Liquid junction potentials calculated from numerical solutions of the Nernst-Planck and Poisson equations

We present numerical solutions for the one-dimensional Nernst-Planck and Poisson system of equations for steady-state electrodiffusion. Commonly used approximate solutions to these equations invoke assumptions of local electroneutrality (Planck approximation) or constant electric field (Goldman approximation). Calculations were performed to test the ranges over which these approximate theories are valid. For a dilutional junction of a 1:1 electrolyte, separated from adjoining perfectly stirred solutions by sharp boundaries, the Planck approximation is valid for values of kappa dL greater than 10, where 1/kappa d is the Debye length of the more dilute solution. The Goldman approximation is valid for kappa cL less than 0.1 where 1/kappa c is the Debye length of the more concentrated solution. These results suggest that the modeling of electrodiffusive flows in and near membrane ion channels may require numerical solutions of this set of equations rather than the use of either limiting case.     

Analytical solution to the initial-value problem for traveling bands of chemotactic bacteria

The governing parabolic partial differential equations for the diffusion and chemotactic transport of a distribution of bacteria and for the diffusion and bacterial degradation of a distribution of chemotactic agent are supplemented with boundary and initial conditions that model the recent capillary tube experiments on the formation and propagation of traveling bands of chemotactic bacteria. An iteration procedure that takes the exact solution to the “diffusionless” problem as a first approximation is applied to solve the equations of the complete theoretical model. It is shown that satisfactory agreement with experiment obtains for the analytical results of the first approximation which relate the velocity of propagation and total number of bacteria cells per unit cross-sectional area in a traveling band to the constant parameters in the governing equations and supplementary conditions. The second approximation is shown to yield approximate analytical expressions for the solution functions which are in close correspondence with previously derived traveling band solutions for values of time after the initial period of formation.     

System of Kinetic Equations for Collisionless Space Plasma in the Approximation of Field-Aligned Force Equilibrium for Electrons

A system of kinetic equations describing relatively slow large-scale processes in collisionless magnetoplasma structures with a spatial resolution on the order of the proton thermal gyroradius is derived. The system correctly takes into account the electrostatic effects in the approximation of field-aligned force equilibrium for electrons. The plasma is considered quasineutral, and the magnetic field is described by the Ampère equation. The longitudinal component of the electric field is found explicitly from the equality of the field-aligned component of the electric force acting on plasma electrons and the divergence of the electron pressure tensor. The electric field component orthogonal to the magnetic field is determined by the distributions of the number densities, current densities, and stress tensors of all plasma species in the instantaneous long-range approximation described by a system of time-independent elliptic equations. Versions of the system of equations adapted to the case of magnetized electrons described by the Vlasov equation in the drift approximation, as well as to the case in which all plasma species are magnetized, are derived. The resulting systems of equations allow creating numerical models capable of describing large-scale processes in nonuniform collisionless space plasma.     

Validity of the rapid buffering approximation near a point source of calcium ions.

In the presence of rapid buffers the full reaction-diffusion equations describing Ca2+ transport can be reduced using the rapid buffering approximation to a single transport equation for [Ca2+]. Here we simulate the full and reduced equations, exploring the conditions necessary for the validity of the rapid buffering approximation for an isolated Ca2+ channel or a cluster of channels. Using a point source and performing numerical simulations of different durations, we quantify the error of the rapid buffering approximation as a function of buffer and source parameters as well as the time and spatial scale set by the resolution of confocal microscopic measurements. We carry out simulations of Ca2+ "sparks" and "puffs," both with and without the indicator dye Ca2+ Green-1, and find that the rapid buffering approximation is excellent. These calculations also show that the traditional calculation of [Ca2+] from a fluorescence signal may grossly underestimate the true value of [Ca2+] near a source. Finally, we use the full model to simulate the transient Ca2+ domain near the pore of an open Ca2+ channel in a cell dialyzed with millimolar concentrations of 1,2-bis(2-aminophenoxy)ethane-N,N,N,N-tetraacetic acid or EGTA. In this regime, where the rapid buffering approximation is poor. Neher's equation for the steady-state Ca2+ profile is shown to be a reliable approximation adjacent to the pore.     

Prediction of the power of detection of marker-quantitative trait locus linkages using analysis of variance

Analysis of variance can be used to detect the linkage of segregating quantitative trait loci (QTLs) to molecular markers in outbred populations. Using independent full-sib families and assuming linkage equilibrium, equations to predict the power of detection of a QTL are described. These equations are based on an hierarchical analysis of variance assuming either a completely random model or a mixed model, in which the QTL effect is fixed. A simple prediction of power from the mean squares is used that assumes a random model so that in the mixed-model situation this is an approximation. Simulation is used to illustrate the failure of the random model to predict mean squares and, hence, the power. The mixed model is shown to provide accurate prediction of the mean squares and, using the approximation, of power.     

The numerical method for the optimal supporting position and related optimal control for the catalytic reaction system

This paper considers the numerical approximation for the optimal supporting position and related optimal control of a catalytic reaction system with some control and state constraints, which is governed by a nonlinear partial differential equations with given initial and boundary conditions. By the Galerkin finite element method, the original problem is projected into a semi-discrete optimal control problem governed by a system of ordinary differential equations. Then the control parameterization method is applied to approximate the control and reduce the original system to an optimal parameter selection problem, in which both the position and related control are taken as decision variables to be optimized. This problem can be solved as a nonlinear optimization problem by a particle swarm optimization algorithm. The numerical simulations are given to illustrate the effectiveness of the proposed numerical approximation method.     

Analysis of time hierarchy in plant cell volume changes

A simple model of plant cell volume changes is presented. It is based on Kedem-Katchalsky equations for water and solute transport and on linear approximation of the dependence of intracellular hydrostatic pressure on the cell volume. Active transport of solute is also included. The time hierarchy within the system is analyzed by appropriate normalization of variables and by the assessment of the numerical values of model coefficients. The dynamics of the system comprises a slow process of solute exchange and a fast process of water transport. This explains the wellknown biphasic response of the cell volume to a sudden change in external conditions. An approximation of equations describing the system behaviour on the basis of the Tikhonov's theorem is proposed. The approximative solution is compared with the exact numerical solution of the original equations. The approximation is very good under physiological conditions, but it ceases to hold when the solute permeability of the cell membrane increases causing the breakdown of the entire time hierarchy within the system.     

Interaction energies in non-covalently bound intermolecular complexes derived using the subsystem formulation of density functional theory

Interaction energies for a representative sample of 39 intermolecular complexes are calculated using two computational approaches based on the subsystem formulation of density functional theory introduced by Cortona (Phys. Rev. B 44:8454, 1991), adopted for studies of intermolecular complexes (Wesolowski and Weber in Chem. Phys. Lett. 248:71, 1996). The energy components (exchange-correlation and non-additive kinetic) expressed as explicit density functionals are approximated by means of gradient-free- (local density approximation) of gradient-dependent- (generalized gradient approximation) approximations. The sample of the considered intermolecular complexes was used previously by Zhao and Truhlar to compare the interaction energies derived using various methods based on the Kohn-Sham equations with high-level quantum chemistry results considered as the reference. It stretches from rare gas dimers up to strong hydrogen bonds. Our results indicate that the subsystem-based methods provide an interesting alternative to that based on the Kohn-Sham equations. Local density approximation, which is the simplest approximation for the relevant density functionals and which does not rely on any empirical data, leads to a computational approach comparing favorably with more than twenty methods based on the Kohn-Sham equations including the ones, which use extensively empirical parameterizations. For various types of non-bonding interactions, the strengths and weaknesses of gradient-free and gradient-dependent approximations to exchange-correlation and non-additive kinetic energy density functionals are discussed in detail.     

System of kinetic equations describing large-scale processes in collisionless space plasma

A system of kinetic equations describing relatively slow large-scale processes in collisionless magnetoplasma structures with a spatial resolution of about the characteristic gyroradius is derived. Plasma is assumed to be quasineutral, while the magnetic and electric fields are determined by the instantaneous distributions of the particle and current densities and the stress tensor of all plasma components in the longrange instantaneous interaction approximation. A special version of equations is derived for the case of magnetized electrons described by the Vlasov equation in the drift approximation. The obtained system of equations can be used to develop a global numerical kinetic model of the Earth’s magnetosphere with a spatial resolution of about 100 km, as well as local models of certain regions of the Earth’s magnetosphere with a higher resolution.     

On learning dynamics underlying the evolution of learning rules

In order to understand the development of non-genetically encoded actions during an animal’s lifespan, it is necessary to analyze the dynamics and evolution of learning rules producing behavior. Owing to the intrinsic stochastic and frequency-dependent nature of learning dynamics, these rules are often studied in evolutionary biology via agent-based computer simulations. In this paper, we show that stochastic approximation theory can help to qualitatively understand learning dynamics and formulate analytical models for the evolution of learning rules. We consider a population of individuals repeatedly interacting during their lifespan, and where the stage game faced by the individuals fluctuates according to an environmental stochastic process. Individuals adjust their behavioral actions according to learning rules belonging to the class of experience-weighted attraction learning mechanisms, which includes standard reinforcement and Bayesian learning as special cases. We use stochastic approximation theory in order to derive differential equations governing action play probabilities, which turn out to have qualitative features of mutator-selection equations. We then perform agent-based simulations to find the conditions where the deterministic approximation is closest to the original stochastic learning process for standard 2-action 2-player fluctuating games, where interaction between learning rules and preference reversal may occur. Finally, we analyze a simplified model for the evolution of learning in a producer–scrounger game, which shows that the exploration rate can interact in a non-intuitive way with other features of co-evolving learning rules. Overall, our analyses illustrate the usefulness of applying stochastic approximation theory in the study of animal learning.     

Alternative solution of the simplest model of enzymatic synthesis of nucleic acids by homotopy perturbation method

Development of methods for obtaining approximate analytical solutions of nonlinear differential equations and their systems is a rapidly developing field of mathematical physics. Earlier, an approximate solution of the simplest system of kinetic enzymatic equations for calculating dynamics of complementary strands of nucleic acids was obtained. In this study, we consider an alternative approach to selecting the basic linear approximation of the used method, which makes it possible to obtain more accurate analytical solutions of the set problem.     

Analysis of the distribution of materials within the blood-brain-cerebrospinal fluid system

When material is introduced into the blood-brain-cerebrospinal fluid system, it will distribute throughout the system in a manner dependent upon the geometrical characteristics and the physical and chemical parameters of the system. Since only average values of the concentration of the material are known in each of the parts of the system, and approximation approach is used in analyzing this distribution theoretically. A simplified model is chosen for the system and equations are derived. These equations are then applied to the results of four papers in the literature dealing with the distribution of thiocyanate. A fifth paper dealing with the sulfate extracellular space of brain is also analyzed.     

Use of the z-transform to investigate nanopulse penetration of biological matter

Short duration, fast rise time electromagnetic ultra-wideband (UWB) pulses ("nanopulses") are generated by numerous electronic devices. Many new technologies involving nanopulses are under development and expected to become widely available soon. Study of nanopulse bioeffects therefore is needed to ensure human safety and to probe the useful range of nanopulses in possible biomedical and biotechnological applications. In this article, we present a new approximation of the Cole-Cole expression for the frequency dependence of the dielectric properties of tissues. The approximation is based on a z-transformation of the electric displacement and a second-order Taylor approximation of the Cole-Cole expression. The approach has been applied to investigating the penetration of nanopulses into biological matter as a function of the dielectric properties of tissue and pulse width. Solutions to Maxwell's equations are calculated using the finite difference time domain method (FDTD).     

Linear noise approximation method for calculating nonequilibrium fluctuations of the occupation numbers in radiative-collisional average ion models

A novel method is proposed for calculating nonequilibrium fluctuations of the mean occupation numbers of the electron shells in the radiative-collisional average-ion models of multicharged plasma kinetics. For the class of Slater ionic models, equations are derived for the mean occupation numbers of the electron shells and their fluctuations in the Fokker-Planck approximation. To calculate the fluctuations, the Fokker-Planck equation is linearized in the vicinity of the steady-state nonequilibrium solution to the kinetic equations (linear noise approximation). The method proposed allows one to take into account both the nonequilibrium correlations of the occupation-number fluctuations and the thermodynamically equilibrium statistical correlations related to the Coulomb interaction among bound electrons. The relation among the coefficients in the Fokker-Planck equation for the occupation-number fluctuations of the electron shells is discussed based on the fluctuation-dissipative theorem.     

Kinetic analysis of the chemotaxis of bacteria

On the basis of a kinetic model of bacterial chemotactic movement the system of differential equations was reduced to describe the phenomenon of bacterial bonds migration. It follows that Keller-Segel equation is a private case of a more general "diffusion approximation" of the kinetic model. The functional parameters of the reduced equation for E. coli K-12 are estimated.     

Approximate treatment of the formation of a difference in the concentrations of an ion at the two sides of a membrane

The recent extension of the approximation method is applied to enable us to arrive at the time course of the concentrations at both sides of a membrane. From the differential equations which govern these, the steady-state solution is obtained in terms of the parameters, which are determined by the thickness of the diffusion layers, the chemical composition and reactions, and the diffusion constant of the membrane.     

Rate of excitation propagation in a reduced Hodgkins-Huxley model. III. Integrodifferential equations]

The Hodgkin - Huxley system of equations is reduced to single integral-differential equation in neglection of slow variables dynamics. Two limiting cases of fast and slow sodium activation processes are considered. The first case leads to a nonlinear differential equation for the potential, the second one - to an ordinary differential equation with a known source as a function of coordinate. Such a simplification is due to approximation of steady-state sodium activation variable with the help of Heviside function. The validity of this approximation is discussed; the corresponding error is estimated by calculation of the second approximation for the source function.