Research
Research
Research
Research
46+ open-access research outputs.
We present a computational platform for modeling chemical reactions in complex molecular environments, focused on ligand-protein binding in drug discovery. The platform implements our new quantum-in-q…
Chemical systems are traditionally described by lists of species, reactions, and externally imposed kinetic laws, a framework that lacks an intrinsic algebraic structure governing how transformations …
SpectraMatcher is a cross-platform desktop application for interactive comparison of experimental and computed vibronic spectra, designed to assist in the recognition and assignment of spectral patter…
Previous studies have primarily focused on the nonequilibrium thermodynamics of chemical reaction networks (CRNs) occurring in closed systems. In contrast, CRNs in open systems exhibit much richer non…
The application of the standard quasi-steady-state approximation to the Michaelis--Menten reaction mechanism is a textbook example of biochemical model reduction, derived using singular perturbation t…
Fluctuations-driven complex oscillations are experimentally observed in cellular systems such as hepatocytes, cardiac cells, neuronal cells, etc. These systems are generally operating in regimes far f…
Metal-organic skeleton materials have been widely used in catalysis with their porous structure and adsorption properties. Precious metal nanoparticles have good catalytic properties. If the noble met…
The ability to mimic protein-based oxidase with multi-functional inorganic nanozymes would greatly advance biomedical and clinical practices. Praseodymia (PrOx) nanorods (NRs) and nanoparticles (NPs) …
Easy and effective usage of computational resources is crucial for scientific calculations. Following our recent work of machine-learning (ML) assisted scheduling optimization [Ref: J. Comput. Chem. 2…
Partial equilibrium approximation (PEA) and quasi-steady-state approximation (QSSA) are two classical methods for reducing complex macroscopic chemical reactions into simple computable ones. Previous …
The development of modern civil industry, energy and information technology is inseparable from the rapid explorations of new materials, which are hampered by months to years of painstaking attempts, …
Investigating a reactive chemical system with automated reaction network exploration algorithms provides a more detailed picture of its chemical mechanism than what would be accessible by manual inves…
The paper presents the algorithm of a code written for computing the cross section for a charge transfer process involving a neutral molecule and a monatomic ion. The entrance and exit potential energ…
Identifying reaction coordinates(RCs) is an active area of research, given the crucial role RCs play in determining the progress of a chemical reaction. The choice of the reaction coordinate is often …
Quasi-steady state reductions for the irreversible Michaelis--Menten reaction mechanism are of interest both from a theoretical and an experimental design perspective. A number of publications have be…
In this paper, we propose a data-driven method to discover multiscale chemical reactions governed by the law of mass action. First, we use a single matrix to represent the stoichiometric coefficients …
The linear noise approximation models the random fluctuations from the mean-field model of a chemical reaction that unfolds near the thermodynamic limit. Specifically, the fluctuations obey a linear L…
Automatic differentiation is a tool for numerically calculating derivatives of a given function up to machine precision. This tool is useful for quantum chemistry methods, which require the calculatio…
A variety of simulation methodologies have been used for modeling reaction-diffusion dynamics -- including approaches based on Differential Equations (DE), the Stochastic Simulation Algorithm (SSA), B…
In a recent comment, Ruth Signorell raises a number of issues that she considers to question the validity of our approach to determine mean free paths for electron scattering in liquid water and our c…
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