相关论文: Secondary Structures in Long Compact Polymers
The conformations of topologically constrained double-folded ring polymers can be described as wrappings of randomly branched primitive trees. We extend previous work on the tree statistics under different (solvent) conditions to explore…
We consider Monte Carlo algorithms for the simulation of charged lattice gases with purely local dynamics. We study the mobility of particles as a function of temperature and show that the poor mobility of particles at low temperatures is…
We argue that the mean crossing number of a random polymer configuration is simply a measure of opacity, without being closely related to entanglement as claimed by several authors. We present an easy way of estimating its asymptotic…
Protein aggregation is of great importance in biology, e.g., in amyloid fibrillation. The aggregation processes that occur at the cellular scale must be highly stochastic in nature because of the statistical number fluctuations that arise…
Based on large-scale Monte Carlo simulations on lattice the energy probability distribution functions are investigated for a large set of primary sequences in distinct models of copolymers at low temperatures below transitions to compacted…
We introduce a `virtual-move' Monte Carlo (VMMC) algorithm for systems of pairwise-interacting particles. This algorithm facilitates the simulation of particles possessing attractions of short range and arbitrary strength and geometry, an…
The statistical mechanics of a long knotted collapsed polymer is determined by a free-energy with a knot-dependent subleading term, which is linked to the length of the shortest polymer that can hold such knot. The only other parameter…
We perform equilibrium computer simulations of a two-dimensional pinned flexible polymer exposed to a quenched disorder potential consisting of hard disks. We are especially interested in the high-density regime of the disorder, where…
One emerging approach for the fabrication of complex architectures on the nanoscale is to utilize particles customized to intrinsically self-assemble into a desired structure. Inverse methods of statistical mechanics have proven…
We perform extensive Monte Carlo simulations of a lattice model and the Go potential to investigate the existence of folding pathways at the level of contact cluster formation for two native structures with markedly different geometries.…
We propose three novel gerrymandering algorithms which incorporate the spatial distribution of voters with the aim of constructing gerrymandered, equal-population, connected districts. Moreover, we develop lattice models of voter…
Many disordered crystalline materials show chemical short range order and relaxation of neighboring atoms. Local structural information can be obtained by analyzing the atomic pair distribution function (PDF). The viability of reverse Monte…
We study the dynamics of a single chain polymer confined to a two dimensional cell. We introduce a kinetically constrained lattice gas model that preserves the connectivity of the chain, and we use this kinetically constrained model to…
While recent work towards the development of tight-binding and ab-initio algorithms has focused on molecular dynamics, Monte Carlo methods can often lead to better results with relatively little effort. We present here a multi-step Monte…
A contact map is a simple representation of the structure of proteins and other chain-like macromolecules. This representation is quite amenable to numerical studies of folding. We show that the number of contact maps corresponding to the…
A model for a monolayer of two types of particles spontaneously forming ordered patterns is studied by a mesoscopic theory and by MC simulations. We assume hard-cores of the same size for both components, short-range attraction long-range…
Through extensive Monte Carlo simulations, we systematically study the effect of chain stiffness on the packing ability of linear polymers composed of hard spheres in extremely confined monolayers, corresponding effectively to 2D films.…
Mining frequent subgraphs is an area of research where we have a given set of graphs (each graph can be seen as a transaction), and we search for (connected) subgraphs contained in many of these graphs. In this work we will discuss…
Powdered materials of sizes ranging from nanometers to microns are widely used in materials science and are carefully selected to enhance the performance of a matrix. Fillers have been used in order to improve, among the others, mechanical,…
We study the influence of structural obstacles in a disordered environment on the size and shape characteristics of long flexible polymer macromolecules. We use the model of self-avoiding random walks on diluted regular lattices at the…