The fractal theory of electrochemical diffusion noise: Correlations of the third and fourth order

Based on the Langevin linear stochastic equation, the correlations of the 3rd and 4th order for thermal fluctuations of the electrode potential are studied in an electrochemical ac circuit involving an electric double layer capacitance, a resistance of steady-state diffusion, and a Warburg impedance. The presence of the noisy Warburg impedance in the ac circuit makes the Langevin linear stochastic equation fractal. The analogy with the steady-state diffusion noise and with the noise of the barrierless-activationless slow discharge is used. Equations for bispectrum and trispectrum of electrode-potential activation are shown. It is demonstrated that the intensity of bispectrum and trispectrum is determined exclusively by the noise of the steady-state diffusion resistance if one of frequency arguments in the polyspectrum is zero. It is found that in an electrochemical ac circuit containing the noisy Warburg impedance, the asymptotics of establishment of equilibrium values of asymmetry and excess of electrode-potential fluctuations (thermalization) obeys the power law rather than the exponential law. Furthermore, the excess thermalization proceeds faster as compared with asymmetry thermalization. The performed theoretical analysis of correlations of the 3rd and 4th order of the fractal noise of electrochemical diffusion is of practical interest. For instance, the concepts of the fractal electrochemical noise can be used in the noise diagnostics of devices of electrochemical power engineering and in the noise methods for studying corrosion systems.     

Electrochemical symmetric stochastic diffusion

Symmetric stochastic diffusion in an equilibrium electrochemical ac circuit is studied theoretically. The electrochemical circuit included double layer capacitance and slow discharge resistance. Electrochemical analog of the stochastic Einstein formula is found. An equation is obtained for the excess of electrochemical stochastic diffusion. It is shown that an excess of electrochemical stochastic diffusion increases at high relaxation times in proportion to the observation time. It is found that excess is related to correlation between the phenomenon of electrochemical stochastic diffusion and the central limiting theorem.     

Diffusion NMR for determining the homogeneous length-scale in lamellar phases

The size of the anisotropic domains in a lyotropic liquid crystal is estimated using a new protocol for diffusion NMR. Echo attenuation decays are recorded for different durations of the displacement-encoding gradient pulses, while keeping the effective diffusion time and the range of the wave vectors constant. Deviations between the sets of data appear if there are non-Gaussian diffusion processes occurring on the time-scale defined by the gradient pulse duration and the length-scale defined by the wave vector. The homogeneous length-scale is defined as the minimum length-scale for which the diffusion appears to be Gaussian. Simulations are performed to show that spatial variation of the director orientation in an otherwise homogeneous system is sufficient to induce non-Gaussian diffusion. The method is demonstrated by numerical solutions of the Bloch-Torrey equation and experiments on a range of lamellar liquid crystals with different domain sizes.     

Theory of asymmetric electrochemical stochastic diffusion

Strict analysis of electrochemical strochastic diffusion due to asymmetric Brownian motion of electric charge in an equilibrium electrochemical ac circuit containing double electric layer capacitance and noisy Faradaic resistance is carried out. Cumulant analogs (for 3rd and 5th order correlations) of the Einstein formula are obtained. It is proved that equilibrium asymmetric (nongauss) stochastic diffusion is in agreement with the central limiting theorem of the probability theory. The Hurst exponent was found in the case of the nongauss components of the process of equilibrium stochastic diffusion. Apart from electrochemistry, the performed stochastic analysis of equilibrium electrochemical nongauss diffusion is also of general theoretical interest, including its application in the stochastic theory of asymmetric anomalous transport and strict theory of fluctuations at large deviations from equilibrium.     

受主方程控制的化学反应体系非平衡定态宏观稳定性判据之随机推广

借助扰动按分布参数分离法及主方程的Kramers-Moyal展开证明,随机熵相应于对最可几路径偏离的偏超量之时间导数与体系对外部扰动的响应性直接相关.该演变速率等价于偏超随机熵产生,并与根据随机位方法提出的随机超熵产生速率等效.对Poisson分布,该量表现为Gibbs超熵产生的等价量.局域平衡假定失效后,化学反应体系的宏观稳定性即决定于这个新的随机量.     

Theory of the first encounter with the boundary by a stochastic diffusion process in an equilibrium electrochemical <Emphasis Type="Italic">RC</Emphasis>-circuit

The methodology of electrochemial impedance is used for finding the characteristic function of the random time of the first encounter with the boundary by a process of electrochemical stochastic diffusion in an equilibrium ac circuit containing a double layer capacitance and a noisy charge-transfer resistance. The Nyquist diagram of the characteristic function suggests that the method of the first random encounter with the boundary by electrochemical stochastic diffusion may prove to be useful in the noise diagnosis of objects and devices of electrochemical power engineering and also in comparative studies of electrochemical corrosion processes.     

受高斯白噪声影响的有限化学反应体系的随机热力学——外噪声对化学反应体系影响的有效热力学量度

通过分析噪声对跃迁概率的不同影响,借助Novikov定理及MSR理论,建立了受多源白噪声影响的有限化学反应体系的有效主方程及有效熵平衡方程,导出非平衡定态时这类噪声体系熵产生的一般表达式,揭示涨落熵产生的统计内涵及噪声贡献,并针对非宏观量级的外噪声,借助扰动按分布参数分离法及有效主方程的Kramers-Moyal展开,进一步对简单加合性噪声建立了非平衡定态宏观稳定性判据的随机模拟,论证了噪声对化学反应体系定态稳定性的弱化作用.     

Propagators and related descriptors for non-Markovian asymmetric random walks with and without boundaries

There are many current applications of the continuous-time random walk (CTRW), particularly in describing kinetic and transport processes in different chemical and biophysical phenomena. We derive exact solutions for the Laplace transforms of the propagators for non-Markovian asymmetric one-dimensional CTRW's in an infinite space and in the presence of an absorbing boundary. The former is used to produce exact results for the Laplace transforms of the first two moments of the displacement of the random walker, the asymptotic behavior of the moments as t-->infinity, and the effective diffusion constant. We show that in the infinite space, the propagator satisfies a relation that can be interpreted as a generalized fluctuation theorem since it reduces to the conventional fluctuation theorem at large times. Based on the Laplace transform of the propagator in the presence of an absorbing boundary, we derive the Laplace transform of the survival probability of the random walker, which is then used to find the mean lifetime for terminated trajectories of the random walk.     

Electrochemical noise generated by anodic dissolution or diffusion processes

A model of the noise generated by electrochemical reactions and by diffusion is proposed. The elementary fluctuations are supposed to be the particle fluxes which are Poisson white noise. This model is successfully used to describe the experimental stochastic behaviour of two cases of non-equilibrium electrochemical interfaces: the noise generated by anodic dissolution of iron in acidic medium and that by diffusion of a reacting species in the bulk of the electrolyte.     

Asymmetric rotor-like probes to polarized fluorescence study of the macroscopically oriented uniaxial media: Model parameters recognition

In this paper the possibility of the numerical data modelling in the case of angle- and time-resolved fluorescence spectroscopy is investigated. The asymmetric fluorescence probes are assumed to undergo the restricted rotational diffusion in a hosting medium. This process is described quantitatively by the diffusion tensor and the aligning potential. The evolution of the system is expressed in terms of the Smoluchowski equation with an appropriate time-developing operator. A matrix representation of this operator is calculated, then symmetrized and diagonalized. The resulting propagator is used to generate the synthetic noisy data set that imitates results of experimental measurements. The data set serves as a groundwork to the χ² optimization, performed by the genetic algorithm followed by the gradient search, in order to recover model parameters, which are diagonal elements of the diffusion tensor, aligning potential expansion coefficients and directions of the electronic dipole moments. This whole procedure properly identifies model parameters, showing that the outlined formalism should be taken in the account in the case of analysing real experimental data.     

A hybrid fluctuating hydrodynamics and kinetic Monte Carlo method for modeling chemically-powered nanoscale motion

We present a stochastic multiscale method for modeling heterogeneous catalysis at the nanoscale. The system is decomposed into the fluid domain and the catalyst-fluid interface. We implemented the fluctuating hydrodynamics framework to model the diffusion of the chemical species in the fluid domain, and the chemical master equation to describe the catalytic activity at the interface. The coupling between the domains occurs simultaneously. Using a simple one-dimensional (1D) linear model, we showed that the predictions of our scheme are in excellent agreement with deterministic simulations. The method was specifically developed to model the spatially asymmetric catalysis on the surface of self-propelled nanoswimmers. Numerical simulations showed that our approach can estimate the uncertainty in the swimming velocity resulting from inherent stochastic nature of the chemical reactions at the catalytic interface. Although the method has been applied to simple 1D and 2D models, it can be generalized to handle different geometries and more sophisticated chemical reactions. Therefore, it can serve as a practical mathematical tool to study how the efficiency of chemically powered nanomachines is affected by the interplay between structural complexity, nonlinear reactivity, and nonequilibrium fluctuations.     

Non-exponential non-Arrhenius relaxation in the course of CO rebinding to heme proteins

The dispersive transport model for relaxation of photolyzed heme proteins has been improved to take into account the coupling of the ligand-heme geminate recombination and the non-Gaussian diffusive dynamics of conformational changes in heme proteins. Contrary to the earlier deterministic version of the model, the present more rigorous formulation is based on the stochastic approach to the problem. This implies that the time evolution of protein conformations should be described in terms of the transient distribution which satisfies the Smoluchowski-type differential equation with a time-dependent diffusion coefficient. The obtained analytical solution of this equation enables us to relate main kinetic parameters of the geminate recombination and quantities characterizing the ligand-heme interaction. The derived expressions demonstrate that the reaction barrier shifts with time towards higher values following the near-stretched exponential behavior in agreement with experiment. Such a behavior is governed by the non-exponential non-Arrhenius conformational relaxation. The latter process can be identified by the characteristics “footprint” left on the experimental rebinding curve and is shown to be responsible for some kinetically different phases of the ligand-heme geminate recombination observed within distinct temperature ranges.     

A master equation investigation of coagulation reactions: Sol-gel transition

The kinetics of irreversible coagulation phenomena in spatially homogeneous systems is formulated in terms of a multivariate stochastic process. The latter is governed by a master equation for the joint probability distribution of the numbers of reacting species. An efficient numerical algorithm is used to simulate the complete time evolution of the stochastic process. The method is illustrated by simulating the coagulation reaction with configuration-dependent reaction kernels, K_ij = (ij)^ω, for clusters of mass i and j with 1/2 < ω ⩽ 1, which are designed to model gelation phenomena. It is demonstrated that the stochastic simulation allows the determination of critical exponents and the gel point directly from the master equation. The results are compared to predictions of the rate equation approach to the sol-gel transition.     

The sorting direct method for stochastic simulation of biochemical systems with varying reaction execution behavior

A key to advancing the understanding of molecular biology in the post-genomic age is the development of accurate predictive models for genetic regulation, protein interaction, metabolism, and other biochemical processes. To facilitate model development, simulation algorithms must provide an accurate representation of the system, while performing the simulation in a reasonable amount of time. Gillespie's stochastic simulation algorithm (SSA) accurately depicts spatially homogeneous models with small populations of chemical species and properly represents noise, but it is often abandoned when modeling larger systems because of its computational complexity. In this work, we examine the performance of different versions of the SSA when applied to several biochemical models. Through our analysis, we discover that transient changes in reaction execution frequencies, which are typical of biochemical models with gene induction and repression, can dramatically affect simulator performance. To account for these shifts, we propose a new algorithm called the sorting direct method that maintains a loosely sorted order of the reactions as the simulation executes. Our measurements show that the sorting direct method performs favorably when compared to other well-known exact stochastic simulation algorithms.     

非恒稳含时电极过程中涨落-耗散的电化学效应——恒电势滴汞电极体系的随机热力学模型

以滴汞电极体系为模型,对非恒稳恒电势动态不可逆电极过程中的耗散-涨落效应进行了系统的研究.基于滴汞电极体系的电化学特征,提出了一个简化的含时随机热力学模型,从而可能对这类重要的含时物理化学过程进行涨落和耗散的定量分析.借助该简化的模型,成功地建立了恒电势滴汞电极过程的基本随机热力学公式,由此推出耗散-涨落效应的理论极谱曲线.在滴汞电极生长缓慢及扩散步骤严重滞后情况下,含时的滴汞电极过程将趋于在有效扩散层厚度演化的慢流型上的准定态过程.在这种准定态近似下,具体分析了涨落对极谱曲线的影响.结果表明,在涨落影响可以忽略的近平衡区,从耗散-涨落导出的极谱方程与从平衡态Nernst公式导出的极谱方程完全吻合.还计算了一个涨落诱导的极谱曲线偏离的典型范例.     

Fluctuation–Dissipation Theorem for Triple Correlations of Electric Noise

Electric fluctuation and noise accompany all electrode processes and can be employed for creating useful information technologies. Severe nonlinearity of electrochemical systems gives rise to a perceptible component of abnormal (non-Gaussian) electric noise. In this paper a fluctuation–dissipation theorem is formulated, which connects third-order noise spectra with faradaic low-level rectification. An analogue is provided: the Schottky formulas for the spectrum of third-order shot noise.     

First passage times for a tracer particle in single file diffusion and fractional Brownian motion

We investigate the full functional form of the first passage time density (FPTD) of a tracer particle in a single-file diffusion (SFD) system whose population is: (i) homogeneous, i.e., all particles having the same diffusion constant and (ii) heterogeneous, with diffusion constants drawn from a heavy-tailed power-law distribution. In parallel, the full FPTD for fractional Brownian motion [fBm-defined by the Hurst parameter, H ∈ (0, 1)] is studied, of interest here as fBm and SFD systems belong to the same universality class. Extensive stochastic (non-Markovian) SFD and fBm simulations are performed and compared to two analytical Markovian techniques: the method of images approximation (MIA) and the Willemski-Fixman approximation (WFA). We find that the MIA cannot approximate well any temporal scale of the SFD FPTD. Our exact inversion of the Willemski-Fixman integral equation captures the long-time power-law exponent, when H ≥ 1/3, as predicted by Molchan [Commun. Math. Phys. 205, 97 (1999)] for fBm. When H < 1/3, which includes homogeneous SFD (H = 1/4), and heterogeneous SFD (H < 1/4), the WFA fails to agree with any temporal scale of the simulations and Molchan's long-time result. SFD systems are compared to their fBm counter parts; and in the homogeneous system both scaled FPTDs agree on all temporal scales including also, the result by Molchan, thus affirming that SFD and fBm dynamics belong to the same universality class. In the heterogeneous case SFD and fBm results for heterogeneity-averaged FPTDs agree in the asymptotic time limit. The non-averaged heterogeneous SFD systems display a lack of self-averaging. An exponential with a power-law argument, multiplied by a power-law pre-factor is shown to describe well the FPTD for all times for homogeneous SFD and sub-diffusive fBm systems.     

Heavy (or large) ions in a fluid in an electric field: The diffusion equation exactly following from the Fokker-Planck equation

The problem of the derivation of the diffusion equation exactly following from the Fokker-Planck (or Klein-Kramers) equation for heavy (or large) particles in a fluid in an external force field is solved in the case in which the particles are ions subject to a uniform (but in general time-varying) electric field. It is found that such a diffusion equation maintains memory of the initial ion velocity distribution, unless sufficiently large values of time are considered. In such temporal asymptotic limit, the diffusion equation exactly becomes (i) the Smoluchowski equation when the electric field is constant in time, and (ii) a new equation generalizing the Smoluchowski equation, when the electric field is arbitrarily time varying. Finally, it is shown that the obtained exact (or asymptotic) results make questionable the procedures and the results of approximate theories developed in the past to get a "corrected" Smoluchowski equation when the external force can also be, in general, position dependent.