arXiv subjects

Alexander S. Mikhailov

Publications and source records attributed to Alexander S. Mikhailov.

At least 19 recordsLinked to original sources

arXiv2023

Reaction-induced molecular dancing and boosted diffusion of enzymes

A novel mechanism of reaction-induced active molecular motion, not involving any kind of self-propulsion, is proposed and analyzed. Because of the momentum exchange with the surrounding solvent, conformational transitions in mechano-chemical enzymes are accompanied by motions of their centers of mass. As we show, in combination with rotational diffusion, such repeated reciprocal motions generate an additional random walk - or molecular dancing - and hence boost translational diffusion of an enzyme. A systematic theory of this phenomenon is developed, using as an example a simple enzyme model of a rigid two-state dumbbell. To support the analysis, numerical simulations are performed. Our conclusion is that the phenomenon of molecular dancing could underlie the observations of reaction-induced diffusion enhancement in enzymes. Major experimental findings, such as the occurrence of leaps, the anti-chemotaxis, the linear dependence on the reaction turnover rate and on the rate of energy supply, become thus explained. Moreover, the dancing behavior is possible in other systems, natural and synthetic, too. In the future, interesting biotechnology applications may be developed using such effects.

cond-mat.soft↗

arXiv2020

Mechanochemical enzymes and protein machines as hydrodynamic force dipoles: The active dimer model

Mechanochemically active enzymes change their shapes within every turnover cycle. Therefore, they induce circulating flows in the solvent around them and behave as oscillating hydrodynamic force dipoles. Because of non-equilibrium fluctuating flows collectively generated by the enzymes, mixing in the solution and diffusion of passive particles within it are expected to get enhanced. Here, we investigate the intensity and statistical properties of such force dipoles in the minimal active dimer model of a mechanochemical enzyme. In the framework of this model, novel estimates for hydrodynamic collective effects in solution and in lipid bilayers under rapid rotational diffusion are derived, and available experimental and computational data is examined.

cond-mat.soft↗

arXiv2020

Diffusion in crowded colloids of particles cyclically changing their shapes

A simple model of an active colloid consisting of dumbbell-shaped particles that cyclically change their length without propelling themselves is proposed and analyzed. At nanoscales, it represents an idealization for bacterial cytoplasm or for a biomembrane with active protein inclusions. Our numerical simulations demonstrate that non-equilibrium conformational activity of particles can strongly affect diffusion and structural relaxation: while a passive colloid behaves as a glass, it gets progressively fluidized when the activity is turned on. Qualitatively, this agrees with experimental results on optical tracking of probe particles in bacterial and yeast cells where metabolism-induced fluidization of cytoplasm was observed.

nlin.AO↗

arXiv2017

Localization and diffusion of tracer particles in viscoelastic media with active force dipoles

Optical tracking in vivo experiments reveal that diffusion of particles in biological cells is strongly enhanced in the presence of ATP and the experimental data for animal cells could previously be reproduced within a phenomenological model of a gel with myosin motors acting within it [EPL 110, 48005 (2015)]. Here, the two-fluid model of a gel is considered where active macromolecules, described as force dipoles, cyclically operate both in the elastic and the fluid components. Through coarse-graining, effective equations of motions for tracer particles displaying local deformations and local fluid flows are derived. The equation for deformation tracers coincides with the earlier phenomenological model and thus confirms it. For flow tracers, diffusion enhancement caused by active force dipoles in the fluid component, and thus due to metabolic activity, is found. The latter effect may explain why ATP-dependent diffusion enhancement could also be observed in bacteria that lack molecular motors in their skeleton or when the activity of myosin motors was chemically inhibited.

cond-mat.soft↗

arXiv2016

Autonomous Learning by Dynamical Systems with Inertial or Delayed Feedbacks

Dynamical systems can autonomously adapt their organization so that the required target dynamics is reproduced. In the previous Rapid Communication [Phys. Rev. E 90,030901(R) (2014)], it was shown how such systems can be designed using delayed feedbacks. Here, the proposed method is further analyzed and improved. Its extension to adaptable systems, where delays are absent and inertial feedbacks are instead employed, is suggested. Numerical tests for three different models, including networks of phase and amplitude oscillators, are performed.

nlin.AO↗

arXiv2016

Hydrodynamic collective effects of active proteins in biological membranes

Lipid bilayers forming biological membranes are known to behave as viscous 2D fluids on submicrometer scales; usually they contain a large number of active protein inclusions. Recently, it has been shown [Proc. Nat. Acad. Sci. USA 112, E3639 (2015)] that such active proteins should in- duce non-thermal fluctuating lipid flows leading to diffusion enhancement and chemotaxis-like drift for passive inclusions in biomembranes. Here, a detailed analytical and numerical investigation of such effects is performed. The attention is focused on the situations when proteins are concentrated within lipid rafts. We demonstrate that passive particles tend to become attracted by active rafts and are accumulated inside them.

cond-mat.soft↗

arXiv2015

Equilibrium microphase separation in the two-leaflet model of lipid membranes

A novel two-leaflet description of lipid membranes is proposed. Within its framework, phase separation phenomena in multicomponent biological membranes are analyzed. As we show, interactions between the leaflets tend to suppress macroscopic phase segregation (i.e., complete demixing of lipids) in such systems. Instead, microphase separation characterized by formation of equilibrium nanoscale domains can take place. The phase diagram is constructed and numerical simulations revealing nanostructures of different morphology are performed.

physics.bio-ph↗

arXiv2014

Autonomous Learning by Simple Dynamical Systems with Delayed Feedbacks

A general scheme for construction of dynamical systems able to learn generation of the desired kinds of dynamics through adjustment of their internal structure is proposed. The scheme involves intrinsic time-delayed feedback to steer the dynamics towards the target performance. As an example, a system of coupled phase oscillators, which can by changing the weights of connections between its elements evolve to a dynamical state with the prescribed (low or high) synchronization level, is considered and investigated.

nlin.AO↗

arXiv2014

Propagation failure of excitation waves on trees and random networks

Excitation waves are studied on trees and random networks of coupled active elements. Undamped propagation of such waves is observed in those networks. It represents an excursion from the resting state and a relaxation back to it for each node. However, the degrees of the nodes influence drastically the dynamics. Excitation propagates more slowly through nodes with larger degrees and beyond some critical degree waves lose their stability and disappear. For regular trees with a fixed branching ratio, the critical degree is determined with an approximate analytical theory which also holds locally for the early stage of excitation spreading in random networks.

nlin.PS↗

arXiv2014

Self-propulsion through symmetry breaking

In addition to self-propulsion by phoretic mechanisms that arises from an asymmetric distribution of reactive species around a catalytic motor, spherical particles with a uniform distribution of catalytic activity may also propel themselves under suitable conditions. Reactive fluctuation-induced asymmetry can give rise to transient concentration gradients which may persist under certain conditions, giving rise to a bifurcation to self-propulsion. The nature of this phenomenon is analyzed in detail, and particle-level simulations are carried out to demonstrate its existence.

cond-mat.stat-mech↗

arXiv2013

Advection of passive particles over flow networks

The problem of stochastic advection of passive particles by circulating conserved flows on networks is formulated and investigated. The particles undergo transitions between the nodes with the transition rates determined by the flows passing through the links. Such stochastic advection processes lead to mixing of particles in the network and, in the final equilibrium state, concentration of particles in all nodes become equal. As we find, equilibration begins in the subset of nodes, representing flow hubs, and extends to the periphery nodes with weak flows. This behavior is related to the effect of localization of the eigenvectors of the advection matrix for considered networks. Applications of the results to problems involving spreading of infections or pollutants by traffic networks are discussed.

cond-mat.stat-mech↗

arXiv2013

Dispersal-induced destabilization of metapopulations and oscillatory Turing patterns in ecological networks

As proposed by Alan Turing in 1952 as a ubiquitous mechanism for nonequilibrium pattern formation, diffusional effects may destabilize uniform distributions of reacting chemical species and lead to both spatially and temporally heterogeneous patterns. While stationary Turing patterns are broadly known, the oscillatory instability, leading to traveling waves in continuous media and also called the wave bifurcation, is rare for chemical systems. Here, we extend the analysis by Turing to general networks and apply it to ecological metapopulations of biological species with dispersal connections between habitats. Remarkably, the oscillatory Turing instability does not lead to wave patterns in networks, but to spontaneous development of heterogeneous oscillations and possible extinction of some species, even though they are absent for isolated populations. Furthermore, our theoretical analysis reveals that this instability is more common in ecological metapopulations than in chemical reactions. Indeed, we find the instabilities for all possible food webs with three predator or prey species, under various assumptions about the mobility of individual species and nonlinear interactions between them. Therefore, we suggest that the oscillatory Turing instability is generic and must play a fundamental role in metapopulation dynamics, providing a common mechanism for dispersal-induced destabilization of ecosystems.

nlin.PS↗

arXiv2013

Effective harmonic potentials: insights into the internal cooperativity and sequence-specificity of protein dynamics

The proper biological functioning of proteins often relies on the occurrence of coordinated fluctuations around their native structure, or of wider and sometimes highly elaborated motions. Coarse-grained elastic-network descriptions are known to capture essential aspects of conformational dynamics in proteins, but have so far remained mostly phenomenological, and unable to account for the chemical specificities of amino acids. Here, we propose a method to derive residue- and distance-specific effective harmonic potentials from the statistical analysis of an extensive dataset of NMR conformational ensembles. These potentials constitute dynamical counterparts to the mean-force statistical potentials commonly used for static analyses of protein structures. In the context of the elastic network model, they yield a strongly improved description of the cooperative aspects of residue motions, and give the opportunity to systematically explore the influence of sequence details on protein dynamics.

q-bio.BM↗

arXiv2013

Sufficient conditions for wave instability in three-component reaction-diffusion systems

Sufficient conditions for the wave instability in general three-component reaction-diffusion systems are derived. These conditions are expressed in terms of the Jacobian matrix of the uniform steady state of the system, and enable us to determine whether the wave instability can be observed as the mobility of one of the species is gradually increased. It is found that the instability can also occur if one of the three species does not diffuse. Our results provide a useful criterion for searching wave instabilities in reaction-diffusion systems of various origins.

nlin.PS↗

arXiv2013

Feedback-induced stationary localized patterns in networks of diffusively coupled bistable elements

Effects of feedbacks on self-organization phenomena in networks of diffusively coupled bistable elements are investigated. For regular trees, an approximate analytical theory for localized stationary patterns under application of global feedbacks is constructed. Using it, properties of such patterns in different parts of the parameter space are discussed. Numerical investigations are performed for large random Erdös-Rényi and scale-free networks. In both kinds of systems, localized stationary activation patterns have been observed. The active nodes in such a pattern form a subnetwork, whose size decreases as the feedback intensity is increased. For strong feedbacks, active subnetworks are organized as trees. Additionally, local feedbacks affecting only the nodes with high degrees (i.e. hubs) or the periphery nodes are considered.

nlin.AO↗

arXiv2012

Traveling and pinned fronts in bistable reaction-diffusion systems on network

Traveling fronts and stationary localized patterns in bistable reaction-diffusion systems have been broadly studied for classical continuous media and regular lattices. Analogs of such non-equilibrium patterns are also possible in networks. Here, we consider traveling and stationary patterns in bistable one-component systems on random Erdös-Rényi, scale-free and hierarchical tree networks. As revealed through numerical simulations, traveling fronts exist in network-organized systems. They represent waves of transition from one stable state into another, spreading over the entire network. The fronts can furthermore be pinned, thus forming stationary structures. While pinning of fronts has previously been considered for chains of diffusively coupled bistable elements, the network architecture brings about significant differences. An important role is played by the degree (the number of connections) of a node. For regular trees with a fixed branching factor, the pinning conditions are analytically determined. For large Erdös-Rényi and scale-free networks, the mean-field theory for stationary patterns is constructed.

nlin.PS↗

arXiv2012

Coarse-Grain Model for Lipid Bilayer Self-Assembly and Dynamics: Multiparticle Collision Description of the Solvent

A mesoscopic coarse-grain model for computationally-efficient simulations of biomembranes is presented. It combines molecular dynamics simulations for the lipids, modeled as elastic chains of beads, with multiparticle collision dynamics for the solvent. Self-assembly of a membrane from a uniform mixture of lipids is observed. Simulations at different temperatures demonstrate that it reproduces the gel and liquid phases of lipid bilayers. Investigations of lipid diffusion in different phases reveals a crossover from subdiffusion to normal diffusion at long times. Macroscopic membrane properties, such as stretching and bending elastic moduli, are determined directly from the mesoscopic simulations. Velocity correlation functions for membrane flows are determined and analyzed.

cond-mat.soft↗

arXiv2012

Design of Oscillator Networks with Enhanced Synchronization Tolerance against Noise

Can synchronization properties of a network of identical oscillators in the presence of noise be improved through appropriate rewiring of its connections? What are the optimal network architectures for a given total number of connections? We address these questions by running the optimization process, using the stochastic Markov Chain Monte Carlo method with replica exchange, to design the networks of phase oscillators with the increased tolerance against noise. As we find, the synchronization of a network, characterized by the Kuramoto order parameter, can be increased up to 40 %, as compared to that of the randomly generated networks, when the optimization is applied. Large ensembles of optimized networks are obtained and their statistical properties are investigated.

nlin.AO↗