Research
Research
Research
Research
39+ 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…
The rigorous description of Conical Intersections (CIs) remains the central challenge of non-adiabatic quantum chemistry. While the ``Yarkony Seam'' -- the $(3N-8)$-dimensional manifold of degeneracy …
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…
The study of cycloaddition mechanisms is central to the fabrication of extended sp2 carbon nanostructures. Reaction modeling in this context has focused mostly on putative, energetically preferred, ex…
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…
Following previous work of M.H. Garner, R. Hoffmann, S. Rettrup and G.C. Solomon, we discuss the generation of helical molecular orbitals (MOs) for linear chains of atoms. We first give a definition o…
Conformational isomers or conformers of molecules play a decisive role in chemistry and biology. However, experimental methods to investigate chemical reaction dynamics are typically not conformer-sen…
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…
In this paper, a topological classification of molecules and their chemical reactions is proposed on a single particle level . We consider zero-dimensional electronic Hamiltonians in a real-space tigh…
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…
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