Related papers: Efficiency of the Incomplete Enumeration algorithm…
We propose new polymer models for Monte Carlo simulation and apply them to a polymer chain confined in a relatively thin box which has both curved and flat sides, and show that either an ideal or an excluded-volume chain spends more time in…
Monte Carlo computer simulations are used to study the segregation behaviour of two polymers under cylindrical confinement. Using a multiple-histogram method, the conformational free energy, F, of the polymers was measured as a function of…
Primitive path analyses of entanglements are performed over a wide range of chain lengths for both bead spring and atomistic polyethylene polymer melts. Estimators for the entanglement length N_e which operate on results for a single chain…
We present the first polynomial-time algorithm to exactly compute the number of labeled chordal graphs on $n$ vertices. Our algorithm solves a more general problem: given $n$ and $\omega$ as input, it computes the number of…
We report results of extensive Dynamical Monte Carlo investigations on self-assembled Equilibrium Polymers (EP) without loops in good solvent. (This is thought to provide a good model of giant surfactant micelles.) Using a novel algorithm…
Pre-calculated libraries of molecular fragment configurations have previously been used as a basis for both equilibrium sampling (via "library-based Monte Carlo") and for obtaining absolute free energies using a polymer-growth formalism.…
Monte Carlo simulations of coarse-grained polymers provide a useful tool to deepen the understanding of conformational and statistical properties of polymers both in physical as well as in biological systems. In this study we sample compact…
We consider flexible branched polymer, with quenched branch structure, and show that its conformational entropy as a function of its gyration radius $R$, at large $R$, obeys, in the scaling sense, $\Delta S \sim R^2/(a^2L)$, with $a$ bond…
Leverage scores, loosely speaking, reflect the importance of the rows and columns of a matrix. Ideally, given the leverage scores of a rank-$r$ matrix $M\in\mathbb{R}^{n\times n}$, that matrix can be reliably completed from just…
We present a detailed analysis of the error budget for the TreePM method for doing cosmological N-Body simulations. It is shown that the choice of filter for splitting the inverse square force into short and long range components suggested…
We present a method to generate realistic, three-dimensional networks of crosslinked semiflexible polymers. The free energy of these networks is obtained from the force-extension characteristics of the individual polymers and their…
We propose efficient algorithms for enumerating maximal common subsequences (MCSs) of two strings. Efficiency of the algorithms are estimated by the preprocessing-time, space, and delay-time complexities. One algorithm prepares a…
Uncertainty estimation in deep models is essential in many real-world applications and has benefited from developments over the last several years. Recent evidence suggests that existing solutions dependent on simple Gaussian formulations…
We give an algorithm that generates a uniformly random contingency table with specified marginals, i.e. a matrix with non-negative integer values and specified row and column sums. Such algorithms are useful in statistics and combinatorics.…
Effective sample size is a standard summary of Markov chain Monte Carlo output, but it is usually attached to scalar or Euclidean summaries chosen by the analyst. For manifold-valued samples this choice is not canonical: coordinate-wise…
Recent developments of microscopic mechanical experiments allow the manipulation of individual polymer molecules in two main ways: \textit{uniform} stretching by external forces and \textit{non-uniform} stretching by external fields. Many…
In Monte Carlo integration an accurate and reliable determination of the numerical intregration error is essential. We point out the need for an independent estimate of the error on this error, for which we present an unbiased estimator. In…
Given a source of iid samples of edges of an input graph $G$ with $n$ vertices and $m$ edges, how many samples does one need to compute a constant factor approximation to the maximum matching size in $G$? Moreover, is it possible to obtain…
Given a way to evaluate an unknown polynomial with integer coefficients, we present new algorithms to recover its nonzero coefficients and corresponding exponents. As an application, we adapt this interpolation algorithm to the problem of…
This paper studies the mixing time of certain adaptive Markov Chain Monte Carlo algorithms. Under some regularity conditions, we show that the convergence rate of Importance Resampling MCMC (IRMCMC) algorithm, measured in terms of the total…