分数阶布朗马达在闪烁棘齿势中的合作输运现象

引入分数阶微积分理论,建立耦合分数阶布朗马达在闪烁棘齿势中的合作输运模型, 利用分数阶差分法求得模型数值解并分析了模型参数对合作定向输运性质的影响. 发现在具有记忆性的分数阶棘齿系统中, 系统阶数与粒子间耦合强度不仅可影响粒子链输运速度, 还可使粒子链出现与整数阶方向相反的定向流; 在阶数固定下, 定向输运速度将随参数(噪声强度、耦合强度、棘齿势峰值高度)变化出现广义随机共振现象. 关键词： 分数阶布朗马达 闪烁棘齿势 合作定向输运 广义随机共振     

Two-dimensional model of elastically coupled molecular motors

A flashing ratchet model of a two-headed molecular motor in a two-dimensional potential is proposed to simulate the hand-over-hand motion of kinesins.Extensive Langevin simulations of the model are performed.We discuss the dependences of motion and efficiency on the model parameters,including the external force and the temperature.A good qualitative agreement with the expected behavior is observed.     

Symmetric linear potential and imperfect Brownian ratchet in molecular motor function

Biomolecular motors are tiny engines that transport materials at the microscopic level within biological cells. In recent years, Elston and Peskin et al have investigated the effect of the elastic properties of the tether that connects the motor to its cargo at the speed of the motor. In this paper we extend their work and present a tether in the form of symmetric linear potential.Our results show that when the driving mechanism is an imperfect Brownian ratchet, the average speed decreases as the stiffness of the tether increases in the limit of large motor diffusion coefficient, which is similar to the results of Elston and Peskin.However, a threshold for the stiffness of the tether connecting the motor to its cargo is found in our model. Only when the tether is stiffer than the threshold can the motor and its cargo function co-operatively, otherwise, the motor and its cargo depart from each other. This result is more realistic than that of the spring model of Elston and Peskin.     

Two-dimensional model of elastically coupled molecular motors

A flashing ratchet model of a two-headed molecular motor in a two-dimensional potential is proposed to simulate the hand-over-hand motion of kinesins. Extensive Langevin simulations of the model are performed. We discuss the dependences of motion and efficiency on the model parameters, including the external force and the temperature. A good qualitative agreement with the expected behavior is observed.     

Feedback control in a coupled Brownian ratchet

On the basis of the double-well ratchet potential which can be calculated theoretically and implemented experimentally, the influences of the time delay, the coupling constant, and the asymmetric parameter of the potential on the performance of a delayed feedback ratchet consisting of two Brownian particles coupled mutually with a linear elastic force are investigated. The centre-of-mass velocity of two coupled Brownian particles, the average effective diffusion coefficient, and the Pe number are calculated. It is found that the parameters are affected by not only the time delay and coupling constant but also the asymmetric parameter of the double-well ratchet potential. It is also found that the enhancement of the current may be obtained by varying the coupling constant of the system for the weak coupling case. It is expected that the results obtained here may be observed in some physical and biological systems.     

Collective dynamics of two-dimensional coupled Brownian motors

The transport properties of coupled Brownian particles in a two-dimensional rocking ratchet are investigated via Langevin simulation. The results show that the average center-of-mass velocity is multi-peaks function of the frequency of the driving force. Furthermore, in the 2D coupled Brownian motor system there are the collective effect and ratchet behavior, which can switch depending on the frequency of driving force. It turns out that the cooperative effect between the interaction of coupled particles and external rocking driving force facilitates collective directional motion and energy conversion.     

带反馈的分数阶耦合布朗马达的定向输运

研究具有幂律记忆性的带反馈耦合布朗马达的定向输运现象, 引入分数阶理论, 建立了带反馈的分数阶耦合布朗马达模型, 利用分数阶差分法求得模型数值解并分析了模型参数对合作定向输运性质的影响. 仿真结果表明, 系统的记忆性通过影响带反馈的棘齿势的打开和闭合而影响粒子的定向输运, 即当系统的阶数在较小的范围内, 系统的记忆性会使带反馈的棘齿势的开关频率增加, 从而增大定向流速; 当系统其他参数(势垒高度、噪声强度等)固定时, 输运速度随着阶数的变化出现广义随机共振现象.     

Coulomb Friction Driving Brownian Motors

We review a family of models recently introduced to describe Brownian motors under the influence of Coulomb friction, or more general non-linear friction laws. It is known that, if the heat bath is modeled as the usual Langevin equation (linear viscosity plus white noise), additional non-linear friction forces are not sufficient to break detailed balance, i.e. cannot produce a motor effect. We discuss two possibile mechanisms to elude this problem. A first possibility, exploited in several models inspired to recent experiments, is to replace the heat bath's white noise by a "collisional noise", that is the effect of random collisions with an external equilibrium gas of particles. A second possibility is enlarging the phase space, e.g. by adding an external potential which couples velocity to position, as in a Klein-Kramers equation. In both cases, non-linear friction becomes sufficient to achieve a non-equilibrium steady state and, in the presence of an even small spatial asymmetry, a motor effect is produced.     

Feedback control in a collective flashing ratchet

An ensemble of Brownian particles in a feedback controlled flashing ratchet is studied. The ratchet potential is switched on and off depending on the position of the particles, with the aim of maximizing the current. We study in detail a protocol which maximizes the instant velocity of the center of mass of the ensemble at any time. This protocol is optimal for one particle and performs better than any periodic flashing for ensembles of moderate size, but is defeated by a random or periodic switching for large ensembles.     

外力作用下反馈耦合布朗棘轮的定向输运

本文研究了处于外力作用下双阱棘轮势中两个反馈耦合布朗粒子的定向输运性能. 通过对过阻尼朗之万方程的数值求解, 详细讨论了外力、热噪声与势阱的不对称参数等对耦合布朗粒子的平均速度、 有效扩散系数及Pe数的影响. 研究发现, 平均速度随外力呈周期性的变化规律. 同时耦合系统存在最优噪声强度会使定向输运达到最强. 值得指出的是棘轮系统可通过改变双阱势的结构来获得较强的定向流. 关键词： 耦合布朗棘轮 外力 双阱棘轮势 平均速度     

Asymmetric step-like characteristics in a tilted rocking ratchet potential

The overdamped Langevin dynamics has been employed to study the directional transport of particles driven in a tilted rocking ratchet potential. The system subjected to a constant direct force undergoes an asymmetrical dynamic transition from a static state to a sliding state at two different critical forces that are consistent with the predicted values. When an additional alternating force is applied to the system, the time-averaged velocity shows several steps of equal height as the direct force increases. These steps are similar to the Shapiro steps in an rf-driven Josephson junction, and appear whenever the system's natural frequency given by the direct force matches an integer multiple of the applied frequency. When the alternating force exceeds a certain critical value which can be also estimated for a slow rocking, a directional motion known as the rectification effect occurs even at zero direct force.     

Current reversal and mass separation of inertial Brownian motors in a two-noise ratchet

Transport of an inertial Brownian motor moving in an asymmetric periodic potential driven by an external force and correlated noises is investigated. Using the numerical algorithm, the asymptotic mean velocity (AMV) for characterizing directed transport is obtained. The effects of the external driving force f and the correlation λ between the two noises on the AMV are discussed. The results manifest: (1) the external driving force and the correlation between the two noises can lead to the phenomena like current reversal. (2) The competitions among the external driving force and the correlation between the two noises are necessary for current reversal, i.e., fλ>0. (3) Different directions of transport are found for different masses of the Brownian particles under the condition fλ>0. Therefore a theoretical study is suggested for separating Brownian particles according to their different masses in the ratchet system.     

布朗马达的非均匀高斯跃迁模型

提出了布朗马达的非均匀高斯跃迁理论，用布朗粒子在多态之间的跃迁模型描述分子马达的定向运动.假定跃迁速率与位置有关，且在跃迁点附近具有高斯函数形式，将布朗粒子在x处的概率密度Pm(x,t)在跃迁点附近展开，可以进行任意阶的近似计算.这一理论涵盖了以往的定点跃迁模型和均匀跃迁模型.作为具体例子，研究了系统在两态之间的跃迁问题.假定在一个周期内有两个跃迁点，讨论了布朗粒子定向运动产生的概率流随温度、跃迁速率和 跃迁宽度的变化关系. 关键词： 布朗马达 高斯跃迁 概率流     

脉冲式棘齿势场作用下囚禁离子的规则与混沌运动

考虑赝势近似下囚禁于Paul阱中的单离子与由脉冲式双激光驻波构成的棘齿势场的相互作用.应用积分方程方法得到系统的经典运动精确解，通过数值方法作出相空间轨道并计算由平均速度定义的流，结合分析与数值结果研究囚禁离子的规则与混沌运动特性.与单驻波型激光脉冲情形相比，发现两个重要的棘齿效应：一是脉冲式棘齿势场的作用导致参数空间混沌区域的改变，从而适当调节第二驻波参数，可使离子的规则运动变为混沌运动，或者混沌运动变为规则运动；二是通过分析平均流随激光参数的变化，发现棘齿势场的介入能使囚禁离子作平均意义下的单向输运，随着势场强度增加到混沌区域，流的强度明显减小并改变方向，系统进入混沌运动. 关键词： 脉冲式棘齿势 囚禁离子 混沌 输运     

反馈脉冲棘轮的能量转化效率研究

研究了反馈脉冲棘轮的定向输运及能量转化效率.详细讨论了弹簧自由长度、耦合强度及脉冲相位等参量对耦合布朗粒子定向输运性能的影响.研究发现,一定自由长度和耦合强度都能促进反馈脉冲棘轮的定向输运,并能使耦合粒子拖动负载做功时的能量转化效率达到最大.此外,通过调节脉冲相位能使反馈棘轮在一个演化周期内获得两次流反转,且合适的相位还能增强反馈棘轮的定向输运.所得结论不仅可为实验上设计合适的反馈脉冲作用来优化棘轮的定向输运性能,而且还能为生物医疗上药物的精准投放提供一定的理论参考.     

Quantitative simulations of ratchet potential in a dusty plasma ratchet

Using a dusty plasma ratchet, one can realize the rectification of charged dust particle in a plasma. To obtain the ratchet potential dominating the rectification, here we perform quantitative simulations based on a two-dimensional fluid model of capacitively coupled plasma. Plasma parameters are firstly calculated in two typical cross sections of the dusty plasma ratchet which cut vertically the saw channel at different azimuthal positions. The balance positions of charged dust particle in the two cross sections then can be found exactly. The electric potentials at the two balance positions have different values. Using interpolation in term of a double-sine function from previous experimental measurement, an asymmetrical ratchet potential along the saw channel is finally obtained. The asymmetrical orientation of the ratchet potential depends on discharge conditions. Quantitative simulations further reproduce our previous experimental phenomena such as the rectification of dust particle in the dusty plasma ratchet.     

Brownian motors: Joint effect of non-Gaussian noise and time asymmetric forcing

Previous works have shown that time asymmetric forcing on the one hand, as well as non-Gaussian noises on the other, can separately enhance the efficiency and current of a Brownian motor. Here, we study the result of subjecting a Brownian motor to both effects simultaneously. Our results have been compared with those obtained for the Gaussian white noise regime in the adiabatic limit. We find that, although the inclusion of the time asymmetry parameter increases the efficiency value up to a certain extent, for the present case this increase is much less appreciable than in the white noise case. We also present a comparative study of the transport coherence in the context of colored noise. Though the efficiency in some cases becomes higher for the non-Gaussian case, the Péclet number is always higher in the Gaussian colored noise case than in the white noise as well as non-Gaussian colored noise cases.     

过阻尼布朗棘轮的斯托克斯效率研究

根据随机能量理论解析得到阻尼环境中布朗粒子的概率流和斯托克斯效率,并进一步研究布朗粒子的输运性能.详细讨论了空间的不对称性、外偏置力及外势结构等对棘轮定向输运的影响.研究发现,合适的外偏置力能使棘轮的定向输运达到最强.通过调节外势的不对称性可使棘轮中粒子的运动反向,当选择合适的空间不对称性时布朗粒子的反向输运可获得最强.此外,一定条件下合适的外势高度也能增强棘轮输运,且能使粒子克服黏滞阻力的斯托克斯效率达到最大.所得结论能够启发实验上设计合适的外势及外偏置来优化布朗棘轮的定向输运性能,并为生物纳米器件的研制提供一定的理论参考.     

Brownian diode: Molecular motor based on a semi-permeable Brownian particle with internal potential drop

A model of an autonomous isothermal Brownian motor with an internal propulsion mechanism is considered. The motor is a Brownian particle which is semi-transparent for molecules of surrounding ideal gas. Molecular passage through the particle is controlled by a potential similar to that in the transition rate theory, i.e. characterized by two stationary states with a finite energy difference separated by a potential barrier. The internal potential drop maintains the diode-like asymmetry of molecular fluxes through the particle, which results in the particle?s stationary drift.     

Brownian ratchet mechanism of translocation in T7 RNA polymerase facilitated by a post-translocation energy bias arising from the conformational change of the enzyme

T7 RNA polymerase can transcribe DNA to RNA by translocating along the DNA. Structural studies suggest that the pivoting rotation of the O helix in the fingers domain may drive the movement of the O helix C-terminal Tyr639 from pre- to post-translocation positions. In a series of all-atom molecular dynamics simulations, we show that the movement of Tyr639 is not tightly coupled to the rotation of the O helix, and that the two processes are only weakly dependent on each other. We also show that the internal potential of the enzyme itself generates a small difference in free energy (ΔE) between the post- and pre-translocation positions of Tyr639. The calculated value of ΔE is consistent with that obtained from single-molecule experimental data. These findings lend support to a model in which the translocation takes place via a Brownian ratchet mechanism, with the small free energy bias ΔE arising from the conformational change of the enzyme itself.