Related papers: Automated transition state theory calculations for…
Computing reaction rates in biomolecular systems is a common goal of molecular dynamics simulations. The reactions considered often involve conformational changes in the molecule, either changes in the structure of a protein or the relative…
Molecule-text modeling, which aims to facilitate molecule-relevant tasks with a textual interface and textual knowledge, is an emerging research direction. Beyond single molecules, studying reaction-text modeling holds promise for helping…
Ring-polymer instanton theory has been developed to simulate the quantum dynamics of molecular systems at low temperatures. Chemical reaction rates can be obtained by locating the dominant tunneling pathway and analyzing fluctuations around…
Several different methods exist for efficient approximation of paths in multiscale stochastic chemical systems. Another approach is to use bursts of stochastic simulation to estimate the parameters of a stochastic differential equation…
The dynamics of molecules are governed by rare event transitions between long-lived (metastable) states. To explore these transitions efficiently, many enhanced sampling protocols have been introduced that involve using simulations with…
The use of machine learning algorithms is an attractive way to produce very fast detector simulations for scattering reactions that can otherwise be computationally expensive. Here we develop a factorised approach where we deal with each…
We develop a stochastic approximation-type algorithm to solve finite state/action, infinite-horizon, risk-aware Markov decision processes. Our algorithm has two loops. The inner loop computes the risk by solving a stochastic saddle-point…
Simulations with an adaptive time-dependent bias, such as metadynamics, enable an efficient exploration of the conformational space of a system. However, the dynamic information of the system is altered by the bias. With infrequent…
Stochastic reaction network models are widely utilized in biology and chemistry to describe the probabilistic dynamics of biochemical systems in general, and gene interaction networks in particular. Most often, statistical analysis and…
The concentration of radiation-induced point defects in general materials under irradiation is commonly described by the point defect kinetics equations based on rate theory. However, the parametric uncertainty in describing the rate…
We report a globally-optimal approach to robotic path planning under uncertainty, based on the theory of quantitative measures of formal languages. A significant generalization to the language-measure-theoretic path planning algorithm…
Many processes of scientific and technological interest are characterized by time scales that render their simulation impossible if one uses present day simulation capabilities. To overcome this challenge a variety of enhanced simulation…
This Feature Article presents an overview of the current status of Ring Polymer Molecular Dynamics (RPMD) rate theory. We first analyze the RPMD approach and its connection to quantum transition-state theory. We then focus on its practical…
The first step to realize automatic experimental data analysis for fusion plasma experiments is fitting noisy data of temperature and density spatial profiles, which are obtained routinely. However, it has been difficult to construct…
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…
Our knowledge about the "cold" Universe often relies on molecular spectra. A general property of such spectra is that the energy level populations are rarely at local thermodynamic equilibrium. Solving the radiative transfer thus requires…
We consider stochastic descriptions of chemical reaction networks in which there are both fast and slow reactions, and for which the time scales are widely separated. We develop a computational algorithm that produces the generator of the…
The nonlinear gyrokinetic equations describe plasma turbulence in laboratory and astrophysical plasmas. To solve these equations, massively parallel codes have been developed and run on present-day supercomputers. This paper describes…
Embedding tables are usually huge in click-through rate (CTR) prediction models. To train and deploy the CTR models efficiently and economically, it is necessary to compress their embedding tables at the training stage. To this end, we…
We present a family of algorithms for the fast determination of reaction paths and barriers in phase space and the computation of the corresponding rates. The method requires the reaction times be large compared to the microscopic time,…