Related papers: Path-accelerated molecular dynamics: Parallel-in-t…
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 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…
Large molecular dynamics simulations (millions of atoms, tens of microseconds, thousands of processors) hit the strong scalability wall: simulation on twice as many processors does not take half the time. Inspired by large N-body space…
Molecular dynamics (MD) simulation is essential for various scientific domains but computationally expensive. Learning-based force fields have made significant progress in accelerating ab-initio MD simulation but are not fast enough for…
Multiple time-scale algorithms exploit the natural separation of time-scales in chemical systems to greatly accelerate the efficiency of molecular dynamics simulations. Although the utility of these methods in systems where the interactions…
Despite its widespread use in materials science, conventional molecular dynamics (MD) simulations are severely constrained by timescale limitations. To address this shortcoming, we propose an empirical formulation of accelerated MD method,…
Molecular dynamics facilitates the simulation of a complex system to be analyzed at molecular and atomic levels. Simulations can last a long period of time, even months. Due to this cause the graphics processing units (GPUs) and multi-core…
An adpative integration technique for time advancement of particle motion in the context of coupled computational fluid dynamics (CFD) - discrete element method (DEM) simulations is presented in this work. CFD-DEM models provide an accurate…
We present the design of a new large scale orchestration layer for accelerators. Our system, Pathways, is explicitly designed to enable exploration of new systems and ML research ideas, while retaining state of the art performance for…
We introduce mapping-variable ring polymer molecular dynamics (MV-RPMD), a model dynamics for the direct simulation of multi-electron processes. An extension of the RPMD idea, this method is based on an exact, imaginary time path-integral…
Quantum effects due to the spatial delocalization of light atoms are treated in molecular simulation via the path integral technique. Among several methods, Path Integral (PI) Molecular Dynamics (MD) is nowadays a powerful tool to…
Understanding the complex behavior of molecular systems is fundamental to fields such as physics, materials science, and biology. Molecular dynamics (MD) simulations are crucial tools for studying atomic-level dynamics. This work focuses on…
In this talk I discuss the general question of the portability of Molecular Dynamics codes for diffusive systems on parallel computers of the APE family. The intrinsic single precision arithmetics of the today available APE platforms does…
We develop an efficient parallel multiscale method that bridges the atomistic and mesoscale regimes, from nanometer to micron and beyond, via concurrent coupling of atomistic simulation and mesoscopic dynamics. In particular, we combine an…
Optimization has been widely used to generate smooth trajectories for motion planning. However, existing trajectory optimization methods show weakness when dealing with large-scale long trajectories. Recent advances in parallel computing…
We present a molecular simulation method to simultaneously find multiple transition pathways, and their associated free-energy profiles. The scheme extends path-metadynamics (PMD) [Phys. Rev. Lett. 109, 020601 (2012)] with multiple paths…
Density functionals at the level of the Generalized Gradient Approximation (GGA) and a plane-wave basis set are widely used today to perform ab initio molecular dynamics (AIMD) simulations. Going up in the ladder of accuracy of density…
Efficient implementations of the classical molecular dynamics (MD) method for Lennard-Jones particle systems are considered. Not only general algorithms but also techniques that are efficient for some specific CPU architectures are also…
We discuss the computational bottlenecks in molecular dynamics (MD) and describe the challenges in parallelizing the computation intensive tasks. We present a hybrid algorithm using MPI (Message Passing Interface) with OpenMP threads for…
A fundamental objective of materials modeling is identifying atomic structures that align with experimental observables. Conventional approaches for disordered materials involve sampling from thermodynamic ensembles and hoping for an…