Configurational entropy of network-forming materials

We present a computationally efficient method to calculate the configurational entropy of network-forming materials. The method requires only the atomic coordinates and bonds of a single well-relaxed configuration. This is in contrast to the multiple simulations that are required for other methods to determine entropy, such as thermodynamic integration. We use our method to obtain the configurational entropy of well-relaxed networks of amorphous silicon and vitreous silica. For these materials we find configurational entropies of 0.93k(B) and 0.88k(B) per silicon atom, respectively.     

Control of structure formation in phase-separating systems

In this paper, we study the evolution of phase-separating binary mixtures which are subjected to alternate cooling and heating cycles. An initially homogeneous mixture is rapidly quenched to a temperature T(1)T(c). These cycles are repeated to create a domain morphology with multiple length scales, i.e., the structure factor is characterized by multiple peaks. For phase separation in d = 2 systems, we present numerical and analytical results for the emergence and growth of this multiple-scale morphology.     

Lattice models of DNA electrophoresis

This article presents an overview of lattice polymer models used to study DNA electrophoresis. Three commonly used models--the bond fluctuation model, the cage model, and the repton model--are discussed, as well their extension to include electric fields, and simulation results obtained. Physical properties that are shared amongst these models are identified, and differences between the models are discussed.     

Desorption of polymers: role of the stagnant layer

The desorption of polymers is studied theoretically and with Monte Carlo simulations. Two regimes can be distinguished: in one regime the detachment of the polymer from the surface is the slowest process, and in the other it is the diffusion of the polymer away from the surface. In both regimes the desorption rate depends on the thickness H of the stagnant layer, i.e. the layer in which the polymer movement is dominated by diffusion. In the diffusion-limited regime the desorption rate scales as H ^{? 2}, as expected for diffusive processes. In the detachment-limited regime the desorption rate scales as H ^{? 1}. The importance of the thickness of the stagnant layer in the detachment-limited regime is due to the fact that the polymer, after it has detached, will most likely readsorb soon after: the probability that the polymer does not readsorb, but crosses the stagnant layer, is inversely proportional to the thickness of the stagnant layer.     

Two-Dimensional Oriented Self-Avoiding Walks with Parallel Contacts

Two closely related models of oriented self-avoiding walks (OSAWs) on a square lattice are studied. We use the pruned-enriched Rosenbluth method to determine numerically the phase diagram. Both models have three phases: a tight-spiral phase in which the binding of parallel steps dominates, a collapsed phase when the binding of antiparallel steps dominates, and a free (open coil) phase. We show that the system features a first-order phase transition from the free phase to the tight-spiral phase, while both other transitions are continuous. The location of the phases is determined accurately. We also study turning numbers and gamma exponents in various regions of the phase diagram.     

Unbiased computation of transition times by pathway recombination

In many systems, the time scales of the microscopic dynamics and macroscopic dynamics of interest are separated by many orders of magnitude. Examples abound, for instance, nucleation, protein folding, and chemical reactions. For these systems, direct simulation of phase space trajectories does not efficiently determine most physical quantities of interest. The past decade has seen the advent of methods circumventing brute force simulation. For most dynamical quantities, these methods all share the drawback of systematical errors. We present a novel method for generating ensembles of phase space trajectories. By sampling small pieces of these trajectories in different phase space domains and piecing them together in a smart way using equilibrium properties, we obtain physical quantities such as transition times. This method does not have any systematical error and is very efficient; the computational effort to calculate the first passage time across a free energy barrier does not increase with the height of the barrier. The strength of the method is shown in the Ising model. Accurate measurements of nucleation times span almost ten orders of magnitude and reveal corrections to classical nucleation theory.