Prediction of ion channel transport from Grote—Hynes and Kramers theories

Generalized Langevin equation based Grote—Hynes (GH) theory and Langevin equation based Kramers theory are used to calculate the transmission coefficient for K⁺ diffusion through a model of the biological potassium ion channel IRK1, which contains a high potential barrier in the selectivity filter. The ion friction kernel is determined from a molecular dynamics (MD) simulation of the force on a stationary ion at the barrier top. The GH and Kramers estimates of the transmission coefficient are compared with those obtained from MD simulations of ion diffusion at the barrier top of the IRK1 channel. It is found that the GH estimate agrees with the value determined by rigorous MD, but the Kramers estimate is about 40% too small. The success or failure of GH and Kramers theories for various other systems is discussed and compared with these results.     

Probing microscopic chaotic dynamics by observing macroscopic transport processes

We derive the Kramers equation, namely, the Fokker-Planck equation for an oscillator, from a completely deterministic picture. The oscillator is coupled to a “booster”, i.e., a deterministic system in a fully chaotic state, wherein diffusion is derived from the sensitive dependence of chaos on initial conditions and friction is a consequence of the linear response of the booster to the action exerted on it by the oscillator. To deal with the Hamiltonian nature of the system of interest and of its coupling to the booster, we extend the earlier theoretical derivation of macroscopic transport coefficients from deterministic dynamics. We show that the frequency of the oscillator can be tuned to the microscopic frequencies of the booster without affecting the canonical nature of the “macroscopic” statistics. The theoretical predictions are supported by numerical simulations.     

Solvent-induced acceleration of the rate of activation of a molecular reaction

An increase in the rates of activated processes with the coupling to the solvent has long been predicted through the phenomenological Langevin equation in the weak coupling regime. However, its direct observation in particle-based models has been elusive because the coupling typically places the processes in the spacial-diffusion limited regime wherein rates decrease with increasing friction. In this work, the forward and backward reaction rates of the LiNC<==>LiCN isomerization reaction in a bath of argon atoms at various densities have been calculated directly using molecular dynamics trajectories. The so-called Kramers turnover in the rate with microscopic friction is clearly visible, thus providing direct and unambiguous evidence for the energy-diffusion regime in which rates increase with friction.     

Reaction rate theory: what it was, where is it today, and where is it going?

A brief history is presented, outlining the development of rate theory during the past century. Starting from Arrhenius [Z. Phys. Chem. 4, 226 (1889)], we follow especially the formulation of transition state theory by Wigner [Z. Phys. Chem. Abt. B 19, 203 (1932)] and Eyring [J. Chem. Phys. 3, 107 (1935)]. Transition state theory (TST) made it possible to obtain quick estimates for reaction rates for a broad variety of processes even during the days when sophisticated computers were not available. Arrhenius' suggestion that a transition state exists which is intermediate between reactants and products was central to the development of rate theory. Although Wigner gave an abstract definition of the transition state as a surface of minimal unidirectional flux, it took almost half of a century until the transition state was precisely defined by Pechukas [Dynamics of Molecular Collisions B, edited by W. H. Miller (Plenum, New York, 1976)], but even this only in the realm of classical mechanics. Eyring, considered by many to be the father of TST, never resolved the question as to the definition of the activation energy for which Arrhenius became famous. In 1978, Chandler [J. Chem. Phys. 68, 2959 (1978)] finally showed that especially when considering condensed phases, the activation energy is a free energy, it is the barrier height in the potential of mean force felt by the reacting system. Parallel to the development of rate theory in the chemistry community, Kramers published in 1940 [Physica (Amsterdam) 7, 284 (1940)] a seminal paper on the relation between Einstein's theory of Brownian motion [Einstein, Ann. Phys. 17, 549 (1905)] and rate theory. Kramers' paper provided a solution for the effect of friction on reaction rates but left us also with some challenges. He could not derive a uniform expression for the rate, valid for all values of the friction coefficient, known as the Kramers turnover problem. He also did not establish the connection between his approach and the TST developed by the chemistry community. For many years, Kramers' theory was considered as providing a dynamic correction to the thermodynamic TST. Both of these questions were resolved in the 1980s when Pollak [J. Chem. Phys. 85, 865 (1986)] showed that Kramers' expression in the moderate to strong friction regime could be derived from TST, provided that the bath, which is the source of the friction, is handled at the same level as the system which is observed. This then led to the Mel'nikov-Pollak-Grabert-Hanggi [Mel'nikov and Meshkov, J. Chem. Phys. 85, 1018 (1986); Pollak, Grabert, and Hanggi, ibid. 91, 4073 (1989)] solution of the turnover problem posed by Kramers. Although classical rate theory reached a high level of maturity, its quantum analog leaves the theorist with serious challenges to this very day. As noted by Wigner [Trans. Faraday Soc. 34, 29 (1938)], TST is an inherently classical theory. A definite quantum TST has not been formulated to date although some very useful approximate quantum rate theories have been invented. The successes and challenges facing quantum rate theory are outlined. An open problem which is being investigated intensively is rate theory away from equilibrium. TST is no longer valid and cannot even serve as a conceptual guide for understanding the critical factors which determine rates away from equilibrium. The nonequilibrium quantum theory is even less well developed than the classical, and suffers from the fact that even today, we do not know how to solve the real time quantum dynamics for systems with "many" degrees of freedom.     

模耦合理论计算纳米粒子在聚合物熔体中的含时扩散系数与常规扩散常数 (cited: 2)

分析和计算了纳米粒子在聚合物熔体中的含时扩散系数与常规扩散常数. 采用广义朗之万方程描述扩散动力学,并通过模耦合理论计算摩擦记忆内核.为简单起见,只考虑了来自两体碰撞和溶剂密度涨落耦合作用两类微观因素对摩擦记忆内核的贡献. 采用聚合物参考作用点模型以及Percus-Yevick闭合条件计算了聚合物-纳米粒子复合溶液的平衡态结构信息函数;详尽分析了纳米粒子的尺寸与聚合物链的尺寸对扩散动力学的影响. 揭示了结构函数、摩擦记忆内核以及扩散系数等随着纳米粒子半径和聚合物链长的变化关系. 结果表明,对于小尺寸的纳米粒子或者短链的聚合物,短时间的非马尔可夫扩散 动力学特征比较显著,含时扩散系数需要更长的时间弛豫到常规扩散常数. 微观因素对扩散常数的贡献随着纳米粒子尺寸的增加而减小,却随着聚合物链长的增加而增大. 此外,模耦合理论得到的扩散常数与Stokes-Einstein关系的预测值进行比较,发现对于小尺寸的纳米粒子或者长链的聚合物,微观因素对扩散常数的的贡献占主导地位. 相反,当纳米粒子较大或者聚合物链长较短时,流体力学的贡献会发挥重要作用.     

Noise-induced transitions in a double-well potential at low friction

A new integral representation of the transition rate holds for any friction and is shown to allow a feasible evaluation in a wide friction range. Analytic approximations include the (high-friction) Kramers result with the leading correction, as well as a low-friction case. The method is complementary to a recent one of Melnikov and Meshkov.     

Noise-induced dynamical transition in systems with symmetric absorbing states

We investigate the effect of noise strength on the macroscopic ordering dynamics of systems with symmetric absorbing states. Using an explicit stochastic microscopic model, we present evidence for a phase transition in the coarsening dynamics, from an Ising-like to a voter-like behavior, as the noise strength is increased past a nontrivial critical value. By mapping to a thermal diffusion process, we argue that the transition arises due to locally-absorbing states being entered more readily in the high-noise regime, which in turn prevents surface tension from driving the ordering process.     

Transition from static to kinetic friction: insights from a 2D model

We describe a 2D spring-block model for the transition from static to kinetic friction at an elastic-slider-rigid-substrate interface obeying a minimalistic friction law (Amontons-Coulomb). By using realistic boundary conditions, a number of previously unexplained experimental results on precursory microslip fronts are successfully reproduced. From the analysis of the interfacial stresses, we derive a prediction for the evolution of the precursor length as a function of the applied loads, as well as an approximate relationship between microscopic and macroscopic friction coefficients. We show that the stress buildup due to both elastic loading and microslip-related relaxations depends only weakly on the underlying shear crack propagation dynamics. Conversely, crack speed depends strongly on both the instantaneous stresses and the friction coefficients, through a nontrivial scaling parameter.     

Kinetic Monte Carlo simulations of electrodeposition: Crossover from continuous to instantaneous homogeneous nucleation within Avrami’s law

The influence of lateral adsorbate diffusion on the dynamics of the first-order phase transition in a two-dimensional Ising lattice gas with attractive nearest-neighbor interactions is investigated by means of kinetic Monte Carlo simulations. For example, electrochemical underpotential deposition proceeds by this mechanism. One major difference from adsorption in vacuum surface science is that under control of the electrode potential and in the absence of mass-transport limitations, local adsorption equilibrium is approximately established. We analyze our results using the theory of Kolmogorov, Johnson and Mehl, and Avrami (KJMA), which we extend to an exponentially decaying nucleation rate. Such a decay may occur due to a suppression of nucleation around existing clusters in the presence of lateral adsorbate diffusion. Correlation functions prove the existence of such exclusion zones. By comparison with microscopic results for the nucleation rate I and the interface velocity of the growing clusters v, we can show that the KJMA theory yields the correct order of magnitude for Iv². This is true even though the spatial correlations mediated by diffusion are neglected. The decaying nucleation rate causes a gradual crossover from continuous to instantaneous nucleation, which is complete when the decay of the nucleation rate is very fast on the time scale of the phase transformation. Hence, instantaneous nucleation can be homogeneous, producing negative minima in the two-point correlation functions. We also present in this paper an n-fold way Monte Carlo algorithm for a square lattice gas with adsorption/desorption and lateral diffusion.     

Sol-Gel transition of concentrated colloidal suspensions

Diffusing-wave spectroscopy (DWS) was used to follow the sol-gel transition of concentrated colloidal suspensions. We present a new technique based on a sandwich of two scattering cells aimed to overcome the problem of nonergodicity in DWS of solidlike systems. Using this technique we obtain quantitative information about the microscopic dynamics all the way from an aggregating suspension to the final gel, thereby covering the whole sol-gel transition. At the gel point a dramatic change of the particle dynamics from diffusion to a subdiffusive arrested motion is observed. A critical-power-law behavior is found for the time evolution of the maximum mean square displacement delta(2) probed by a single particle in the gel.     

Modified Kramers formulas for the decay rate in agreement with dynamical modeling

Accuracy of the Kramers approximate formulas for the thermal decay rate of the metastable state is studied for the anharmonic shapes of the potential pocket and the barrier. This is done by the comparison with the quasistationary rate resulting from the dynamical modeling. Disagreement between the Kramers rate and the dynamical one is shown to reach 15% in the cases when much better agreement is expected. Corrections to the Kramers formulas accounting for the higher derivatives of the potential are obtained. The small parameters are the ratios of the thermal energy to the stiffnesses at the extremes of the potential. The distance between the potential barrier and the absorptive border is accounted for as well. This corrected Kramers rate is demonstrated to agree with the dynamical rate typically within 2%. Probably the most interesting result is that despite the corrections are derived in the case of the overdamped Brownian motion, the above 2% agreement holds even in the case of medium friction.     

Energy diffusion controlled reaction rate in dissipative Hamiltonian systems

In this paper the energy diffusion controlled reaction rate in dissipative Hamiltonian systems is investigated by using the stochastic averaging method for quasi Hamiltonian systems. The boundary value problem of mean first-passage time (MFPT) of averaged system is formulated and the energy diffusion controlled reaction rate is obtained as the inverse of MFPT. The energy diffusion controlled reaction rate in the classical Kramers bistable potential and in a two-dimensional bistable potential with a heat bath are obtained by using the proposed approach respectively. The obtained results are then compared with those from Monte Carlo simulation of original systems and from the classical Kramers theory. It is shown that the reaction rate obtained by using the proposed approach agrees well with that from Monte Carlo simulation and is more accurate than the classical Kramers rate.     

Brownian motion in a periodic potential: Application to dielectric relaxation

The relaxational dynamics of a planar rotator in anM-fold cosine potential subject to a random torque is investigated in detail. For the case of a periodic potential with large barrier height, the numerical results of the relaxation dynamics are in complete agreement with an approximate analytical solution. The latter, is derived on assuming a harmonic potential at the bottom of the potential minima and a large time-scale separation between the short-time libration inside each potential minima and a long-time hopping phenomenon over the potential barriers. ForM2, the hopping phenomenon is found to be the dominant feature of the orientational autocorrelation function. The average hopping time is explained satisfactorily in terms of the Kramers activation rate theory. In particular a complete agreement is found between the numerical results of the escape rate and those obtained from the modified Kramers' predictions valid for low friction coefficient. The cosine model is applied to the study of dielectric spectroscopy. The particle mobility and the complex permitivity, of a dielectric material are calculated by numerical solutions for rotational velocity and orientational auto-correlation functions, respectively. The main features of the experimental observables are determined analytically and compared to the corresponding numerical results. The applicability of the plane rotator model to dielectric spectroscopy is also discussed.From Jan. 1^st 1985: Institut für Theoretische Physik, RWTH, Aachen, FRG     

Diffusion in a bistable potential

The problem of diffusion of a particle in a bistable potential is studied on the basis of the one-dimensional Smoluchowski equation for the space- and time-dependent probability distribution. The potential is modeled as two parabolic wells separated by a parabolic barrier. For the model potential the Smoluchowski equation is solved exactly by a Laplace transform with respect to time for the initial condition that at time zero the probability distribution is given by a thermal equilibrium distribution in one of the wells. In the limit of a high barrier the rate of transition to the other well is given by an asymptotic result due to Kramers. For a potential barrier of moderate height there are significant corrections to the asymptotic result.     

Two state behavior in a solvable model of beta-hairpin folding

Understanding the mechanism of protein secondary structure formation is an essential part of the protein-folding puzzle. Here we describe a simple model for the formation of a beta hairpin, motivated by the fact that folding of a beta hairpin captures much of the basic physics of protein folding. The modeled hairpin is composed of two interacting Gaussian chains with one pairwise (two-body) and two many-body interactions. We show that these many-body interactions, arising from side chain packing effects, are responsible for producing an "all-or-none" folding transition. We also estimate the (single exponential) folding/unfolding rate via calculating the thermodynamic weight of the "critical" droplet/bubble.     

Force-driven micro-rheology

Within a microscopic formalism for the nonequilibrium response of colloidal suspensions driven by an external force, we study the active micro-rheology of a glass-forming colloidal suspensions. In this technique, a probe particle is subject to an external force, and its nonequilibrium dynamics is monitored. Strong external forcing delocalizes the particle from its nearest-neighbor cage, resulting in a pronounced force-thinning behavior of the single-particle friction. We discuss the dynamics in the vicinity of this delocalization transition, and how long-range transport is induced for a particle that is localized in the quiescent case.     

A theoretical model for the collective motion of proteins by means of principal component analysis

A coarse grained model in the frame work of principal component analysis is presented. We used a bath of harmonic oscillators approach, based on classical mechanics, to derive the generalized Langevin equations of motion for the collective coordinates. The dynamics of the protein collective coordinates derived from molecular dynamics simulations have been studied for the Bovine Pancreatic Trypsin Inhibitor. We analyzed the stability of the method by studying structural fluctuations of the C _a atoms obtained from a 20 ns molecular dynamics simulation. Subsequently, the dynamics of the collective coordinates of protein were characterized by calculating the dynamical friction coefficient and diffusion coefficients along with time-dependent correlation functions of collective coordinates. A dual diffusion behavior was observed with a fast relaxation time of short diffusion regime 0.2–0.4 ps and slow relaxation time of long diffusion about 1–2 ps. In addition, we observed a power law decay of dynamical friction coefficient with exponent for the first five collective coordinates varying from −0.746 to −0.938 for the real part and from −0.528 to −0.665 for its magnitude. It was found that only the first ten collective coordinates are responsible for configuration transitions occurring on time scale longer than 50 ps.     

Transition probabilities and stochastic equations for the mean field ising model

The microscopic transition rate is briefly calculated from quantum principles to derive the microscopic master equation. By introducing _p, the phenomenological time, and coarse graining W_p, the transition rate, a complete normalized phenomenological transition rate is obtained. The Langer form is then approximately obtained.Supported in part by the Robert A. Welch Foundation.On leave of absence from the Institute of Theoretical Physics, Academia Sinica, Beijing, China.