相关论文: Constant-temperature molecular-dynamics algorithms…
We show that for any liquid or solid with strong correlation between its $NVT$ virial and potential-energy equilibrium fluctuations, the temperature is a product of a function of excess entropy per particle and a function of density,…
In this paper we develop a direct simulation Monte Carlo (DSMC) method for simulating highly nonequilibrium dynamics of nearly degenerate ultra-cold gases. We show that our method can simulate the high-energy collision of two thermal clouds…
A recent article in J. Chem. Phys. argues that the two algorithms, the velocity-Verlet, and position-Verlet integrators, commonly used in Molecular Dynamics (MD) simulations, are different \cite{Ni2024}. But not only are the two algorithms…
We propose a neural operator framework, termed mixture density nonlinear manifold decoder (MD-NOMAD), for stochastic simulators. Our approach leverages an amalgamation of the pointwise operator learning neural architecture nonlinear…
The nested sampling algorithm has been shown to be a general method for calculating the pressure-temperature-composition phase diagrams of materials. While the previous implementation used single-particle Monte Carlo moves, these are…
Order(N) Tight-Binding Molecular Dynamics (TBMD) simulations are performed to investigate the thermal stability of (10,10) metallic Single-Walled Carbon Nanotubes (SWCNT). Periodic boundary conditions (PBC) are applied in axial direction.…
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…
A method for integrating the chemical equations associated with nuclear combustion at high temperature is presented and extensively checked. Following the idea of E. M\"uller, the feedback between nuclear rates and temperature was taken…
The synchronized molecular dynamics simulation via macroscopic heat and momentum transfer is proposed for the non-isothermal flow behaviors of complex fluids. In this method, the molecular dynamics simulations are assigned to small fluid…
Developing efficient and accurate algorithms for chemistry integration is a challenging task due to its strong stiffness and high dimensionality. The current work presents a deep learning-based numerical method called DeepCombustion0.0 to…
Simulating the dynamics of ions near polarizable nanoparticles (NPs) using coarse-grained models is extremely challenging due to the need to solve the Poisson equation at every simulation timestep. Recently, a molecular dynamics (MD) method…
In this paper, a high order implicit Method of Line Transpose (MOL$^T$ ) method based on a weighted essentially non-oscillatory (WENO) methodology is developed for one-dimensional linear transport equations and further applied to the…
We study the tensor-optimized antisymmetrized molecular dynamics (TOAMD) as a successive variational method in many-body systems with strong interaction for nuclei. In TOAMD, the correlation functions for the tensor force and the…
In this paper, we generalize the idea in our previous work for the Vlasov-Amp\`{e}re (VA) system \cite{cheng_va} and develop energy-conserving discontinuous Galerkin (DG) methods for the Vlasov-Maxwell (VM) system. The VM system is a…
In this paper we present a new variable time step criterion for the velocity-Verlet algorithm allowing to correctly simulate the dynamics of charged particles exchanging energy via Coulomb collisions while minimising simulation time. We…
Classical Molecular Dynamics (MD) simulations are employed as a tool to investigate structural properties of ice crystals under several temperature and pressure conditions. All ice crystal phases are analyzed by means of a computational…
We investigate the ergodicity and "hot solvent/cold solute" problems in molecular dynamics simulations. While the kinetic moments and the stimulated Nos\'e--Hoover methods improve the ergodicity of a harmonic-oscillator system, both methods…
The authors present a new molecular dynamics algorithm for sampling the isothermal-isobaric ensemble. In this approach the velocities of all particles and volume degrees of freedom are rescaled by a properly chosen random factor. The…
For Hamiltonian systems, simulation algorithms that exactly conserve numerical energy or pseudo-energy have seen extensive investigation. Most available methods either require the iterative solution of nonlinear algebraic equations at each…
The increasing number of protein-based metamaterials demands reliable and efficient theoretical and computational methods to study the physicochemical properties they may display. In this regard, we develop a simulation strategy based on…