Related papers: Accelerating Molecular Dynamics Simulations using …
Molecular dynamics (MD) simulations have transformed our understanding of the nanoscale, driving breakthroughs in materials science, computational chemistry, and several other fields, including biophysics and drug design. Even on exascale…
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…
In this work, the development and implementation of the effective stochastic potential (ESP) method is presented to perform efficient conformational sampling of molecules. The overarching goal of this work is to alleviate the computational…
The limits of molecular dynamics (MD) simulations of macromolecules are steadily pushed forward by the relentless developments of computer architectures and algorithms. This explosion in the number and extent (in size and time) of MD…
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…
We present a rigorous Ewald summation formula to evaluate the electrostatic interactions in two-dimensionally periodic planar interfaces of three-dimensional systems. By rewriting the Fourier part of the summation formula of the original…
High resolution molecular dynamics simulations with full Coulomb interactions of electrons are used to investigate field emission from a prolate spheroidal tip. The space charge limited current is several times lower than the current…
We derive a Ewald decomposition for the Stokeslet in planar periodicity and a novel PME-type O(N log N) method for the fast evaluation of the resulting sums. The decomposition is the natural 2P counterpart to the classical 3P decomposition…
To further develop accurate and large-scale simulations of electrochemical interfaces, we propose a unified explicit electric potential framework to simultaneously predict atomic forces and electron density distributions. The framework…
Polymer electrolytes are promising candidates for the next generation lithium-ion battery technology. Large scale screening of polymer electrolytes is hindered by the significant cost of molecular dynamics (MD) simulation in amorphous…
The computational bottleneck of molecular dynamics is the pairwise additive long-range interactions between particles. The random batch Ewald (RBE) method provides a highly efficient and superscalable solver for long-range interactions, but…
Quantum computation offers significant potential for accelerating the simulation of molecules and materials through algorithms such as quantum phase estimation (QPE). However, the expected speedup in ground-state energy estimation depends…
Behavior-cloning based visuomotor policies enable precise manipulation but often inherit the slow, cautious tempo of human demonstrations, limiting practical deployment. However, prior studies on acceleration methods mainly rely on…
We study the influence of truncating the electrostatic interactions in a fully hydrated pure dipalmitoylphosphatidylcholine (DPPC) bilayer through 20 ns molecular dynamics simulations. The computations in which the electrostatic…
We present an optimized implementation of the recently proposed symmetric gradient domain machine learning (sGDML) model. The sGDML model is able to faithfully reproduce global potential energy surfaces (PES) for molecules with a few dozen…
Large language models (LLMs) deliver impressive generation quality, but incur very high inference cost because each output token is generated auto-regressively through all model layers. Early-exit based self-speculative decoding (EESD) has…
Simulating charged many-body systems has been a computational demanding task due to the long-range nature of electrostatic interaction. For the multi-scale model of electrolytes which combines the strengths of atomistic/continuum…
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…
High-order accurate summation-by-parts (SBP) finite difference (FD) methods constitute efficient numerical methods for simulating large-scale hyperbolic wave propagation problems. Traditional SBP FD operators that approximate first-order…
In a previous paper a method was developed to subtract the interactions due to periodically replicated charges (or other long-range entities) in one spatial dimension. The method constitutes a generalized "electrostatic layer correction"…