Analytical solution of equations describing slow axonal transport based on the stop-and-go hypothesis

This paper presents an analytical solution for slow axonal transport in an axon. The governing equations for slow axonal transport are based on the stop-and-go hypothesis which assumes that organelles alternate between short periods of rapid movement on microtubules (MTs), short on-track pauses, and prolonged off-track pauses, when they temporarily disengage from MTs. The model includes six kinetic states for organelles: two for off-track organelles (anterograde and retrograde), two for running organelles, and two for pausing organelles. An analytical solution is obtained for a steady-state situation. To obtain the analytical solution, the governing equations are uncoupled by using a perturbation method. The solution is validated by comparing it with a high-accuracy numerical solution. Results are presented for neurofilaments (NFs), which are characterized by small diffusivity, and for tubulin oligomers, which are characterized by large diffusivity. The difference in transport modes between these two types of organelles in a short axon is discussed. A comparison between zero-order and first-order approximations makes it possible to obtain a physical insight into the effects of organelle reversals (when organelles change the type of a molecular motor they are attached to, an anterograde versus retrograde motor).     

Effect of cytoskeletal element degradation on merging of concentration waves in slow axonal transport

The aim of this paper is to investigate, by means of a numerical simulation, the effect of the half-life of cytoskeletal elements (CEs) on superposition of several waves representing concentrations of running, pausing, and off-track anterograde and retrograde CE populations. The waves can be induced by simultaneous microinjections of radiolabeled CEs in different locations in the vicinity of a neuron body; alternatively, the waves can be induced by microinjecting CEs at the same location several times, with a time interval between the injections. Since the waves spread out as they propagate downstream, unless their amplitude decreases too fast, they eventually superimpose. As a result of superposition and merging of several waves, for the case with a large half-life of CEs, a single wave is formed. For the case with a small half-life the waves vanish before they have enough time to merge.     

Detectable states,cycle fluxes,and motility scaling of molecular motor kinesin: An integrative kinetic graph theory analysis

The process by which a kinesin motor couples its ATPase activity with concerted mechanical hand-over-hand steps is a foremost topic of molecular motor physics. Two major routes toward elucidating kinesin mechanisms are the motility performance characterization of velocity and run length, and single-molecular state detection experiments. However, these two sets of experimental approaches are largely uncoupled to date. Here, we introduce an integrative motility state analysis based on a theorized kinetic graph theory for kinesin, which, on one hand, is validated by a wealth of accumulated motility data, and, on the other hand, allows for rigorous quantification of state occurrences and chemomechanical cycling probabilities. An interesting linear scaling for kinesin motility performance across species is discussed as well. An integrative kinetic graph theory analysis provides a powerful tool to bridge motility and state characterization experiments, so as to forge a unified effort for the elucidation of the working mechanisms of molecular motors.     

Merging of viral concentration waves in retrograde viral transport in axons

This paper develops an analytical solution describing propagation of two viral waves in an axon and applies the obtained analytical solution to investigating the dynamics of merging of these two waves as they move retrogradely toward the neuron body. The viral diffusivity and viral degradation are accounted for in the model. Computational results are presented for two situations: when all dynein motors move with the same velocity and when dynein motor velocity distribution is characterized by a probability density function (pdf). The effect of various model parameters on the time it takes for the waves to merge is discussed. It is proposed that observing the dynamics of wave merging can be used for determining parameters characterizing viral transport, such as the viral diffusivity. This may contribute toward better understanding of viral transport properties and potentially help in developing novel viral detection techniques.     

Elastic waves in non-Newtonian (Maxwell) fluid-saturated porous media

This paper studies the elastic waves in non-Newtonian (Maxwell) fluid-saturated porous media with the nonzero boundary slip velocity for pore size distribution. The coefficient bF_m(ω) that measures the deviation from Poiseuille flow friction in such media is presented. Based on this coefficient, we investigate the properties of elastic waves by calculating their phase velocities and attenuation coefficients as functions of frequency and the behaviour of the dynamic permeability. The study shows that the pore size distribution removes oscillations in all physical quantities in the non-Newtonian regime. Consideration of the nonzero boundary slip effect in non-Newtonian (Maxwell) fluid-saturated porous media results in (a) an overall increase of the dynamic permeability, (b) an increase of phase velocities of fast Biot waves and shear waves except in the low frequency domain and an overall increase of phase velocity of slow Biot waves and (c) an overall increase of the attenuation of three Biot waves in the intermediate frequency domain except in the deeply non-Newtonian regime. The study also shows that the attenuation coefficient of slow Biot waves is small in the deeply non-Newtonian regime at higher frequency, which encourages us to detect slow Biot waves in oil-saturated porous rock.     

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.     

Dynamics of cooperative transport by multiple kinesin motors and diffusing microtubule-associated proteins

In eukaryote cells, cargos are often transported cooperatively by kinesin motors and nonmotor microtubule-associated proteins (MAPs). The prior in vitro experimental data showed that the velocity of the cargo transported by kinesin motors and Ndc80 (a member of MAP) proteins of truncated coiled-coil stalks decreases sensitively with the increase of the ratio of Ndc80 to motor number. However, the underlying mechanism of Ndc80 affecting sensitively the cooperative cargo transport by kinesin motors is unclear. To understand the mechanism, here we study numerically the cooperative cargo transport by kinesin motors and Ndc80 proteins. Our results showed that for the case of the motors and Ndc80 proteins with truncated short stalks, as used in the experiments, the calculated results reproduce quantitatively the prior experimental data. The mechanism of the cargo velocity decreasing sensitively with the ratio of Ndc80 to motor number is revealed. By contrast, for the case of the motors and Ndc80 proteins with full-length long stalks, the velocity of the cargo decreases slowly with the increase in the ratio of Ndc80 to kinesin number. Our results thus give an explanation of why the kinesin motors working in the cell have long stalks.     

Elastic waves in non-Newtonian (Maxwell) fluid-saturated porous media

Abstract

This paper studies the elastic waves in non-Newtonian (Maxwell) fluid-saturated porous media with the nonzero boundary slip velocity for pore size distribution. The coefficient bF _m (ω) that measures the deviation from Poiseuille flow friction in such media is presented. Based on this coefficient, we investigate the properties of elastic waves by calculating their phase velocities and attenuation coefficients as functions of frequency and the behaviour of the dynamic permeability. The study shows that the pore size distribution removes oscillations in all physical quantities in the non-Newtonian regime. Consideration of the nonzero boundary slip effect in non-Newtonian (Maxwell) fluid-saturated porous media results in (a) an overall increase of the dynamic permeability, (b) an increase of phase velocities of fast Biot waves and shear waves except in the low frequency domain and an overall increase of phase velocity of slow Biot waves and (c) an overall increase of the attenuation of three Biot waves in the intermediate frequency domain except in the deeply non-Newtonian regime. The study also shows that the attenuation coefficient of slow Biot waves is small in the deeply non-Newtonian regime at higher frequency, which encourages us to detect slow Biot waves in oil-saturated porous rock.     

The neck linker of kinesin 1 seems optimally designed to approach the largest stepping velocity: a simulation study of an ideal model

The neck linker is widely believed to play a critical role in the hand-over-hand walking of conventional kinesin 1. Experiments have shown that change of the neck linker length will significantly change the stepping velocity of the motor. In this paper, we studied this length effect based on a highly simplified chemically powered ratchet model. In this model, we assume that the chemical steps (ATP hydrolysis, ADP and P(i) release, ATP binding, neck linker docking) are fast enough under conditions far from equilibrium and the mechanical steps (detachment, diffusional search and re-attachment of the free head) are rate-limiting in kinesin walking. According to this model, and regarding the neck linker as a worm-like-chain polypeptide, we can calculate the steady state stepping velocity of the motor for different neck linker lengths. Our results show, under the actual values of binding energy between kinesin head and microtubule (~15k(B)T) and the persistence length of neck linker (~0.5 nm), that there is an optimal neck linker length (~14-16 a.a.) corresponding to the maximal velocity, which implies that the length of the wild-type neck linker (~15 a.a.) might be optimally designed for kinesin 1 to approach the largest stepping velocity.     

用求解概率密度函数输运方程的方法模拟湍流自由射流

用求解概率密度函数输运方程的方法模拟湍流自由射流周向阳，郑楚光，马毓义（华中理工大学煤燃烧国家重点实验室武汉４３００７４）关键词概率密度函数；湍流；自由射流１前言和通常的湍流统计矩模型（如ｋ－ε模型或Ｒｅｙｎｏｌｄｓ应力模型等）相比，用求解速度和标量...     

Wave motion of incompressible turbulent fluid

Evolution of small disturbances in a fully developed incompressible turbulent flow is considered on the base of the transport equation for the single-point probability density function (PDF) of velocity fluctuations. It is shown that at high frequencies this equation is similar to the Vlasov equation for charged plasma in a self-consistent electromagnetic field having longitudinal wave solutions for turbulent stresses similar to Langmuir waves. It is found that the longitudinal waves of turbulent stresses have a constant phase velocity and can be damped, neutral, or growing waves, depending on the type of undisturbed probability density function of velocity fluctuations. The obtained result differs from the previously published solutions to this problem using the statistical moments closures according to which the wave disturbances should be neutral or damped. The possibilities of experimental observation of longitudinal waves of turbulent stresses are analyzed.     

Velocity locking of incoherent nonlinear wave packets

We show both theoretically and experimentally in an optical fiber system that a set of incoherent nonlinear waves irreversibly evolves to a specific equilibrium state, in which the individual wave packets propagate with identical group velocities. This intriguing process of velocity locking can be explained in detail by simple thermodynamic arguments based on the kinetic wave theory. Accordingly, the selection of the velocity-locked state is shown to result from the natural tendency of the isolated wave system to approach the state that maximizes the nonequilibrium entropy.     

驱动马达定向运动的随机动力学模型

本文在非对称周期势中考虑驱动马达的机械化学耦合,基于布朗马达的工作原理,利用MATLAB数值模拟驱动马达在一定实验条件下的运动特征.我们首先模拟了单个驱动马达的位移和速度随时间变化的图像,然后分别计算了多个驱动马达运动的平均速度,最后计算了不同负载力条件下马达运动速度的系综平均值.模拟结果表明驱动马达在定向运动中存在等待态和行走态,行走步长约为8.2nm,且马达运动具有一定的随机性.通过与实验比较,发现模型计算结果与实验吻合.     

Cancellous bone analysis with modified least squares Prony's method and chirp filter: phantom experiments and simulation

The presence of two longitudinal waves in porous media is predicted by Biot's theory and has been confirmed experimentally in cancellous bone. When cancellous bone samples are interrogated in through-transmission, these two waves can overlap in time. Previously, the Modified Least-Squares Prony's (MLSP) method was validated for estimation of amplitudes, attenuation coefficients, and phase velocities of fast and slow waves, but tended to overestimate phase velocities by up to about 5%. In the present paper, a pre-processing chirp filter to mitigate the phase velocity bias is derived. The MLSP/chirp filter (MLSPCF) method was tested for decomposition of a 500 kHz-center-frequency signal containing two overlapping components: one passing through a low-density-polyethylene plate (fast wave) and another passing through a cancellous-bone-mimicking phantom material (slow wave). The chirp filter reduced phase velocity bias from 100 m/s (5.1%) to 69 m/s (3.5%) (fast wave) and from 29 m/s (1.9%) to 10 m/s (0.7%) (slow wave). Similar improvements were found for 1) measurements in polycarbonate (fast wave) and a cancellous-bone-mimicking phantom (slow wave), and 2) a simulation based on parameters mimicking bovine cancellous bone. The MLSPCF method did not offer consistent improvement in estimates of attenuation coefficient or amplitude.     

Dispersion of interface waves in sediments with power-law shear speed profiles. I. Exact and approximate analytical results.

In the upper tens of meters of ocean bottom, unconsolidated marine sediments consisting of clay, silt, or fine sand with high porosity are "almost incompressible" in the sense that the shear wave velocity is much smaller than the compressional wave velocity. The shear velocity has very large gradients close to the ocean floor leading to strong coupling of compressional and shear waves in such "soft" sediments. The weak compressibility opens an avenue for developing a theory of elastic wave propagation in continuously stratified soft sediments that fully accounts for the coupling. Elastic waves in soft sediments consist of "fast" waves propagating with velocities close to the compressional velocity and "slow" waves propagating with velocities on the order of the shear velocity. For the slow waves, the theory predicts the existence of surface waves at the ocean-sediment boundary. In the important special case of the power-law depth-dependence of shear rigidity, phase and group velocities of the interface waves are shown to scale as a certain power of frequency. An explicit, exact solution was obtained for the surface waves in sediments characterized by constant density and a linear increase of shear rigidity with depth, that is, for the case of shear speed proportional to the square root of the depth below the sediment-water interface. Asymptotic and perturbation techniques were used to extend the result to more general environments. Theoretical dispersion relations agreed well with numerical simulations and available experimental data and, as demonstrated in a companion paper [D. M. F. Chapman and O. A. Godin, J. Acoust. Soc. Am 110, 1908 (2001)] led to a simple and robust inversion of interface wave travel times for shear velocity profiles in the sediment.     

Reconceptualizing kinesin’s working cycle as separate chemical and mechanical processes

The biomolecular motor kinesin uses chemical energy released from a fuel reaction to generate directional movement and produce mechanical work. The underlying physical mechanism is not fully understood yet. To analyze the energetics of the motor, we reconceptualize its chemomechanical cycle in terms of separate fuel reaction and work production processes and introduce a thermodynamic constraint to optimize the cycle. The model predicts that the load dependences of the motor’s velocity, stepping ratio, and dwell time are determined by the mechanical parameters of the motor–track system rather than the fuel reaction rate. This behavior is verified using reported experimental data from wild-type and elongated kinesins. The fuel reaction and work production processes indicate that kinesin is driven by switching between two chemical states, probably following a general pattern for molecular motors. The comparison with experimental data indicates that the fuel reaction processes are close to adiabatic, which is important for efficient operation of the motor. The model also suggests that a soft, short neck linker is important for the motor to maintain its load transport velocity.     

无旋性前进重力波传递在均匀流中的Lagrangen解析解与试验验证Ⅱ.试验验证

针对文献[1]中的无旋性自由表面周期性规则前进重力波传递在均匀流中,本文以与前进波波向同向与反向的均匀流两种特例情况,进行试验测量,所得的波形曲线、流速分布、流体质点的运动轨迹与运动周期及其质量传输速率与Lagrange平均高程等特性,均与文献[1]中全以Lagrange方式所得的三阶解结果符合得很好.这证实本研究取定的标注流体质点的参数,正好为其在原静止水中的位置坐标值.同时亦证实波流场中由流体质点所构成的波形曲线,其波长皆同于(纯)前进波,而其传播速度为(纯)前进波波速与均匀流流速之和是具Doppler效应的;而流体质点的运动周期与其运动周期平均高程、及其质量传输速率扣掉均匀流流速等,都与(纯)前进波的相符.另外,亦揭示出流体质点的运动轨迹,在前进波波向与均匀流同向中,当流体质点在波谷断面处时沿前进波波向的流速分量为反向、零与正向时,则其形状分别为朝波向前进的扁长辐状余摆线、在波谷断面处成尖点朝下的滚轮状线与短辐形余摆线;而在前进波波向与均匀流反向中,当流体质点的质量传输速率为沿前进波波向为正向与零时,则其形状分别为朝波向前进的缩短的扁长辐形余摆线与长轴在前进波波向上椭圆形封闭曲线;而当流体质点的质量传输速率为反前进波波向,但质点在波峰断面处时沿前进波波向的流速分量分别为正向、零与反向时,则其形状分别为反波向前进的倒扁长辐形余摆线、在波峰断面处成尖点朝上的倒滚轮状线与倒短辐形余摆线.     

两相壁面射流PDF方程有限分析方法及数值模拟

提出求解位置-速度相空间中高维两相流PDF(probability density function)方程的有限分析方法,将位置-速度相空间颗粒PDF方程约化到速度空间,并解析求解,颗粒的位置PDF用轨道方法求解.对壁面射流两相流动进行数值模拟,并与颗粒雷诺应力轨道方法进行比较计算,结果优于颗粒雷诺应力轨道方法.     

Cooling kinetics of a granular gas of viscoelastic particles

The evolution of a granular gas of viscoelastic particles in the homogeneous cooling state is studied. The velocity distribution function of granular particles and the time dependence of the mean kinetic energy of particles (granular temperature) are found. The noticeable deviation of the distribution function from the Maxwell distribution and its non-monotonous evolution are established. The perturbation theory with respect to the small dispersion parameter is elaborated and the analytical expressions for the asymptotic time dependence of the velocity distribution function and the granular gas temperature are derived.