Jul 2026· Journal of Chemical Physics· Vol 165 4· 0 citations· 28 references
Medicine
Abstract
The kinetic Monte Carlo (KMC) method is becoming increasingly popular in the research of heterogeneous catalysts, yielding fundamental understanding of, e.g., their activity, selectivity, and rate of poisoning. KMC simulations can provide a link between ab initio electronic structure calculations and experiments by simulating at larger scales than is feasible for other methods, such as molecular dynamics (MD). A common problem for many systems studied using KMC, however, is the timescale separation of events considered, often leading to considerable computational effort and time spent on modeling fast events that are quasi-equilibrated and, thus, "uninteresting" from a kinetics perspective. In an attempt to make these simulations more efficient, two broad classes of schemes have been developed: those separating the state-space into "superbasins" and treating the fast events in approximate ways, and those employing absorbing Markov chain theory. In this paper, we consider the master equation underpinning KMC simulations in cases where the slow and fast events can be clearly defined, allowing us to "lump" the states into superbasins and use a perturbation expansion to derive approximations of the full solution. We thus develop a framework that unifies these two classes of schemes and enables us to derive a hierarchy of approximations that transcend the quasi-equilibration approximation. The validity of these approximations is then examined by testing them on four model systems, two of them relevant to on-lattice reaction kinetics.
A common operator viewpoint is developed connecting generator-based partial differential equations, variational principles, Markov state models, dynamical Galerkin approximation, and neural networks with an emphasis on self-supervised methods that learn solutions of their defining dynamical equations rather than relyin...
Molecular dynamics (MD) simulations rely on accurate numerical integration of the equations of motion, where the choice of the timestep (Δt) critically affects stability and precision. Rather than aiming to recover an exact atomic trajectory, second-order integrators, such as those implemented in LAMMPS with the Nosé–H...
L. Selis, Mauricio P. Galvez-Legua, Jorge G. Butler-Blacker· Computation· 0 citations
A framework for constructing a continuous-time Markov chain (CTMC) from a static, Boltzmann-weighted ensemble is presented, enabling the generation of physically plausible kinetic trajectories without requiring extensive molecular dynamics simulation.
Krishna Praneet Mulukutla, Marimuthu Krishnan· Journal of Chemical Informat...· 0 citations
QuantaMind is presented, a machine learning force field framework that attains density functional theory–level accuracy, enabling fully reactive simulations of complex molecular systems, and establishes a paradigm for long-timescale, fully reactive molecular simulation.
Song Xia, De-Qiang Zhang, Xue-Dong Shang et al.· Science Advances· 0 citations
Water exhibits anomalous thermodynamic and structural behaviour as it approaches and crosses below its melting point. Modelling this behaviour computationally remains challenging: as temperature decreases, nuclear quantum effects (NQEs) become increasingly significant, sampling efficiency deteriorates, and the choice o...
Francisco Carrascoza, Konrad Gorzelanczyk, J. Błażewicz· Entropy· 0 citations
We present a direct simulation Monte Carlo (DSMC) method for the kinetic theory of ordered fluids recently introduced by the authors. The microscopic constituents of these fluids carry an order parameter belonging to a manifold. The method applies Strang splitting to couple a Monte Carlo treatment of the binary collisi...
J. A. Carrillo, P. E. Farrell, Andrea Medaglia et al.· 0 citations
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