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We introduce an algorithm based on Generalized Dual Method (GDM) to efficiently study the dynamics of a particle in quasiperiodic environments without the need to use periodic approximations or to save the information of the vertices that…
Quantum mechanical control of the position of a particle by using a trapping potential well is an important problem for the manipulation of a quantum particle. We study the probability of successful conveyance of a particle trapping in a…
According to the topological design theory and method of parallel mechanism (PM) based on position and orientation characteristic (POC) equations, this paper design a novel 3-translation (3T) PM that has three advantages, i.e., 1) it…
A recently proposed method for computer simulations in the isothermal-isobaric (NPT) ensemble, based on Langevin-type equations of motion for the particle coordinates and the ``piston'' degree of freedom, is re-derived by straightforward…
A recent proposal to connect the loop quantization with the spin foam model for cosmology via the path integral is hereby adapted to the case of mechanical systems within the framework of the so called polymer quantum mechanics. The…
We have developed efficient numerical algorithms for solving 3D steady-state Poisson-Nernst-Planck (PNP) equations with excess chemical potentials described by the classical density functional theory (cDFT). The coupled PNP equations are…
The embedded atom method (EAM) is one of the most widely used many-body, short-range potentials in molecular dynamics simulations, particularly for metallic systems. To enhance the efficiency of calculating these short-range interactions,…
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…
Most of the theoretical models describing the translocation of a polymer chain through a nanopore use the hypothesis that the polymer is always relaxed during the complete process. In other words, models generally assume that the…
The computer simulation of many molecular processes is complicated by long time scales caused by rare transitions between long-lived states. Here, we propose a new approach to simulate such rare events, which combines transition path…
We explore the possibility of modifying the multiplicity of the basic cluster in the entropy functional used in the cluster variation method so that truncation errors owing to finite size of the basic cluster may be corrected. The numerical…
The ability to understand spatial-temporal patterns for crowds of people is crucial for achieving long-term autonomy of mobile robots deployed in human environments. However, traditional historical data-driven memory models are inadequate…
Popular methods for identifying transition paths between energy minima, such as the nudged elastic band and string methods, typically do not incorporate potential energy curvature information, leading to slow relaxation to the minimum…
A transition of quantum walk induced by classical randomness changes the probability distribution of the walker from a two-peak structure to a single-peak one when the random parameter exceeds a critical value. We first establish the…
A general, variational approach to derive low-order reduced systems is presented. The approach is based on the concept of optimal parameterizing manifold (OPM) that substitutes the more classical notions of invariant or slow manifold when…
We introduce a computational method to discover polymorphs in molecular crystals at finite temperature. The method is based on reproducing the crystallization process starting from the liquid and letting the system discover the relevant…
The nematic ordering in semiflexible polymers with contour length $L$ exceeding their persistence length $\ell_p$ is described by a confinement of the polymers in a cylinder of radius $r_{eff}$ much larger than the radius $r_\rho$, expected…
We present a quantum Monte-Carlo simulation for a pumped atom in a strong coupling cavity with dissipation, where two ordered spatial modes are formed for the atomic probability density, with the peaks distributed either only in the odd…
We have developed a multi-scale self-consistent method to study the charge conductivity of a porous system or a metallic matrix alloyed by randomly distributed nonmetallic grains and vacancies by incorporating Schr\"{o}dinger's equation and…
We discuss and analyze the virtual element method on general polygonal meshes for the time-dependent Poisson-Nernst-Planck equations, which are a nonlinear coupled system widely used in semiconductors and ion channels. The spatial…