Electrodynamics of Media

Contains reports on two research projects.Joint Services Electronics Programs (U. S. Army, U. S. Navy, and U. S. Air Force) under Contract DA 28-043-AMC-02536(E

Electrodynamics of Media

Contains reports on two research projects.Joint Services Electronics Programs (U. S. Army, U.S. Navy, and U.S. Air Force) under Contract DA 28-043-AMC-02536(E)U. S. Air Force (ESD) Contract F19628-70-C-006

Relaxation Dynamics of Semiflexible Polymers

We study the relaxation dynamics of a semiflexible chain by introducing a time-dependent tension. The chain has one of its ends attached to a large bead, and the other end is fixed. We focus on the initial relaxation of the chain that is initially strongly stretched. Using a tension that is self-consistently determined, we obtain the evolution of the end-to-end distance with no free parameters. Our results are in good agreement with single molecule experiments on double stranded DNA

Electrodynamics of Media

Contains research objectives and reports on two research projects.Joint Services Electronics Programs (U. S. Army, U. S. Navy, and U. S. Air Force) under Contract DA 28-043-AMC-02536(E)National Science Foundation (Grant GK-3370

TransFind—predicting transcriptional regulators for gene sets

The analysis of putative transcription factor binding sites in promoter regions of coregulated genes allows to infer the transcription factors that underlie observed changes in gene expression. While such analyses constitute a central component of the in-silico characterization of transcriptional regulatory networks, there is still a lack of simple-to-use web servers able to combine state-of-the-art prediction methods with phylogenetic analysis and appropriate multiple testing corrected statistics, which returns the results within a short time. Having these aims in mind we developed TransFind, which is freely available at http://transfind.sys-bio.net/

Anomalous fluctuations of active polar filaments

Using a simple model, we study the fluctuating dynamics of inextensible, semiflexible polar filaments interacting with active and directed force generating centres such as molecular motors. Taking into account the fact that the activity occurs on time-scales comparable to the filament relaxation time, we obtain some unexpected differences between both the steady-state and dynamical behaviour of active as compared to passive filaments. For the statics, the filaments have a {novel} length-scale dependent rigidity. Dynamically, we find strongly enhanced anomalous diffusion.Comment: 5 pages, 3 figure

Generalized model for dynamic percolation

We study the dynamics of a carrier, which performs a biased motion under the influence of an external field E, in an environment which is modeled by dynamic percolation and created by hard-core particles. The particles move randomly on a simple cubic lattice, constrained by hard-core exclusion, and they spontaneously annihilate and re-appear at some prescribed rates. Using decoupling of the third-order correlation functions into the product of the pairwise carrier-particle correlations we determine the density profiles of the "environment" particles, as seen from the stationary moving carrier, and calculate its terminal velocity, V_c, as the function of the applied field and other system parameters. We find that for sufficiently small driving forces the force exerted on the carrier by the "environment" particles shows a viscous-like behavior. An analog Stokes formula for such dynamic percolative environments and the corresponding friction coefficient are derived. We show that the density profile of the environment particles is strongly inhomogeneous: In front of the stationary moving carrier the density is higher than the average density, $\rho_s$, and approaches the average value as an exponential function of the distance from the carrier. Past the carrier the local density is lower than $\rho_s$ and the relaxation towards $\rho_s$ may proceed differently depending on whether the particles number is or is not explicitly conserved.Comment: Latex, 32 pages, 4 ps-figures, submitted to PR

Pearling and Pinching: Propagation of Rayleigh Instabilities

A new category of front propagation problems is proposed in which a spreading instability evolves through a singular configuration before saturating. We examine the nature of this front for the viscous Rayleigh instability of a column of one fluid immersed in another, using the marginal stability criterion to estimate the front velocity, front width, and the selected wavelength in terms of the surface tension and viscosity contrast. Experiments are suggested on systems that may display this phenomenon, including droplets elongated in extensional flows, capillary bridges, liquid crystal tethers, and viscoelastic fluids. The related problem of propagation in Rayleigh-like systems that do not fission is also considered.Comment: Revtex, 7 pages, 4 ps figs, PR

Random Walks on a Fluctuating Lattice: A Renormalization Group Approach Applied in One Dimension

We study the problem of a random walk on a lattice in which bonds connecting nearest neighbor sites open and close randomly in time, a situation often encountered in fluctuating media. We present a simple renormalization group technique to solve for the effective diffusive behavior at long times. For one-dimensional lattices we obtain better quantitative agreement with simulation data than earlier effective medium results. Our technique works in principle in any dimension, although the amount of computation required rises with dimensionality of the lattice.Comment: PostScript file including 2 figures, total 15 pages, 8 other figures obtainable by mail from D.L. Stei

Dynamics of viscoelastic membranes

We determine both the in-plane and out-of-plane dynamics of viscoelastic membranes separating two viscous fluids in order to understand microrheological studies of such membranes. We demonstrate the general viscoelastic signatures in the dynamics of shear, bending, and compression modes. We also find a screening of the otherwise two-dimensional character of the response to point forces due to the presence of solvent. Finally, we show that there is a linear, hydrodynamic coupling between the in-plane compression modes of the membrane and the out-of-plane bending modes in the case where the membrane separates two different fluids or environments