相关论文: Secondary Structures in Long Compact Polymers

Sequential Monte Carlo methods are typically not straightforward to implement on parallel architectures. This is because standard resampling schemes involve communication between all particles. The $\alpha$-sequential Monte Carlo method was…

In simple models side chains are often represented implicitly (e.g., by spin-states) or simplified as one atom. We study side chain effects using square lattice and tetrahedral lattice models, with explicitly side chains of two atoms. We…

We study classical hard-core dimer models on the square lattice with links extending beyond nearest-neighbors. Numerically, using a directed-loop Monte Carlo algorithm, we find that, in the presence of longer dimers preserving the bipartite…

We simulate structural phase behavior of polymer-grafted colloidal particles by molecular Monte Carlo technique. Interparticle potential, which has a finite repulsive square-step outside a rigid core of the colloid, was previously confirmed…

Motivated by the problem of domain formation in chromosomes, we studied a co--polymer model where only a subset of the monomers feel attractive interactions. These monomers are displaced randomly from a regularly-spaced pattern, thus…

In the context of Monte Carlo sampling for lattice models, the complexity of the energy landscape often leads to Markov chains being trapped in local optima, thereby increasing the correlation between samples and reducing sampling…

Space filling designs are central to studying complex systems in various areas of science. They are used for obtaining an overall understanding of the behaviour of the response over the input space, model construction and uncertainty…

A polymer folding model on the square lattice is constructed with attractive contact interactions of strength 1/c^2, 0<c<1. The corresponding model on a dynamical random lattice, with freely fluctuating co-ordination number at each vertex,…

This paper concerns the approximation of smooth, high-dimensional functions from limited samples using polynomials. This task lies at the heart of many applications in computational science and engineering - notably, some of those arising…

Granular material is showing very often in geotechnical engineering, petroleum engineering, material science and physics. The packings of the granular material play a very important role in their mechanical behaviors, such as stress-strain…

Langevin algorithms are popular Markov chain Monte Carlo (MCMC) methods for large-scale sampling problems that often arise in data science. We propose Monte Carlo algorithms based on the discretizations of $P$-th order Langevin dynamics for…

This is a brief survey of certain constants associated with random lattice models, including self-avoiding walks, polyominoes, the Lenz-Ising model, monomers and dimers, ice models, hard squares and hexagons, and percolation models.

We present a lattice Monte Carlo algorithm based on the one originally proposed by Maggs and Rossetto for simulating electrostatic interactions in inhomogeneous dielectric media. The original algorithm is known to produce attractive…

Markov chain Monte Carlo algorithms are invaluable tools for exploring stationary properties of physical systems, especially in situations where direct sampling is unfeasible. Common implementations of Monte Carlo algorithms employ…

Constraints can be interpreted in a broad sense as any kind of explicit restriction over the parameters. While some constraints are defined directly on the parameter space, when they are instead defined by known behaviour on the model,…

We show how to obtain a fast component-by-component construction algorithm for higher order polynomial lattice rules. Such rules are useful for multivariate quadrature of high-dimensional smooth functions over the unit cube as they achieve…

The scaling behaviour of randomly branched polymers in a good solvent is studied in two to nine dimensions, using as microscopic models lattice animals and lattice trees on simple hypercubic lattices. As a stochastic sampling method we use…

Topologically constrained genome-like polymers often double-fold into tree-like configurations. Here we calculate the exact number of tightly double-folded configurations available to a ring polymer in ideal conditions. For this purpose, we…

A polymer chain tethered to a surface may be compact or extended, adsorbed or desorbed, depending on interactions with the surface and the surrounding solvent. This leads to a rich phase diagram with a variety of transitions. To investigate…

Many soft-matter and biophysical systems are composed of monomers which reversibly assemble into rod-like aggregates. The aggregates can then order into liquid-crystal phases if the density is high enough, and liquid-crystal ordering…