Related papers: Modeling a simple enzyme reaction with delay and d…
Classical descriptions of enzyme kinetics ignore the physical nature of the intracellular environment. Main implicit assumptions behind such approaches are that reactions occur in compartment volumes which are large enough so that molecular…
In this work we study a kinetic model of active particles with delayed dynamics, and its limit when the number of particles goes to infinity. This limit turns out to be related to delayed differential equations with random initial…
Catalysis lies at the heart of chemical reactivity, yet its foundational principles remain fragmented across the distinct domains of homogeneous, heterogeneous, and enzymatic systems Here, we propose a unifying theoretical model that…
Complex systems often have features that can be modeled by advanced mathematical tools [1]. Of special interests are the features of complex systems that have a network structure as such systems are important for modeling technological and…
Biomolecular condensates in cells are often rich in catalytically-active enzymes. This is particularly true in the case of the large enzymatic complexes known as metabolons, which contain different enzymes that participate in the same…
Inspired by active shape morphing in developing tissues and biomaterials, we investigate two generic mechanochemical models where the deformations of a thin elastic sheet are driven by, and in turn affect, the concentration gradients of a…
Event-driven molecular dynamics simulations are carried out on two rigid body systems which differ in the symmetry of their molecular mass distributions. First, simulations of methane in which the molecules interact via discontinuous…
The interactions between diffusing molecules and membrane-bound receptors drive numerous cellular processes. In this work, we develop a spatial model of molecular interactions with membrane receptors by homogenizing the cell membrane and…
We have proposed the neck linker swing model to investigate the mechanism of mechanochemical coupling of kinesin. The Michaelis-Menten-like curve for velocity vs ATP concentration at different loads has been obtained, which is in agreement…
Several different enzymes display an apparent diffusion coefficient that increases with the concentration of their substrate. Moreover, their motion becomes directed in substrate gradients. Currently, there are several competing models for…
Dynamic facilitation theory assumes short-ranged dynamic constraints to be the essential feature of supercooled liquids and draws much of its conclusions from the study of kinetically constrained models. While deceptively simple, these…
A chemical kinetic model of the elongation dynamics of RNA polymerase along a DNA sequence is introduced. The proposed model governs the discrete movement of the RNA polymerase along a DNA template, with no consideration given to elastic…
Conventional kinesin is a homodimeric motor protein that unidirectionally transports organelles along filamentous microtubule (MT) by hydrolyzing ATP molecules. This study shows that the load modulations of ATP turnover and head diffusion…
The paper gives a systematic analysis of singularities of transition processes in dynamical systems. General dynamical systems with dependence on parameter are studied. A system of relaxation times is constructed. Each relaxation time…
The concept of allostery in which macromolecules switch between two different conformations is a central theme in biological processes ranging from gene regulation to cell signaling to enzymology. Allosteric enzymes pervade metabolic…
Many chemical reactions in biological cells occur at very low concentrations of constituent molecules. Thus, transcriptional gene-regulation is often controlled by poorly expressed transcription-factors, such as E.coli lac repressor with…
This study presents a dynamic modeling approach for precipitation in electrolyte systems, focusing on the crystallization of an aromatic amine through continuous processes. A novel model, integrating equilibrium and crystallization…
Biomolecular condensates are small droplets forming spontaneously in biological cells via phase separation. They play a role in many cellular processes, but it is unclear how cells control them. Cellular regulation often relies on…
Nucleation is a key step in the synthesis of new material from solution. Well-established lattice-gas models can be used to gain insight into the basic physics of nucleation pathways involving a single nucleus type. In many situations a…
With potential relevance to biomechanics, an interesting problem in statistical mechanics not previously solved is a binary mechanical model system. Discrete chemical states of proteins are often associated with discrete metastable…