studied in mathematics and statistics, sometimes even referred to as "the random graph." In a dynamic context it reflects best the idea of loose social ties. We find that if the evolution of the interaction structure is based on a binomial random graph and if just a few players choose the risk dominant action initially, then with positive probability, contagion with respect to the risk dominant action occurs very rapidly; but in a large population, it is much more likely that contagion with respect to the alternative action occurs. The latter means that high connectivity does not necessarily favor contagion with respect to the risk dominant action.

Hosted by Beate Schmittmann.

Nanostructured materials are of considerable interest for both fundamental studies and potential devices. The synthesis of nanoparticles can be complicated because of multiple steps required to obtain the desired composition, structure, and particle size and particle size distribution. In our research, we are utilizing pulsed laser deposition to achieve the desired composition, structure, and particle size in one step for a variety of nanoparticle based thin film composites. The nanoparticles evolve as three dimensional clusters because of the respective surface and interface energies. We have demonstrated the ability to control the size of magnetic nanoparticles by tailoring the magnetic properties from superparamagnetic to ferromagnetic. In this talk, I will discuss our experimental approach and give an overview of some our efforts on magnetic nanoparticles in various thin film matrices, including some intriguing results with gold nanoparticles.

Hosted by Giti Khodaparast.

The Casimir effect in quantum electrodynamics (QED) is perhaps the best-known example of fluctuation-induced long-ranged forces acting on objects (conducting plates) immersed in a fluctuating medium (quantum electromagnetic field in vacuum). A similar effect emerges in statistical physics, where, e.g., colloidal particles immersed in a binary liquid mixture experience an additional force due to the classical thermal fluctuations occurring in the surrounding medium. This Casimir-like force acquires universal features upon approaching a critical point of the medium and becomes long-ranged at criticality. In turn, this universality allows the theoretical investigation of the force via representative models and also a stringent experimental test of the corresponding predictions.

In contrast to QED, the strenght and sign of the Casimir force resulting from critical fluctuations can be easily tuned by surface treatments and temperature control. The talk reviews some recent advances in the theoretical study of the universal properties of the critical Casimir force arising in thin films. Our predictions compare very well with the experimental results obtained for wetting layers of fluids. We discuss how the Casimir force between a colloidal particle and a planar wall immersed in a binary liquid mixture has been measured with femto-Newton accuracy, comparing these experimental results with the corresponding theoretical predictions.

1. O. Vasilyev, A. Gambassi, A. Maciolek, S. Dietrich, Europhys. Lett. 80, 60009 (2007).
2. C. Hertlein, L. Helden, A. Gambassi, S. Dietrich, C. Bechinger, Nature 451, 172 (2008).

Hosted by Royce Zia.

Isovalent doping has been used for many years to improve the physical properties of compound semiconductors. This approach may prove to be of particular import for the group III nitride alloys since they are “defect semiconductors” in the sense that the concentrations of native point defects, residual chemical impurities, and threading dislocations typically approach or exceed those of doping atoms introduced intentionally during crystal growth. These electrically active defects degrade the majority carrier transport properties of n- and p-type GaN films, and, in addition, make it difficult to synthesize good semi-insulating material. Group III nitride semiconductor alloys with mixing on the anion sublattice are also of considerable interest because of their potential application to a wide range of optoelectronic devices. The large difference in bond lengths between group III nitrides and arsenides results in an enormous miscibility gap, making it difficult to grow ternary alloys in the intermediate composition range. While nitrogen-doped GaAs and arsenic-rich GaAsN alloys have been studied by many research groups, there has been comparatively little work done at and/or near the nitrogen-rich side of the phase diagram, which is the primary focus of this seminar. Arsenic-doped GaN and nitrogen-rich GaNAs alloys have been grown by metal-organic chemical vapor deposition (MOCVD) and characterized using a wide range of measurement techniques. Representative experimental data will be shown to demonstrate the structural, chemical, and electronic quality of these materials and the observed physical trends will be compared against predictions derived from contemporary theoretical models.

Hosted by Giti Khodaparast.

Practical applications of superconductors rely not only on high critical temperatures, below which these materials exhibit zero resistivity, but also depend on the maximum current density which superconductors can carry before entering the normal state, and the maximum magnetic field strength to which they can be exposed. For type-II superconductors in the mixed state, these crucial quantities are directly related to the flux pinning of quantized magnetic vortices through intrinsic or fabricated material defects.

In this talk I will discuss the characterization of non-equilibrium steady states of driven flux lines in type-II superconductors subject to strong point or columnar pinning centers. Three-dimensional Metropolis Monte Carlo simulations are employed to obtain physical observables such as the current-voltage (I-V) curve, static structure factor, radius of gyration, and voltage noise power spectra. I will also briefly discuss my current research on the slow relaxation and aging dynamics of disordered interacting magnetic flux line systems.

The last twenty years has seen remarkable improvement in the development of methods to generate and detect pulsed terahertz (100 GHz - 10 THz) radiation. Terahertz spectroscopy has already been shown to be a powerful tool for the characterization of gases, semiconductors, plastics, etc. Due to the transparent properties of many non-metallic materials at terahertz frequencies, both the security and the manufacturing inspection sectors are interested in developing terahertz imaging systems. In order for pulsed terahertz applications to be realized beyond the laboratory bench, the reliance on the use of bulky free-space optics must be addressed. A crucial enabling step in the advancement of terahertz technology is the development of waveguides for use at these frequencies. This step is comparable to the large growth in laser telecommunications that followed the birth of low-cost fiberoptics. The physics and engineering associated with developing terahertz waveguides is quite difficult due to material constraints and concerns about pulse attenuation and dispersion. In this talk, I will describe the generation and detection of pulsed terahertz radiation and highlight several of its potential applications. I will show how a simple metal wire has turned into one of the most interesting and successful terahertz waveguides to date. These wire waveguides are so effective due to a physical phenomenon known as surface plasmon polaritons (SPPs). I will present results from both finite element method simulations and experimental measurements that explain the excitation and emission properties of SPPs at terahertz frequencies. I will conclude the talk with a discussion of how the use of terahertz plasmonics coupled with the relatively young field of terahertz metamaterials will lead to improved terahertz-based spectroscopic and imaging techniques such as near-field scanning microscopy.

Hosted by Giti Khodaparast.