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This article introduces a highly parallel algorithm for molecular dynamics simulations with short-range forces on single node multi- and many-core systems. The algorithm is designed to achieve high parallel speedups for strongly…
We have extended the Large-scale Atomic/Molecular Massively Parallel Simulator (LAMMPS) to support directional bonds and dynamic bonding. The framework supports stochastic formation of new bonds, breakage of existing bonds, and conversion…
The ever-increasing power of supercomputers coupled with highly scalable simulation codes have made molecular dynamics an indispensable tool in applications ranging from predictive modeling of materials to computational design and discovery…
The simulation of chemical reactions and mechanical properties including failure from atoms to the micrometer scale remains a longstanding challenge in chemistry and materials science. Bottlenecks include computational feasibility,…
In order to accelerate molecular dynamics simulations, it is very common to impose holonomic constraints on their hardest degrees of freedom. In this way, the time step used to integrate the equations of motion can be increased, thus…
Most current machine learning interatomic potentials (MLIPs) rely on short-range approximations, without explicit treatment of long-range electrostatics. To address this, we recently developed the Latent Ewald Summation (LES) method, which…
A number of problems arise when long-range forces, such as those governed by Bessel functions, are used in particle-particle simulations. If a simple cut-off for the interaction is used, the system may find an equilibrium configuration at…
Adaptive lattice Boltzmann methods (LBMs) are based on velocity discretizations that self-adjust to local macroscopic conditions such as velocity and temperature. While this feature improves the accuracy and the stability of LBMs for large…
We present a simple and robust technique to extract kinetic rate models and thermodynamic quantities from single molecule time traces. SMACKS (Single Molecule Analysis of Complex Kinetic Sequences) is a maximum likelihood approach that…
Polymerases are protein enzymes that move along nucleic acid chains and catalyze template-based polymerization reactions during gene transcription and replication. The polymerases also substantially improve transcription or replication…
In-context learning (ICL) effectively conditions large language models (LLMs) for molecular tasks, such as property prediction and molecule captioning, by embedding carefully selected demonstration examples into the input prompt. This…
Surface integral equation (SIE) methods are of great interest for the efficient electromagnetic modeling of various devices, from integrated circuits to antenna arrays. Existing acceleration algorithms for SIEs, such as the adaptive…
A parallel implementation of coupled spin-lattice dynamics in the LAMMPS molecular dynamics package is presented. The equations of motion for both spin only and coupled spin-lattice dynamics are first reviewed, including a detailed account…
This is the final paper in a series that introduces geodesic molecular dynamics at constant potential energy. This dynamics is entitled NVU dynamics in analogy to standard energy-conserving Newtonian NVE dynamics. In the first two papers…
A multi-scale framework was recently proposed for more realistic molecular dynamics simulations in continuum solvent models by coupling a molecular mechanics treatment of solute with a fluid mechanics treatment of solvent, where we…
In this paper, a new progressive mesh algorithm is introduced in order to perform fast physical simulations by the use of a lattice Boltzmann method (LBM) on a single-node multi-GPU architecture. This algorithm is able to mesh automatically…
Interatomic potentials (IPs) are reduced-order models for calculating the potential energy of a system of atoms given their positions in space and species. IPs treat atoms as classical particles without explicitly modeling electrons and…
First-principles particle-in-cell (PIC) simulation is a powerful tool for understanding plasma behavior, but this power often comes at great computational expense. Artificially reducing the ion/electron mass ratio is a time-honored practice…
We study the convergence and the stability of fictitious dynamical methods for electrons. First, we show that a particular damped second-order dynamics has a much faster rate of convergence to the ground-state than first-order steepest…
As compute power increases with time, more involved and larger simulations become possible. However, it gets increasingly difficult to efficiently use the provided computational resources. Especially in particle-based simulations with a…