Entropic particle transport in periodic channels

The dynamics of Brownian motion has widespread applications extending from transport in designed micro-channels up to its prominent role for inducing transport in molecular motors and Brownian motors. Here, Brownian transport is studied in micro-sized, two-dimensional periodic channels, exhibiting periodically varying cross-sections. The particles in addition are subjected to an external force acting alongside the direction of the longitudinal channel axis. For a fixed channel geometry, the dynamics of the two-dimensional problem is characterized by a single dimensionless parameter which is proportional to the ratio of the applied force and the temperature of the particle environment. In such structures entropic effects may play a dominant role. Under certain conditions the two-dimensional dynamics can be approximated by an effective one-dimensional motion of the particle in the longitudinal direction. The Langevin equation describing this reduced, one-dimensional process is of the type of the Fick-Jacobs equation. It contains an entropic potential determined by the varying extension of the eliminated channel direction, and a correction to the diffusion constant that introduces a space dependent diffusion. Different forms of this correction term have been suggested before, which we here compare for a particular class of models. We analyze the regime of validity of the Fick-Jacobs equation, both by means of analytical estimates and the comparisons with numerical results for the full two-dimensional stochastic dynamics. For the nonlinear mobility we find a temperature dependence which is opposite to that known for particle transport in periodic potentials. The influence of entropic effects is discussed for both, the nonlinear mobility and the effective diffusion constant.     

Characteristic features of electron-ion collisions in strong electric fields

The classical motion of an electron in the Coulomb field of an ion and in a uniform external electric field is analyzed. A nondimensionalization method that makes it possible to study electron motion in arbitrarily strong electric fields is proposed. The possible electron trajectories in the plane of motion in a static field are classified. It is noted that, from a practical standpoint, the most interesting trajectories are snakelike trajectories, which are absent in the problem with a weak external field. An adiabatic approximation for transverse electron motions in quasistatic (strong) fields is constructed. A one-dimensional equation of motion is derived that accounts for transverse electron oscillations and the increase in the effective electron mass as an electron approaches an ion. An analytic model is used to calculate the spectra of bremsstrahlung generated by individual electrons. The calculated results are shown to agree well with the results of direct numerical integration of the basic equations. It is predicted that, at frequencies higher than the frequency of the incident light, pronounced peaks can appear in the spectrum of the transverse dipole moment of an electron; as a result, an electron is expected to effectively emit radiation at these frequencies in the direction of the external field.     

Formulation of Statistical Equation of Motion of Blood

A general form of the statistical equation of motion of the blood is derived by averaging the motion of individual elements of the blood over a small volume in space. This equation can be transformed into an explicit form to find the constitutive equations of the blood provided the detailed motion of the plasma in some neighborhood of a suspended particle is known. As a demonstration of such transformation, the general form of the statistical equation of motion is applied to the suspension of sphere with a very low concentration to find the effective viscosity.     

Kinetic criteria of solid state mechanisms in biology

Kinetic criteria for solid state physical mechanisms of electron and ion transport in biological systems are summarized, and the mechanisms are discussed. A reaction which is rate-limited by electron or ion transport across a particle or membrane in accord with Ohm's law will show first order kinetics, with an hyperbolic relationship between rate constant and the sum of substrate plus product. Larger initial substrate concentrations produce smaller rate constants, thus giving the appearance of substrate inhibition. Examples are cytochrome oxidase and peroxidase, and pyruvate carboxylase. Ohmic transport mechanisms may be caused by electron conduction or superconduction through protein, by electron conduction through water, or by conduction of ions through membranes. A reaction which is rate-limited by charge transport across an activation energy barrier at an interface in accord with a logarithmic voltage-current law will show reaction kinetics conforming to the Elovich equation, and will have the appearance of a pair of simultaneous first order processes. Examples include decay of photogenerated free radicals in eye melanin particles and in photosynthetic particles of bacteria, and sodium and potassium ion transport across cell surfaces. The logarithmic voltage-current law may be regarded as an empirical relationship describing behavior of interfaces, justified by extensive experimental data on many types of interfaces, or it may be derived theoretically for individual cases from statistical mechanical and/or solid state physical considerations. Dedicated to Prof. N. Rashevsky and to his enlightened editorial policy, especially to his policy of publishing that which is new, even when he disagrees with it.     

Estimating equations for spatially correlated data in multi-dimensional space

We use the quasilikelihood concept to propose an estimatingequation for spatial data with correlation across the studyregion in a multi-dimensional space. With appropriate mixingconditions, we develop a central limit theorem for a randomfield under various L_p metrics. The consistency and asymptoticnormality of quasilikelihood estimators can then be derived.We also conduct simulations to evaluate the performance of theproposed estimating equation, and a dataset from East LansingWoods is used to illustrate the method.     

The random walk of Azospirillum brasilense

The bacterium Azospirillum brasilense has been frequently studied in laboratory experiments. It performs movements in space where long forward and backward runs on a straight line occur simultaneously with slow changes of direction of the line. A model is presented in which a correlated random walk on a line is joined to diffusion on a sphere of directions. For this transport system, a hierarchy of moment approximations is derived, ranging from a hyperbolic system with four dependent variables to a scalar damped wave equation (telegraph equation) and then to a single diffusion equation for particle density. The original parameters are compounded in the diffusion quotient. The effects of these parameters, such as particle speed or turning rate, on the diffusion coefficient are discussed in detail.     

Description of turbulent convection in a plasma with the help of interacting Lorentz oscillators

A four-field model is proposed that describes turbulent plasma convection inside the separatrix during the L-H transition. It is shown that the Braginskii four-field hydrodynamic equations, which describe fluctuations of the electron and ion temperatures, plasma density, and electrostatic potential in tokamak edge plasmas, can be reduced to three Lorentz-like systems of equations coupled through the equation for the kinetic energy of the fluctuations, i.e., to a four-field edge turbulent layer model describing the nonlinear dynamics of convective cells in the presence of a sheared flow. For three coupled oscillators, the critical pressure gradient corresponding to transitions to both L-and H-modes is found to be much lower than that for an individual oscillator, which describes turbulent convection driven by fluctuations of one type. The edge turbulent layer model makes it possible to describe the formation of a transport barrier inside the separatrix during the L-H transition; calculate heat and particle fluxes via ion and electron channels; and, in combination with the transport code for a core plasma, compute the auxiliary heating power required for a transition to the H-mode.     

Evaluation of the effect of water on the kinetics of transmembrane transport of ions along narrow ionic channels

An equation for the velocity of ion transport along channels with a unidirectional flux of water molecules and ions was derived. It has been shown that the ionic flux linked between water transport is negligible as compared with the overall ionic flux. The effect of water is to diminish the maximum transport velocity only.     

Brownian dynamics study of ion transport in the vestibule of membrane channels.

Brownian dynamics simulations have been carried out to study the transport of ions in a vestibular geometry, which offers a more realistic shape for membrane channels than cylindrical tubes. Specifically, we consider a torus-shaped channel, for which the analytical solution of Poisson's equation is possible. The system is composed of the toroidal channel, with length and radius of the constricted region of 80 A and 4 A, respectively, and two reservoirs containing 50 sodium ions and 50 chloride ions. The positions of each of these ions executing Brownian motion under the influence of a stochastic force and a systematic electric force are determined at discrete time steps of 50 fs for up to 2.5 ns. All of the systematic forces acting on an ion due to the other ions, an external electric field, fixed charges in the channel protein, and the image charges induced at the water-protein boundary are explicitly included in the calculations. We find that the repulsive dielectric force arising from the induced surface charges plays a dominant role in channel dynamics. It expels an ion from the vestibule when it is deliberately put in it. Even in the presence of an applied electric potential of 100 mV, an ion cannot overcome this repulsive force and permeate the channel. Only when dipoles of a favorable orientation are placed along the sides of the transmembrane segment can an ion traverse the channel under the influence of a membrane potential. When the strength of the dipoles is further increased, an ion becomes detained in a potential well, and the driving force provided by the applied field is not sufficient to drive the ion out of the well. The trajectory of an ion navigating across the channel mostly remains close to the central axis of the pore lumen. Finally, we discuss the implications of these findings for the transport of ions across the membrane.     

Recent progress in membrane protein dynamics revealed by X-ray free electron lasers: Molecular movies of microbial rhodopsins

Microbial rhodopsin is a membrane protein with a domain of seven-transmembrane helices and a retinal chromophore. The main function of this protein is to perform light-induced ion transport, either actively or passively, by acting as pumps, channels, and light sensors. It is widely used for optogenetic application to control the activity of specific cells in living tissues by light. Time-resolved serial femtosecond crystallography (TR-SFX) with the use of X-ray free electron lasers is an effective technique for capturing dynamic ion transport and efflux structures across membranes with high spatial and temporal resolutions. Here, we outline recent TR-SFX studies of microbial rhodopsins, including a pump and a channel. We also discuss differences and similarities observed in the structural dynamics derived from the TR-SFX structures.     

Random walk with persistence and external bias

The partial differential equation of the random walk problem with persistence of direction and external bias is derived. By persistence of direction or internal bias we mean that the probability a particle will travel in a given direction need not be the same for all directions, but depends solely upon the particle's previous direction of motion. The external bias arises from an anisotropy of the medium or an external force on the particle. The problem is treated by considering that the net displacement of a particle arises from two factors, namely, that neither the probability of the particle traveling in any direction after turning nor the distance the particle travels in a given direction need be the same for all directions. A modified Fokker-Planck equation is first obtained using the assumptions that the particles have a distribution of travel times and speeds and that the average time of travel between turns need not be zero. The fional equation incopporating the assumption of a persistence of direction and an external bias is then derived. Applications to the study of diffusion and to long-chain polymers are then made. This work was done while the author was Public Health Service Research Fellow of The National Institute of Mental Health, Federal Security Agency.     

The reliability of relative anion-cation permeabilities deduced from reversal (Dilution) potential measurements in ion channel studies

Measurements of anion-cation permeability ratios (e.g., P _Cl/P _Na) are most readily made by measuring changes in zero-current reversal potential when the salt concentration on one side of the membrane (e.g., external NaCl) is decreased. This is particularly useful for measuring changes in ion selectivity in wild-type and mutant channels, such as those of the ligand-gated ion channel superfamily, and has shown that many of these channels have a significant permeability to counter-ions. One Brownian dynamics study of ion permeation through such narrow ion channels failed to observe such counter-ion movement, although later, another Brownian dynamics study did observe counter-ion movement through simulations of the same channels. The question has been raised as to the reliability of such reversal potential measurements for determining permeability ratios, particularly given the use of an equation such as the Goldman-Hodgkin-Katz (GHK) equation, which is often used to calculate such ratios. A new derivation of the GHK equation in terms of activity coefficients is also included. The application of irreversible thermodynamics will be shown to qualitatively support the reliability of such experimental anion-cation permeability values derived from reversal potential measurements. It will then be shown that for such zero-current situations, different electrodiffusion models, with very different underlying assumptions, produce almost identical relative permeabilities (and reversal potentials). Finally, the results of the two Brownian dynamics simulation studies and the relationship between reversal potentials and relative permeability will be discussed.     

The drift approximation solves the Poisson, Nernst-Planck, and continuum equations in the limit of large external voltages

Nearly linear current-voltage curves are frequently found in biological ion channels. Using the drift limit of the substantially non-linear Poisson-Nernst-Planck equations, we explain such behavior of diffusion-controlled charge transport systems. Starting from Gauss' law, drift, and continuity equations we derive a simple analytical current-voltage relation, which accounts for this deviation from linearity. As shown previously, the drift limit of the Nernst-Planck equation applies if the total electric current is dominated by the electric field, and integral contributions from concentration gradients are small. The simple analytical form of the drift current-voltage relations makes it an ideal tool to analyze experiment current-voltage curves. We also solved the complete Poisson-Nernst-Planck equations numerically, and determined current-voltage curves over a wide range of voltages, concentrations, and Debye lengths. The simulation fully supports the analytical estimate that the current-voltage curves of simple charge transport systems are dominated by the drift mechanism. Even those relations containing the most extensive approximations remained qualitatively within the correct order of magnitude. Received: 24 September 1998 / Revised version: 22 January 1999 / Accepted: 22 January 1999     

Instabilities on Prey Dynamics in Jellyfish Feeding

We study the dynamics of plankton in the wake of a jellyfish. Using an analytical approach, we derive a reduced-order equation that governs the prey motion which is modeled as neutrally-buoyant inertial particle. This modified equation takes into account both the effects of prey inertia and self-propulsion and enables us to calculate both the attracting and repelling Lagrangian coherent structures for the prey motion. For the case of zero self-propulsion, it is simplified to the equation of motion for infinitesimal fluid particles. Additionally, we determine the critical size of prey over which instabilities on its motion occur resulting in different dynamics from those predicted by the reduced-order equation even for the case of zero self-propulsion. We illustrate our theoretical findings through an experimentally measured velocity field of a jellyfish. Using the inertial equation, we calculate the Lagrangian coherent structures that characterize prey motion as well as the instability regions over which larger prey will have different dynamics even for the case of zero self-propulsion.     

Suppression of the neoclassical tearing modes in tokamaks under anomalous transverse transport conditions when the magnetic well effect predominates over the bootstrap drive

A study is made of the suppression of neoclassical tearing modes in tokamaks under anomalous transverse transport conditions when the magnetic well effect predominates over the bootstrap drive. It is stressed that the corresponding effect, which is called the compound suppression effect, depends strongly on the profiles of the electron and ion temperature perturbations. Account is taken of the fact that the temperature profile can be established as a result of the competition between anomalous transverse heat transport, on the one hand, and longitudinal collisional heat transport, longitudinal heat convection, longitudinal inertial transport, and transport due to the rotation of magnetic islands, on the other hand. The role of geodesic effects is discussed. The cases of competition just mentioned are described by the model sets of reduced transport equations, which are called, respectively, collisional, convective, inertial, and rotational plasmophysical models. The magnetic well is calculated with allowance for geodesic effects. It is shown that, for strong anomalous heat transport conditions, the contribution of the magnetic well to the generalized Rutherford equation for the island width W is independent of W not only in the collisional model (which has been investigated earlier) but also in the convective and inertial models and depends very weakly (logarithmically) on W in the rotational model. It is this weak dependence that gives rise to the compound effect, which is the subject of the present study. A criterion for the stabilization of neoclassical tearing modes by the compound effect at an arbitrary level of the transverse heat transport by electrons and ions is derived and is analyzed for two cases: when the electron heat transport and ion heat transport are both strong, and when the electron heat transport is strong and the ion heat transport is weak.     

Multiscale analysis of collective motion and decision-making in swarms: An advection-diffusion equation with memory approach

We propose a (time) multiscale method for the coarse-grained analysis of collective motion and decision-making in self-propelled particle models of swarms comprising a mixture of ‘naïve’ and ‘informed’ individuals. The method is based on projecting the particle configuration onto a single ‘meta-particle’ that consists of the elongation of the flock together with the mean group velocity and position. We find that the collective states can be associated with the transient and asymptotic transport properties of the random walk followed by the meta-particle, which we assume follows a continuous time random walk (CTRW). These properties can be accurately predicted at the macroscopic level by an advection-diffusion equation with memory (ADEM) whose parameters are obtained from a mean group velocity time series obtained from a single simulation run of the individual-based model.