Related papers: The Quasi-Steady State Assumption in an Enzymatica…
A frequently desirable characteristic of chemical kinetics systems is that of persistence, the property that if all the species are initially present then none of them may tend toward extinction. It is known that solutions of…
Why reaction rate constants for enzymatic reactions are typically inversely proportional to fractional power exponents of solvent viscosity remains to be already a thirty years old puzzle. Available interpretations of the phenomenon invoke…
Comprehensive and predictive simulation of coupled reaction networks has long been a goal of biology and other fields. Currently, metabolic network models that utilize enzyme mass action kinetics have predictive power but are limited in…
The possibility that a short-range interacting system exhibits nonadditivity is investigated. After the discussion on the precise definition of additivity and its consequence, we show that it is possible when the system is in a…
We discuss the nature of quasi-stationary states (QSS) with non-Boltzmannian distribution in systems with long-range interactions in relation with a process of incomplete violent relaxation based on the Vlasov equation. We discuss several…
A stochastic model for the dynamics of enzymatic catalysis in explicit, effective solvents under physiological conditions is presented. Analytically-computed first passage time densities of a diffusing particle in a spherical shell with…
Hybrid quantum mechanical-molecular mechanical (QM/MM) simulations are widely used in enzyme simulation. Over ten convergence studies of QM/MM methods have revealed over the past several years that key energetic and structural properties…
Many experiments in recent years have reported that, when exposed to their corresponding substrate, catalytic enzymes undergo enhanced diffusion as well as chemotaxis (biased motion in the direction of a substrate gradient). Among other…
We suggest a natural approach that leads to a modification of classical quasispecies models and incorporates the possibility of population extinction in addition to growth. The resulting modified models are called open. Their essential…
We construct the {\it quasi-stationary} (QS) probability distribution for the Domany-Kinzel stochastic cellular automaton (DKCA), a discrete-time Markov process with an absorbing state. QS distributions are derived at both the one- and…
We describe a quantum electromechanical system(QEMS) comprising a single quantum dot harmonically bound between two electrodes and facilitating a tunneling current between them. An example of such a system is a fullerene molecule between…
The adiabatic approximation in open systems is formulated through the effective Hamiltonian approach. By introducing an ancilla, we embed the open system dynamics into a non-Hermitian quantum dynamics of a composite system, the adiabatic…
We study a Michaelis-Menten reaction for a single two-state enzyme molecule, whose transition rates between the two conformations are modulated by an harmonically oscillating external force. In particular, we obtain a range of optimal…
In the framework of the theory of open systems based on completely positive quantum dynamical semigroups, we give a description of the dynamics of entanglement for a system consisting of two uncoupled harmonic oscillators interacting with a…
Simulations of biophysical systems inevitably include steps that correspond to time integrations of ordinary differential equations. These equations are often related to enzyme action in the synthesis and destruction of molecular species,…
An open system is not conservative because energy can escape to the outside. An open system by itself is thus not conservative. As a result, the time-evolution operator is not hermitian in the usual sense and the eigenfunctions (factorized…
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…
Truly stable metastable states are an artifact of the mean-field approximation or the zero temperature limit. If such appealing concepts in glass theory as configurational entropy are to have a meaning beyond these approximations, one needs…
Initially far out-of-equilibrium self-gravitating systems form, through a collisionless relaxation dynamics, quasi-stationary states (QSS). These may arise from a bottom-up aggregation of structures or in a top-down frame; their…
In the framework of the theory of open systems based on completely positive quantum dynamical semigroups, we give a description of the continuous-variable entanglement for a system consisting of two independent harmonic oscillators…