Stochastic Four-State Mechanochemical Model of F1-ATPase

F₁-ATPase, a part of ATP synthase, can synthesize and hydrolyze ATP moleculars in which the central γ-subunit rotates inside the α₃β₃ cylinder. Astochastic four-state mechanochemical coupling model of F$_{1}$-ATPase isstudied with the aid of the master equation. In this model, the ATPhydrolysis and synthesis are dependent on ATP, ADP, and Pi concentrations.The effects of ATP concentration, ADP concentration, and the external torqueon the occupation probability of binding-state, the rotation rate and thediffusion coefficient of F₁-ATPase are investigated. Moreover, theresults from this model are compared with experiments. The mechanochemicalmechanism F₁-ATPase is qualitatively explained by the model.     

Directed Motion of a Molecular Motor Based on the Four-State Model with Unequal Substeps

A periodic one-dimensional four-state hopping model is proposed. In the model, the substeps betweenarbitrary adjacent states are unequal, and an explicit solution of the master equation is first obtained for the probabilitydistribution as a function of the time and position for any initial distribution with all the transients included. Next, thetransient behaviors in the initial period of time and the characteristic time to reach the steady state for the molecularmotor are discussed. Finally, we compare the steady state results to experiments and illustrate qualitatively the kineticbehaviors of a molecular motor under external load F.     

Directed Motion of a Molecular Motor Based Qn the Four－State Model with Unequal Substeps

A periodic one-dimensional four-state hopping model is proposed. In the model, the substeps between arbitrary adjacent states are unequal, and an explicit solution of the master equation is first obtained for the probability distribution as a function of the time and position for any initial distribution with all the transients included. Next, the transient behaviors in the initial period of time and the characteristic time to reach the steady state for the molecular motor are discussed. Finally, we compare the steady state results to experiments and illustrate qualitatively the kinetic behaviors of a molecular motor under external load F.     

Four-State Quantum Chain as a Model of Sequence Evolution

A variety of selection-mutation models for DNA (or RNA) sequences, well known in molecular evolution, can be translated into a model of coupled Ising quantum chains. This correspondence is used to investigate the genetic variability and error threshold behaviour in dependence of possible fitness landscapes. In contrast to the two-state models treated hitherto, the model explicitly takes the four-state nature of the nucleotide alphabet into account and allows for the distinction of mutation rates for the different base substitutions, as given by standard mutation schemes of molecular phylogeny. As a consequence of this refined treatment, new phase diagrams for the error threshold behaviour are obtained, with appearance of a novel phase in which the nucleotide ordering of the wildtype sequence is only partially conserved. Explicit analytical and numerical results are presented for evolution dynamics and equilibrium behaviour in a number of accessible situations, such as quadratic fitness landscapes and the Kimura 2 parameter mutation scheme.     

Stochastic theory for clustering of quenched-in vacancies—1. General mathematical properties

The problem of clustering of quenched-in vacancies into various types of extended defects is considered. A master equation for the evolution of the concentration of clusters of various sizes is written down with general transition rates. It is shown that this model represents a continuous time non-stationary Markoff process. A particular choice of transition rates corresponding to the formation of vacancy loops and stacking fault tetrahedra is considered in some detail. It is shown that this choice of transition rates allows us to obtain the solution for the concentration of the single vacancy units, and hence yields some information on the nucleation time. Further, the transition matrix becomes stationary and doubly stochastic due to the short time constant of the concentration of single vacancy units. This in turn leads to an unphysical stationary state. Finally we show how the rate equations for the irradiated situation can be written down and derive the phenomenological rate equations that are conventionally used.     

Data-Driven Model Reduction for Stochastic Burgers Equations

We present a class of efficient parametric closure models for 1D stochastic Burgers equations. Casting it as statistical learning of the flow map, we derive the parametric form by representing the unresolved high wavenumber Fourier modes as functionals of the resolved variable’s trajectory. The reduced models are nonlinear autoregression (NAR) time series models, with coefficients estimated from data by least squares. The NAR models can accurately reproduce the energy spectrum, the invariant densities, and the autocorrelations. Taking advantage of the simplicity of the NAR models, we investigate maximal space-time reduction. Reduction in space dimension is unlimited, and NAR models with two Fourier modes can perform well. The NAR model’s stability limits time reduction, with a maximal time step smaller than that of the K-mode Galerkin system. We report a potential criterion for optimal space-time reduction: the NAR models achieve minimal relative error in the energy spectrum at the time step, where the K-mode Galerkin system’s mean Courant–Friedrichs–Lewy (CFL) number agrees with that of the full model.     

Stochastic analysis of symmetry-breaking bifurcations: Master equation approach

The multivariate master equation for a general reaction-diffusion system is solved perturbatively, in the vicinity of a bifurcation point leading to symmetry-breaking transitions. The possibility to express the result through a Brazovskii type of potential is examined, and a comparison with the Langevin analysis of Walgraefet al. [Adv. Chem. Phys. 49:311 (1982)] is performed.     

Coherence Loss of Two-Photon Jaynes-Cummings Model in Dispersive Approximation

Completely solving the dissipative dynamics of nonlinear Jaynes-Cumming model is a very difficult task.In our recent work (Phys. Lett. A284 (2001) 156), we just obtained analytical results of the field dissipative dynamics of the nonlinear JCM. In the present paper, employing the perturbative expansion of master equation, we obtain the density operator of the system (field +atom). The coherence losses of the system and of the atom are investigated when two-photon process is involved. We also study the effect of different atomic initial states and the influence of the field amplitude on the atomic coherence loss.     

A Stochastic LWR Model with Consideration of the Driver's Individual Property

In this paper,we develop a stochastic LWR model based on the influences of the driver's individual property on his/her perceived density and speed deviation.The numerical results show that the driver's individual property has great effects on traffic flow only when the initial density is moderate,i.e.,at this time,oscillating traffic flow will occur and the oscillating phenomena in the traffic system consisting of the conservative and aggressive drivers is more serious than that in the traffic system consisting of the conservative (aggressive) drivers.     

变密度随机涡模型在湍流射流扩散火焰中的应用

采用变密度随机涡模型,对H₂/O₂/N₂湍流射流扩散火焰进行数值模拟,湍流过程通过涡的采样、涡的抑制和涡的翻转实现.其中,针对变密度反应流问题,提出一种大涡抑制的新机制,并详细讨论各种参数对模型预测效果的影响.计算结果表明,修改后的模型可以合理预测H₂/O₂/N₂射流火焰结构,能够反映湍流的涡特性;模型中与涡采样和涡抑制有关的参数对预测结果有一定影响.     

A_(n-1)~((1))面模型反射方程的多参数解

利用面型因式化Ｌ算子,通过面模型反射方程的对角解,构造了一个含有ｎ＋１个任意参数的非对角解．     

Entropy and Entanglement in Master Equation of Effective Hamiltonian for Jaynes-Cummings Model

In this paper, we analytically solve the master equation for Jaynes-Cummings model in the dispersive regime including phase damping and the field is assumed to be initially in a superposition of coherent states. Using an established entanglement measure based on the negativity of the eigenvalues of the partially transposed density matrix we find a very strong sensitivity of the maximally generated entanglement to the amount of phase damping. Qualitatively this behavior is also reflected in alternative entanglement measures, but the quantitative agreement between different measures depends on the chosen noise model. The phase decoherence for this model results in monotonic increase in the total entropy while the atomic sub-entropy keeps its periodic behaviour without any effect.     

Zn Belavin模型反射方程的多参数解

利用A_(n－1)⁽¹⁾面模型反射方程的对角解,得到了ZnBelavin模型反射方程的含有n+1个参数的解.当n=2时,其结果与侯伯宇等人给出的8项角反射方程的解是一致的.     

Theoretical Model Calculation for d ＋^8Li Reaction

Based on the theoretical models for light nuclei, the calculations of reaction cross sections and the angular distributions for d ＋^8Li reaction are performed. Since all of the particle emissions are from the compound nucleus to the discrete levels, the angular momentum coupling effect in pre-equilibrium mechanism is taken into account. The three- body break-up process and the recoil effect are involved. The theoretical calculated results are compared to existing experimental data.     

Theoretical Model Calculation for d+8Li Reaction

Based on the theoretical models for light nuclei, the calculations of reaction cross sections and the angular distributions for d+⁸Li reaction are performed. Since all of the particle emissions are from the compound nucleus to the discrete levels, the angular momentum coupling effect in pre-equilibrium mechanism is taken into account. The three-body break-up process and the recoil effect are involved. The theoretical calculated results are compared to existing experimental data.     

15顶角模型反射方程的常数解

得到了15顶角模型A2(1)模型和超对称t–J模型反射方程的非对角解,结果发现,A2(1)模型具有三种形式的非对角解,超对称t–J模型具有一种形式的非对角解,每种形式的非对角解均含有两个解,每个非对角解中均含有三个任意参数.关于对角解也得到了一些新的形式的解.     

Relative Energy Shift of a Two-Level Atom in a Cylindrical Spacetime

We investigate the evolution dynamics of a two-level atom system interacting with the massless scalar field in a Cylindrical spacetime. We find that both the energy shifts of ground state and excited state can be separated into two parts due to the vacuum fluctuations. One is the corresponding energy shift for a rest atom in four-dimensional Minkowski space without spatial compactification, the other is just the modification of the spatial compactified periodic length. It will reveal that the influence of the presence of one spatial compactified dimension can not be neglected in Lamb shift as the relative energy level shift of an atom.     

单电子晶体管电流解析模型及数值分析

本文首先建立单电子晶体管的电流解析模型, 然后将蒙特卡罗法与主方程法结合进行数值分析, 研究了栅极偏压、漏极偏压、温度与隧道结电阻等参数对器件特性的影响. 结果表明: 对于对称结, 库仑台阶随栅极偏压增大而漂移; 漏极电压增大, 库仑振荡振幅增强, 库仑阻塞则衰减; 温度升高将导致库仑台阶和库仑振荡现象消失. 对于非对称结, 源漏隧道结电阻比率增大, 库仑阻塞现象越明显. 关键词： 单电子晶体管 解析模型 蒙特卡罗法 主方程法     

利用热纠缠态表象获得Caldeira-Leggett密度算符方程的积分形式解

开放量子系统,即系统-热库模型,可以用一个关于密度算符的主方程来描述,比如,用来描述固态物理中耗散现象的Caldeira.Leggett主方程.虽然已经有人为了求解此主方程的约化密度矩阵的精确表达式而做过一些努力,但迄今还未见有解答.本文使用了一种全新的方法来求解Caldeira-Leggett方程,用这个新方法可以得到积分形式的显式表达.该方法的要点在于利用有序算符内积分技术把关于密度算符的微分方程首先转化成关于密度态矢量的微分方程,再将密度态矢量投影到热纠缠态表象中,Caldeira-Leggett方程就转变成了关于波函数的微分方程,而波函数是函数.这样就可以使用数学中求解微分方程的方法来求解出波函数.再次利用有序算符内积分技术,再将波函数转化为态矢量和算符,就得到了Caldeira-Leggett方程的积分形势解.