Related papers: Modeling a simple enzyme reaction with delay and d…
Different simplified and detailed chemical models and their impact on simulations of combustion regimes initiating by the initial temperature gradient in methane/air mixtures are studied. The limits of the regimes of reaction wave…
Co-existence of phase segregation and \emph{interconversion} or \emph{isomerization} reaction among molecular species leads to fascinating structure formation in biological and chemical world. Using Monte Carlo simulations of the prototype…
The role of retardation in the entanglement dynamics of two distant atoms interacting with a multi-mode field of a ring cavity is discussed. The retardation is associated with a finite time required for light to travel between the atoms…
The progress of the successive rounds of catalytic conversion of substrates into product(s) by a single enzyme is characterized by the distribution of turnover times. Establishing the most general form of dependence of this distribution on…
We propose a two-dimensional model for a complete description of the dynamics of molecular motors, including both the processive movement along track filaments and the dissociation from the filaments. The theoretical results on the…
Chemically reacting systems exhibiting a repeatable delay period before a visible and sudden change are referred to as clock reactions; they have a long history in education and provide an idealisation of various biochemical and industrial…
Enzyme kinetics is very often characterised by the irreversible Michaelis-Menten (MM) equation. However, in open chemical reaction networks such as metabolic pathways, this approach can lead to significant kinetic and thermodynamic…
To study the dynamics of chemical processes, we often adopt rate equations to observe the change in chemical concentrations. However, when the number of the molecules is small, the fluctuations cannot be neglected. We often study the…
We study the reaction kinetics of end-functionalized polymer chains dispersed in an unreactive polymer melt. Starting from an infinite hierarchy of coupled equations for many-chain correlation functions, a closed equation is derived for the…
F1-ATPase catalyses ATP hydrolysis and converts the cellular chemical energy into mechanical rotation. The hydrolysis reaction in F1-ATPase does not follow the widely believed Michaelis-Menten mechanism. Instead, the hydrolysis mechanism…
In this paper we extend the Gaussian self-consistent method to permit study of the equilibrium and kinetics of conformational transitions for heteropolymers with any given primary sequence. The kinetic equations earlier derived by us are…
We propose two dynamical models with delay taking advantage of their complex dynamics for information processing tasks. The first model incorporates coupled delayed dynamics of multiple bits, which is shown to have desirable properties as…
Kinetic Monte Carlo methods such as the Gillespie algorithm model chemical reactions as random walks in particle number space. The inter-reaction times are exponentially distributed under the assumption that the system is well mixed. We…
We investigate the heterogeneous dynamics in a model, where chemical gelation and glass transition interplay, focusing on the dynamical susceptibility. Two independent mechanisms give raise to the correlations, which are manifested in the…
Anaerobic glycolysis in yeast perturbed by the reduction of xenobiotic ketones is studied numerically in two models which possess the same topology but different levels of complexity. By comparing both models' predictions for concentrations…
Millisecond crystal relaxation has been used to explain anomalous decay in doped alkali halides. We attribute this slowness to Fermi-Pasta-Ulam solitons. Our model exhibits confinement of mechanical energy released by excitation. Extending…
Some general dynamical properties of models for compaction of granular media based on master equations are analyzed. In particular, a one-dimensional lattice model with short-ranged dynamical constraints is considered. The stationary state…
Mathematical modeling based on time-delay differential equations is an important tool to study the role of delay in biological systems and to evaluate its impact on the asymptotic behavior of their dynamics. Delays are indeed found in many…
The interrelation of dynamic processes active on separated time-scales in glasses and viscous liquids is investigated using a model displaying two time-scale bifurcations both between fast and secondary relaxation and between secondary and…
We present molecular dynamics simulations on the slow dynamics of a mixture of big and small soft-spheres with a large size disparity. Dynamics are investigated in a broad range of temperature and mixture composition. As a consequence of…