Defect fluctuations and lifetimes in disordered Yukawa systems.

We examine the time-dependent defect fluctuations and lifetimes for a bidisperse disordered assembly of Yukawa particles. At high temperatures, the noise spectrum of fluctuations is white and the coordination number lifetimes have a stretched exponential distribution. At lower temperatures, the system dynamically freezes, the defect fluctuations exhibit a 1/f spectrum, and there is a power law distribution of the coordination number lifetimes.

Optimization in gradient networks.

Gradient networks can be used to model the dominant structure of complex networks. Previous work has focused on random gradient networks. Here we study gradient networks that minimize jamming on substrate networks with scale-free and Erdos-Renyi structure.

Stripes, clusters, and nonequilibrium ordering for bidisperse colloids with repulsive interactions.

We show that two-dimensional bidisperse assemblies of colloids with strictly repulsive interactions exhibit stripe, cluster, and partially crystallized states when driven over a quenched random substrate. The nonequilibrium states on a substrate are significantly more ordered than equilibrium states both with and without substrates. A minimum substrate strength is necessary to induce the nonequilibrium pattern formation.

Dependence of Spurious Charge-Transfer Excited States on Orbital Exchange in TDDFT: Large Molecules and Clusters.

Time-dependent density functional theory (TDDFT) is a powerful tool allowing for accurate description of excited states in many nanoscale molecular systems; however, its application to large molecules may be plagued with difficulties that are not immediately obvious from previous experiences of applying TDDFT to small molecules. In TDDFT, the appearance of spurious charge-transfer states below the first optical excited state is shown to have significant effects on the predicted absorption and emission spectra of several donor-acceptor substituted molecules. The same problem affects the predictions of electronic spectra of molecular aggregates formed from weakly interacting chromophores.

Condensates in driven aggregation processes.

We investigate aggregation driven by mass injection. In this stochastic process, mass is added with constant rate r and clusters merge at a constant total rate 1 , so that both the total number of clusters and the total mass steadily grow with time. Analytic results are presented for the three classic aggregation rates K{i,j} between clusters of size i and j .

Molecular dynamics study of small PNA molecules in lipid-water system.

We present the results of molecular dynamics simulations of small peptide nucleic acid (PNA) molecules, synthetic analogs of DNA, at a lipid bilayer in water. At neutral pH, without any salt, and in the NP(n)gammaT ensemble, two similar PNA molecules (6-mers) with the same nucleic base sequence and different terminal groups are investigated at the interface between water and a 1-palmitoyl-2-oleoylphosphatidylcholine lipid bilayer. The results of our simulations suggest that at low ionic strength of the solution, both PNA molecules adsorb at the lipid-water interface.

Electrophoresis of DNA on a disordered two-dimensional substrate.

We propose a method for electrophoretic separation of DNA in which adsorbed polymers are driven over a disordered two-dimensional substrate which contains attractive sites for the polymers. Using simulations of a model for long polymer chains, we show that the mobility increases with polymer length, in contrast to gel electrophoresis techniques, and that separation can be achieved for a range of length scales. We demonstrate that the separation mechanism relies on steric interactions between polymer segments, which prevent substrate disorder sites from trapping more than one DNA segment each.

Probing the mechanical unzipping of DNA.

A study of the micromechanical unzipping of DNA in the framework of the Peyrard-Bishop-Dauxois model is presented. We introduce a Monte Carlo technique that allows accurate determination of the dependence of the unzipping forces on unzipping speed and temperature. Our findings agree quantitatively with experimental results for homogeneous DNA, and for lamda-phage DNA we reproduce the recently obtained experimental force-temperature phase diagram.

Loop calculus in statistical physics and information science.

Considering a discrete and finite statistical model of a general position we introduce an exact expression for the partition function in terms of a finite series. The leading term in the series is the Bethe-Peierls (belief propagation) (BP) contribution; the rest are expressed as loop contributions on the factor graph and calculated directly using the BP solution. The series unveils a small parameter that often makes the BP approximation so successful.

Sequencing DNA by dynamic force spectroscopy: limitations and prospects.

Using a well established model, we systematically analyze fundamental limitations on the viability of using mechanical unzipping of DNA as a fast and inexpensive sequencing method. Standard unzipping techniques, where double-stranded DNA is unzipped through the application of a force at one end of the molecule, are shown to be inadequate. Emerging techniques that unzip DNA by local force application are more promising, and we establish the necessary experimental requirements that must be met for these techniques to succeed as single molecule sequencing tools.

Coarsening of topological defects in oscillating systems with quenched disorder.

We use large scale simulations to study interacting particles in two dimensions in the presence of both an ac drive and quenched disorder. As a function of ac amplitude, there is a crossover from a low drive regime where the colloid positions are highly disordered to a higher ac drive regime where the system dynamically reorders. We examine the coarsening of topological defects formed when the system is quenched from a disordered low ac amplitude state to a high ac amplitude state.

Alignment of rods and partition of integers.

We study dynamical ordering of rods. In this process, rod alignment via pairwise interactions competes with diffusive wiggling. Under strong diffusion, the system is disordered, but at weak diffusion, the system is ordered.

Crossover from intermittent to continuum dynamics for locally driven colloids.

We simulate a colloid with charge q(d) driven through a disordered assembly of interacting colloids with charge q and show that, for q(d) approximately q, the velocity-force relation is nonlinear and the velocity fluctuations of the driven particle are highly intermittent with a 1/f characteristic. When g(d) >>q , the average velocity drops, the velocity-force relation becomes linear, and the velocity fluctuations are Gaussian. We discuss the results in terms of a crossover from strongly intermittent heterogeneous dynamics to continuum dynamics.

Power-law velocity distributions in granular gases.

The kinetic theory of granular gases is studied for spatially homogeneous systems. At large velocities, the equation governing the velocity distribution becomes linear, and it admits stationary solutions with a power-law tail, f (v) approximately v(-sigma) . This behavior holds in arbitrary dimension for arbitrary collision rates including both hard spheres and Maxwell molecules.

Application of the extended RSA models in studies of particle deposition at partially covered surfaces.

This paper reviews the application of the extended random sequential adsorption (RSA) approaches to the modeling of colloid-particle deposition (irreversible adsorption) on surfaces precovered with smaller particles. Hard (noninteracting) particle systems are discussed first. We report on the numerical simulations we performed to determine the available surface function, jamming coverage, and pair-correlation function of the larger particles.

Theoretical study of the effects of solvent environment on photophysical properties and electronic structure of paracyclophane chromophores.

We use first-principles quantum-chemical approaches to study absorption and emission properties of recently synthesized distyrylbenzene (DSB) derivative chromophores and their dimers (two DSB molecules linked through a [2.2]paracyclophane moiety). Several solvent models are applied to model experimentally observed shifts and radiative lifetimes in Stokes nonpolar organic solvents (toluene) and water.

Stationary states and energy cascades in inelastic gases.

We find a general class of nontrivial stationary states in inelastic gases where, due to dissipation, energy is transferred from large velocity scales to small velocity scales. These steady states exist for arbitrary collision rules and arbitrary dimension. Their signature is a stationary velocity distribution f(v) with an algebraic high-energy tail, f(v) approximately v(-sigma).

Kinetic theory of random graphs: from paths to cycles.

The structural properties of evolving random graphs are investigated. Treating linking as a dynamic aggregation process, rate equations for the distribution of node to node distances (paths) and of cycles are formulated and solved analytically. At the gelation point, the typical length of paths and cycles, l , scales with the component size k as l approximately k(1/2) .

Bubble nucleation and cooperativity in DNA melting.

The onset of intermediate states (denaturation bubbles) and their role during the melting transition of DNA are studied using the Peyrard-Bishop-Dauxois model by Monte Carlo simulations with no adjustable parameters. Comparison is made with previously published experimental results finding excellent agreement. Melting curves, critical DNA segment length for stability of bubbles, and the possibility of a two-state transition are studied.

Electron-vibrational dynamics of photoexcited polyfluorenes.

The highly polarizable pi-electron system of conjugated molecules forms the basis for their unique electronic and photophysical properties, which play an important role in numerous biological phenomena and make them important materials for technological applications. We present a theoretical investigation of the dynamics and relaxation of photoexcited states in conjugated polyfluorenes, which are promising materials for display applications. Our analysis shows that both fast (approximately 20 fs) and slow (approximately 1 ps) nuclear motions couple to the electronic degrees of freedom during the excited-state dynamics.

Size of outbreaks near the epidemic threshold.

The spread of infectious diseases near the epidemic threshold is investigated. Scaling laws for the size and the duration of outbreaks originating from a single infected individual in a large susceptible population are obtained. The maximal size of an outbreak n(*) scales as N(2/3) with N the population size.

Finite-size fluctuations in interacting particle systems.

Fluctuations may govern the fate of an interacting particle system even on the mean-field level. This is demonstrated via a three species cyclic trapping reaction with a large, yet finite number of particles, where the final number of particles N(f) scales logarithmically with the system size N, N(f) approximately ln N. Statistical fluctuations, that become significant as the number of particles diminishes, are responsible for this behavior.

Impurity in a Maxwellian unforced granular fluid.

We investigate velocity statistics of an impurity immersed in a uniform granular fluid. We consider the cooling phase, and obtain scaling solutions of the inelastic Maxwell model analytically. First, we analyze identical fluid-fluid and fluid-impurity collision rates.

Exchange-driven growth.

We study a class of growth processes in which clusters evolve via exchange of particles. We show that depending on the rate of exchange there are three possibilities: (I) Growth-clusters grow indefinitely, (II) gelation-all mass is transformed into an infinite gel in a finite time, and (III) instant gelation. In regimes I and II, the cluster size distribution attains a self-similar form.

Discrete vector solitons in two-dimensional nonlinear waveguide arrays: solutions, stability, and dynamics.

We identify and investigate bimodal (vector) solitons in models of square-lattice arrays of nonlinear optical waveguides. These vector self-localized states are, in fact, self-induced channels in a nonlinear photonic-crystal matrix. Such two-dimensional discrete vector solitons are possible in waveguide arrays in which each element carries two light beams that are either orthogonally polarized or have different carrier wavelengths.