Related papers: Prediction of Peptide Conformation by the Multican…
For solving the discretized three-temperature energy linear systems, Xu et al. proposed a physical-variable based coarsening two-level iterative method (PCTL algorithm) in 2009 and verified its efficiency by numerical experiments in…
Automated identification of protein conformational states from simulation of an ensemble of structures is a hard problem because it requires teaching a computer to recognize shapes. We adapt the naive Bayes classifier from the machine…
We aim to investigate relationships between select processing parameters or inputs (composition, temperature, annealing time) and two structural parameters, specifically, the mean radius and volume fraction of the Fe$_3$Si nanocrystals. To…
Coarse-grained models are a core computational tool in theoretical chemistry and biophysics. A judicious choice of a coarse-grained model can yield physical insight by isolating the essential degrees of freedom that dictate the…
We study the 38-atom Lennard-Jones cluster with parallel tempering Monte Carlo methods in the microcanonical and molecular dynamics ensembles. A new Monte Carlo algorithm is presented that samples rigorously the molecular dynamics ensemble…
In this study, internal energy (U), electric field (E) and particle number (N) which specify the system quantities i.e. thermodynamical quantities for the proteins. In the frame of thermodynamical formalism, the relation between the heat…
It is generally believed that, in the thermodynamic limit, the microcanonical description as a function of energy coincides with the canonical description as a function of temperature. However, various examples of systems for which the…
A general discussion is made concerning the ways in which one can get signatures about a possible liquid-gas phase transition in nuclear matter. Microcanonical temperature, heat capacity and second order derivative of the entropy versus…
Equilibrium statistics of finite Hamiltonian systems is fundamentally described by the microcanonical ensemble (ME). Canonical, or grand-canonical partition functions are deduced from this by Laplace transform. Only in the thermodynamic…
We prove several theorems to give sufficient conditions for convergence of quantum annealing, which is a protocol to solve generic optimization problems by quantum dynamics. In particular the property of strong ergodicity is proved for the…
Monte Carlo simulation code has been developed and tested for studying the passage of charged particle beams and radiation through the crystalline matter at energies from tens of MeV up to hundreds of GeV. The developed Monte Carlo code…
Machine learning interatomic potentials (MLIPs) are routinely used to model diverse atomistic phenomena, yet parameterizing them to accurately capture solid-state phase transformations remains difficult. We present error metrics and…
A novel approach designed to directly estimate microcanonical quantities from energy histograms is proposed, which enables the immediate systematic identification and classification of phase transitions in physical systems of any size by…
Lithium is a typical quantum solid, characterized by cubic structures at ambient pressure. As the pressure increases, it forms more complex structures and undergoes a metal-to-semiconductor transformation, complicating theoretical and…
Equilibrium canonical distribution in statistical mechanics assumes weak system-bath coupling (SBC). In real physical situations this assumption can be invalid and equilibrium quantum statistics of the system may be non-canonical. By…
Multi-energy computed tomography (ME-CT) is an x-ray transmission imaging technique that uses the energy dependence of x-ray photon attenuation to determine the elemental composition of an object of interest. Mathematically, forward ME-CT…
The time sequences of the molecular dynamics simulation for the folding process of a protein is analyzed with the inherent structure landscape which focuses on configurational dynamics of the system. Time dependent energy and entropy for…
We demonstrate that substantial progress can be achieved in the study of the phase structure of 4-dimensional compact QED by a joint use of hybrid Monte Carlo and multicanonical algorithms, through an efficient parallel implementation. This…
This paper presents a canonical duality approach for solving a general topology optimization problem of nonlinear elastic structures. By using finite element method, this most challenging problem can be formulated as a mixed integer…
We propose an algorithm for molecular dynamics or Monte Carlo simulations that uses an interpolation procedure to estimate potential energy values from energies and gradients evaluated previously at points of a simplicial mesh. We chose an…