Denis S. Goldobin

Dynamics of Limit-Cycle Oscillators Subject to General Noise

The phase description is a powerful tool for analyzing noisy limit-cycle oscillators. The method, however, has found only limited applications so far, because the present theory is applicable only to Gaussian noise while noise in the real world often has non-Gaussian statistics. Here, we provide the phase reduction method for limit-cycle oscillators subject to general, colored and non-Gaussian, noise including a heavy-tailed one. We derive quantifiers like mean frequency, diffusion constant, and the Lyapunov exponent to confirm consistency of the results. Applying our results, we additionally study a resonance between the phase and noise.

Coherence of noisy oscillators with delayed feedback

A theory of effect of delayed feedback on the coherence of the noisy self-sustained oscillations is developed. In the Gaussian approximation a closed system of equations is derived for the phase diffusion constant and the mean frequency. A comparison with numerics shows that the theory works well for weak feedback and strong noise.

Effective long-time phase dynamics of limit-cycle oscillators driven by weak colored noise

An effective white-noise Langevin equation is derived that describes long-time phase dynamics of a limit-cycle oscillator driven by weak stationary colored noise. Effective drift and diffusion coefficients are given in terms of the phase sensitivity of the oscillator and the correlation function of the noise, and are explicitly calculated for oscillators with sinusoidal phase sensitivity functions driven by two typical colored Gaussian processes. The results are verified by numerical simulations using several types of stochastic or chaotic noise. The drift and diffusion coefficients of oscillators driven by chaotic noise exhibit anomalous dependence on the oscillator frequency, reflecting the peculiar power spectrum of the chaotic noise.

Diffusive counter dispersion of mass in bubbly media

We consider a liquid bearing gas bubbles in a porous medium. When gas bubbles are immovably trapped in a porous matrix by surface-tension forces, the dominant mechanism of transfer of gas mass becomes the diffusion of gas molecules through the liquid. Essentially, the gas solution is in local thermodynamic equilibrium with vapor phase all over the system, i.e., the solute concentration equals the solubility. When temperature and/or pressure gradients are applied, diffusion fluxes appear and these fluxes are faithfully determined by the temperature and pressure fields, not by the local solute concentration, which is enslaved by the former. We derive the equations governing such systems, accounting for thermodiffusion and gravitational segregation effects, which are shown not to be neglected for geological systems-marine sediments, terrestrial aquifers, etc. The results are applied for the treatment of non-high-pressure systems and real geological systems bearing methane or carbon dioxide, where we find a potential possibility of the formation of gaseous horizons deep below a porous medium surface. The reported effects are of particular importance for natural methane hydrate deposits and the problem of burial of industrial production of carbon dioxide in deep aquifers.

Comment on "Time-averaged properties of unstable periodic orbits and chaotic orbits in ordinary differential equation systems".

A recent paper claims that mean characteristics of chaotic orbits differ from the corresponding values averaged over the set of unstable periodic orbits, embedded in the chaotic attractor. We demonstrate that the alleged discrepancy is an artifact of the improper averaging. Since the natural measure is nonuniformly distributed over the attractor, different periodic orbits make different contributions into the time averages. As soon as the corresponding weights are accounted for, the discrepancy disappears.

Towards quantitative prediction of proteasomal digestion patterns of proteins

We discuss the problem of proteasomal degradation of proteins. Though proteasomes are important for all aspects of cellular metabolism, some details of the physical mechanism of the process remain unknown. We introduce a stochastic model of the proteasomal degradation of proteins, which accounts for the protein translocation and the topology of the positioning of cleavage centers of a proteasome from first principles. For this model we develop a mathematical description based on a master equation and techniques for reconstruction of the cleavage specificity inherent to proteins and the proteasomal translocation rates, which are a property of the proteasome species, from mass spectroscopy data on digestion patterns. With these properties determined, one can quantitatively predict digestion patterns for new experimental set-ups. Additionally we design an experimental set-up for a synthetic polypeptide with a periodic sequence of amino acids, which enables especially reliable determination of translocation rates.

Uncertainty principle for control of ensembles of oscillators driven by common noise

We discuss control techniques for noisy self-sustained oscillators with a focus on reliability, stability of the response to noisy driving, and oscillation coherence understood in the sense of constancy of oscillation frequency. For any kind of linear feedback control — single and recursive delay feedback, linear frequency filter, etc. — the phase diffusion constant, quantifying coherence, and the Lyapunov exponent, quantifying reliability, can be efficiently controlled but their ratio remains constant. Thus, an “uncertainty principle” can be formulated: the loss of reliability occurs when coherence is enhanced and, vice versa, coherence is weakened when reliability is enhanced. Treatment of this principle for ensembles of oscillators synchronized by common noise or global coupling reveals a substantial difference between the cases of slightly non-identical oscillators and identical ones with intrinsic noise.

Non-Fickian diffusion affects the relation between the salinity and hydrate capacity profiles in marine sediments

Abstract On-site measurements of water salinity (which can be directly evaluated from the electrical conductivity) in deep-sea sediments is technically the primary source of indirect information on the capacity of the marine deposits of methane hydrates. We show the relation between the salinity (chlorinity) profile and the hydrate volume in pores to be significantly affected by non-Fickian contributions to the diffusion flux—the thermal diffusion and the gravitational segregation—which have been previously ignored in the literature on the subject and the analysis of surveys data. We provide amended relations and utilize them for an analysis of field measurements for a real hydrate deposit.

Scaling of transport coefficients of porous media under compaction

Porous sediments in geological systems are exposed to stress by the above-laying mass and consequent compaction, which may be significantly nonuniform across the massif. We derive scaling laws for the compaction of sediments of similar geological origin. With these laws, we evaluate the dependence of the transport properties of a fluid-saturated porous medium (permeability, effective molecular diffusivity, hydrodynamic dispersion, electrical and thermal conductivities) on its porosity. In particular, we demonstrate that the assumption of a uniform geothermal gradient is not adequate for systems with nonuniform compaction and show the importance of the derived scaling laws for mathematical modelling of methane hydrate deposits; these deposits are believed to have potential for impact on global climate change and Glacial-Interglacial cycles.

Interplay of coupling and common noise at the transition to synchrony in oscillator populations

There are two ways to synchronize oscillators: by coupling and by common forcing, which can be pure noise. By virtue of the Ott-Antonsen ansatz for sine-coupled phase oscillators, we obtain analytically tractable equations for the case where both coupling and common noise are present. While noise always tends to synchronize the phase oscillators, the repulsive coupling can act against synchrony, and we focus on this nontrivial situation. For identical oscillators, the fully synchronous state remains stable for small repulsive coupling; moreover it is an absorbing state which always wins over the asynchronous regime. For oscillators with a distribution of natural frequencies, we report on a counter-intuitive effect of dispersion (instead of usual convergence) of the oscillators frequencies at synchrony; the latter effect disappears if noise vanishes.