Brownian motion in fluctuating periodic potentials

This work deals with the overdamped motion of a particle in a fluctuating one-dimensional periodic potential. If the potential has no inversion symmetry and its fluctuations are asymmetric and correlated in time, a net flow can be generated at finite temperatures. We present results for the stationary current for the case of a piecewise linear potential, especially for potentials being close to the case with inversion symmetry. The aim is to study the stationary current as a function of the potential. Depending on the form of the potential, the current changes sign once or even twice as a function of the correlation time of the potential fluctuations. To explain these current reversals, several mechanisms are proposed. Finally, we discuss to what extent the model is useful to understand the motion of biomolecular motors.     

Protein motors induced enhanced diffusion in intracellular transport

Diffusion of transported particles in the intracellular medium is described by means of a generalized diffusion equation containing forces due to the cytoskeleton network and to the protein motors. We find that the enhanced diffusion observed in experiments depends on the nature of the force exerted by the protein motors and on parameters characterizing the intracellular medium which is described in terms of a generalized Debye spectrum for the noise density of states.     

Transport in a fluctuating potential

We study the overdamped motion of a particle in a fluctuating one-dimensional periodic potential. The potential has no inversion symmetry, and the fluctuations are correlated in time. At finite temperatures, a stationary current is induced. The amplitude and the direction of the current depend on the details of the noise process that is responsible for the potential fluctuations. We discuss several limiting situations for a general case. Furthermore we calculate the current in the case of a piecewise linear potential for different noise processes and parameters. A detailed discussion of the results is given, including a discussion of the mechanism that is responsible for the current reversal. We compare the present results with results for transport in a ratchet-like potential due to a fluctuating force. We also discuss the biological relevance of the present models for molecular motors. We present a model for the motion of molecular motors that explains why similar molecular motors can move in different directions.     

Noise induced intercellular propagation of calcium waves

In this paper, we investigate the spatiotemporal dynamics of a bidirectional coupled chain of cells, in which a cell is subjected to an external noise. Noisy oscillations of calcium (Ca²⁺), that is, a bursting-like phenomenon induced by noise with fluctuations in the baseline values of calcium, are induced in the first cell and propagated along the chain with noise suppression. This phenomenon of noise suppression is further investigated by computing the normalized fluctuation of pulse durations. It is therefore found that the noise induced coherence resonance phenomenon occurs at the cellular level. Coherence biresonance behaviour appears in the transmission of noise induced oscillations at appropriate noise intensity or noise coupling (for low noise intensity) and the information flow in each cell can be simultaneously optimized at the optimal value of noise or coupling.     

The Efficiency of Molecular Motors

Molecular motors convert chemical energy into mechanical work while operating in an environment dominated by Brownian motion. The aim of this paper is to explore the flow of energy between the molecular motors and its surroundings, in particular, its efficiency. Based on the Fokker-Planck equation with either N or infinite chemical states, we find that the energy efficiency of molecular motors, whether the Stokes efficiency or the usual thermodynamic efficiency, is strictly less than one, because of the dissipation of the energy in both the overdamped surroundings and in the process of the chemical reaction.     

Effects of rebinding rate and asymmetry in unbinding rate on cargo transport by multiple kinesin motors

Many intracellular transports are performed by multiple molecular motors in a cooperative manner.Here,we use stochastic simulations to study the cooperative transport by multiple kinesin motors,focusing mainly on effects of the form of unbinding rate versus force and the rebinding rate of single motors on the cooperative transport.We consider two forms of the unbinding rate.One is the symmetric form with respect to the force direction,which is obtained according to Kramers theory.The other is the asymmetric form,which is obtained from the prior studies for the single kinesin motor.With the asymmetric form the simulated results of both velocity and run length of the cooperative transport by two identical motors and those by a kinesin-1 motor and a kinesin-2 motor are in quantitative agreement with the available experimental data,whereas with the symmetric form the simulated results are inconsistent with the experimental data.For the cooperative transport by a faster motor and a much slower motor,the asymmetric form can give both larger velocity and longer run length than the symmetric form,giving an explanation for why kinesin adopts the asymmetric form of the unbinding rate rather than the symmetric form.For the cooperative transport by two identical motors,while the velocity is nearly independent of the rebinding rate,the run length increases linearly with the rebinding rate.For the cooperative transport by two different motors,the increase of the rebinding rate of one motor also enhances the run length of the cooperative transport.The dynamics of transport by N(N=3,4,5,6,7 and 8)motors is also studied.     

Noise in Genotype Selection Model

We study the steady state properties ofa genotype selection model in presence of correlated Gaussian whitenoise. The effect of the noise on the genotype selection model is discussed. It is found that correlated noise can breakthe balance of gene selection and induce the phase transition which can makes us select one type gene haploid from agene group.     

A discretized spectral approximation in neutron transport theory. Some numerical considerations

The half-range weight function, orthogonality integrals, and completeness theorems in the theory of kinetic equations are often not known, or when they are, are too complicated to be of much practical use. This suggests the use of full-range relations to solve half-range problems, and in this paper we investigate the adaptability of such an approach in the theory of one-speed neutron transport by a discretized spectral approximation formulated recently.     

Special solutions of the Fokker-Planck transport equation for arbitrary band structures; Mobility and diffusivity in a uniform field of force

A Fokker-Planck equation can be derived from a transition-type transport equation if the transition rates are nearly local in momentum space compared with the inhomogeneity length of the distribution. It is a second-order differential equation, whose coefficients depend on the band structureE(k), the viscosity tensor (k), and the temperatureT. Classical solutions of the Fokker-Planck equation deal with the parabolic band structure of free Brownian particles in a field of force. Mobility and diffusivity are then independent of the applied field. Here the explicit solution for the stationary state and the time-integrated conditional probability will be given in one dimension. This suffices to determine mobility and diffusivity. Assuming = 1, these quantities become independent of the field and the band structure, if the latter is nonperiodic, though the distribution still depends on it. This property even holds in three dimensions fork-independent viscosity tensors. Field-dependent mobility and diffusivity are obtained for ak-dependent viscosity or = 1 and periodic band structures. The latter is demonstrated for the caseE-cosk, which is also related to the noise problem in Josephson junctions.     

On the solution of Fokker-Planck equation for electron transport

Two different techniques have been used to solve the Fokker-Planck equation for electron transport in infinite homogeneous medium namely, maximum entropy and flux-limited approach. The solutions obtained for the scalar flux function φ₀(x,s) by both methods are numerically compared.     

稀疏膨胀过程中几何位形对于电子非局域热传导的影响

发展了考虑一维柱对称、球对称位型下流体演化的Fokker-Planck程序, 在流体力学极限下对程序进行了校验. 利用程序模拟研究了球对称位型、平板位型下等离子体在自由稀疏演化过程中电子热流的非局域热输运行为, 分析了几何位型对电子非局域热传导的影响. 非局域卷积理论的计算研究发现, 稀疏过程中空间的几何效应会减小外向电子热输运的非局域性.     

Analytical investigation of transient molecular-motor-assisted transport in elongated cells

This paper investigates analytically the molecular-motor-assisted transport between the cell nucleus and cell membrane in an elongated cell, which allows the formulation of governing equations in a cylindrical coordinate system. This problem is relevant to biomimetic transport systems as well as to many biological processes occurring in living cells, such as the viral infection of a cell. The obtained analytical solution is shown to agree well with a high-accuracy numerical solution of the same problem. The developed analytical technique extends the applicability of the generalized Fourier series method to a new type of problems involving intracellular transport of organelles.      

The operator method for solving the fractional Fokker-Planck equation

The operator method has been used to solve the fractional Fokker-Planck equation (FPE) which recently formulated as a model for the anomalous transport process. Two classes of special interest of fractional F-P equations coming from plasma physics and charged particle transport problem has been considered. It is shown that the mean square-displacement 〈x²(t)〉 satisfy the universal power law characterized the anomalous time evolution i.e. .     

Numerical solution of the Fokker-Planck equation with variable coefficients

We study the numerical solution of the Fokker-Planck equation. This equation gives a good approximation to the radiative transport equation when scattering is peaked sharply in the forward direction which is the case for light propagation in tissues, for example. We derive first the numerical solution for the problem with constant coefficients. This numerical solution is constructed as an expansion in plane wave solutions. Then we extend that result to take into account coefficients that vary spatially. This extension leads to a coupled system of initial and final value problems. We solve this system iteratively. Numerical results show the utility of this method.     

Effects of Noise on Ecological Invasion Processes: Bacteriophage-Mediated Competition in Bacteria

Pathogen-mediated competition, through which an invasive species carrying and transmitting a pathogen can be a superior competitor to a more vulnerable resident species, is one of the principle driving forces influencing biodiversity in nature. Using an experimental system of bacteriophage-mediated competition in bacterial populations and a deterministic model, we have shown in Joo et al. [Proc. R. Soc. B 273,1843–1848 (2006)] that the competitive advantage conferred by the phage depends only on the relative phage pathology and is independent of the initial phage concentration and other phage and host parameters such as the infection-causing contact rate, the spontaneous and infection-induced lysis rates, and the phage burst size. Here we investigate the effects of stochastic fluctuations on bacterial invasion facilitated by bacteriophage, and examine the validity of the deterministic approach. We use both numerical and analytical methods of stochastic processes to identify the source of noise and assess its magnitude. We show that the conclusions obtained from the deterministic model are robust against stochastic fluctuations, yet deviations become prominently large when the phage are more pathological to the invading bacterial strain.     

Directed transport in equilibrium: A model study

It is generally believed that sustained directed transport in mechanical systems is not achievable under equilibrium conditions. In this article, by analyzing a simple model, we will show that directed motion under equilibrium conditions can take place and is not inconsistent with conservation of energy and the second law of thermodynamics. Our model demonstrates a novel symmetry breaking mechanism sustainable under equilibrium conditions and average uniform motion of the center of mass is a consequence of the sustained broken symmetry. The most important consequence of our results is that, no current condition for mechanical equilibrium is possibly non-universal.     

Brownian Ratchet Driven by a Rocking Forcing with Broken Temporal Symmetry

The ratchet motion of a Brownian particle in a symmetric periodic potential under a rocking force thatbreaks the temporal symmetry is studied. As long as the relaxation time in the thermal background is much shorter thanthe forcing period, the unidirectional transport can be analytically treated. By solving the Fokker-Planck equations, weget an analytical expression of the current. This result indicates that with an appropriate match between the potentialfield, the asymmetric ac force and the thermal noise, a net current can be achieved. The current versus thermal noiseexhibits a stochastic-resonance-like behavior.     

电流驱动磁化翻转中的热效应

从理论上研究了电流驱动磁开关中的热效应,在Neel-Brown弛豫时间理论和Li等的有效温度的工作基础上作了改进.在对称系综模型的Landau-Lifshitz-Gilbert和Fokker-Planck方程的基础上,分析了电流驱动磁动力学开关过程和电流引起磁势能的变化,提出一个新的电流感应磁势垒降低模型.新模型是非线性的,与Li等的有效温度模型不同.在此模型的基础上,讨论了开关临界电流对温度、开关时间的依赖关系,理论与实验相符合.对电流引起的样品温升的实验曲线进行了修正,实验结果与文中的非线性势垒降低模 关键词： 热效应 自旋传输矩 Neel-Brown弛豫时间 Fokker-Planck方程     

Time Dependence of Entropy Flux and Entropy Production of a Dissipative Dynamical System Driven by Non-Gaussian Noise

A stochastic dissipative dynamical system driven by non-Gaussian noise is investigated. A general approximate Fokker-Planck equation of the system is derived through a path-integral approach. Based on the definition of Shannon＇s information entropy, the exact time dependence of entropy flux and entropy production of the system is calculated both in the absence and in the presence of non-equilibrium constraint. The present calculation can be used to interpret the interplay of the dissipative constant and non-Gaussian noise on the entropy flux and entropy production.