相关论文: Implementing Dimer Metadynamics using GROMACS

The tribology between surfaces can have a profound impact on the response of a mechanical system, such as how granular particles are driven to flow. In this work, we perform experiments that time-resolve the tangential and normal components…

Work presented in this paper describes a general algorithm and its finite element implementation for performing concurrent multiple sub-domain simulations in linear structural dynamics. Using this approach one can solve problems in which…

(Abbreviated) In this paper we report on the development of a multiscale method for simulating complex liquid-liquid systems such as water in contact with oil containing asphaltenes. We consider simulations where water drops covered with…

Several recently proposed semi--automatic and fully--automatic coarse--graining schemes for polymer simulations are discussed. All these techniques derive effective potentials for multi--atom units or super--atoms from atomistic…

The Multiparticle Collision Dynamics technique (MPC) for hydrodynamics simulations is generalized to binary fluid mixtures and multiphase flows, by coupling the particle-based fluid dynamics to a Ginzburg-Landau free-energy functional for…

Temperature is a fundamental regulator of chemical and biochemical kinetics, yet capturing nonlinear thermal effects directly from experimental data remains a major challenge due to limited throughput and model flexibility. Recent advances…

We present a GPU implementation of LAMMPS, a widely-used parallel molecular dynamics (MD) software package, and show 5x to 13x single node speedups versus the CPU-only version of LAMMPS. This new CUDA package for LAMMPS also enables…

A new method based on quasi-independent parallel simulations approach, replica-averaging, has been developed to study the influence of flow on mechanical force-mediated polymer processes such as denaturation and breaking of bonds. This…

Multiple time scale molecular dynamics enhances computational efficiency by updating slow motions less frequently than fast motions. However, in practice the largest outer time step possible is limited not by the physical forces but by…

A new gradient-based adaptive sampling method is proposed for design of experiments applications which balances space filling, local refinement, and error minimization objectives while reducing reliance on delicate tuning parameters. High…

We present a novel framework for assimilating planar PIV experimental data using a variational approach to enhance the predictions of the Spalart-Allmaras RANS turbulence model. Our method applies three-dimensional constraints to the…

Structural and thermodynamic consistency of coarse-graining models across multiple length scales is essential for the predictive role of multi-scale modeling and molecular dynamic simulations that use mesoscale descriptions. Our approach is…

Simulations of nano- to micro-meter scale fluidic systems under thermal gradients require consistent mesoscopic methods accounting for both hydrodynamic interactions and proper transport of energy. One such method is dissipative particle…

We present a new adaptive particle-based data assimilation scheme for cryospheric applications that leverages promising developments in importance sampling. The proposed approach seeks to combine some of the advantages of two widely used…

State-of-the-art AI deep potentials provide ab initio-quality results, but at a fraction of the computational cost of first-principles quantum mechanical calculations, such as density functional theory. In this work, we bring AI deep…

We review some recent coarse-graining and multi-scale methods, but also put forward some new ideas for addressing such issues. We find that, if one is guided by nonequilibrium statistical mechanics and thermodynamics, it is possible to…

Accurately modeling chemical reactions in molecular dynamics simulations requires detailed pre- and post-reaction templates, often created through labor-intensive manual workflows. This work introduces a Python-based algorithm that…

Numerical simulations of two-phase flow and fluid structure interaction problems are of great interest in many environmental problems and engineering applications. To capture the complex physical processes involved in these problems, a high…

This paper contains the latest installment of the authors' project on developing ensemble based data assimilation methodology for high dimensional fluid dynamics models. The algorithm presented here is a particle filter that combines model…

We show that simulations of polymer rheology at a fluctuating mesoscopic scale and at the macroscopic scale where flow instabilities occur can be achieved at the same time with dissipative particle dynamics (DPD) technique.} We model the…