Related papers: An empirical formulation of accelerated molecular …
One important problem in constructing the reduced dynamics of molecular systems is the accurate modeling of the non-Markovian behavior arising from the dynamics of unresolved variables. The main complication emerges from the lack of scale…
Molecular dynamics (MD) is a widely-used tool for simulating the molecular and materials properties. It is a common wisdom that molecular dynamics simulations should obey physical laws and, hence, lots of effort is put into ensuring that…
In drug discovery, molecular dynamics (MD) simulation for protein-ligand binding provides a powerful tool for predicting binding affinities, estimating transport properties, and exploring pocket sites. There has been a long history of…
Molecular Dynamics (MD) simulations are essential for understanding the atomic-level behavior of molecular systems, giving insights into their transitions and interactions. However, classical MD techniques are limited by the trade-off…
We present the molecular hyperdynamics algorithm and its implementation to the nonorthogonal tight-binding model NTBM and the corresponding software. Due to its multiscale structure, the proposed approach provides the long time scale…
The rapid evolution of molecular dynamics (MD) methods, including machine-learned dynamics, has outpaced the development of standardized tools for method validation. Objective comparison between simulation approaches is often hindered by…
Simulating large-scale protein dynamics using traditional all-atom molecular dynamics (MD) remains computationally prohibitive. We present a unified, universal framework for coarse-grained molecular dynamics (CG-MD) that achieves…
Unlike most static material properties widely studied in the machine learning literature, ionic transport properties are inherently dynamic, making their fast and accurate prediction from static atomic structures challenging. The current…
Event-driven molecular dynamics is a valuable tool in condensed and soft matter physics when particles can be modeled as hard objects or more generally if their interaction potential can be modeled in a stepwise fashion. Hard spheres model…
Molecular dynamics (MD) simulations are a central tool in science and engineering enabling the study of dynamical behavior and the link between microscopic structure and macroscopic function. Their high computational cost, however, has…
Understanding and predicting microstructure evolution is fundamental to materials science, as it governs the resulting properties and performance of materials. Traditional simulation methods, such as phase-field models, offer high-fidelity…
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…
Geometry optimization is an important part of both computational materials and surface science because it is the path to finding ground state atomic structures and reaction pathways. These properties are used in the estimation of…
Molecular dynamics simulations are an important tool for describing the evolution of a chemical system with time. However, these simulations are inherently held back either by the prohibitive cost of accurate electronic structure theory…
Molecular dynamics (MD) is a powerful technique for studying microscopic phenomena, but its computational cost has driven significant interest in the development of deep learning-based surrogate models. We introduce generative modeling of…
An issue for molecular dynamics simulations is that events of interest often involve timescales that are much longer than the simulation time step, which is set by the fastest timescales of the model. Because of this timescale separation,…
We introduce a new adaptive decomposition tool, which we refer to as Nonlinear Mode Decomposition (NMD). It decomposes a given signal into a set of physically meaningful oscillations for any waveform, simultaneously removing the noise. NMD…
We study the nucleation dynamics of a model solid state transformation and the criterion for microstructure selection using a molecular dynamics (MD) simulation. Our simulations show a range of microstructures depending on the depth of…
We propose a multiscale computational method for thin-layer flows of complex fluids, termed the synchronized molecular dynamics (SMD) method, which directly couples local molecular dynamics (MD) simulations with a macroscopic lubrication…
Direct simulation of biomolecular dynamics in thermal equilibrium is challenging due to the metastable nature of conformation dynamics and the computational cost of molecular dynamics. Biased or enhanced sampling methods may improve the…