arXiv subjects

Igor Goychuk

Publications and source records attributed to Igor Goychuk.

At least 37 records · Page 2Linked to original sources

arXiv2013

Coexistence and efficiency of normal and anomalous transport by molecular motors in living cells

Recent experiments reveal both passive subdiffusion of various nanoparticles and anomalous active transport of such particles by molecular motors in the molecularly crowded environment of living biological cells. Passive and active microrheology reveals that the origin of this anomalous dynamics is due to the viscoelasticity of the intracellular fluid. How do molecular motors perform in such a highly viscous, dissipative environment? Can we explain the observed co-existence of the anomalous transport of relatively large particles of 100 to 500 nm in size by kinesin motors with the normal transport of smaller particles by the same molecular motors? What is the efficiency of molecular motors in the anomalous transport regime? Here we answer these seemingly conflicting questions and consistently explain experimental findings in a generalization of the well-known continuous diffusion model for molecular motors with two conformational states in which viscoelastic effects are included.

physics.bio-ph↗

arXiv2012

Fractional time random walk subdiffusion and anomalous transport with finite mean residence times: faster, not slower

Continuous time random walk (CTRW) subdiffusion along with the associated fractional Fokker-Planck equation (FFPE) is traditionally based on the premise of random clock with divergent mean period. This work considers an alternative CTRW and FFPE description which is featured by finite mean residence times (MRTs) in any spatial domain of finite size. Transient subdiffusive transport can occur on a very large time scale $τ_c$ which can greatly exceed mean residence time in any trap, $τ_c\gg <τ>$, and even not being related to it. Asymptotically, on a macroscale transport becomes normal for $t\ggτ_c$. However, mesoscopic transport is anomalous. Differently from viscoelastic subdiffusion no long-range anti-correlations among position increments are required. Moreover, our study makes it obvious that the transient subdiffusion and transport are faster than one expects from their normal asymptotic limit on a macroscale. This observation has profound implications for anomalous mesoscopic transport processes in biological cells because of macroscopic viscosity of cytoplasm is finite.

cond-mat.stat-mech↗

arXiv2012

Flashing subdiffusive ratchets in viscoelastic media

We study subdiffusive ratchet transport in periodically and randomly flashing potentials. Central Brownian particle is elastically coupled to surrounding auxiliary Brownian quasi-particles which account for the influence of viscoelastic environment. Similar to standard dynamical modeling of Brownian motion, the external force influences only the motion of central particle not affecting directly the environmental degrees of freedom (see video). Just a handful of auxiliary Brownian particles suffice to model subdiffusion over many temporal decades. Time-modulation of the potential violates the symmetry of thermal detailed balance and induces anomalous subdiffusive current which exhibits a remarkable quality at low temperatures, as well as a number of other surprising features such as saturation at low temperatures, and multiple inversions of the transport direction upon a change of the driving frequency in nonadiabatic regime. Our study generalizes classical Brownian motors towards operating in sticky viscoelastic environments like cytosol of biological cells or dense polymer solutions.

cond-mat.stat-mech↗

arXiv2012

Is subdiffusional transport slower than normal?

We consider anomalous non-Markovian transport of Brownian particles in viscoelastic fluid-like media with very large but finite macroscopic viscosity under the influence of a constant force field F. The viscoelastic properties of the medium are characterized by a power-law viscoelastic memory kernel which ultra slow decays in time on the time scale τof strong viscoelastic correlations. The subdiffusive transport regime emerges transiently for t<τ. However, the transport becomes asymptotically normal for t>>τ. It is shown that even though transiently the mean displacement and the variance both scale sublinearly, i.e. anomalously slow, in time, <δx(t)> ~ F t^α, <δx^2(t)> ~ t^α, 0<α<1, the mean displacement at each instant of time is nevertheless always larger than one obtained for normal transport in a purely viscous medium with the same macroscopic viscosity obtained in the Markovian approximation. This can have profound implications for the subdiffusive transport in biological cells as the notion of "ultra-slowness" can be misleading in the context of anomalous diffusion-limited transport and reaction processes occurring on nano- and mesoscales.

cond-mat.stat-mech↗

arXiv2011

Fractional Brownian motors and Stochastic Resonance

We study fluctuating tilt Brownian ratchets based on fractional subdiffusion in sticky viscoelastic media characterized by a power law memory kernel. Unlike the normal diffusion case the rectification effect vanishes in the adiabatically slow modulation limit and optimizes in a driving frequency range. It is shown also that anomalous rectification effect is maximal (stochastic resonance effect) at optimal temperature and can exhibit a surprisingly good quality. Moreover, subdiffusive current can flow in the counter-intuitive direction upon a change of temperature or driving frequency. The dependence of anomalous transport on load exhibits a remarkably simple universality.

cond-mat.stat-mech↗

arXiv2011

Subdiffusive dynamics in washboard potentials: two different approaches and different universality classes

We consider and compare two different approaches to the fractional subdiffusion and transport in washboard potentials. One is based on the concept of random fractal time and is associated with the fractional Fokker-Planck equation. Another approach is based on the fractional generalized Langevin dynamics and is associated with anti-persistent fractional Brownian motion and its generalizations. Profound differences between these two different approaches sharing the common adjective "fractional" are explained in spite of some similarities they share in the absence of a nonlinear force. In particular, we show that the asymptotic dynamics in tilted washboard potentials obey two different universality classes independently of the form of potential.

cond-mat.stat-mech↗

arXiv2010

Subdiffusive Brownian ratchets rocked by a periodic force

This work puts forward a generalization of the well-known rocking Markovian Brownian ratchets to the realm of antipersistent non-Markovian subdiffusion in viscoelastic media. A periodically forced subdiffusion in a parity-broken ratchet potential is considered within the non-Markovian generalized Langevin equation (GLE) description with a power-law memory kernel $η(t)\propto t^{-α}$ ($0<α<1$). It is shown that subdiffusive rectification currents, defined through the mean displacement and subvelocity $v_α$, $<δx(t)>\sim v_α t^α/ Γ(1+α)$, emerge asymptotically due to the breaking of the detailed balance symmetry by driving. The asymptotic exponent is $α$, the same as for free subdiffusion, $<δx^2(t)>\propto t^α$. However, a transient to this regime with some time-dependent $α_{\rm eff}(t)$ gradually decaying in time, $α\leq α_{\rm eff}(t)\leq 1$, can be very slow depending on the barrier height and the driving field strength. In striking contrast to its normal diffusion counterpart, the anomalous rectification current is absent asymptotically in the limit of adiabatic driving with frequency $Ω\to 0$, displaying a resonance like dependence on the driving frequency. However, an anomalous current inversion occurs for a sufficiently fast driving, like in the normal diffusion case. In the lowest order of the driving field, such a rectification current presents a quadratic response effect. Beyond perturbation regime it exhibits a broad maximum versus the driving field strength. Moreover, anomalous current exhibits a maximum versus the potential amplitude.

cond-mat.stat-mech↗

arXiv2010

Markovian embedding of non-Markovian superdiffusion

We consider different Markovian embedding schemes of non-Markovian stochastic processes that are described by generalized Langevin equations (GLE) and obey thermal detailed balance under equilibrium conditions. At thermal equilibrium superdiffusive behavior can emerge if the total integral of the memory kernel vanishes. Such a situation of vanishing static friction is caused by a super-Ohmic thermal bath. One of the simplest models of ballistic superdiffusion is determined by a bi-exponential memory kernel that was proposed by Bao [J.-D. Bao, J. Stat. Phys. 114, 503 (2004)]. We show that this non-Markovian model has infinitely many different 4-dimensional Markovian embeddings. Implementing numerically the simplest one, we demonstrate that (i) the presence of a periodic potential with arbitrarily low barriers changes the asymptotic large time behavior from free ballistic superdiffusion into normal diffusion; (ii) an additional biasing force renders the asymptotic dynamics superdiffusive again. The development of transients that display a qualitatively different behavior compared to the true large-time asymptotics presents a general feature of this non-Markovian dynamics. These transients though may be extremely long. As a consequence, they can be even mistaken as the true asymptotics. We find that such intermediate asymptotics exhibit a giant enhancement of superdiffusion in tilted washboard potentials and it is accompanied by a giant transient superballistic current growing proportional to $t^{α_{\rm eff}}$ with an exponent $α_{\rm eff}$ that can exceed the ballistic value of two.

cond-mat.stat-mech↗

arXiv2009

Viscoelastic subdiffusion: from anomalous to normal

We study viscoelastic subdiffusion in bistable and periodic potentials within the Generalized Langevin Equation approach. Our results justify the (ultra)slow fluctuating rate view of the corresponding bistable non-Markovian dynamics which displays bursting and anti-correlation of the residence times in two potential wells. The transition kinetics is asymptotically stretched-exponential when the potential barrier $V_0$ several times exceeds thermal energy $k_BT$ ($V_0\sim 2 - 10 k_BT$) and it cannot be described by the non-Markovian rate theory (NMRT). The well-known NMRT result approximates, however, ever better with the increasing barrier height, the most probable logarithm of the residence times. Moreover, the rate description is gradually restored when the barrier height exceeds a fuzzy borderline which depends on the power law exponent of free subdiffusion $α$. Such a potential-free subdiffusion is ergodic. Surprisingly, in periodic potentials it is not sensitive to the barrier height in the long time asymptotic limit. However, the transient to this asymptotic regime is extremally slow and it does profoundly depend on the barrier height. The time-scale of such subdiffusion can exceed the mean residence time in a potential well, or in a finite spatial domain by many orders of magnitude. All these features are in sharp contrast with an alternative subdiffusion mechanism involving jumps among traps with the divergent mean residence time in these traps.

cond-mat.soft↗

arXiv2009

Nonstationary stochastic resonance viewed through the lens of information theory

In biological systems, information is frequently transferred with Poisson like spike processes (shot noise) modulated in time by information-carrying signals. How then to quantify information transfer for the output for such nonstationary input signals of finite duration? Is there some minimal length of the input signal duration versus its strength? Can such signals be better detected when immersed in noise stemming from the surroundings by increasing the stochastic intensity? These are some basic questions which we attempt to address within an analytical theory based on the Kullback-Leibler information concept applied to random processes.

physics.bio-ph↗

arXiv2008

Noise-assisted spike propagation in myelinated neurons

We consider noise-assisted spike propagation in myelinated axons within a multi-compartment stochastic Hodgkin-Huxley model. The noise originates from a finite number of ion channels in each node of Ranvier. For the subthreshold internodal electric coupling, we show that (i) intrinsic noise removes the sharply defined threshold for spike propagation from node to node, and (ii) there exists an optimum number of ion channels which allows for the most efficient signal propagation and it corresponds to the actual physiological values.

q-bio.NC↗

arXiv2006

Chemically driven electron tunnelling pumps

The simplest mechanism for molecular electron pumps is discussed which is based on nonadiabatic electron tunnelling and nonequilibrium conformational fluctuations. Such fluctuations can be induced, e.g. by random binding of negatively charged ATP molecules to the electron-transferring molecular complex, their subsequent hydrolysis and the products dissociation. The pumping rate can be controlled by the ATP concentration in solution. Depending on the model parameters there may exist a critical ATP concentration for the pump to function. Alternatively, nonequilibrium fluctuations can be induced by externally applied stochastic electric fields. For realistically chosen parameters, the mechanism is shown to be robust and highly efficient.

physics.bio-ph↗

arXiv2006

Quantum Stochastic Synchronization

We study within the spin-boson dynamics the synchronization of quantum tunneling with an external periodic driving signal. As a main result we find that at a sufficiently large system-bath coupling strength (Kondo parameter a>1) the thermal noise plays a constructive role in yielding both a frequency and a phase synchronization in a symmetric two-level system. Such riveting synchronization occurs when the driving frequency supersedes the zero temperature tunneling rate. As an application evidencing the effect, we consider a charge transfer dynamics in molecular complexes.

cond-mat.stat-mech↗

arXiv2006

Quantum Two-State Dynamics Driven by Stationary Non-Markovian Discrete Noise: Exact Results

We consider the problem of stochastic averaging of a quantum two-state dynamics driven by non-Markovian, discrete noises of the continuous time random walk type (multistate renewal processes). The emphasis is put on the proper averaging over the stationary noise realizations corresponding, e.g., to a stationary environment. A two state non-Markovian process with an arbitrary non-exponential distribution of residence times (RTDs) in its states with a finite mean residence time provides a paradigm. For the case of a two-state quantum relaxation caused by such a classical stochastic field we obtain the explicit exact, analytical expression for the averaged Laplace-transformed relaxation dynamics. In the limit of Markovian noise (implying an exponential RTD), all previously known results are recovered. We exemplify new more general results for the case of non-Markovian noise with a biexponential RTD. The averaged, real-time relaxation dynamics is obtained in this case by numerically exact solving of a resulting algebraic polynomial problem. Moreover, the case of manifest non-Markovian noise with an infinite range of temporal autocorrelation (which in principle is not accessible to any kind of perturbative treatment) is studied, both analytically (asymptotic long-time dynamics) and numerically (by a precise numerical inversion of the Laplace-transformed averaged quantum relaxation).

cond-mat.stat-mech↗

arXiv2006

The role of conformational diffusion in ion channel gating

We consider an exactly tractable model of the Kramers type for the voltage-dependent gating dynamics of single ion channels. It is assumed that the gating dynamics is caused by the thermally activated transitions in a bistable potential. Moreover, the closed state of the channel is highly degenerate and embraces the whole manifold of closed substates. Opening of the ion channel is energetically prohibited from most of the closed substates and requires a special conformation where the voltage sensor can move along an activation pathway and trigger the transition into the open conformation. When the corresponding activation barrier towards the channel's opening is removed by the applied voltage, the statistics of non-conducting time intervals become strongly influenced by the conformational diffusion. For the corresponding supra-threshold voltages, our model explains the origin of the power law distribution of the closed time intervals. The exponential-linear dependence of the opening rate on voltage, often used as an experimental fit, is also reproduced by our model.

physics.bio-ph↗

arXiv2006

Rate processes with non-Markovian dynamical disorder

Rate processes with dynamical disorder are investigated within a simple framework provided by unidirectional electron transfer (ET) with fluctuating transfer rate. The rate fluctuations are assumed to be described by a non-Markovian stochastic jump process which reflects conformational dynamics of an electron transferring donor-acceptor molecular complex. A tractable analytical expression is obtained for the relaxation of the donor population (in the Laplace-transformed time domain) averaged over the stationary conformational fluctuations. The corresponding mean transfer time is also obtained in an analytical form. The case of two-state fluctuations is studied in detail for a model incorporating substate diffusion within one of the conformations. It is shown that an increase of the conformational diffusion time results in a gradual transition from the regime of fast modulation characterized by the averaged ET rate to the regime of quasi-static disorder. This transition occurs at the conformational mean residence time intervals fixed much less than the inverse of the corresponding ET rates. An explanation of this paradoxical effect is provided. Moreover, its presence is also manifested for the simplest, exactly solvable non-Markovian model with a biexponential distribution of the residence times in one of the conformations. The nontrivial conditions for this phenomenon to occur are found.

cond-mat.stat-mech↗

arXiv2006

Effect of channel block on the spiking activity of excitable membranes in a stochastic Hodgkin-Huxley model

The influence of intrinsic channel noise on the spontaneous spiking activity of poisoned excitable membrane patches is studied by use of a stochastic generalization of the Hodgkin-Huxley model. Internal noise stemming from the stochastic dynamics of individual ion channels is known to affect the collective properties of the whole ion channel cluster. For example, there exists an optimal size of the membrane patch for which the internal noise alone causes a regular spontaneous generation of action potentials. In addition to varying the size of ion channel clusters, living organisms may adapt the densities of ion channels in order to optimally regulate the spontaneous spiking activity. The influence of channel block on the excitability of a membrane patch of certain size is twofold: First, a variation of ion channel densities primarily yields a change of the conductance level. Second, a down-regulation of working ion channels always increases the channel noise. While the former effect dominates in the case of sodium channel block resulting in a reduced spiking activity, the latter enhances the generation of spontaneous action potentials in the case of a tailored potassium channel blocking. Moreover, by blocking some portion of either potassium or sodium ion channels, it is possible to either increase or to decrease the regularity of the spike train.

q-bio.SC↗

arXiv2006

Channel noise and synchronization in excitable membranes

Using a stochastic generalization of the Hodgkin–Huxley model, we consider the influence of intrinsic channel noise on the synchronization between the spiking activity of the excitable membrane and an externally applied periodic signal. For small patches, i.e., when the channel noise dominates the excitable dynamics, we find the phenomenon of intrinsic coherence resonance. In this case, the relatively regular spiking behavior is practically independent of the applied external driving; therefore no synchronization occurs. Synchronization takes place, however, only for sufficiently large ion channel assemblies. The neuronal signal processing is thus likely rooted in the collective properties of optimally large assemblies of ion channels.

physics.bio-ph↗