Related papers: Parallel Algorithm for Calculation of the Exact Pa…
We discuss two topics that we have encountered in our lattice-Boltzmann simulations of complex fluids: the sizes of droplets in particle-stabilised emulsions and deformable particles in fluid flow. The common factor in these seemingly…
A novel family of dynamical Monte Carlo algorithms for lattice polymers is proposed. Our central idea is to simulate an extended ensemble in which the self-avoiding condition is systematically weakened. The degree of the self-overlap is…
Parallel algorithms for ab initio calculations of vibrations modes of solids are presented and implemented under PVM. Load balancing and communication problems are dealt with in order to increase parallelism efficiency. For accurate time…
In this work we propose a new algorithm for the computation of statistical equilibrium quantities on a cubic lattice when both an energy and a statistical temperature are involved. We demonstrate that the pivot algorithm used in situations…
The monomer-dimer model is fundamental in statistical mechanics. However, it is $#P$-complete in computation, even for two dimensional problems. A formulation in matrix permanent for the partition function of the monomer-dimer model is…
A parallel implementation of coupled spin-lattice dynamics in the LAMMPS molecular dynamics package is presented. The equations of motion for both spin only and coupled spin-lattice dynamics are first reviewed, including a detailed account…
We consider a refinement of the partition function of graph homomorphisms and present a quasi-polynomial algorithm to compute it in a certain domain. As a corollary, we obtain quasi-polynomial algorithms for computing partition functions…
High-throughput computational screening of polymers offers a powerful way to address the imbalance between the vast number of polymers synthesised for diverse applications and the relatively small subset that can be studied using atomistic…
It has been shown that the parallel Lattice Linear Predicate (LLP) algorithm solves many combinatorial optimization problems such as the shortest path problem, the stable marriage problem and the market clearing price problem. In this…
We give efficient quantum algorithms to estimate the partition function of (i) the six vertex model on a two-dimensional (2D) square lattice, (ii) the Ising model with magnetic fields on a planar graph, (iii) the Potts model on a quasi 2D…
We apply a recently developed adaptive algorithm that systematically improves the efficiency of parallel tempering or replica exchange methods in the numerical simulation of small proteins. Feedback iterations allow us to identify an…
The Cooperative Motion Algorithm is an efficient lattice method to simulate dense polymer systems and is often used with two different criteria to generate a Markov chain in the configuration space. While the first method is the…
The effect of different move sets on the folding kinetics of the Monte Carlo simulations is analysed based on the conformation-network and the temperature-dependent folding kinetics. A new scheme of implementing Metropolis algorithm is…
In this article we present a parallel algorithm for simulation of the heat conduction process inside the so-called pulse cryogenic cell. This simulation is important for designing the device for portion injection of working gases into…
We present an algorithm for the exhaustive enumeration of all monomer sequences and conformations of short lattice proteins as described by the hydrophobic-polar (HP) model. The algorithm is used for an exact identification of all designing…
A new algorithm for simulating compact U(1) lattice gauge theory in three dimensions is presented which is based on global changes in the configuration space. We show that this algorithm provides an effective way to extract partition…
The graphical realization of a given degree sequence and given partition adjacency matrix simultaneously is a relevant problem in data driven modeling of networks. Here we formulate common generalizations of this problem and the Exact…
The sheer sizes of modern datasets are forcing data-structure designers to consider seriously both parallel construction and compactness. To achieve those goals we need to design a parallel algorithm with good scalability and with low…
We show that predicting the HPP or FHP III lattice gas for finite time is equivalent to calculating the output of an arbitrary Boolean circuit, and is therefore P-complete: that is, it is just as hard as any other problem solvable by a…
A method is proposed for exactly calculating the partition function of a rectangular Ising lattice with the presence of a uniform external field. This approach is based on the method of the transfer matrix developed about seventy years ago…