Related papers: Fast and accurate committor estimation for kinetic…
Milestoning is an accurate and efficient method for rare event kinetics calculations by constructing a continuous-time kinetic network connecting the reactant and product states. However, even with adequate sampling, its accuracy can also…
We report the quantum computing of reacting flows by simulating the Hamiltonian dynamics. The scalar transport equation for reacting flows is transformed into a Hamiltonian system, mapping the dissipative and non-Hermitian problem in…
A highly efficient formulation of moment equations for stochastic reaction networks is introduced. It is based on a set of binomial moments that capture the combinatorics of the reaction processes. The resulting set of equations can be…
We propose a novel approach for computing committor functions, which describe transitions of a stochastic process between metastable states. The committor function satisfies a backward Kolmogorov equation, and in typical high-dimensional…
A computer simulation has to be fast to be helpful, if it is employed to study the behavior of a multicomponent dynamic system. This paper discusses modeling concepts and algorithmic techniques useful for creating such fast simulations.…
Recent years have seen unprecedented advance in the design and control of quantum computers. Nonetheless, their applicability is still restricted and access remains expensive. Therefore, a substantial amount of quantum algorithms research…
This article proposes a new way to construct computationally efficient `wrappers' around fine scale, microscopic, detailed descriptions of dynamical systems, such as molecular dynamics, to make predictions at the macroscale `continuum'…
Path integral implementation of the quantum instanton approximation currently belongs among the most accurate methods for computing quantum rate constants and kinetic isotope effects, but its use has been limited due to the rather high…
This paper proposes several explicit and implicit multistep frequency response optimized integrators considering first or second order derivative. A prediction-based method aiming at accelerating a novel power system transient simulation…
A version of the time-parallel algorithm parareal is analyzed and applied to stochastic models in chemical kinetics. A fast predictor at the macroscopic scale (evaluated in serial) is available in the form of the usual reaction rate…
The problem of studying rare events is central to many areas of computer simulations. In a recent paper [Kang, P., et al., Nat. Comput. Sci. 4, 451-460, 2024], we have shown that a powerful way of solving this problem passes through the…
Determining the kinetic bottlenecks that make transitions between metastable states difficult is key to understanding important physical problems like crystallization, chemical reactions, or protein folding. In all these phenomena, the…
We propose a computationally efficient method to solve the dynamics of operators of bosonic quantum systems coupled to their environments. The method maps the operator under interest to a set of complex-valued functions, and its adjoint…
We report a novel hybrid method of simultaneous atomistic simulation of solids in critical regions (contacts surfaces, cracks areas, etc.), along with continuum modeling of other parts. The continuum is treated in terms of quasi-atoms of…
Computational chemistry allows researchers to experiment in sillico: by running a computer simulations of a biological or chemical processes of interest. Molecular dynamics with molecular mechanics model of interactions simulates N-body…
We analyze several optimal transportation problems between de-terminantal point processes. We show how to estimate some of the distances between distributions of DPP they induce. We then apply these results to evaluate the accuracy of a new…
We report a novel approach for the efficient computation of solutions of a broad class of large-scale systems of non-linear ordinary differential equations, describing aggregation kinetics. The method is based on a new take on the…
Consider scene understanding problems such as predicting where a person is probably reaching, or inferring the pose of 3D objects from depth images, or inferring the probable street crossings of pedestrians at a busy intersection. This…
The ability to predict accurate thermodynamic and kinetic properties in biomolecular systems is of both scientific and practical utility. While both remain very difficult, predictions of kinetics are particularly difficult because rates, in…
Molecular dynamics simulates the~movements of atoms. Due to its high cost, many methods have been developed to "push the~simulation forward". One of them, metadynamics, can hasten the~molecular dynamics with the~help of variables describing…