相关论文: A Much better replacement of the Michaelis-Menten …
This paper studies a mathematical formalism of nonequilibrium thermodynamics for chemical reaction models with $N$ species, $M$ reactions, and general rate law. We establish a mathematical basis for J. W. Gibbs' macroscopic chemical…
Starting from the detailed catalytic mechanism of a biocatalyst we provide a coarse-graining procedure which, by construction, is thermodynamically consistent. This procedure provides stoichiometries, reaction fluxes (rate laws), and…
The molecular energies of chemical systems have been successfully calculated on quantum computers, however, more attention has been paid to the dynamic process of chemical reactions in practical application, especially in catalyst design,…
We shall revisit the conventional adiabatic or Markov approximation, which --contrary to the semiclassical case-- does not preserve the positive-definite character of the corresponding density matrix, thus leading to highly non-physical…
Enzyme kinetics are cyclic. A more realistic reversible three-step mechanism of the Michaelis-Menten kinetics is investigated in detail, and three kinds of waiting cycle times $T$, $T_{+}$, $T_{-}$ are defined. It is shown that the mean…
Recent fluorescence spectroscopy measurements of the turnover time distribution of single-enzyme turnover kinetics of $\beta$-galactosidase provide evidence of Michaelis-Menten kinetics at low substrate concentration. However, at high…
We review the non-relativistic Green's-function approach to the kinetic equations for Fermi liquids far from equilibrium. The emphasis is on the consistent treatment of the off-shell motion between collisions and on the non-instant and…
Complex systems can be advantageously modeled by formal reaction systems (RS), a.k.a. chemical reaction networks in chemistry. Reaction-based models can indeed be interpreted in a hierarchy of semantics, depending on the question at hand,…
We consider a Markov process in continuous time with a finite number of discrete states. The time-dependent probabilities of being in any state of the Markov chain are governed by a set of ordinary differential equations, whose dimension…
Chemotaxis describes the movement of an organism, such as single or multi-cellular organisms and bacteria, in response to a chemical stimulus. Two widely used models to describe the phenomenon are the celebrated Keller-Segel equation and a…
Approximations based on moment-closure (MA) are commonly used to obtain estimates of the mean molecule numbers and of the variance of fluctuations in the number of molecules of chemical systems. The advantage of this approach is that it can…
Quantum mechanics/molecular mechanics (QM/MM) is a standard computational tool for describing chemical reactivity in systems with many degrees of freedom, including polymers, enzymes, and reacting molecules in complex solvents. However,…
A recently developed model chemistry (jun-Cheap) has been slightly modified and proposed as an effective, reliable and parameter-free scheme for the computation of accurate reaction rates with special reference to astrochemical and…
Starting from the coherent state representation of the evolution operator with the help of the path-integral, we derive a formula for the low-lying levels $E = \epsilon_0 - 2\triangle\epsilon cos (s+\xi)\pi$ of a quantum spin system. The…
Quasiparticle dynamics in relativistic plasmas associated with hot, weakly-coupled gauge theories (such as QCD at asymptotically high temperature $T$) can be described by an effective kinetic theory, valid on sufficiently large time and…
The aim of this work is to investigate the application of partial moment approximations to kinetic chemotaxis equations in one and two spatial dimensions. Starting with a kinetic equation for the cell densities we apply a…
There are several important solid-state systems, such as defects in solids, superconducting circuits and molecular qubits, for attractive candidates of quantum computations. Molecular qubits, which benefit from the power of chemistry for…
Quantum Gibbs state sampling algorithms generally suffer from either scaling exponentially with system size or requiring specific knowledge of spectral properties \textit{a priori}. Also, these algorithms require a large overhead of bath or…
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 consider a~quasilinear model arising from dynamical magnetization. This model is described by a~magneto-quasistatic (MQS) approximation of Maxwell's equations. Assuming that the medium consists of a~conducting and a~non-conducting part,…