相关论文: A Much better replacement of the Michaelis-Menten …
We develop an general formalism of single enzyme kinetics in two dimension where substrates diffuse stochastically on a square lattice in presence of disorder. The dynamics of the model could be decoupled effectively to two stochastic…
The Quasi Steady-State (QSS) model of long-term dynamics relies on the idea of time-scale decomposition. Assuming that the fast variables are infinitely fast and are stable in the long-term, the QSS model replaces the differential equations…
In this paper, we develop a method for obtaining the approximate solution for the evolution of single-step transformations under non-isothermal conditions. We have applied it to many reaction models and obtained very simple analytical…
The first experimental demonstration of an adaptive quantum state estimation (AQSE) is reported. The strong consistency and asymptotic efficiency of AQSE have been mathematically proven [ A. Fujiwara J. Phys. A 39 12489 (2006)]. In this…
Mathematical analysis of mass action models of large complex chemical systems is typically only possible if the models are reduced. The most common reduction technique is based on quasi-steady state assumptions. To increase the accuracy of…
We present a model of an ATP-fueled molecular machine which push a polymer through a pore channel. The machine acts between two levels (working-waiting), and the working one remains active for a fixed time giving a constant force. The…
We consider the application of Kramers theory to the microscopic calculation of rates of conformational transitions of macromolecules. The main difficulty in such an approach is to locate the transition state in a huge configuration space.…
Quasicentroid molecular dynamics (QCMD) is a path-integral method for approximating nuclear quantum effects in dynamics simulations, which has given promising results for gas- and condensed-phase water. Here, by simulating the infrared…
Finding optimal reaction coordinates and predicting accurate kinetic rates for activated processes are two of the foremost challenges of molecular simulations. We introduce an algorithm that tackles the two problems at once: starting from a…
Previous studies have primarily focused on the nonequilibrium thermodynamics of chemical reaction networks (CRNs) occurring in closed systems. In contrast, CRNs in open systems exhibit much richer nonequilibrium phenomena due to sustained…
Results are presented for the quench dynamics of a clean and interacting electron system, where the quench involves varying the strength of the attractive interaction along arbitrary quench trajectories. The initial state before the quench…
The concept of entropy and the correct application of the Second Law of thermodynamics are essential in order to understand the reason why quantum error correction is thermodynamically possible and no violation of the Second Law occurs…
The chemical birth-death process, whose chemical master equation (CME) is exactly solvable, is a paradigmatic toy problem often used to get intuition for how stochasticity affects chemical kinetics. In a certain limit, it can be…
The statistical problem of the distribution of $s$ quanta of equal energy $\epsilon_0$ and total energy $E$ among $N$ distinguishable particles is resolved using the conventional theory based on Boltzmann's principle of equal probabilities…
Particle-based simulations are an essential tool for the study of biochemical systems for scales between molecular/Brownian dynamics and the reaction-diffusion master equation. These simulations utilise proximity-based reaction conditions…
Applying probabilistic techniques we study regularity properties of quantum master equations (QMEs) in the Lindblad form with unbounded coefficients; a density operator is regular if, roughly speaking, it describes a quantum state with…
The quantum relative entropy is a fundamental quantity in quantum information science, characterizing the distinguishability between two quantum states. However, this quantity is not additive in general for correlated quantum states,…
Models invoking the chemical master equation are used in many areas of science, and, hence, their simulation is of interest to many researchers. The complexity of the problems at hand often requires considerable computational power, so a…
Antisymmetrized molecular dynamics (AMD) with quantum branching processes is reformulated so that it can be applicable to the collisions of heavy nuclei such as Au + Au multifragmentation reactions. The quantum branching process due to the…
We study networks of biochemical reactions modelled by continuous-time Markov processes. Such networks typically contain many molecular species and reactions and are hard to study analytically as well as by simulation. Particularly, we are…