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Fluctuation-dissipation relations for Markov processes.

The fluctuation-dissipation relation is calculated for stochastic models obeying a master equation with continuous time. In the general case of a nonstationary process, there appears to be no simple relation between the response and the correlation. Also, if one considers stationary processes, the linear response cannot be expressed via time-derivatives of the correlation function alone. In this case, an additional function, which has rarely been discussed previously, is required. This so-called asymmetry depends on the two times also relevant for the response and the correlation and it vanishes under equilibrium conditions. The asymmetry can be expressed in terms of the propagators and the transition rates of the master equation but it is not related to any physical observable in an obvious way. It is found that the behavior of the asymmetry strongly depends on the nature of the dynamical variable considered in the calculation of the correlation and the response. If one is concerned with a variable which randomizes with any transition among the states of the system, the asymmetry vanishes in most cases. This is in contrast to the situation for other classes of variables. In particular, for trap models of glassy relaxation, the fluctuation-dissipation ratio strongly depends on the observable and the asymmetry plays a dominant role in the determination of this ratio also if only neutral variables are considered. Some implications of a nonvanishing asymmetry with regard to the definition of an effective temperature are discussed.

Journal Article↗

Energetics from slow infrared multiphoton dissociation of biomolecules.

Photodissociation kinetics of the protonated pentapeptide leucine enkephalin measured using a cw CO(2) laser and a Fourier-transform mass spectrometer are reported. A short induction period, corresponding to the time required to raise the internal energy of the ion population to a (dissociating) steady state, is observed. After this induction period, the dissociation data are accurately fit by first-order kinetics. A plot of the log of the unimolecular dissociation rate constant, k(uni), as a function of the log of laser power is linear at low laser powers (<9 W, k(uni) <0.05 s(-1)), but tapers off at high laser power (9-33 W, k(uni) = 0.05-7 s(-1)). The entire measured dissociation curve can be accurately fit by an exponential function plus a constant. The experiment is simulated using a master equation formalism. In the model, the laser radiation is described as an energetically flat-topped distribution which is spatially uniform. This description is consistent with experimental results which indicate that ion motion within the cell averages out spatial inhomogeneities in the laser light. The model has several adjustable parameters. The effect of varying these parameters on the calculated kinetics and power dependence curves is discussed. A procedure for determining a limited range of threshold dissociation energy, E(o), which fits both the measured induction period and power dependence curves, is presented. Using this procedure, E(o) of leucine enkephalin is determined to be 1.12-1.46 eV. This result is consistent with, although less precise than, values measured previously using blackbody infrared radiative dissociation. Although the blackbody dissociation results were used as a starting point to search for fits of the master equation model to experiment, these results demonstrate that it is, in principle, possible to determine a limited range of E(o) from slow infrared multiphoton dissociation data alone.

Journal Article↗

A stochastic analysis of first-order reaction networks.

A stochastic model for a general system of first-order reactions in which each reaction may be either a conversion reaction or a catalytic reaction is derived. The governing master equation is formulated in a manner that explicitly separates the effects of network topology from other aspects, and the evolution equations for the first two moments are derived. We find the surprising, and apparently unknown, result that the time evolution of the second moments can be represented explicitly in terms of the eigenvalues and projections of the matrix that governs the evolution of the means. The model is used to analyze the effects of network topology and the reaction type on the moments of the probability distribution. In particular, it is shown that for an open system of first-order conversion reactions, the distribution of all the system components is a Poisson distribution at steady state. Two different measures of the noise have been used previously, and it is shown that different qualitative and quantitative conclusions can result, depending on which measure is used. The effect of catalytic reactions on the variance of the system components is also analyzed, and the master equation for a coupled system of first-order reactions and diffusion is derived.

Algorithms↗

CF3CH3 --> HF + CF2CH2: a non-RRKM reaction?

The experimental shock tube data recently reported by Kiefer et al. [J. Phys. Chem. A 2004, 108, 2443-2450] for the title reaction at temperatures between 1600 and 2400 K have been compared to master equation simulations using three models: (a) standard RRKM theory, (b) RRKM theory modified by local random matrix theory, which introduces dynamical corrections arising from slow intramolecular vibrational energy randomization, and (c) an ad hoc empirical non-RRKM model. Only the third model provides a good fit of the Kiefer et al. unimolecular reaction rate data. In separate simulations, all three models accurately reproduce the experimental 300 K chemical activation data of Marcoux and Setser [J. Phys. Chem. 1978, 82, 97-108] when the energy transfer parameters are freely varied to fit the data. When experimental energy transfer parameters for a geometrical isomer (1,1,2-trifluoroethane) are used, the standard RRKM model fits the chemical activation data better than the other models, but if energy transfer in the 1,1,1-trifluoroethane is significantly reduced in comparison to the 1,1,2 isomer, then the empirical ad hoc non-RRKM model also gives a good fit. While the ad hoc empirical non-RRKM model can be made to fit the data, it is not based on theory, and we argue that it is physically unrealistic. We also show that the master equation simulations can mimic the Kiefer et al. vibrational relaxation data, which was the first shock tube observation of double-exponential relaxation. We conclude that, until more data on the trifluoroethanes become available, the current evidence is insufficient to decide with confidence whether non-RRKM effects are important in this reaction, or whether the Kiefer et al. data can be explained in some other way.

Journal Article↗

Linear response to perturbation of nonexponential renewal processes.

We study the linear response of a two-state stochastic process, obeying the renewal condition, by means of a stochastic rate equation equivalent to a master equation with infinite memory. We show that the condition of perennial aging makes the response to coherent perturbation vanish in the long-time limit.

Journal Article↗

Kinetic equation with exact charge conservation.

A kinetic master equation for multiplicity distributions is formulated for charged particles which are created or destroyed only in pairs due to the conservation of their Abelian charge. It allows one to study time evolution of the multiplicity distributions in a relativistic many-body system with arbitrary average particle multiplicities. It is shown to reproduce the equilibrium results for both canonical (rare particles) and grand canonical (abundant particles) systems. For canonical systems, the equilibrium multiplicity is much lower and the relaxation time is much shorter than the naive extrapolation from grand canonical results. Implications for chemical equilibration in heavy-ion collisions are also discussed.

Journal Article↗

Radiation of solitons described by a high-order cubic nonlinear Schrodinger equation

The resonant radiation of solitons due to higher order dispersion, described by an extended nonlinear Schrodinger (NLS) equation with nonlinear (cubic) dispersive terms and linear terms with third and fourth derivatives, is studied. The basic equation includes, as a particular case, a higher order derivative NLS equation. General properties of the master equation, such as conservation laws, Hamiltonian structures (in important particular cases), and Galilei transformation are studied. Explicit asymptotic expressions, describing the radiation at different initial conditions, are derived. The obtained results, in particular, provide a basis for the study of soliton losses, caused by the radiation, in optical fibers.

Journal Article↗

A theoretical approach to cluster formation in biological membranes.

A theoretical analysis of cluster formation within the lipid matrix of biological membranes is presented. Various models are analysed: (a) one-dimensional monolayer, (b) two-dimensional monolayer and (c) one dimensional bilayer. Furthermore, lipid-protein interactions are considered. The model is based on differential equations for the probabilities ai and bi which characterize the occupation of the lattice site i by the lipids A and B, respectively. These differential equations are an approximation of the Master-equation. Steady states as well as time-dependent variations are analysed. Depending on the interaction energies of the two lipids, different stationary lipid distributions are obtained, including clusters of lipids A or B and alternating structures. The distributions may be dynamically stable or unstable. It is shown that phase transitions within the lipid matrix may be induced by alteration of the composition of the membrane, by changing the interaction energies of the lipids, by variation of the temperature or by lipid-protein interactions. The transitions between different stationary distributions are studied by use of bifurcation diagrams. The analysis of time-dependent states reveals that unstable structures of the membrane may be important for certain time periods. Consideration of the lipid bilayer leads to a great number of possible distributions, which may be symmetric or asymmetric with respect to the outer and inner leaflets of the membrane.

Membrane Lipids↗

Entropy production along a stochastic trajectory and an integral fluctuation theorem.

For stochastic nonequilibrium dynamics like a Langevin equation for a colloidal particle or a master equation for discrete states, entropy production along a single trajectory is studied. It involves both genuine particle entropy and entropy production in the surrounding medium. The integrated sum of both Delatas(tot) is shown to obey a fluctuation theorem (exp([-Deltas(tot) = 1 for arbitrary initial conditions and arbitrary time-dependent driving over a finite time interval.

Journal Article↗

Quantum dissipation in unbounded systems.

In recent years trajectory based methodologies have become increasingly popular for evaluating the time evolution of quantum systems. A revival of the de Broglie--Bohm interpretation of quantum mechanics has spawned several such techniques for examining quantum dynamics from a hydrodynamic perspective. Using techniques similar to those found in computational fluid dynamics one can construct the wave function of a quantum system at any time from the trajectories of a discrete ensemble of hydrodynamic fluid elements (Bohm particles) which evolve according to nonclassical equations of motion. Until very recently these schemes have been limited to conservative systems. In this paper, we present our methodology for including the effects of a thermal environment into the hydrodynamic formulation of quantum dynamics. We derive hydrodynamic equations of motion from the Caldeira-Leggett master equation for the reduced density matrix and give a brief overview of our computational scheme that incorporates an adaptive Lagrangian mesh. Our applications focus upon the dissipative dynamics of open unbounded quantum systems. Using both the Wigner phase space representation and the linear entropy, we probe the breakdown of the Markov approximation of the bath dynamics at low temperatures. We suggest a criteria for rationalizing the validity of the Markov approximation in open unbound systems and discuss decoherence, energy relaxation, and quantum/classical correspondence in the context of the Bohmian paths.

Journal Article↗

Dynamics of a tracer granular particle as a nonequilibrium Markov process.

The dynamics of a tracer particle in a stationary driven granular gas is investigated. We show how to transform the linear Boltzmann equation, describing the dynamics of the tracer into a master equation for a continuous Markov process. The transition rates depend on the stationary velocity distribution of the gas. When the gas has a Gaussian velocity probability distribution function (PDF), the stationary velocity PDF of the tracer is Gaussian with a lower temperature and satisfies detailed balance for any value of the restitution coefficient alpha. As soon as the velocity PDF of the gas departs from the Gaussian form, detailed balance is violated. This nonequilibrium state can be characterized in terms of a Lebowitz-Spohn action functional W(tau) defined over trajectories of time duration tau. We discuss the properties of this functional and of a similar functional W(tau), which differs from the first for a term that is nonextensive in time. On the one hand, we show that in numerical experiments (i.e., at finite times tau), the two functionals have different fluctuations and W always satisfies an Evans-Searles-like symmetry. On the other hand, we cannot observe the verification of the Lebowitz-Spohn-Gallavotti-Cohen (LS-GC) relation, which is expected for W(tau) at very large times tau. We give an argument for the possible failure of the LS-GC relation in this situation. We also suggest practical recipes for measuring W(tau) and W(tau) in experiments.

Journal Article↗

Universal equations for linear adiabatic pulses and characterization of partial adiabaticity.

A numerical analysis of the sech/tanh (or hyperbolic secant) and tanh/tan adiabatic inversion pulses provides a set of master equations for each type of pulse that guarantee their optimal implementation over a wide range of practical conditions without needing to further simulate the inversion profiles of the pulses. These simple equations determine the necessary maximum RF amplitude (RF(max)) required for a preselected degree of inversion across a chosen effective bandwidth (bw(eff)) and for a chosen pulse length (T(p)). The two types of pulse function differently: The sech/tanh pulse provides a rectangular inversion profile with bw(eff) being a large fraction of the adiabatic frequency sweep (bwdth), whereas for tanh/tan bw(eff) is < or =bwdth/20. If the quality of inversion is defined as the minimum allowable extent of inversion, iota(bw), at the boundaries of bw(eff), two basic linear equations are found for both types of pulse and these are of the form (RF(max)T(p))(2)=m(1)T(p)bwdth+c(1) and T(p)bwdth=m(3)T(p)bw(eff)+c(3). The different behavior of the two pulses is expressed as different dependencies of the slopes m(n) and intercepts c(n) on iota(bw) and allowances are made for second order effects within these equations. The availability of these master relationships enables a direct comparison of the two types of adiabatic pulse and it is found that tanh/tan requires about half the pulse length of an equivalent sech/tanh pulse and also has the advantage of being less sensitive to the effects of scalar coupling. In contrast sech/tanh delivers about half the total RF power of an equivalent tanh/tan pulse. It is expected that the forms of these two basic linear equations are generally applicable to adiabatic inversion pulses and thus define the concept of "linear adiabaticity." At low values of T(p)bwdth or T(p)bw(eff) the linear equations no longer apply, defining a region of "partial adiabaticity." Normal adiabatic pulses in the middle of this partial region are more efficient in terms of RF(max) or T(p) but are moderately less tolerant to RF inhomogeneity. A class of numerically optimized pulses has recently been developed that specifically trades adiabaticity in an attempt to gain RF(max) or T(p) efficiency. In comparison to normal adiabatic pulses implemented under optimal conditions, these new partially adiabatic pulses show only marginal improvements; they are restricted to single values of T(p)bw(eff), and they are vastly less tolerant to RF inhomogeneity. These comparisons, and direct comparisons between any types of inversion pulse, adiabatic or otherwise, can be made using plots of (RF(max)T(p))(2) or (Total Power) T(p) versus T(p)bw(eff).

Magnetic Resonance Spectroscopy↗

Noisy spiking neurons and networks: useful approximations for firing probabilities and global behavior.

Electrophysiological properties of spiking neurons receiving complex stimuli perturbed by noise are investigated. A semi-analytical estimate of firing probabilities and subthreshold behavior of the stochastic system can be made in terms of the solution of a purely deterministic system. The method comes from an approximation for the distribution function and moments of the underlying non linear multidimensional diffusion process. This so called moment method works for general conductance-based systems and an application is presented for the Hodgkin-Huxley neuronal model. Statistical properties obtained from the moment method are compared with direct numerical integration of the stochastic system. The firing probability due to external noise is derived as a closed formula. Results are given for different forms of the deterministic component of the stimulus. A generalization to neural networks of conductance-based systems with internal currents perturbed by noise can be obtained using the same approach. In the case of fully connected networks, a mean field population equation is derived which may be compared to Kuramoto's master equation for weakly coupled neural oscillators.

Action Potentials↗

A derivation of the mixed quantum-classical Liouville equation from the influence functional formalism.

We show that the mixed quantum-classical Liouville equation is equivalent to linearizing the forward-backward action in the influence functional. Derivations are provided in terms of either the diabatic or adiabatic basis sets. An application of the mixed quantum-classical Liouville equation for calculating the memory kernel of the generalized quantum master equation is also presented. The accuracy and computational feasibility of such an approach is demonstrated in the case of a two-level system nonlinearly coupled to an anharmonic bath.

Journal Article↗

Systematic derivation of reaction-diffusion equations with distributed delays and relations to fractional reaction-diffusion equations and hyperbolic transport equations: application to the theory of Neolithic transition.

We introduce a general method for the systematic derivation of nonlinear reaction-diffusion equations with distributed delays. We study the interactions among different types of moving individuals (atoms, molecules, quasiparticles, biological organisms, etc). The motion of each species is described by the continuous time random walk theory, analyzed in the literature for transport problems, whereas the interactions among the species are described by a set of transformation rates, which are nonlinear functions of the local concentrations of the different types of individuals. We use the time interval between two jumps (the transition time) as an additional state variable and obtain a set of evolution equations, which are local in time. In order to make a connection with the transport models used in the literature, we make transformations which eliminate the transition time and derive a set of nonlocal equations which are nonlinear generalizations of the so-called generalized master equations. The method leads under different specified conditions to various types of nonlocal transport equations including a nonlinear generalization of fractional diffusion equations, hyperbolic reaction-diffusion equations, and delay-differential reaction-diffusion equations. Thus in the analysis of a given problem we can fit to the data the type of reaction-diffusion equation and the corresponding physical and kinetic parameters. The method is illustrated, as a test case, by the study of the neolithic transition. We introduce a set of assumptions which makes it possible to describe the transition from hunting and gathering to agriculture economics by a differential delay reaction-diffusion equation for the population density. We derive a delay evolution equation for the rate of advance of agriculture, which illustrates an application of our analysis.

Biophysical Phenomena↗

Nonequilibrium voltage fluctuations in biological membranes. I. General framework of charge transport in discrete systems and related voltage noise.

This paper continues our work on the theory of nonequilibrium voltage noise generated by electric transport processes in membranes. Introducing the membrane voltage as a further variable, a system of kinetic equations linearized in voltage is derived by which generally the time-dependent behaviour of charge-transport processes under varying voltage can be discussed. Using these equations, the treatment of voltage noise can be based on the usual master equation approach to steady-state fluctuations of scalar quantities. Thus, a general theoretical approach to nonequilibrium voltage noise is presented, completing our approach to current fluctuations which had been developed some years ago. It is explicitly shown that at equilibrium the approach yields agreement with the Nyquist relation, while at nonequilibrium this relation is not valid. A further general property of voltage noise is the reduction of low-frequency noise with increasing number of transport units as a consequence of the interactions via the electric field. In a second paper, the approach will be applied for a number of special transport mechanisms, such as ionic channels, carriers or electrogenic pumps.

Kinetics↗