A generalized Langevin algorithm for studying permeation across biological ion channels

We present a new leapfrog algorithm for the numerical solution of the generalized Langevin equation (GLE) in the case where the friction kernel is exponentially decaying. Like other leapfrog and Verlet algorithms, our algorithm is second order in velocity and third order in position. It is relatively easy to implement compared with other available algorithms, and would therefore make a good candidate for exploring the effects of finite memory time-scales in situations where modelling the precise functional form of the memory kernel was not important. We have tested this algorithm on a one-dimensional barrier crossing model, and found good asymptotic agreement with limits obtained using Brownian dynamics (BD) simulations, as well as with a theoretical asymptotic limit. We have also used the algorithm to perform a more sophisticated simulation of ion conduction through a KcsA channel. The results are a close match to corresponding results obtained using the Langevin equation, thereby helping to justify the use of Brownian dynamics in KcsA and other similar ion channels.     

On the quantum langevin equation

The quantum Langevin equation is the Heisenberg equation of motion for the (operator) coordinate of a Brownian particle coupled to a heat bath. We give an elementary derivation of this equation for a simple coupled-oscillator model of the heat bath.Deceased.     

外力作用下反馈耦合布朗棘轮的定向输运

本文研究了处于外力作用下双阱棘轮势中两个反馈耦合布朗粒子的定向输运性能. 通过对过阻尼朗之万方程的数值求解, 详细讨论了外力、热噪声与势阱的不对称参数等对耦合布朗粒子的平均速度、 有效扩散系数及Pe数的影响. 研究发现, 平均速度随外力呈周期性的变化规律. 同时耦合系统存在最优噪声强度会使定向输运达到最强. 值得指出的是棘轮系统可通过改变双阱势的结构来获得较强的定向流. 关键词： 耦合布朗棘轮 外力 双阱棘轮势 平均速度     

Strategies for fluctuation renormalization in nonlinear transport theory

We are concerned here with the problems encountered in the derivation of nonlinear transport equations from a correspondingly nonlinear Langevin equation. A dynamical coupling between the time-dependent averages and the fluctuations must be accounted for by a procedure which leads to a renormalization of the nonlinear transport equation. Generalizing the familiar phenomenological approach to Brownian motion to nonlinear dynamics, we illustrate how the problem arises and show how the fluctuation renormalization can be obtained exactly by a formal procedure or approximately by more tractable methods.     

Friction tensor for a pair of Brownian particles: Spurious finite-size effects and molecular dynamics estimates

In this work, we show thatin any finite system, the binary friction tensor for two Brownian particlescannot be directly estimated from an evaluation of the microscopic Green-Kubo formula, involving the time integral of force-force autocorrelation functions. This pitfall is associated with a subtle inversion of the thermodynamic and long-time limits and leads to spurious results for the estimates of the friction matrix based on molecular dynamics simulations. Starting from a careful analysis of the coupled Langevin equations for two interacting Brownian particles, we derive a method to circumvent these effects and extract the binary friction tensor from the correlation function matrix of the instantaneous forces exerted by the bath particles on the fixed Brownian particles, and from the relaxation of the total momentum of the bath in afinite system. The general methodology is applied to the case of two hard or soft Brownian spheres in a bath of light particles. Numerical estimates of the relevant correlation functions and of the resulting self and mutual components of the matrix of friction tensors are obtained by molecular dynamics simulations for various spacings between the Brownian particles. This paper is dedicated to B. Jancovici on the occassion of his 65th birthday.     

The generalized Schrödinger–Langevin equation

In this work, for a Brownian particle interacting with a heat bath, we derive a generalization of the so-called Schrödinger–Langevin or Kostin equation. This generalization is based on a nonlinear interaction model providing a state-dependent dissipation process exhibiting multiplicative noise. Two straightforward applications to the measurement process are then analyzed, continuous and weak measurements in terms of the quantum Bohmian trajectory formalism. Finally, it is also shown that the generalized uncertainty principle, which appears in some approaches to quantum gravity, can be expressed in terms of this generalized equation.     

Generalized Langevin theory of multiphoton absorption dynamics of polyatomic molecules and the nature of laser-selective effects

The generalized Langevin equation (GLE) with memory effects describing the dynamical behavior of the multiphoton processes of polyatomic molecules is presented. The temperature-dependent absorption cross section is obtained by solving the Laplace-Fourier transform of the velocity autocorrelation function governed by the GLE. It is shown that the nature of the multiphoton absorption is characterized by the memory effects of the damping kernel, the dephasing rate and the intramolecular vibration relaxation rate. The laser-selective effects are discussed in terms of the multiquantum exchange processes and the related “internal resonant” condition.     

Dynamics of ions in the selectivity filter of the KcsA channel

The statistical and dynamical properties of ions in the selectivity filter of the KcsA ion channel are considered on the basis of molecular dynamics (MD) simulations of the KcsA protein embedded in a lipid membrane surrounded by an ionic solution. A new approach to the derivation of a Brownian dynamics (BD) model of ion permeation through the filter is discussed, based on unbiased MD simulations. It is shown that depending on additional assumptions, ion’s dynamics can be described either by under-damped Langevin equation with constant damping and white noise or by Langevin equation with a fractional memory kernel. A comparison of the potential of the mean force derived from unbiased MD simulations with the potential produced by the umbrella sampling method demonstrates significant differences in these potentials. The origin of these differences is an open question that requires further clarifications.     

Hydrodynamics of Brownian particles

When considering the hydrodynamics of Brownian particles, one is confronted to a difficult closure problem. One possibility to close the hierarchy of hydrodynamic equations is to consider a strong friction limit. This leads to the Smoluchowski equation that reduces to the ordinary diffusion equation in the absence of external forces. Unfortunately, this equation has infinite propagation speed leading to some difficulties. Another possibility is to make a Local Thermodynamic Equilibrium (L.T.E) assumption. This leads to the damped Euler equation with an isothermal equation of state. However, this approach is purely phenomenological. In this paper, we provide a preliminary discussion of the validity of the L.T.E assumption. To that purpose, we consider the case of free Brownian particles and harmonically bound Brownian particles for which exact analytical results can be obtained [S. Chandrasekhar, Rev. Mod. Phys. 15, 1 (1943)]. For these systems, we find that the L.T.E. assumption is not unreasonable and that it can be improved by introducing a time dependent kinetic temperature T_kin(t)=γ(t)T instead of the bath temperature T. We also compare hydrodynamic equations and generalized diffusion equations with time dependent diffusion coefficients.     

The precise time-dependent solution of the Fokker–Planck equation with anomalous diffusion

We study the time behavior of the Fokker–Planck equation in Zwanzig’s rule (the backward-Ito’s rule) based on the Langevin equation of Brownian motion with an anomalous diffusion in a complex medium. The diffusion coefficient is a function in momentum space and follows a generalized fluctuation–dissipation relation. We obtain the precise time-dependent analytical solution of the Fokker–Planck equation and at long time the solution approaches to a stationary power-law distribution in nonextensive statistics. As a test, numerically we have demonstrated the accuracy and validity of the time-dependent solution.     

Injected Power Fluctuations in Langevin Equation

In this paper, we consider the Langevin equation from an unusual point of view, that is as an archetype for a dissipative system driven out of equilibrium by an external excitation. Using path integral method, we compute exactly the probability density function of the power (averaged over a time interval of length ) injected (and dissipated) by the random force into a Brownian particle driven by a Langevin equation. The resulting distribution, as well as the associated large deviation function, display strong asymmetry, whose origin is explained. Connections with the so-called Fluctuation Theorem are thereafter discussed. Finally, considering Langevin equations with a pinning potential, we show that the large deviation function associated with the injected power is completely insensitive to the presence of a potential.     

Computing the non-linear anomalous diffusion equation from first principles

We investigate asymptotically the occurrence of anomalous diffusion and its associated family of statistical evolution equations. Starting from a non-Markovian process à la Langevin we show that the mean probability distribution of the displacement of a particle follows a generalized non-linear Fokker-Planck equation. Thus we show that the anomalous behavior can be linked to a fast fluctuation process with memory from a microscopic dynamics level, and slow fluctuations of the dissipative variable. The general results can be applied to a wide range of physical systems that present a departure from the Brownian regime.     

The kinetic boundary layer for the Klein-Kramers equation; A new numerical approach

We explore a numerical technique for determining the structure of the kinetic boundary layer of the Klein-Kramers equation for noninteracting Brownian particles in a fluid near a wall that absorbs the Brownian particles. The equation is of interest in the theory of diffusion-controlled reactions and of the coagulation of colloidal suspensions. By numerical simulation of the Langevin equation equivalent to the Klein-Kramers equation we amass statistics of the velocities at the first return to the wall and of the return times for particles injected into the fluid at the wall with given velocities. The data can be used to construct the solutions of the standard problems at an absorbing wall, the Milne and the albedo problem. We confirm and extend earlier results by Burschka and Titulaer, obtained by a variational method vexed by the slow convergence of the underlying eigenfunction expansion. We briefly discuss some further boundary layer problems that can be attacked by exploiting the results reported here.     

Quantum stochastic differential equations for boson and fermion systems—method of non-equilibrium thermo field dynamics

A unified canonical operator formalism for quantum stochastic differential equations, including the quantum stochastic Liouville equation and the quantum Langevin equation both of the Itô and the Stratonovich types, is presented within the framework of non-equilibrium thermo field dynamics (NETFD). It is performed by introducing an appropriate martingale operator in the Schrödinger and the Heisenberg representations with fermionic and bosonic Brownian motions. In order to decide the double tilde conjugation rule and the thermal state conditions for fermions, a generalization of the system consisting of a vector field and Faddeev-Popov ghosts to dissipative open situations is carried out within NETFD.     

Scaling laws and memory effects in the dynamics of liquids and proteins

Recent progress in the numerical calculation of memory functions from molecular dynamics simulations allowed the gaining of deeper insight into the relaxation dynamics of liquids and proteins. The concept of memory functions goes back to the work of R. Zwanzig on the generalized Langevin equation, and it was the basis for the development of various dynamical models for liquids. In this article we present briefly a method for the numerical calculation of memory functions, which is then applied to study their scaling behavior in normal and fractional Brownian dynamics. It has been shown recently that the model of fractional Brownian dynamics constitutes effectively a link between protein dynamics on the nanosecond time scale, which is accessible to molecular dynamics simulations and thermal neutron scattering, and the much longer time scale of functional protein dynamics, which can be studied by fluorescence correlation spectroscopy. The text was submitted by the authors in English. Affiliated with the University of Orléans.