准稳态系统向最可几动力学态的转变

On the anti-quasi-steady-state conditions of enzyme kinetics

Quasi-steady state reductions for the irreversible Michaelis--Menten reaction mechanism are of interest both from a theoretical and an experimental design perspective. A number of publications have been devoted to extending the parameter range where reduction is possible, via improved sufficient conditions. In the present note, we complement these results by exhibiting local conditions that preclude quasi-steady-state reductions (anti-quasi-steady-state), in the classical as well as in a broader sense. To this end, one needs to obtain necessary (as opposed to sufficient) conditions and determi…

Quantum Kinetic Rates within the Nonequilibrium Steady State

The nonequilibrium steady state (NESS) of a quantum network is central to a host of physical and biological scenarios. Examples include natural processes such as vision and photosynthesis, as well as technical devices such as photocells, both activated by incoherent light (e.g. sunlight) and leading to quantum transport. Here, a completely general approach to defining components of a quantum network in the NESS, and obtaining rates of processes between these components is provided. Quantum effects are explicitly included throughout, both in (a) defining network components via projection operat…

Stochastic enzyme kinetics and the quasi-steady-state reductions: Application of the slow scale linear noise approximation à la Fenichel

The linear noise approximation models the random fluctuations from the mean-field model of a chemical reaction that unfolds near the thermodynamic limit. Specifically, the fluctuations obey a linear Langevin equation up to order $Ω^{-1/2}$, where $Ω$ is the size of the chemical system (usually the volume). In the presence of disparate timescales, the linear noise approximation admits a quasi-steady-state reduction referred to as the \textit{slow scale} linear noise approximation (ssLNA). Curiously, the ssLNAs reported in the literature are slightly different. The differences in the reported ss…

Accelerated estimation of long-timescale kinetics by combining weighted ensemble simulation with Markov model "microstates" using non-Markovian theory

The weighted ensemble (WE) simulation strategy provides unbiased sampling of non-equilibrium processes, such as molecular folding or binding, but the extraction of rate constants relies on characterizing steady state behavior. Unfortunately, WE simulations of sufficiently complex systems will not relax to steady state on observed simulation times. Here we show that a post-simulation clustering of molecular configurations into "microbins" using methods developed in the Markov State Model (MSM) community, can yield unbiased kinetics from WE data before steady-state convergence of the WE simulati…

熵与动力学之间的普适关系

Universal Relation between Entropy and Kinetics

该研究基于第一性原理推导出联系熵与粒子构型动态传播子的普适严格不等式，适用于任意远离热平衡的稳态，可用于扩散系数界的获取或熵的估算，经实例验证有效且应用广泛。

质疑酶抑制剂常数估计的可靠性：竞争性抑制的情况

Questioning the reliability of estimates of enzyme inhibitor constant: Case of competitive inhibition

动力学参数的可靠性是理解细胞系统内酶动力学的关键。本研究提出了使用Lineweaver-Burk图估计K（M），V（max）和K（I）等参数时需要反思的一些注意事项。IC（50）的质量也需要彻底的重新研究，因为它与K（I）和K（M）值直接相关。稳态和非稳态条件下的抑制动力学进行了研究，估计参数的误差与实际值进行比较，以解决其充分性的问题。

Towards a full quantitative description of single-molecule reaction kinetics in biological cells

The first-passage time (FPT), i.e., the moment when a stochastic process reaches a given threshold value for the first time, is a fundamental mathematical concept with immediate applications. In particular, it quantifies the statistics of instances when biomolecules in a biological cell reach their specific binding sites and trigger cellular regulation. Typically, the first-passage properties are given in terms of mean first-passage times. However, modern experiments now monitor single-molecular binding-processes in living cells and thus provide access to the full statistics of the underlying …

An efficient Kinetic Monte Carlo to study analyte capture by a nanopore: Transients, boundary conditions and time-dependent fields

To better understand the capture process by a nanopore, we introduce an efficient Kinetic Monte Carlo (KMC) algorithm that can simulate long times and large system sizes by mapping the dynamic of a point-like particle in a 3D spherically symmetric system onto the 1D biased random walk. Our algorithm recovers the steady-state analytical solution and allows us to study time-dependent processes such as transients. Simulation results show that the steady-state depletion zone near pore is barely larger than the pore radius and narrows at higher field intensities; as a result, the time to reach stea…

随机化学反应网络中的缺陷、动力学可逆性与催化作用

Deficiency, Kinetic Invertibility, and Catalysis in Stochastic Chemical Reaction Networks

本文研究随机化学反应网络中对偶主方程的质量作用相容性及催化网络缺陷，证明仅零缺陷网络可反转稳态流，而非平衡催化网络并非零缺陷。

Kinetic Expression for Optimal Catalyst Electronic Configuration: The Case of Ammonia Decomposition

A new steady-state kinetic model of ammonia decomposition is presented and analyzed regarding the electronic properties of metal catalysts. The model is based on the classical Temkin-Ertl mechanism and modified in accordance with Wolkenstein electronic theory by implementing participation of free electrons of the catalyst to change the chemical nature of adsorbed species. Wolkenstein original theory only applied to semiconductors but by including the d-band model, the electronic theory can be extended to metals. For both simplified and full reaction mechanisms, including electronic steps, we p…

Transient probability currents provide upper and lower bounds on non-equilibrium steady-state currents in the Smoluchowski picture

Probability currents are fundamental in characterizing the kinetics of non-equilibrium processes. Notably, the steady-state current $J_{ss}$ for a source-sink system can provide the exact mean-first-passage time (MFPT) for the transition from source to sink. Because transient non-equilibrium behavior is quantified in some modern path sampling approaches, such as the "weighted ensemble" strategy, there is strong motivation to determine bounds on $J_{ss}$ -- and hence on the MFPT -- as the system evolves in time. Here we show that $J_{ss}$ is bounded from above and below by the maximum and minim…