Related papers: Accelerating Molecular Dynamics Simulations using …
It was recently demonstrated that a simple Monte Carlo (MC) algorithm involving the swap of particle pairs dramatically accelerates the equilibrium sampling of simulated supercooled liquids. We propose two numerical schemes integrating the…
With the rapid advancement of computational techniques, Molecular Dynamics (MD) simulations have emerged as powerful tools in biomedical research, enabling in-depth investigations of biological systems at the atomic level. Among the diverse…
Characterizing conformational transitions in physical systems remains a fundamental challenge, as traditional sampling methods struggle with the high-dimensional nature of molecular systems and high-energy barriers between stable states.…
Accurately predicting protein-ligand binding free energies (BFEs) remains a central challenge in drug discovery, particularly because the most reliable methods, such as free energy perturbation (FEP), are computationally intensive and…
Molecular dynamics (MD)-based path sampling algorithms are a very important class of methods used to study the energetics and kinetics of rare (bio)molecular events. They sample the highly informative but highly unlikely reactive…
Speculative decoding (SD) accelerates large language model (LLM) reasoning by using a small draft model to generate candidate tokens, which the target LLM either accepts directly or regenerates upon rejection. However, excessive alignment…
We present a fast and spectrally accurate method for efficient computation of the three dimensional Coulomb potential with periodicity in one direction. The algorithm is FFT-based and uses the so-called Ewald decomposition, which is…
We present a data-driven reduced-order modeling of the space-charge dynamics for electromagnetic particle-in-cell (EMPIC) plasma simulations based on dynamic mode decomposition (DMD). The dynamics of the charged particles in kinetic plasma…
In the first part of a series of two papers, we present in considerable detail a collision-driven molecular dynamics algorithm for a system of nonspherical particles, within a parallelepiped simulation domain, under both periodic or…
We present a highly efficient molecular dynamics scheme for calculating the concentration profile of dopants implanted in group-IV alloy, and III-V zinc blende structure materials. Our program incorporates methods for reducing computational…
The Ewald summation technique is generalised to power-law 1/|r|^k potentials in three-, two- and one-dimensional geometries with explicit formulae for all the components of the sums. The cases of short-range, long-range and "marginal"…
The extended quantum molecular dynamics (EQMD) model is one of the few quantum molecular dynamics (QMD)-like transport approaches that can be used to study the effective clustering structure as well as heavily deformed nuclei in both ground…
Coordinating the design of sampling and sparse-dense matrix multiplication (SpMM) is crucial for accelerating graph neural networks (GNNs). However, due to irrational sampling strategies, existing methods face a trade-off between accuracy…
Predicting the binding affinity between small molecules and target macromolecules while combining both speed and accuracy, is a cornerstone of modern computational drug discovery which is critical for accelerating therapeutic development.…
An efficient parallelization approach to simulate optical properties of ensembles of quantum emitters in realistic electromagnetic environments is considered. It relies on balancing computing load of utilized processors and is built into…
This paper explores the integration of symmetries into the Koopman-operator framework for the analysis and efficient learning of equivariant dynamical systems using a group-convolutional approach. Approximating the Koopman operator by…
The Energetic Particle Radiation Environment Model (EPREM) solves the focused transport equation (FTE) on a Lagrangian grid in a frame co-moving with the solar wind plasma and simulates the acceleration and transport of solar energetic…
We design a quantum molecular dynamics method for strongly correlated electron metals. The strong electronic correlation effects are treated within a real-space version of the Gutzwiller variational approximation (GA), which is suitable for…
We propose a new route to accelerate molecular dynamics through the use of velocity jump processes allowing for an adaptive time-step specific to each atom-atom pair (2-body) interactions. We start by introducing the formalism of the new…
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…