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.     

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.     

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.     

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.     

Passage times for unbiased polymer translocation through a narrow pore

We study the translocation process of a polymer in the absence of external fields for various pore diameters b and membrane thickness L. The polymer performs Rouse and reptation dynamics. The mean translocation time (tau(t)) that the polymer needs to escape from a cell and the mean dwell time (tau(d)) that the polymer spends in the pore during the translocation process obey scaling relations in terms of the polymer length N, L, and b/R(g), where R(g) is the radius of gyration for the polymer. We explain these relations using simple arguments based on polymer dynamics and the equilibrium properties of polymers.