基于三磷酸腺苷调节的分子马达单向能量跃迁模型

分子马达的梯跳运动和在过阻尼溶液中动力学原理尚未揭示清楚, 从分子马达输运特点和实验现象出发, 构建满足朗之万方程的单向能量跃迁模型, 并通过Monte Carlo方法分析了分子马达的随机动力学行为. 结果表明, 在合适的跃迁能量作用下, 分子马达可以利用噪声进行稳定的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; 轨道周期势虽影响分子马达速度的大小但不会改变其运动方向, 分子马达运动方向由跃迁能量决定; 另外, 虽然在不同的噪声强度时平均速度不为零, 但是分子马达系统的高效输运对噪声有一定选择性. 关键词： 分子马达 能量跃迁 朗之万方程 噪声强度     

Collective motion of active Brownian particles in one dimension

We analyze a model of active Brownian particles with non-linear friction and velocity coupling in one spatial dimension. The model exhibits two modes of motion observed in biological swarms: A disordered phase with vanishing mean velocity and an ordered phase with finite mean velocity. Starting from the microscopic Langevin equations, we derive mean-field equations of the collective dynamics. We identify the fixed points of the mean-field equations corresponding to the two modes and analyze their stability with respect to the model parameters. Finally, we compare our analytical findings with numerical simulations of the microscopic model.     

Directed transport of two interacting particles in a washboard potential

We study the conservative and deterministic dynamics of two nonlinearly interacting particles evolving in a one-dimensional spatially periodic washboard potential. A weak tilt of the washboard potential is applied biasing one direction for particle transport. However, the tilt vanishes asymptotically in the direction of bias. Moreover, the total energy content is not enough for both particles to be able to escape simultaneously from an initial potential well; to achieve transport the coupled particles need to interact cooperatively. For low coupling strength the two particles remain trapped inside the starting potential well permanently. For increased coupling strength there exists a regime in which one of the particles transfers the majority of its energy to the other one, as a consequence of which the latter escapes from the potential well and the bond between them breaks. Finally, for suitably large couplings, coordinated energy exchange between the particles allows them to achieve escapes — one particle followed by the other — from consecutive potential wells resulting in directed collective motion. The key mechanism of transport rectification is based on the asymptotically vanishing tilt causing a symmetry breaking of the non-chaotic fraction of the dynamics in the mixed phase space. That is, after a chaotic transient, only at one of the boundaries of the chaotic layer do resonance islands appear. The settling of trajectories in the ballistic channels associated with transporting islands provides long-range directed transport dynamics of the escaping dimer.     

A Locust-Inspired Model of Collective Marching on Rings

We study the collective motion of autonomous mobile agents in a ringlike environment. The agents’ dynamics are inspired by known laboratory experiments on the dynamics of locust swarms. In these experiments, locusts placed at arbitrary locations and initial orientations on a ring-shaped arena are observed to eventually all march in the same direction. In this work we ask whether, and how fast, a similar phenomenon occurs in a stochastic swarm of simple locust-inspired agents. The agents are randomly initiated as marching either clockwise or counterclockwise on a discretized, wide ring-shaped region, which we subdivide into k concentric tracks of length n. Collisions cause agents to change their direction of motion. To avoid this, agents may decide to switch tracks to merge with platoons of agents marching in their direction. We prove that such agents must eventually converge to a local consensus about their direction of motion, meaning that all agents on each narrow track must eventually march in the same direction. We give asymptotic bounds for the expected time it takes for such convergence or “stabilization” to occur, which depends on the number of agents, the length of the tracks, and the number of tracks. We show that when agents also have a small probability of “erratic”, random track-jumping behavior, a global consensus on the direction of motion across all tracks will eventually be reached. Finally, we verify our theoretical findings in numerical simulations.     

Ratchet and switching effects in stochastic kink dynamics

We study collective dynamics in a chain of harmonically coupled particles subjected to degenerate but asymmetric on-site double-well potentials and driven by white and exponentially correlated noise. The difference of frequencies of small-amplitude oscillations in the vicinity of the wells appears to be a sufficient condition for the existence of the soliton ratchet effect. We find directed thermally activated soliton motion while at certain critical values of either the correlation time or noise strength, a reversal (switching) of the direction of motion takes place. Furthermore, we observe stochastic soliton transport directed against an applied d.c. field.     

Ratchet transport of overdamped particles in superimposed driven lattices

Ratchet transport of overdamped particles is investigated in superimposed driven lattices using Langevin dynamics simulations. It is found that noise can strongly affect the transport of the particles. When lattices driving dominates the transport, the noise acts as a disturbance of the directed transport and slows down the average velocity of the particles.When the driving phase has less impact on particle transport, Gaussian white noise can play a positive role. By simply modulating these two parameters, we can control efficiency and the direction of the directed currents.     

Brownian particles far from equilibrium

We study a model of Brownian particles which are pumped with energy by means of a non-linear friction function, for which different types are discussed. A suitable expression for a non-linear, velocity-dependent friction function is derived by considering an internal energy depot of the Brownian particles. In this case, the friction function describes the pumping of energy in the range of small velocities, while in the range of large velocities the known limit of dissipative friction is reached. In order to investigate the influence of additional energy supply, we discuss the velocity distribution function for different cases. Analytical solutions of the corresponding Fokker-Planck equation in 2d are presented and compared with computer simulations. Different to the case of passive Brownian motion, we find several new features of the dynamics, such as the formation of limit cycles in the four-dimensional phase-space, a large mean squared displacement which increases quadratically with the energy supply, or non-equilibrium velocity distributions with crater-like form. Further, we point to some generalizations and possible applications of the model. Received 24 November 1999     

Directed transport of an asymmetric particle pair induced by non-equilibrium conditions

The hopping motion of a classical bounded pair of two particles along a chain is investigated. It is shown that in the asymmetric case of the system dynamics including excited states which differ from the respective ground states by the barrier to be overcome by one of the two particles, the over- and underpopulation of these excited states leads to a directed motion of the particle pair. Thereby, overpopulation results in one direction of motion, whereas underpopulation results in the opposite direction, and the mean velocity is determined by the amount of over-resp. underpopulation. For small deviations from equilibrium, the system exhibits linear response well known from other ratchet-type models. Possible generalizations and applications are discussed. Received 17 August 2001 and Received in final form 11 October 2001     

紧凑型反应堆中的单粒子动力学

针对紧凑型聚变反应堆独特的磁势阱结构, 使用蒙特卡罗方法研究单个高能带电粒子的约束动力学行为。考虑到磁场位型的局域平坦性, 在足够小的计算区域或足够短的时间内, 带电粒子基本上在一个常数磁场中的运动。基于此, 给出精确保证能量守恒的粒子运动方程逐点解析解, 该计算方案具有长时间追踪的能力。模拟结果表明: 对于初始位置和速度方向随机分布的具有1千电子伏能量的高能氘粒子, 大约有7%的概率能够约束至10 ms量级。由于粒子运动方程的求解过程不依赖于具体的磁场位型, 所以它可以方便地应用到具有任意位型的磁约束装置中。     

等单元长度多间隙加速结构的束流动力学特性

等单元长度多间隙加速结构是一种非同步加速结构,当粒子在加速结构中的速度变化很明显时,粒子在每个间隙的相位是不相同的,薄透镜近似下的束流纵向运动方程没有考虑粒子在加速结构中的速度变化,这在单腔的能量增益相对于粒子能量很小的情况下是合理的,但是当粒子在加速结构中的速度有明显变化时,这种处理方式是不够的.本文从带电粒子在电磁...     

Cluster dynamics and cluster size distributions in systems of self-propelled particles

Systems of self-propelled particles (SPP) interacting by a velocity alignment mechanism in the presence of noise exhibit rich clustering dynamics. Often, clusters are responsible for the distribution of (local) information in these systems. Here, we investigate the properties of individual clusters in SPP systems, in particular the asymmetric spreading behavior of clusters with respect to their direction of motion. In addition, we formulate a Smoluchowski-type kinetic model to describe the evolution of the cluster size distribution (CSD). This model predicts the emergence of steady-state CSDs in SPP systems. We test our theoretical predictions in simulations of SPP with nematic interactions and find that our simple kinetic model reproduces qualitatively the transition to aggregation observed in simulations.     

Self-propelled particles with fluctuating speed and direction of motion in two dimensions

We study general aspects of active motion with fluctuations in the speed and the direction of motion in two dimensions. We consider the case in which fluctuations in the speed are not correlated to fluctuations in the direction of motion, and assume that both processes can be described by independent characteristic time scales. We show the occurrence of a complex transient that can exhibit a series of alternating regimes of motion, for two different angular dynamics which correspond to persistent and directed random walks. We also show additive corrections to the diffusion coefficient. The characteristic time scales are also exposed in the velocity autocorrelation, which is a sum of exponential forms.     

Energy Transport Through Rare Collisions

We study a one-dimensional Hamiltonian chain of masses perturbed by an energy conserving noise. The dynamics is such that, according to its Hamiltonian part, particles move freely in cells and interact with their neighbors through collisions, made possible by a small overlap of size ϵ>0 between near cells. The noise only randomly flips the velocity of the particles. If ϵ→0, and if time is rescaled by a factor 1/ϵ, we show that energy evolves autonomously according to a stochastic equation, which hydrodynamic limit is known in some cases. In particular, if only two different energies are present, the limiting process coincides with the simple symmetric exclusion process.     

Ratchet transport of self-propelled chimeras in an asymmetric periodic structure

We studied the rectified transport of underdamped particles subject to phase lag in an asymmetric periodic structure. When the inertia effect is considered, it is possible to observe reversals of the average velocity with small self-propelled force, whereas particles always move in the positive direction with large self-propelled force. The introduction of phase lag leads particles to follow circular orbits and suppress the polar motion. In addition, this can adjust the direction of particle motion. There exists an optimal value of polar interaction strength at which the rectification is maximal. These results open the way for many application processes, such as spatial sorting of particles mixture and separation based on their physical properties.     

Dynamics of viscous vesicles in shear flow

The dynamics of giant lipid vesicles under shear flow is experimentally investigated. Consistent with previous theoretical and numerical studies, two flow regimes are identified depending on the viscosity ratio between the interior and the exterior of the vesicle, and its reduced volume or excess surface. At low viscosity ratios, a tank-treading motion of the membrane takes place, the vesicle assuming a constant orientation with respect to the flow direction. At higher viscosity ratios, a tumbling motion is observed in which the whole vesicle rotates with a periodically modulated velocity. When the shear rate increases, this tumbling motion becomes increasingly sensitive to vesicle deformation due to the elongational component of the flow and significant deviations from simpler models are observed. A good characterization of these various flow regimes is essential for the validation of analytical and numerical models, and to relate microscopic dynamics to macroscopic rheology of suspensions of deformable particles, such as blood.     

Non-Gaussian and Clustering Behavior in One-Dimensional Polydisperse Granular Gas System

We present a one-dimensional dynamic model of polydisperse granular mixture with the fractal characteristic of the particle size distribution, in which the particles are subject to inelastic mutual collisions and are driven by Gaussian white noise. The inhomogeneity of the particle size distribution is described by a fractal dimension D. The stationary state that the mixture reaches is the result of the balance between energy dissipation and energy injection. By molecular dynamics simulations, we have mainly studied how the inhomogeneity of the particle size distribution and the inelasticity of collisions influence the velocity distribution and distribution of interparticle spacing in the steady-state.The simulation results indicate that, in the inelasticity case, the velocity distribution strongly deviates from the Gaussian one and the system has a strong spatial clustering. Thus the inhomogeneity and the inelasticity have great effects on the velocity distribution and distribution of interparticle spacing. The quantitative information of the non-Gaussian velocity distribution and that of clustering are respectively represented.     

Global Pressure of One-Dimensional Polydisperse Granular Gases Driven by Gaussian White Noise

We study the global pressure of a one-dimensional polydisperse granular gases system for the first time,in which the size distribution of particles has the fractal characteristic and the inhomogeneity is described by a fractal dimension D. The particles are driven by Gaussian white noise and subject to inelastic mutual collisions. We define the global pressure P of the system as the impulse transferred across a surface in a unit of time, which has two contributions,one from the translational motion of particles and the other from the collisions. Explicit expression for the global pressure in the steady state is derived. By molecular dynamics simulations, we investigate how the inelasticity of collisions and the inhomogeneity of the particles influence the global pressure. The simulation results indicate that the restitution coefficient e and the fractal dimension D have significant effect on the pressure.     

自扩散泳微观转动马达的介观模拟

转动的微尺度马达是一类重要的微流器件.近年来,因为其重要的应用及理论价值引起了学术界的广泛关注.本文提出了一种新型的自扩散泳驱动的微观转动马达模型.通过介观动力学模拟,验证了该模型的有效性.模拟结果表明,该自扩散泳微观转动马达可以单向地自驱动转动,并且转动速度和马达表面发生的催化化学反应速率(即自产生的浓度梯度场强弱)、以及液体分子与马达之间的相互作用有关.此外,研究了两个转动马达共存时的运动行为,重点考察了马达之间的流体力学相互作用和浓度梯度场效应对马达转动的影响.该自扩散泳微观转动马达为设计实用的微流器件提供了新的思路和参考,也为研究活性胶体系统的集体行为提供了理想模型.     

Global Pressure of One-Dimensional Polydisperse Granular Gases Driven by Gaussian White Noise

We study the global pressure of a one-dimensional polydisperse granular gases system for the first time, in which the size distribution of particles has the fractal characteristic and the inhomogeneity is described by a fractal dimension D. The particles are driven by Gaussian white noise and subject to inelastic mutual collisions. We define the global pressure P of the system as the impulse transferred across a surface in a unit of time, which has two contributions, one from the translational motion of particles and the other from the collisions. Explicit expression for the global pressure in the steady state is derived. By molecular dynamics simulations, we investigate how the inelasticity of collisions and the inhomogeneity of the particles influence the global pressure. The simulation results indicate that the restitution coefficient e and the fractal dimension D have significant effect on the pressure.     

Rate of Entropy Production in Stochastic Mechanical Systems

Entropy production in stochastic mechanical systems is examined here with strict bounds on its rate. Stochastic mechanical systems include pure diffusions in Euclidean space or on Lie groups, as well as systems evolving on phase space for which the fluctuation-dissipation theorem applies, i.e., return-to-equilibrium processes. Two separate ways for ensembles of such mechanical systems forced by noise to reach equilibrium are examined here. First, a restorative potential and damping can be applied, leading to a classical return-to-equilibrium process wherein energy taken out by damping can balance the energy going in from the noise. Second, the process evolves on a compact configuration space (such as random walks on spheres, torsion angles in chain molecules, and rotational Brownian motion) lead to long-time solutions that are constant over the configuration space, regardless of whether or not damping and random forcing balance. This is a kind of potential-free equilibrium distribution resulting from topological constraints. Inertial and noninertial (kinematic) systems are considered. These systems can consist of unconstrained particles or more complex systems with constraints, such as rigid-bodies or linkages. These more complicated systems evolve on Lie groups and model phenomena such as rotational Brownian motion and nonholonomic robotic systems. In all cases, it is shown that the rate of entropy production is closely related to the appropriate concept of Fisher information matrix of the probability density defined by the Fokker–Planck equation. Classical results from information theory are then repurposed to provide computable bounds on the rate of entropy production in stochastic mechanical systems.