Research
Research
Research
Research
33+ 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 …
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…
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) …
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 …
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…
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…
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…
Reaction constants in traditional Michaelis-Menten type enzyme kinetics are most often determined through a linear Lineweaver-Burk plot. While such a graphical plot is sometimes good to achieve the en…
We recall the perturbation expansion for Michaelis-Menten kinetics, beyond the standard quasi-steady-state approximation (sQSSA). Against this background, we are able to appropriately apply the altern…
Dynamic cooperativity in monomeric enzymes is characterized in terms of a non-Michaelis-Menten kinetic behaviour. The latter is believed to be associated with mechanisms that include multiple reaction…
Recent fluorescence spectroscopy measurements of the turnover time distribution of single-enzyme turnover kinetics of $\beta$-galactosidase provide evidence of Michaelis-Menten kinetics at low substra…
In biochemical systems the Michaelis-Menten (MM) scheme is one of the best-known models of the enzyme- catalyzed kinetics. In the academic literature the MM approximation has been thoroughly studied i…
The Michaelis-Menten enzymatic reaction is sufficient to perceive many subtleties of network modeling, including the concentration and time scales separations, the formal equivalence between bulk phas…
The standard two-step model of homogeneous-catalyzed reactions had been theoretically analyzed at various levels of approximations from time to time. The primary aim was to check the validity of the q…
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