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We employ two different atomistic methods to investigate solute-defect interactions in nanosized palladium-hydrogen (Pd-H) systems across multiple time scales. The first method, referred to as Diffusive Molecular Dynamics (DMD), focuses on…
A new approach is described to the evaluation of the S-matrix in three-dimensional atom-diatom reactive quantum scattering theory. The theory is developed based on natural collision coordinates where progress along the reaction coordinate…
Reactive and elastic cross-sections, and rate coefficients, have been calculated for the S(1D)+ D2 (v=0, j=0) reaction using a modified hyperspherical quantum reactive scattering method. The considered collision energy ranges from the…
The factors underlying the experimentally observed branching ratio (70:30) of the (1,3-cyclohexadiene) CHD$\rightarrow$HT (1,3,5-hexatriene) photochemical ring-opening reaction are investigated. The ring-opening reaction path is optimized…
It has been established that there is an inherent limit to the accuracy of the reaction-diffusion master equation. Specifically, there exists a fundamental lower bound on the mesh size, below which the accuracy deteriorates as the mesh is…
Molecular simulations of the forced unfolding and refolding of biomolecules or molecular complexes allow to gain important kinetic, structural and thermodynamic information about the folding process and the underlying energy landscape. In…
The transition states and dividing surfaces used to find rate constants for bimolecular reactions are shown to undergo qualitative changes, known as Morse bifurcations, and to exist for a large range of energies, not just immediately above…
We propose a model based on quantum molecular dynamics (QMD) incorporated with statistical decay model (SDM) to describe various nuclear reactions in an unified way. In this first part of the work, the basic ingredients of the model are…
A fourth-order exponential time differencing (ETD) Runge-Kutta scheme with dimensional splitting is developed to solve multidimensional non-linear systems of reaction-diffusion equations (RDE). By approximating the matrix exponential in the…
The results of accurate quantum reactive scattering calculations for the D + HD($v=4$, $j=0$) $\to$ D + HD($v'$, $j'$), D + HD($v=4$, $j=0$) $\to$ H + D$_2$($v'$, $j'$) and H + D$_2$($v=4$, $j=0$) $\to$ D + HD($v'$,$j'$) reactions are…
The $\Delta \text{NO}$ method for static correlation is combined with second-order M{\o}ller-Plesset perturbation theory (MP2) and coupled-cluster singles and doubles (CCSD) to account for dynamic correlation. The MP2 and CCSD expressions…
This study address the computational determination of catalytic reaction rates by moving beyond traditional Transition State Theory (TST), addressing its limitations in complex systems. The Hill relation framework, integrated with Adaptive…
Neural network-based molecular dynamics (NNMD) simulations incorporating long-range electrostatic interactions have significantly extended the applicability to heterogeneous and ionic systems, enabling effective modeling critical physical…
Probabilistic Manifold Decomposition (PMD)\cite{doi:10.1137/25M1738863}, developed in our earlier work, provides a nonlinear model reduction by embedding high-dimensional dynamics onto low-dimensional probabilistic manifolds. The PMD has…
This article concerns two methods for reducing large systems of chemical kinetics equations, namely, the method of intrinsic low-dimensional manifolds (ILDMs) due to Maas and Pope and an iterative method due to Fraser and further developed…
A second-order $L$-stable exponential time-differencing (ETD) method is developed by combining an ETD scheme with approximating the matrix exponentials by rational functions having real distinct poles (RDP), together with a dimensional…
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 describe a fast implementation of the quasi-centroid molecular dynamics (QCMD) method in which the quasi-centroid potential of mean force is approximated as a separable correction to the classical interaction potential. This correction…
Describing the kinetics of polymer reactions, such as the formation of loops and hairpins in nucleic acids or polypeptides, is complicated by the structural dynamics of their chains. Although both intramolecular reactions, such as…
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…