Related papers: Enzyme kinetics simulation at the scale of individ…
The rate-limiting step of some enzymatic reactions is a physical step, i.e. diffusion. The efficiency of such reactions can be improved through an increase in the arrival rate of the substrate molecules, e.g. by a directed passage of…
Enzyme catalysis in reactors for industrial applications usually require an external intervention of the species involved in the chemical reactions. We analyze the most elementary open enzyme catalysis with competitive inhibition where a…
Chemical reactions are usually studied under the assumption that both substrates and catalysts are well mixed (WM) throughout the system. Although this is often applicable to test-tube experimental conditions, it is not realistic in…
Biomolecular condensates are formed via liquid-liquid phase separation of proteins, often together with nucleic acids, typically driven by interactions between low-affinity binding sites. The computational study of such condensates that…
The classic Michaelis-Menten equation describes the catalytic activities for ensembles of enzyme molecules very well. But recent single-molecule experiment showed that the waiting time distribution and other properties of single enzyme…
We present an inference scheme of long timescale, non-exponential kinetics from Molecular Dynamics simulations accelerated by stochastic resetting. Standard simulations provide valuable insight into chemical processes but are limited to…
Computational screening of naturally occurring proteins has the potential to identify efficient catalysts among the hundreds of millions of sequences that remain uncharacterized. Current experimental methods remain time, cost and labor…
The formation of condensates is now considered as a major organization principle of eukaryotic cells. Several studies have recently shown that the properties of these condensates are affected by enzymatic reactions. We propose here a simple…
Electrostatic forces play many important roles in molecular biology, but are hard to model due to the complicated interactions between biomolecules and the surrounding solvent, a fluid composed of water and dissolved ions. Continuum model…
The microstructure of materials evolves through chemical reactions and mechanical stress, often strongly coupled in phenomena such as pressure solution or crystallization pressure. This article presents MASKE: a simulator to address the…
We study a class of Stochastic Differential Equations (SDEs) with jumps modeling multistage Michaelis--Menten enzyme kinetics, in which a substrate is sequentially transformed into a product via a cascade of intermediate complexes. These…
Massively-parallel molecular dynamics simulation is applied to systems containing electrolytes, vapour-liquid interfaces, and biomolecules in contact with water-oil interfaces. Novel molecular models of alkali halide salts are presented and…
Living cells exhibit a complex organization comprising numerous compartments, among which are RNA- and protein-rich membraneless, liquid-like organelles known as biomolecular condensates. Energy-consuming processes regulate their formation…
Enzymes are essential to maintain organisms alive. Some of the reactions they catalyze are associated with a change in reagents chirality, hence their activity can be tracked by using optical means. However, illumination affects enzyme…
Motivation: The design of enzymes is as challenging as it is consequential for making chemical synthesis in medical and industrial applications more efficient, cost-effective and environmentally friendly. While several aspects of this…
We describe modeling approaches to a "network" of connected enzyme-catalyzed reactions, with added (bio)chemical processes that introduce biochemical filtering steps into the functioning of such a biocatalytic cascade. Theoretical…
Different graphical plots involving the catalytic rate with the (initial) substrate concentration exist in the enzyme kinetics literature to estimate the reaction constants. But, none of these standard plots can unambiguously distinguish…
We study kinetic models of reversible enzyme reactions and compare two techniques for analytic approximate solutions of the model. Analytic approximate solutions of non-linear reaction equations for reversible enzyme reactions are…
Living systems are forced away from thermodynamic equilibrium by exchange of mass and energy with their environment. In order to model a biochemical reaction network in a non-equilibrium state one requires a mathematical formulation to…
Surfaces serve as highly efficient catalysts for a vast variety of chemical reactions. Typically, such surface reactions involve billions of molecules which diffuse and react over macroscopic areas. Therefore, stochastic fluctuations are…