肌球蛋白Ⅵ分子马达周期势场下的弹性扩散模型

肌球蛋白Ⅵ分子马达因其特殊的结构及胞内功能,其动力学原理成为研究的热点. 从肌球蛋白Ⅵ自身结构和实验现象出发,建立其弹性扩散模型,并通过Monte Carlo方法分析了肌球蛋白Ⅵ满足朗之万方程的随机动力学行为. 结果表明,在环境噪声作用下,具有弹性势能和轨道周期势能的肌球蛋白Ⅵ可以进行梯跳运动和有效的输运,但负载力会减弱分子马达系统的输运能力;当弹性系数一定时,弹性链越长平均速度越小,当弹性链长度一定时,合理选择弹性系数平均速度可达到最大值;另外,负载力的存在使肌球蛋白Ⅵ在接触位点的平均驻留时间呈指数增加. 关键词： 分子马达 肌球蛋白Ⅵ 朗之万方程 弹性扩散模型     

System-reservoir interaction with stochastic coupling parameters

We consider the problem of a system coupled to an ensemble of independent harmonic oscillators acting as a reservoir. We use an extension of the functional derivative technique to analyze some of the effects of adding stochastic terms to the system-reservoir coupling parameters. Two approaches (quantum master equation and Langevin equation) are considered and their ranges of validity and differences are examined.     

Impact of receptor-ligand distance on adhesion cluster stability

Cells in multicellular organisms adhere to the extracellular matrix through two-dimensional clusters spanning a size range from very few to thousands of adhesion bonds. For many common receptor-ligand systems, the ligands are tethered to a surface via polymeric spacers with finite binding range, thus adhesion cluster stability crucially depends on receptor-ligand distance. We introduce a one-step master equation which incorporates the effect of cooperative binding through a finite number of polymeric ligand tethers. We also derive Fokker-Planck and mean field equations as continuum limits of the master equation. Polymers are modeled either as harmonic springs or as worm-like chains. In both cases, we find bistability between bound and unbound states for intermediate values of receptor-ligand distance and calculate the corresponding switching times. For small cluster sizes, stochastic effects destabilize the clusters at large separation, as shown by a detailed analysis of the stochastic potential resulting from the Fokker-Planck equation.     

Fluctuation analysis of mechanochemical coupling depending on the type of biomolecular motors

Mechanochemical coupling was studied for myosin II and V consistently. The fluctuation in myosin V motility was determined by correlating the stochasticity of the ATPase reaction with regular displacements per one ATP, consistent with a tight mechanochemical coupling. In contrast, myosin II, working in an ensemble, was explained by a loose coupling, generating variable step sizes which depend on [ATP] and realizing a much larger step (200 nm) per one ATP than myosin V through its cooperativity at zero load. These different mechanics are ideal for their physiological functions.     

Continuous measurements in quantum systems

During a continuous measurement, quantum systems can be described by a stochastic Schrödinger equation which, in the appropriate limit, reproduces the von Neumann wave-function collapse. The average behavior on the ensemble of all measurement results is described by a master equation obtained from a general model of measurement apparatus consisting of an infinite set of degrees of freedom linearly interacting with the measured system and in contact with a reservoir at high temperature.     

A pedestrian approach to transitions and fluctuations in simple nonequilibrium chemical systems

A method is presented for identifying the quasi-stable states of a simple class of spatially homogeneous, nonlinear, nonequilibrium chemical systems, and for numerically calculating the associated mean transition times, mean fluctuation periods and effective fluctuation ranges. The method of analysis is based on a “stochastic simulation” approach instead of a “master equation” approach, and it therefore focuses on the behavior of a typical individual system instead of on the collective behavior of a statistical ensemble of systems. Results of explicit calculations are presented for a model set of reactions proposed by Schlögl, and some clarification is achieved regarding hysteresis effects and the effects of an absorbing null state.     

基于冲击力模型的分子马达动力学分析

从分子马达输运特点和实验现象出发,建立满足朗之万方程的冲击力模型,分析分子马达定向输运的动力学行为.研究发现:在合适的冲击力和噪声强度的共同作用下,分子马达可以稳定的梯跳跃迁运动和有效的输运;分子马达在轨运动的方向由冲击力的方向决定;另外,虽然在不同的噪声强度时平均速度都不为零,但是整个分子马达系综的高效输运对噪声强度有一定的选择性;系综的平均速度随着负载力的增大而减小,甚至会产生反方向的运动.     

On the theory of fluctuations around non-equilibrium steady states: A generalized time-convolutionless projector formalism

A new method of finding nonlinear Langevin type equations of motion for relevant macrovariables and the corresponding master equation for systems far from thermal equilibrium is presented by generalizing the time-convolutionless formalism proposed previously for equilibrium hamiltoian systems by Tokuyama and Mori. The Langevin type equation consists of a fluctuating force, and the nonlinear drift coefficients which are always identical to those of the master equation. A simple formula which relates the drift coefficients to the time correlation of the fluctuating forces is derived. This is a generalization of the fluctuation-dissipation theorem of the second kind in equilibrium systems and is valid not only for transport phenomena due to internal fluctuations but also for transport phenomena due to externally-driven fluctuations. A new cumulant expansion of the master equation is also obtained. The conditions under which a Langevin and a Fokker-Planck equation of a generalized type for non-equilibrium open systems can be derived are clarified.The theory is illustrated by studying hydrodynamic fluctuations near the Rayleigh-Bénard instability. The effects of two kinds of fluctuations, internal fluctuations of irrelevant macrovariables and external (thermal) noises, on the convective instability are investigated. A stochastic Ginzburg-Landau type equation for the order parameter and the corresponding nonlinear Fokker-Planck equation are derived.     

Quantum systems in regular and stochastic fields. Creation and destruction of the coherence

The problem of the coherent state generation with definite parameters for multilevel quantum systems is investigated. The interaction with external environment and stochastic fields can destroy the coherence. The competition of these processes is considered on the basis of the Fokker-Planck equations approach, derived from the master equation for the density matrix of the system. Examples of the coherent states dynamics for two-level atoms in an external stochastic field in a nonideal resonator are considered. Average over the realizations of stochastic fields is performed for the case of the white Gaussian noise and the Kubo-Anderson process. Explicit formulas for probability and shape of radiation line are obtained. The text was submitted by the author in English.     

Motion reversal of molecular motor assemblies due to weak noise

Bidirectional motion is an example of collective behavior of molecular motors. It occurs at finite noise level in a nonequilibrium system. We consider this problem as a first exit problem. We identify the noise strength by doing an expansion of a master equation and apply the Wentzell-Freidlin theory to define an effective nonequilibrium potential and provide analytical estimates of the reversal time. Our results match very well with the results of stochastic simulations.     

Open quantum system approach for heavy quark thermalization

We treat heavy quark as an open quantum system in a hot medium and rederive the stochastic Schr?dinger equation (SSE) from the full Schr?dinger equation for both heavy quarks and the medium. We apply the SSE to the dynamical evolutions of a heavy quark (as a system) in the static hot medium (as an environment). Heavy quarks interact with the medium via random scatterings, which exchange the momentum and phase factor randomly between two wave functions of the system and the environment. The exchange of momentum and phase factor results in the transition between different eigenstates of the system. These are included via an external stochastic potential in the Hamiltonian of SSE. Stochastic wave functions of a heavy quark are evolved with the stochastic external potential. The mean wave functions and corresponding momentum distributions of heavy quarks are obtained after the ensemble average over a large set of stochastic wave functions. We present the thermalization of heavy quarks in the static medium with different coupling strengths.     

Langevin and generalized Langevin types of spontaneous emission of quantum particles

In the effective Hamiltonian representation, we have obtained a quantum stochastic differential equation of a generalized Langevin type for the evolution operator of an atomic ensemble in a microcavity in an external broadband quantized field and in a nonresonant field of the microcavity. We show that, depending on the number of particles in the atomic ensemble, its dynamics demonstrates both the Langevin and the generalized Langevin types of the two-photon spontaneous decay. In this case, one photon is emitted into the cavity mode, whereas the other photon is emitted into the external broadband electromagnetic field. The Langevin type is determined by a considerable Stark interaction of the atomic ensemble with the broadband photon-free quantized field. We show that, here, the Stark interaction is represented by a quantized Poisson process and, depending on its magnitude (at certain numbers of atoms in the ensemble), the two-photon collective spontaneous emission of microcavity atoms can be completely suppressed. In this case, the two-photon spontaneous emission of the singly excited atomic ensemble is described by the two-level model, while the atom-photon cluster of the microcavity under the described conditions is an artificial two-level quantum particle with a strong Stark interaction.     

Finite size effects in stochastically driven systems use of the Poisson representation

A method is presented to take into account finite size effects in a system under the influence of external noise. Inclusion of external noise in a master equation results in an effective master equation in which new transitions among states are possible. The steady state properties of a chemical systems are calculated using the Poisson representation of the master equation.     

Quantum Chaos,Random Matrices,and Irreversibility in Interacting Many-Body Quantum Systems

The Pauli master equation describes the statistical equilibration of a closed quantum system. Simplifying and generalizing an approach developed in two previous papers, we present a derivation of that equation using concepts developed in quantum chaos and random-matrix theory. We assume that the system consists of subsystems with strong internal mixing. We can then model the system as an ensemble of random matrices. Equilibration results from averaging over the ensemble. The direction of the arrow of time is determined by an (ever-so-small) coupling to the outside world. The master equation holds for sufficiently large times if the average level densities in all subsystems are sufficiently smooth. These conditions are quantified in the text, and leading-order correction terms are given.     

A generalized stochastic liouville equation. Non-Markovian versus memoryless master equations

The interrelation between the well-known non-Markovian master equation and the new memoryless one used in the previous paper is clarified on the basis of damping theory. The latter equation is generalized to include cases in which the Hamiltonian or the Liouvillian is a random function of time, and is written in a form feasible for perturbational analysis. Thus, the existing stochastic theory in which those cases mentioned above are discussed is equipped with a more tractable basic equation. Two problems discussed in the previous paper, i.e., the random frequency modulation of a quantal oscillator and the Brownian motion of a spin, are treated from the viewpoint of the stochastic theory without such explicit consideration of external reservoirs as was taken in the previous paper.     

Chemomechanical Coupling of Molecular Motors: Thermodynamics, Network Representations, and Balance Conditions

Molecular motors are considered that convert the chemical energy released from the hydrolysis of adenosine triphosphate (ATP) into mechanical work. Such a motor represents a small system that is coupled to a heat reservoir, a work reservoir, and particle reservoirs for ATP, adenosine diphosphate (ADP), and inorganic phosphate (P). The discrete state space of the motor is defined in terms of the chemical composition of its catalytic domains. Each motor state represents an ensemble of molecular conformations that are thermally equilibrated. The motor states together with the possible transitions between neighboring states define a network representation of the motor. The motor dynamics is described by a continuous-time Markov process (or master equation) on this network. The consistency between thermodynamics and network dynamics implies (i) local and nonlocal balance conditions for the transition rates of the motor and (ii) an underlying landscape of internal energies for the motor states. The local balance conditions can be interpreted in terms of constrained equilibria between neighboring motor states; the nonlocal balance conditions pinpoint chemical and/or mechanical nonequilibrium.     

Master Equation for Quantum Brownian Motion Derived by Stochastic Methods

The master equation for a linear open quantum system in a general environment is derived using a stochastic approach. This is an alternative derivation to that of Hu, Paz, and Zhang, which was based on the direct computation of path integrals, or to that of Halliwell and Yu, based on the evolution of the Wigner function for a linear closed quantum system. We first show by using the influence functional formalism that the reduced Wigner function for the open system coincides with a distribution function resulting from averaging both over the initial conditions and the stochastic source of a formal Langevin equation. The master equation for the reduced Wigner function can then be deduced as a Fokker-Planck equation obtained from the formal Langevin equation.     

Heat transport in quantum spin chains

We discuss the problem of heat conduction in quantum spin chain models. To investigate this problem it is necessary to consider the finite open system connected to heat baths. We describe two different procedures to couple the system with the reservoirs: a model of stochastic heat baths and the quantum trajectories solution of the quantum master equation. The stochastic heat bath procedure operates on the pure wave function of the isolated system, so that it is locally and periodically collapsed to a quantum state consistent with a boundary nonequilibrium state. In contrast, the quantum trajectories procedure evaluates ensemble averages in terms of the reduced density matrix operator of the system. We apply these procedures to different models of quantum spin chains and numerically show their applicability to study the heat flow.     

Synchronization of a large number of continuous one-dimensional stochastic elements with time-delayed mean-field coupling

We study synchronization as a means of control of collective behavior of an ensemble of coupled stochastic units in which oscillations are induced merely by external noise. For a large number of one-dimensional continuous stochastic elements coupled non-homogeneously through the mean field with delay we developed an approach to find a boundary of synchronization domain and the frequency of the mean-field oscillations on it. Namely, the exact location of the synchronization threshold is shown to be a solution of the boundary value problem (BVP) which was derived from the linearized Fokker-Planck equation. Here the synchronization threshold is found by solving this BVP numerically. Approximate analytics is obtained by expanding the solution of the linearized Fokker-Planck equation into a series of eigenfunctions of the stationary Fokker-Planck operator. Bistable systems with a polynomial and piece-wise linear potential are considered as examples. Multistability and hysteresis in the mean-field behavior are observed in the stochastic network at finite noise intensities. In the limit of small noise intensities the critical coupling strength is shown to remain finite, provided that the delay in the coupling function is not infinitely small. Delay in the coupling term can be used as a control parameter that manipulates the location of the synchronization threshold.