arXiv subjects

Gary W. Slater

Publications and source records attributed to Gary W. Slater.

22 records · Page 2Linked to original sources

arXiv2010

Optimizing the accuracy of Lattice Monte Carlo algorithms for simulating diffusion

The behavior of a Lattice Monte Carlo algorithm (if it is designed correctly) must approach that of the continuum system that it is designed to simulate as the time step and the mesh step tend to zero. However, we show for an algorithm for unbiased particle diffusion that if one of these two parameters remains fixed, the accuracy of the algorithm is optimal for a certain finite value of the other parameter. In one dimension, the optimal algorithm with moves to the two nearest neighbor sites reproduces the correct second and fourth moments (and minimizes the error for the higher moments at large times) of the particle distribution and preserves the first two moments of the first-passage time distributions. In two and three dimensions, the same level of accuracy requires simultaneous moves along two axes ("diagonal" moves). Such moves attempting to cross an impenetrable boundary should be projected along the boundary, rather than simply rejected. We also treat the case of absorbing boundaries.

cond-mat.stat-mech↗

arXiv2009

Optimizing end-labeled free-solution electrophoresis by increasing the hydrodynamic friction of the drag-tag

We study the electrophoretic separation of polyelectrolytes of varying lengths by means of end-labeled free-solution electrophoresis (ELFSE). A coarse-grained molecular dynamics simulation model, using full electrostatic interactions and a mesoscopic Lattice Boltzmann fluid to account for hydrodynamic interactions, is used to characterize the drag coefficients of different label types: linear and branched polymeric labels, as well as transiently bound micelles. It is specifically shown that the label's drag coefficient is determined by its hydrodynamic size, and that the drag per label monomer is largest for linear labels. However, the addition of side chains to a linear label offers the possibility to increase the hydrodynamic size, and therefore the label efficiency, without having to increase the linear length of the label, thereby simplifying synthesis. The third class of labels investigated, transiently bound micelles, seems very promising for the usage in ELFSE, as they provide a significant higher hydrodynamic drag than the other label types. The results are compared to theoretical predictions, and we investigate how the efficiency of the ELFSE method can be improved by using smartly designed drag-tags.

cond-mat.soft↗

arXiv2008

Non-driven polymer translocation through a nanopore: computational evidence that the escape and relaxation processes are coupled

Most of the theoretical models describing the translocation of a polymer chain through a nanopore use the hypothesis that the polymer is always relaxed during the complete process. In other words, models generally assume that the characteristic relaxation time of the chain is small enough compared to the translocation time that non-equilibrium molecular conformations can be ignored. In this paper, we use Molecular Dynamics simulations to directly test this hypothesis by looking at the escape time of unbiased polymer chains starting with different initial conditions. We find that the translocation process is not quite in equilibrium for the systems studied, even though the translocation time tau is about 10 times larger than the relaxation time tau_r. Our most striking result is the observation that the last half of the chain escapes in less than ~12% of the total escape time, which implies that there is a large acceleration of the chain at the end of its escape from the channel.

q-bio.BM↗

arXiv2004

A new set of Monte Carlo moves for lattice random-walk models of biased diffusion

We recently demonstrated that standard fixed-time lattice random-walk models cannot be modified to properly represent biased diffusion processes in more than two dimensions. The origin of this fundamental limitation appears to be the fact that traditional Monte Carlo moves do not allow for simultaneous jumps along each spatial direction. We thus propose a new algorithm to transform biased diffusion problems into lattice random walks such that we recover the proper dynamics for any number of spatial dimensions and for arbitrary values of the external field. Using a hypercubic lattice, we redefine the basic Monte Carlo moves, including the transition probabilities and the corresponding time durations, in order to allow for simultaneous jumps along all Cartesian axes. We show that our new algorithm can be used both with computer simulations and with exact numerical methods to obtain the mean velocity and the diffusion coefficient of point-like particles in any dimensions and in the presence of obstacles.

physics.data-an↗