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  1. Article ; Online: Swarmalators with delayed interactions.

    Blum, Nicholas / Li, Andre / O'Keeffe, Kevin / Kogan, Oleg

    Physical review. E

    2024  Volume 109, Issue 1-1, Page(s) 14205

    Abstract: We investigate the effects of delayed interactions in a population of "swarmalators," generalizations of phase oscillators that both synchronize in time and swarm through space. We discover two steady collective states: a state in which swarmalators are ... ...

    Abstract We investigate the effects of delayed interactions in a population of "swarmalators," generalizations of phase oscillators that both synchronize in time and swarm through space. We discover two steady collective states: a state in which swarmalators are essentially motionless in a disk arranged in a pseudocrystalline order, and a boiling state in which the swarmalators again form a disk, but now the swarmalators near the boundary perform boiling-like convective motions. These states are reminiscent of the beating clusters seen in photoactivated colloids and the living crystals of starfish embryos.
    Language English
    Publishing date 2024-02-15
    Publishing country United States
    Document type Journal Article
    ZDB-ID 2844562-4
    ISSN 2470-0053 ; 2470-0045
    ISSN (online) 2470-0053
    ISSN 2470-0045
    DOI 10.1103/PhysRevE.109.014205
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article ; Online: Fisher-Kolmogorov-Petrovsky-Piskunov dynamics mediated by a parent field with a delay.

    Stanley, Steffanie / Kogan, Oleg

    Physical review. E

    2021  Volume 104, Issue 3-1, Page(s) 34415

    Abstract: We examine a modification of the Fisher-Kolmogorov-Petrovsky-Piskunov (FKPP) process in which the diffusing substance requires a parent density field for reproduction. A biological example would be the density of diffusing spores (propagules) and the ... ...

    Abstract We examine a modification of the Fisher-Kolmogorov-Petrovsky-Piskunov (FKPP) process in which the diffusing substance requires a parent density field for reproduction. A biological example would be the density of diffusing spores (propagules) and the density of a stationary fungus (parent). The parent produces propagules at a certain rate, and the propagules turn into the parent substance at another rate. We model this evolution by the FKPP process with delay, which reflects a finite time typically required for a new parent to mature before it begins to produce propagules. Although the FKPP process with other types of delays have been considered in the past as a pure mathematical construct, in our paper a delay in the FKPP model arises in a natural science setting. The speed of the resulting density fronts is shown to decrease with increasing delay time and has a nontrivial dependence on the rate of conversion of propagules into the parent substance. Remarkably, the fronts in this model are always slower than Fisher waves of the classical FKPP model. The largest speed is half the classical value, and it is achieved at zero delay and when the two rates are matched.
    Language English
    Publishing date 2021-08-14
    Publishing country United States
    Document type Journal Article
    ZDB-ID 2844562-4
    ISSN 2470-0053 ; 2470-0045
    ISSN (online) 2470-0053
    ISSN 2470-0045
    DOI 10.1103/PhysRevE.104.034415
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Book ; Online: Tunable intracellular transport on converging microtubule morphologies

    Sarpangala, Niranjan / Randell, Brooke / Gopinathan, Ajay / Kogan, Oleg

    2023  

    Abstract: A common type of cytoskeletal morphology involves multiple converging microbutubules with their minus ends collected and stabilized by a microtubule organizing center (MTOC) in the interior of the cell. This arrangement enables the ballistic transport of ...

    Abstract A common type of cytoskeletal morphology involves multiple converging microbutubules with their minus ends collected and stabilized by a microtubule organizing center (MTOC) in the interior of the cell. This arrangement enables the ballistic transport of cargo bound to microtubules, both dynein mediated transport towards the MTOC and kinesin mediated transport away from it, interspersed with diffusion for unbound cargo-motor complexes. Spatial and temporal positioning of the MTOC allows for bidirectional transport towards and away from specific organelles and locations within the cell and also the sequestering and subsequent dispersal of dynein transported cargo. The general principles governing dynamics, efficiency and tunability of such transport in the MTOC vicinity is not fully understood. To address this, we develop a one-dimensional model that includes advective transport towards an attractor (such as the MTOC), and diffusive transport that allows particles to reach absorbing boundaries (such as cellular membranes). We calculated the mean first passage time (MFPT) for cargo to reach the boundaries as a measure of the effectiveness of sequestering (large MFPT) and diffusive dispersal (low MFPT). The MFPT experiences a dramatic growth in magnitude, transitioning from a low to high MFPT regime (dispersal to sequestering) over a window of cargo attachment/detachment rates that is close to in vivo values. We find that increasing either the attachment or detachment rate, while fixing the other, can result in optimal dispersal when the attractor is placed asymmetrically. Finally, we describe a rare event regime, where the escape location is exponentially sensitive to the attractor positioning. Our results suggest that structures such as the MTOC allow for the sensitive control of the spatial and temporal features of transport and corresponding function under physiological conditions.
    Keywords Quantitative Biology - Cell Behavior ; Condensed Matter - Statistical Mechanics ; Quantitative Biology - Subcellular Processes
    Subject code 612 ; 380
    Publishing date 2023-01-03
    Publishing country us
    Document type Book ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  4. Book ; Online: FKPP dynamics mediated by a parent field with a delay

    Stanley, Steffanie / Kogan, Oleg

    2020  

    Abstract: We examine a modification of the Fisher-Kolmogorov-Petrovsky-Piskunov (FKPP) process in which the diffusing substance requires a parent density field for reproduction. A biological example would be the density of diffusing spores (propagules) and the ... ...

    Abstract We examine a modification of the Fisher-Kolmogorov-Petrovsky-Piskunov (FKPP) process in which the diffusing substance requires a parent density field for reproduction. A biological example would be the density of diffusing spores (propagules) and the density of a stationary fungus (parent). The parent produces propagules at a certain rate, and the propagules turn into the parent substance at another rate. We model this evolution by the FKPP process with delay, which reflects a finite time typically required for a new parent to mature before it begins to produce propagules. While the FKPP process with other types of delays have been considered in the past as a pure mathematical construct, in our work a delay in the FKPP model arises in a natural science setting. The speed of the resulting density fronts is shown to decrease with increasing delay time, and has a non-trivial dependence on the rate of conversion of propagules into the parent substance. Remarkably, the fronts in this model are always slower than Fisher waves of the classical FKPP model. The largest speed is half of the classical value, and it is achieved at zero delay and when the two rates are matched.
    Keywords Quantitative Biology - Populations and Evolution ; Condensed Matter - Statistical Mechanics ; Mathematical Physics ; Nonlinear Sciences - Pattern Formation and Solitons ; Physics - Biological Physics
    Subject code 190
    Publishing date 2020-10-30
    Publishing country us
    Document type Book ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  5. Article: Controlling transitions in a Duffing oscillator by sweeping parameters in time.

    Kogan, Oleg

    Physical review. E, Statistical, nonlinear, and soft matter physics

    2007  Volume 76, Issue 3 Pt 2, Page(s) 37203

    Abstract: We consider a high-Q Duffing oscillator in a weakly nonlinear regime with the driving frequency sigma varying in time between sigma i and sigma f at a characteristic rate r. We found that the frequency sweep can cause controlled transitions between two ... ...

    Abstract We consider a high-Q Duffing oscillator in a weakly nonlinear regime with the driving frequency sigma varying in time between sigma i and sigma f at a characteristic rate r. We found that the frequency sweep can cause controlled transitions between two stable states of the system. Moreover, these transitions are accomplished via a transient that lingers for a long time around the third, unstable fixed point of saddle type. We propose a simple explanation for this phenomenon, and find the transient lifetime to scale as -(ln|r-rc|)lambda r, where rc is the critical rate necessary to induce a transition and lambda r is the repulsive eigenvalue of the saddle. Experimental implications are mentioned.
    Language English
    Publishing date 2007-09
    Publishing country United States
    Document type Journal Article
    ISSN 1539-3755
    ISSN 1539-3755
    DOI 10.1103/PhysRevE.76.037203
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Book ; Online: Path-dependent course of epidemic

    Nimmagadda, Varun / Kogan, Oleg / Khain, Evgeniy

    are two phases of quarantine better than one?

    2020  

    Abstract: The importance of a strict quarantine has been widely debated during the COVID-19 epidemic even from the purely epidemiological point of view. One argument against strict lockdown measures is that once the strict quarantine is lifted, the epidemic comes ... ...

    Abstract The importance of a strict quarantine has been widely debated during the COVID-19 epidemic even from the purely epidemiological point of view. One argument against strict lockdown measures is that once the strict quarantine is lifted, the epidemic comes back, and so the cumulative number of infected individuals during the entire epidemic will stay the same. We consider an SIR model on a network and follow the disease dynamics, modeling the phases of quarantine by changing the node degree distribution. We show that the system reaches different steady states based on the history: the outcome of the epidemic is path-dependent despite the same final node degree distribution. The results indicate that two-phase route to the final node degree distribution (a strict phase followed by a soft phase) are always better than one phase (the same soft one) unless all the individuals have the same number of connections at the end (the same degree); in the latter case, the overall number of infected is indeed history-independent. The modeling also suggests that the optimal procedure of lifting the quarantine consists of releasing nodes in the order of their degree - highest first.

    Comment: 6 pages, 4 figures, accepted to EPL (Europhysics Letters)
    Keywords Physics - Physics and Society ; Condensed Matter - Statistical Mechanics ; Quantitative Biology - Populations and Evolution
    Subject code 612
    Publishing date 2020-11-27
    Publishing country us
    Document type Book ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  7. Book ; Online: Onset of Singularities in the Pattern of Fluctuational Paths of a Nonequilibrium System

    Kogan, Oleg

    2011  

    Abstract: Fluctuations in systems away from thermal equilibrium have features that have no analog in equilibrium systems. One of such features concerns large rare excursions far from the stable state in the space of dynamical variables. For equilibrium systems, ... ...

    Abstract Fluctuations in systems away from thermal equilibrium have features that have no analog in equilibrium systems. One of such features concerns large rare excursions far from the stable state in the space of dynamical variables. For equilibrium systems, the most probable fluctuational trajectory to a given state is related to the fluctuation-free trajectory back to the stable state by time reversal. This is no longer true for nonequilibrium systems, where the pattern of the most probable trajectories generally displays singularities. Here we study how the singularities emerge as the system is driven away from equilibrium, and whether a driving strength threshold is required for their onset. Using a resonantly modulated oscillator as a model, we identify two distinct scenarios, depending on the speed of the optimal path in thermal equilibrium. If the position away from the stable state along the optimal path grows exponentially in time, the singularities emerge without a threshold. We find the scaling of the location of the singularities as a function of the control parameter. If the growth away from the stable state is faster than exponential, characterized by the ability to reach infinity in finite time, there is a threshold for the onset of singularities, which we study for the model.

    Comment: 10 pages, 6 figures
    Keywords Condensed Matter - Statistical Mechanics ; Nonlinear Sciences - Chaotic Dynamics
    Subject code 612
    Publishing date 2011-10-12
    Publishing country us
    Document type Book ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  8. Article ; Online: Fragility of reaction-diffusion models with respect to competing advective processes.

    Kogan, Oleg / O'Keeffe, Kevin / Myers, Christopher R

    Physical review. E

    2017  Volume 96, Issue 2-1, Page(s) 22220

    Abstract: We study the coupling of a Fisher-Kolmogorov-Petrovsky-Piskunov (FKPP) equation to a separate, advection-only transport process. We find that an infinitesimal coupling can cause a finite change in the speed and shape of the reaction front, indicating the ...

    Abstract We study the coupling of a Fisher-Kolmogorov-Petrovsky-Piskunov (FKPP) equation to a separate, advection-only transport process. We find that an infinitesimal coupling can cause a finite change in the speed and shape of the reaction front, indicating the fragility of the FKPP model with respect to such a perturbation. The front dynamics can be mapped to an effective FKPP equation only at sufficiently fast diffusion or large coupling strength. We also discover conditions when the front width diverges and when its speed is insensitive to the coupling. At zero diffusion in our mean-field description, the downwind front speed goes to a finite value as the coupling goes to zero.
    Language English
    Publishing date 2017-08
    Publishing country United States
    Document type Journal Article
    ZDB-ID 2844562-4
    ISSN 2470-0053 ; 2470-0045
    ISSN (online) 2470-0053
    ISSN 2470-0045
    DOI 10.1103/PhysRevE.96.022220
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  9. Book ; Online: Scaling crossovers in activated escape of nonequilibrium systems

    Kogan, Oleg

    a resonantly driven oscillator

    2008  

    Abstract: The rate of metastable decay in nonequilibrium systems is expected to display scaling behavior: i.e., the logarithm of the decay rate should scale as a power of the distance to a bifurcation point where the metastable state disappears. Recently such ... ...

    Abstract The rate of metastable decay in nonequilibrium systems is expected to display scaling behavior: i.e., the logarithm of the decay rate should scale as a power of the distance to a bifurcation point where the metastable state disappears. Recently such behavior was observed and some of the earlier predicted exponents were found in experiments on several types of systems described by a model of a modulated oscillator. Here we establish the range where different scaling behavior is displayed and show how the crossover between different types of scaling occurs. The analysis is done for a nonlinear oscillator with two coexisting stable states of forced vibrations. Our numerical calculations, based on the the instanton method allow the mapping of the entire parameter range of bi-stability. We find the regions where the scaling exponents are 1 or 3/2, depending on the damping. The exponent 3/2 is found to extend much further from the bifurcation then were it would be expected to hold as a result of an over-damped soft mode. We also uncover a new scaling behavior with exponent of $\approx$ 1.3 which extends, numerically, beyond the close vicinity of the bifurcation point.

    Comment: 13 pages, 14 figures
    Keywords Condensed Matter - Statistical Mechanics ; Condensed Matter - Other Condensed Matter
    Subject code 612
    Publishing date 2008-05-07
    Publishing country us
    Document type Book ; Online
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  10. Article ; Online: Two-strain competition in quasineutral stochastic disease dynamics.

    Kogan, Oleg / Khasin, Michael / Meerson, Baruch / Schneider, David / Myers, Christopher R

    Physical review. E, Statistical, nonlinear, and soft matter physics

    2014  Volume 90, Issue 4, Page(s) 42149

    Abstract: We develop a perturbation method for studying quasineutral competition in a broad class of stochastic competition models and apply it to the analysis of fixation of competing strains in two epidemic models. The first model is a two-strain generalization ... ...

    Abstract We develop a perturbation method for studying quasineutral competition in a broad class of stochastic competition models and apply it to the analysis of fixation of competing strains in two epidemic models. The first model is a two-strain generalization of the stochastic susceptible-infected-susceptible (SIS) model. Here we extend previous results due to Parsons and Quince [Theor. Popul. Biol. 72, 468 (2007)], Parsons et al. [Theor. Popul. Biol. 74, 302 (2008)], and Lin, Kim, and Doering [J. Stat. Phys. 148, 646 (2012)]. The second model, a two-strain generalization of the stochastic susceptible-infected-recovered (SIR) model with population turnover, has not been studied previously. In each of the two models, when the basic reproduction numbers of the two strains are identical, a system with an infinite population size approaches a point on the deterministic coexistence line (CL): a straight line of fixed points in the phase space of subpopulation sizes. Shot noise drives one of the strain populations to fixation, and the other to extinction, on a time scale proportional to the total population size. Our perturbation method explicitly tracks the dynamics of the probability distribution of the subpopulations in the vicinity of the CL. We argue that, whereas the slow strain has a competitive advantage for mathematically "typical" initial conditions, it is the fast strain that is more likely to win in the important situation when a few infectives of both strains are introduced into a susceptible population.
    MeSH term(s) Computer Simulation ; Epidemics ; Models, Biological ; Probability ; Stochastic Processes ; Time Factors
    Language English
    Publishing date 2014-10
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
    ISSN 1550-2376
    ISSN (online) 1550-2376
    DOI 10.1103/PhysRevE.90.042149
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