相关论文: Velocity jump processes : an alternative to multi-…

Recent advances in random-walk particle-tracking have enabled direct simulation of mixing and reactions on particles by allowing the particles to interact with each other using a multi-point mass transfer scheme. The mass transfer scheme…

Molecular transitions -- such as protein folding, allostery, and membrane transport -- are central to biology yet remain notoriously difficult to simulate. Their intrinsic rarity pushes them beyond reach of standard molecular dynamics,…

Accelerated molecular dynamics (MD) simulations are implemented to model the sliding process of AFM experiments at speeds close to those found in experiment. In this study the hyperdynamics method, originally devised to extend MD time…

A new, very fast, implementation of the exact (Fock) exchange operator for electronic structure calculations within the plane-wave pseudopotential method is described in detail for both molecular and periodic systems, and carefully…

Infrequent Metadynamics is a popular method to obtain the rates of long timescale processes from accelerated simulations. The inference procedure is based on rescaling the first-passage times of Metadynamics trajectories using a…

Simulating the long-timescale dynamics of biomolecules is a central challenge in computational science. While enhanced sampling methods can accelerate these simulations, they rely on pre-defined collective variables that are often difficult…

The random batch Ewald (RBE) is an efficient and accurate method for molecular dynamics (MD) simulations of physical systems at the nano-/micro- scale. The method shows great potential to solve the computational bottleneck of long-range…

We have developed molecular dynamics codes for a short-range interaction potential that adopt both the flat-MPI and MPI/OpenMP hybrid parallelizations on the basis of a full domain decomposition strategy. Benchmark simulations involving up…

Event-driven molecular dynamics simulations are carried out on two rigid body systems which differ in the symmetry of their molecular mass distributions. First, simulations of methane in which the molecules interact via discontinuous…

This paper proposes several explicit and implicit multistep frequency response optimized integrators considering first or second order derivative. A prediction-based method aiming at accelerating a novel power system transient simulation…

We present a new adaptive resolution technique for efficient particle-based multiscale molecular dynamics (MD) simulations. The presented approach is tailor-made for molecular systems where atomistic resolution is required only in spatially…

All-atom, force field-based molecular dynamics simulations are essential tools in computational chemistry, enabling the prediction and analysis of biomolecular systems with atomic-level resolution. However, as system sizes and simulation…

With the goal to provide absolute lower bounds for the best possible running times that can be achieved by $(1+\lambda)$-type search heuristics on common benchmark problems, we recently suggested a dynamic programming approach that computes…

Conventional molecular dynamics (MD) simulations struggle when simulating particles with steeply varying interaction potentials, due to the need to use a very short time step. Here, we demonstrate that an event-driven Monte Carlo (EDMC)…

The ability to predict accurate thermodynamic and kinetic properties in biomolecular systems is of both scientific and practical utility. While both remain very difficult, predictions of kinetics are particularly difficult because rates, in…

Recent advances in both theory and methods have created opportunities to simulate biomolecular processes more efficiently using adaptive ensemble simulations. Ensemble-based simulations are used widely to compute a number of individual…

A GPU-accelerated version of the lattice Boltzmann method for efficient simulation of soft materials is introduced. Unlike standard approaches, this method reconstructs the distribution functions from available hydrodynamic variables…

Reactive molecular dynamics simulations are computationally demanding. Reaching spatial and temporal scales where interesting scientific phenomena can be observed requires efficient and scalable implementations on modern hardware. In this…

Stochastic kinetic models describe systems across biology, chemistry, and physics where discrete events and small populations render deterministic approximations inadequate. Parameter inference and inverse design in these systems require…

A four-way coupling scheme for the direct numerical simulation of particle-laden flows is developed and analyzed. It employs a novel adaptive multi-relaxation time lattice Boltzmann method to simulate the fluid phase efficiently. The…