Related papers: Kinetically Constrained Ring-Polymer Molecular Dyn…
An exact real time quantum dynamics preaveraged over imaginary time path integral is formulated for general condensed phase equilibrium ensemble. This formulation results in the well-known centroid dynamics approach upon filtering of…
We propose a methodology for fully automated calculation of thermal rate coefficients of gas phase chemical reactions, which is based on combining the ring polymer molecular dynamics (RPMD) with the machine-learning interatomic potentials…
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…
A dynamic mode decomposition (DMD) based reduced-order model (ROM) is developed for tracking, detection, and prediction of kinetic plasma behavior. DMD is applied to the high-fidelity kinetic plasma model based on the electromagnetic…
Centroid molecular dynamics (CMD) incorporates nuclear quantum statistics into the calculation of vibrational spectra. However, when performed in Cartesian coordinates, CMD shows unphysical artifacts in certain vibrational bands, known as…
A kinetic approach for the evolution of ultracold neutral plasmas including interionic correlations and the treatment of ionization/excitation and recombination/deexcitation by rate equations is described in detail. To assess the…
For nearly the past 30 years, Centroid Molecular Dynamics (CMD) has proven to be a viable classical-like phase space formulation for the calculation of quantum dynamical properties. However, calculation of the centroid effective force…
Massively parallel computer architectures create new opportunities for the performance of long-timescale molecular dynamics (MD) simulations. Here, we introduce the path-accelerated molecular dynamics (PAMD) method that takes advantage of…
Mixed-quantum classical (MQC) methods for simulating the dynamics of molecules at metal surfaces have the potential to accurately and efficiently provide mechanistic insight into reactive processes. Here, we introduce simple two-dimensional…
The replica exchange molecular dynamics (REMD) approach is applied to four oligomeric peptide systems. At physiologically relevant temperature values REMD samples conformation space and aggregation transitions more efficiently than constant…
Interacting-Particle Reaction Dynamics (iPRD) simulates the spatiotemporal evolution of particles that experience interaction forces and can react with one another. The combination of interaction forces and reactions enable a wide range of…
This study employed an artificial intelligence-enhanced molecular simulation framework to enable efficient Path Integral Molecular Dynamics (PIMD) simulations. Owing to its modular architecture and high-throughput capabilities, the…
Mass-conserving reaction-diffusion (MCRD) systems are widely used to model phase separation and pattern formation in cell polarity, biomolecular condensates, and ecological systems. Numerical simulations and formal asymptotic analysis…
Mixed-quantum-classical molecular dynamics simulation implies an effective measurement on the electronic states owing to continuously tracking the atomic forces.Based on this insight, we propose a quantum trajectory mean-field approach for…
In this work, rate coefficients of four prototypical insertion reactions, X + H2 -- H + XH (X=C(1D), N(2D), O(1D), S(1D)) and associated isotope reactions are calculated based on ring polymer molecular dynamics (RPMD) with Cayley propagator…
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…
Developing efficient path integral (PI) methods for atomistic simulations of vibrational spectra in heterogeneous condensed phases and interfaces has long been a challenging task. Here, we present the h-CMD method, short for hybrid centroid…
Specialized motions such as jumping are often achieved on quadruped robots by solving a trajectory optimization problem once and executing the trajectory using a tracking controller. This approach is in parallel with Model Predictive…
An accurate treatment of the structures and dynamics that lead to enhanced chemical reactivity in enzymes requires explicit treatment of both electronic and nuclear quantum effects. The former can be captured in ab initio molecular dynamics…
Rare but critical events in complex systems, such as protein folding, chemical reactions, disease progression, and extreme weather or climate phenomena, are governed by complex, high-dimensional, stochastic dynamics. Identifying an optimal…