Optimizing Replica Exchange Moves For Molecular Dynamics

In this short note we sketch the statistical physics framework of the replica exchange technique when applied to molecular dynamics simulations. In particular, we draw attention to generalized move sets that allow a variety of optimizations as well as new applications of the method.Comment: 4 pages, 3 figures; revised version (1 figure added), PRE in pres

On central tendency and dispersion measures for intervals and hypercubes

The uncertainty or the variability of the data may be treated by considering, rather than a single value for each data, the interval of values in which it may fall. This paper studies the derivation of basic description statistics for interval-valued datasets. We propose a geometrical approach in the determination of summary statistics (central tendency and dispersion measures) for interval-valued variables

Ions in Fluctuating Channels: Transistors Alive

Ion channels are proteins with a hole down the middle embedded in cell membranes. Membranes form insulating structures and the channels through them allow and control the movement of charged particles, spherical ions, mostly Na+, K+, Ca++, and Cl-. Membranes contain hundreds or thousands of types of channels, fluctuating between open conducting, and closed insulating states. Channels control an enormous range of biological function by opening and closing in response to specific stimuli using mechanisms that are not yet understood in physical language. Open channels conduct current of charged particles following laws of Brownian movement of charged spheres rather like the laws of electrodiffusion of quasi-particles in semiconductors. Open channels select between similar ions using a combination of electrostatic and 'crowded charge' (Lennard-Jones) forces. The specific location of atoms and the exact atomic structure of the channel protein seems much less important than certain properties of the structure, namely the volume accessible to ions and the effective density of fixed and polarization charge. There is no sign of other chemical effects like delocalization of electron orbitals between ions and the channel protein. Channels play a role in biology as important as transistors in computers, and they use rather similar physics to perform part of that role. Understanding their fluctuations awaits physical insight into the source of the variance and mathematical analysis of the coupling of the fluctuations to the other components and forces of the system.Comment: Revised version of earlier submission, as invited, refereed, and published by journa

Heat Conduction and Entropy Production in a One-Dimensional Hard-Particle Gas

We present large scale simulations for a one-dimensional chain of hard-point particles with alternating masses. We correct several claims in the recent literature based on much smaller simulations. Both for boundary conditions with two heat baths at different temperatures at both ends and from heat current autocorrelations in equilibrium we find heat conductivities kappa to diverge with the number N of particles. These depended very strongly on the mass ratios, and extrapolation to N -> infty resp. t -> infty is difficult due to very large finite-size and finite-time corrections. Nevertheless, our data seem compatible with a universal power law kappa ~ N^alpha with alpha approx 0.33. This suggests a relation to the Kardar-Parisi-Zhang model. We finally show that the hard-point gas with periodic boundary conditions is not chaotic in the usual sense and discuss why the system, when kept out of equilibrium, leads nevertheless to energy dissipation and entropy production.Comment: 4 pages (incl. 5 figures), RevTe

Simulations of grafted polymers in a good solvent

We present improved simulations of three-dimensional self avoiding walks with one end attached to an impenetrable surface on the simple cubic lattice. This surface can either be a-thermal, having thus only an entropic effect, or attractive. In the latter case we concentrate on the adsorption transition, We find clear evidence for the cross-over exponent to be smaller than 1/2, in contrast to all previous simulations but in agreement with a re-summed field theoretic $\epsilon$-expansion. Since we use the pruned-enriched Rosenbluth method (PERM) which allows very precise estimates of the partition sum itself, we also obtain improved estimates for all entropic critical exponents.Comment: 5 pages with 9 figures included; minor change

Development of an IEC neutron source for NDE

This paper concerns the development of a neutron so based on the inertial electrostatic confinement (IEC) of a low density fusion plasma in a gridded, spherically-focusing device. With the motivation of using such sources for nondestructive evaluation (NDE) applications, the focus of the development is on : Small size devices, sealed operation with D{sub 2} or D{sub 2}/T{sub 2} mixtures, Power-utilization and neutron-output optimization, and integration into an assay system. In this paper, we describe an experimental system that has been established for the development and testing of IEC neutron sources, and we present preliminary results of tests conducted for 25-cm and 15-cm diameter IEC devices

Finite size scaling in neural networks

We demonstrate that the fraction of pattern sets that can be stored in single- and hidden-layer perceptrons exhibits finite size scaling. This feature allows to estimate the critical storage capacity \alpha_c from simulations of relatively small systems. We illustrate this approach by determining \alpha_c, together with the finite size scaling exponent \nu, for storing Gaussian patterns in committee and parity machines with binary couplings and up to K=5 hidden units.Comment: 4 pages, RevTex, 5 figures, uses multicol.sty and psfig.st

Reconstruction of a first-order phase transition from computer simulations of individual phases and subphases

We present a new method for investigating first-order phase transitions using Monte Carlo simulations. It relies on the multiple-histogram method and uses solely histograms of individual phases. In addition, we extend the method to include histograms of subphases. The free energy difference between phases, necessary for attributing the correct statistical weights to the histograms, is determined by a detour in control parameter space via auxiliary systems with short relaxation times. We apply this method to a recently introduced model for structure formation in polypeptides for which other methods fail.Comment: 13 pages in preprint mode, REVTeX, 2 Figures available from the authors ([email protected], [email protected]