Diffusion constant for the repton model of gel electrophoresis

The repton model is a simple model of the "reptation" motion by which DNA diffuses through a gel during electrophoresis. In this paper we show that the model can be mapped onto a system consisting of two types of particles with hard-sphere interactions diffusing on a one-dimensional lattice. Using this mapping we formulate an efficient Monte Carlo algorithm for the model which allows us to simulate systems more than twice the size of those studied before. Our results confirm scaling hypotheses which have previously been put forward for the model. We also show how the particle version of the model can be used to construct a transfer matrix which allows us to solve exactly for the diffusion constant of small repton systems. We give results for systems of up to 20 reptons.Comment: 19 pages including five PostScript figures, typeset in LaTeX using RevTeX 3.

Error estimation in the histogram Monte Carlo method

We examine the sources of error in the histogram reweighting method for Monte Carlo data analysis. We demonstrate that, in addition to the standard statistical error which has been studied elsewhere, there are two other sources of error, one arising through correlations in the reweighted samples, and one arising from the finite range of energies sampled by a simulation of finite length. We demonstrate that while the former correction is usually negligible by comparison with statistical fluctuations, the latter may not be, and give criteria for judging the range of validity of histogram extrapolations based on the size of this latter correction.Comment: 7 pages including 3 postscript figures, typeset in LaTeX using the RevTeX macro packag

Large-scale structure of time evolving citation networks

In this paper we examine a number of methods for probing and understanding the large-scale structure of networks that evolve over time. We focus in particular on citation networks, networks of references between documents such as papers, patents, or court cases. We describe three different methods of analysis, one based on an expectation-maximization algorithm, one based on modularity optimization, and one based on eigenvector centrality. Using the network of citations between opinions of the United States Supreme Court as an example, we demonstrate how each of these methods can reveal significant structural divisions in the network, and how, ultimately, the combination of all three can help us develop a coherent overall picture of the network's shape.Comment: 10 pages, 6 figures; journal names for 4 references fixe

Response of strongly-interacting matter to magnetic field: some exact results

We derive some exact results concerning the response of strongly-interacting matter to external magnetic fields. Our results come from consideration of triangle anomalies in medium. First, we define an "axial magnetic susceptibility," then we examine its beahvior in two flavor QCD via response theory. In the chirally restored phase, this quantity is proportional to the fermion chemical potential, while in the phase of broken chiral symmetry it can be related, through triangle anomalies, to an in-medium amplitude for the neutral pion to decay to two photons. We confirm the latter result by calculation in a linear sigma model, where this amplitude is already known in the literature.Comment: 13 pages, no figures, To be submitted to Physical Review D, fixed an omitted referenc

Two-Dimensional Scaling Limits via Marked Nonsimple Loops

We postulate the existence of a natural Poissonian marking of the double (touching) points of SLE(6) and hence of the related continuum nonsimple loop process that describes macroscopic cluster boundaries in 2D critical percolation. We explain how these marked loops should yield continuum versions of near-critical percolation, dynamical percolation, minimal spanning trees and related plane filling curves, and invasion percolation. We show that this yields for some of the continuum objects a conformal covariance property that generalizes the conformal invariance of critical systems. It is an open problem to rigorously construct the continuum objects and to prove that they are indeed the scaling limits of the corresponding lattice objects.Comment: 25 pages, 5 figure