Related papers: Extending ring polymer molecular dynamics rate the…
We investigate the plasma enhancement of nuclear reactions in the intermediate coupling regime using orbital free molecular dynamics (OFMD) simulations. Mixtures of H-Cu and H-Ag serve as prototypes of simultaneous weak and strong couplings…
The reaction-diffusion master equation (RDME) is a lattice-based stochastic model for spatially resolved cellular processes. It is often interpreted as an approximation to spatially continuous reaction-diffusion models, which, in the limit…
We report the implementation of a multi-CPU and multi-GPU massively parallel platform dedicated to the explicit inclusion of nuclear quantum effects (NQEs) in the Tinker-HP molecular dynamics (MD) package. The platform, denoted Quantum-HP,…
Molecular dynamics (MD) simulations can model the interactions between macromolecules with high spatiotemporal resolution but at a high computational cost. By combining high-throughput MD with Markov state models (MSMs), it is now possible…
Morphogenesis is central to biology but remains largely unexplored in chemistry. Reaction-diffusion (RD) mechanisms are, however, essential to understand how shape emerges in the living world. While numerical methods confirm the incredible…
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…
With the path integral approach, the thermal average in a multi-electronic-state quantum systems can be approximated by the ring polymer representation on an extended configuration space, where the additional degrees of freedom are…
Efficient computational methods that are capable of supporting experimental measures obtained at constant values of pH and redox potential are important tools as they serve to, among other things, provide additional atomic level information…
Path integral molecular dynamics (PIMD), which maps a quantum particle onto a fictitious classical system of ring polymers and propagates the "beads" of this extended classical system using molecular dynamics, is widely used to capture…
We present an accelerated ``on-the-fly'' coupled-cluster path-integral molecular dynamics (PIMD) method for finite-temperature simulations in which electron correlation and nuclear quantum effects are treated simultaneously. The approach is…
Accurately modeling chemical reactions at the atomistic level requires high-level electronic structure theory due to the presence of unpaired electrons and the need to properly describe bond breaking and making energetics. Commonly used…
Eyring theory provides a convenient approximation to the rate of a chemical reaction, as it uses only local information evaluated near extremal points of a given potential energy surface. However, in cases of pronounced anharmonicity and…
Response Surface Methodology (RSM) introduced in the paper (Box & Wilson, 1951) explores the relationships between explanatory and response variables in complex settings and provides a framework to identify correct settings for the…
We present here a first application of the Fermionic Molecular Dynamics (FMD) approach to low-energy nuclear reactions, namely the $^3$He($\alpha$,$\gamma$)$^7$Be radiative capture reaction. We divide the Hilbert space into an external…
Particle-based stochastic reaction-diffusion (PBSRD) models are a popular approach for capturing stochasticity in reaction and transport processes across biological systems. In some contexts, the overdamped approximation inherent in such…
We introduce a rigorous method to microscopically compute the observables which characterize the thermodynamics and kinetics of rare macromolecular transitions for which it is possible to identify a priori a slow reaction coordinate. In…
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…
We investigate the fast-reaction asymptotics for a one-dimensional reaction-diffusion (RD) system describing the penetration of the carbonation reaction in concrete. The technique of matched-asymptotics is used to show that the RD system…
Transition State Theory is a central cornerstone in reaction dynamics. Its key step is the identification of a dividing surface that is crossed only once by all reactive trajectories. This assumption is often badly violated, especially when…
Nuclear quantum effects (NQEs) are often central to a predictive understanding of chemical reactions and rates. While their incorporation in gas-phase reactions is well established, studies involving condensed matter often neglect or…