Related papers: Adaptively Biased Molecular Dynamics for Free Ener…
The development of machine-learning (ML) potentials offers significant accuracy improvements compared to molecular mechanics (MM) because of the inclusion of quantum-mechanical effects in molecular interactions. However, ML simulations are…
The increasing number of protein-based metamaterials demands reliable and efficient theoretical and computational methods to study the physicochemical properties they may display. In this regard, we develop a simulation strategy based on…
It is now established that nuclear quantum motion plays an important role in determining water's hydrogen bonding, structure, and dynamics. Such effects are important to include in density functional theory (DFT) based molecular dynamics…
This study proposes a novel adaptive finite volume-particle method (AFVPM) for accurate and efficient free surface flow simulations. The proposed AFVPM synergistically combines the Eulerian finite volume method (FVM) on unstructured meshes…
In this study, we carried out equilibrium molecular dynamics (EMD) simulations of the liquid-liquid interface between two different Lennard-Jones components with varying miscibility, where we examined the relation between the interfacial…
We previously introduced a conformational sampling method, a multi-dimensional virtual-system coupled molecular dynamics (mD-VcMD), to enhance conformational sampling of a biomolecular system by computer simulations. Here, we present a new…
Droplet motion over a surface with wettability gradient has been simulated using molecular dynamics (MD) simulation to highlight the underlying physics. GROMACS and Visual Molecular Dynamics (VMD) were used for simulation and intermittent…
Replica exchange molecular dynamics (REMD) becomes more efficient as the frequency of swap between the temperatures is increased. Recently in [Plattner et al, J. Chem. Phys. 135, 134111 (2011)] a method was proposed to implement infinite…
In this work, we propose a multi-scale protocol for routine theoretical studies of chemical reaction mechanisms. The initial reaction paths of our investigated systems are sampled using the Nudged-Elastic Band (NEB) method driven by a cheap…
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…
We introduce a new numerical technique, namely triangular tessellation, to calculate the free energy associated with the adsorption of a colloidal particle at a flat interface. The theory and numerical scheme presented here are sufficiently…
Metadynamics is an enhanced sampling method of great popularity, based on the on-the-fly construction of a bias potential that is function of a selected number of collective variables. We propose here a change in perspective that shifts the…
Alchemical Grid Dock (AlGDock) is open-source software designed to compute the binding potential of mean force (BPMF) - the binding free energy between a flexible ligand and a rigid receptor - for a small organic ligand and a biological…
We propose a continuous-time scheme for large-scale optimization that introduces individual, adaptive momentum coefficients regulated by the kinetic energy of each model parameter. This approach automatically adjusts to local landscape…
We present a new formulation of ab initio molecular dynamics which exploits the efficiency of plane waves in adaptive curvilinear coordinates, and thus provides an accurate treatment of first-row elements. The method is used to perform a…
We demonstrate how a prior assumption of smoothness can be used to enhance the reconstruction of free energy profiles from multiple umbrella sampling simulations using the Bayesian Gaussian process regression approach. The method we derive…
Ultrafast, time-resolved spectroscopies enable the direct observation of non-equilibrium processes in condensed-phase systems and have revealed key insights into energy transport, hydrogen-bond dynamics, and vibrational coupling. While ab…
We demonstrate an adaptive sampling approach for computing the probability of a rare event for a set of three-dimensional airplane geometries under various flight conditions. We develop a fully automated method to generate parameterized…
Using conservation of energy - a fundamental property of closed classical and quantum mechanical systems - we develop an efficient gradient-domain machine learning (GDML) approach to construct accurate molecular force fields using a…
The interaction of condensed phase systems with external electric fields is crucial in myriad processes in nature and technology ranging from the field-directed motion of cells (galvanotaxis), to energy storage and conversion systems…