arXiv subjects

Mykhailo Potomkin

Publications and source records attributed to Mykhailo Potomkin.

17 recordsLinked to original sources

arXiv2026

Kinetics of an Expanding Bacterial Colony: Continuum Modeling and Analysis

We study the spatiotemporal dynamics of the expansion of a bacterial colony on a hard substrate. Nutrient from the substrate diffuses into the colony and is taken up by the bacterial cells for them to grow and divide, expanding the initial monolayer and then pancake-shaped colony. The concentration of nutrient determines the local cell growth rate in the colony. Mass conservation relates such local growth rate with velocity which is approximated to be proportional to the pressure gradient by Darcy's law. Altogether, the growing colony is modeled as a moving-boundary problem with the nutrient concentration and pressure solving a reaction-diffusion equation and Laplace's equation, respectively. We analyze the self-consistent moving-boundary model with respect to different geometrical setting. For a general three-dimensional cylindrically symmetric model, we study the steady-state nutrient concentration. We construct and analyze a one-dimensional model for vertical expansion and a two-dimensional disk model for radial expansion of the colony. Our analysis finds that the nutrient depletes into the colony and slows down the vertical expansion of the colony. The vertical level where the nutrient concentration reaches the Monod constant, a threshold below which individual bacteria hardly grow, lowers down exponentially fast. We also estimate the asymptotic radial expansion rate. Moreover, we establish that the region where the nutrient concentration is above the threshold, allowing bacteria to grow and the colony to expand radially, is a ring-shaped peripheral region of fixed thickness. All these are consistent with experiment and agent-based simulations reported in literature.

math.AP↗

arXiv2025

Multiscale Analysis of a Kinetic Model of Confined Suspensions of Self-Propelled Rods

The behavior of active matter under confinement poses significant challenges due to the intricate coupling between dynamics near boundaries and those in the bulk. A defining feature of active matter systems is that a substantial portion of their dynamics takes place near confining boundaries. In our previous work, we developed a kinetic framework that enables direct computation of the probability distribution functions for both the position and orientation of active rods. A distinguishing aspect of this approach is its explicit treatment of wall accumulation through the use of two coupled probability distribution functions: one describing the bulk population and the other representing rods accumulated at the boundary. Another novel feature is the structure of the governing equation, which is degenerate: it is second-order in one non-temporal variable and first-order in another. The main focus of this paper is to rigorously justify this model via multi-scale analysis. We first establish well-posedness of the system and then employ two distinct multi-scale derivations to obtain the model as a singular limit of a more classical kinetic system in the regime of vanishing translational diffusion. For analytical clarity, we consider the case in which active rods, once accumulated at the wall, remain permanently confined there. This work provides a rigorous mathematical foundation for reduced kinetic models of confined active matter, bridging microscopic dynamics and macroscopic accumulation phenomena.

math.AP↗

arXiv2024

Boundary accumulations of active rods in microchannels with elliptical cross-section

Many motile microorganisms and bio-mimetic micro-particles have been successfully modeled as active rods - elongated bodies capable of self-propulsion. A hallmark of active rod dynamics under confinement is their tendency to accumulate at the walls. Unlike passive particles, which typically sediment and cease their motion at the wall, accumulated active rods continue to move along the wall, reorient, and may even escape from it. The dynamics of active rods at the wall and those away from it result in complex and non-trivial distributions. In this work, we examine the effects of wall curvature on active rod distribution by studying elliptical perturbations of tube-like microchannels, that is, the cylindrical confinement with a circular cross-section, common in both nature and various applications. By developing a computational model for individual active rods and conducting Monte Carlo simulations, we discovered that active rods tend to concentrate at locations with the highest wall curvature. We then investigated how the distribution of active rod accumulation depends on the background flow and orientation diffusion. Finally, we used a simplified mathematical model to explain why active rods preferentially accumulate at high-curvature locations.

cond-mat.soft↗

arXiv2022

Dynamics and steady state of squirmer motion in liquid crystal

We analyze a nonlinear PDE system describing the motion of a microswimmer in a nematic liquid crystal environment. For the microswimmer's motility, the squirmer model is used in which self-propulsion enters the model through the slip velocity on the microswimmer's surface. The liquid crystal is described using the well-established Beris-Edwards formulation. In previous computational studies, it was shown that the squirmer, regardless of its initial configuration, eventually orients itself either parallel or perpendicular to the preferred orientation dictated by the liquid crystal. Furthermore, the corresponding solution of the coupled nonlinear system converges to a steady state. In this work, we rigorously establish the existence of steady state and also the finite-time existence for the time-dependent problem. Finally, using a two-scale asymptotic expansion we derive a reduced model for the collective swimming of squirmers as they reach their steady state orientation and speed.

math.AP↗

arXiv2020

Motor protein transport along inhomogeneous microtubules

Many cellular processes rely on the cell's ability to transport material to and from the nucleus. Networks consisting of many microtubules and actin filaments are key to this transport. Recently, the inhibition of intracellular transport has been implicated in neurodegenerative diseases such as Alzheimer's disease and Amyotrophic Lateral Sclerosis (ALS). Furthermore, microtubules may contain so-called defective regions where motor protein velocity is reduced due to accumulation of other motors and microtubule associated proteins. In this work, we propose a new mathematical model describing the motion of motor proteins on microtubules which incorporate a defective region. We take a mean-field approach derived from a first principle lattice model to study motor protein dynamics and density profiles. In particular, given a set of model parameters we obtain a closed-form expression for the equilibrium density profile along a given microtubule. We then verify the analytic results using mathematical analysis on the discrete model and Monte Carlo simulations. This work will contribute to the fundamental understanding of inhomogeneous microtubules providing insight into microscopic interactions that may result in the onset of neurodegenerative diseases. Our results for inhomogeneous microtubules are consistent with prior work studying the homogeneous case.

q-bio.SC↗

arXiv2019

A kinetic approach to active rod dynamics in confined domains

The study of active matter consisting of many self-propelled (active) swimmers in an imposed flow is important for many applications. Self-propelled swimmers may represent both living and artificial ones such as bacteria and chemically driven bi-metallic nano-particles. In this work we focus on a kinetic description of active matter represented by self-propelled rods swimming in a viscous fluid confined by a wall. It is well-known that walls may significantly affect the trajectories of active rods in contrast to unbounded or periodic containers. Among such effects are accumulation at walls and upstream motion (also known as negative rheotaxis). Our first main result is the rigorous derivation of boundary conditions for the active rods' probability distribution function in the limit of vanishing inertia. Finding such a limit is important due to (i) the fact that in many examples of active matter inertia is negligible, since swimming occurs in a low Reynolds number regime, and (ii) this limit allows us to reduce the dimension - and so computational complexity - of the kinetic description. For the resulting model, we derive the system in the limit of vanishing translational diffusion which is also typically negligible for active particles. This system allows for tracking separately active particles accumulated at walls and active particles swimming in the bulk of the fluid.

cond-mat.soft↗

arXiv2018

Continuum approximations to systems of correlated interacting particles

We consider a system of interacting particles with random initial conditions. Continuum approximations of the system, based on truncations of the BBGKY hierarchy, are described and simulated for various initial distributions and types of interaction. Specifically, we compare the Mean Field Approximation (MFA), the Kirkwood Superposition Approximation (KSA), and a recently developed truncation of the BBGKY hierarchy (the Truncation Approximation - TA). We show that KSA and TA perform more accurately than MFA in capturing approximate distributions (histograms) obtained from Monte Carlo simulations. Furthermore, TA is more numerically stable and less computationally expensive than KSA.

cond-mat.stat-mech↗

arXiv2017

Focusing of Active Particles in a Converging Flow

We consider active particles swimming in a convergent fluid flow in a trapezoid nozzle with no-slip walls. We use mathematical modeling to analyze trajectories of these particles inside the nozzle. By extensive Monte Carlo simulations, we show that trajectories are strongly affected by the background fluid flow and geometry of the nozzle leading to wall accumulation and upstream motion (rheotaxis). In particular, we describe the non-trivial focusing of active rods depending on physical and geometrical parameters. It is also established that the convergent component of the background flow leads to stability of both downstream and upstream swimming at the centerline. The stability of downstream swimming enhances focusing, and the stability of upstream swimming enables rheotaxis in the bulk.

cond-mat.soft↗

arXiv2016

Flagella bending affects macroscopic properties of bacterial suspensions

To survive in harsh conditions, motile bacteria swim in complex environment and respond to the surrounding flow. Here we develop a PDE model describing how the flagella bending affects macroscopic properties of bacterial suspensions. First, we show how the flagella bending contributes to the decrease of the effective viscosity observed in dilute suspension. Our results do not impose tumbling (random re-orientation) as it was done previously to explain the viscosity reduction. Second, we demonstrate a possibility of bacterium escape from the wall entrapment due to the self-induced buckling of flagella. Our results shed light on the role of flexible bacterial flagella in interactions of bacteria with shear flow and walls or obstacles.

math.AP↗

arXiv2016

Phase field model of cell motility: sharp interface limit in sub-critical case

We consider a system of two PDEs arising in modeling of motility of eukariotic cells on substrates. This system consists of the Allen-Cahn equation for the scalar phase field function coupled with another vectorial parabolic equation for the orientation of the actin filament network. The two key properties of this system are (i) presence of gradients in the coupling terms (gradient coupling) and (ii) mass (volume) preservation constraints. We first prove that the sharp interface property of initial conditions is preserved in time. Next we formally derive the equation of the motion of the interface, which is the mean curvature motion perturbed by a nonlinear term that appears due to the properties (i)-(ii). This novel term leads to surprising features of the the motion of the interface. Because of these properties maximum principle and classical comparison techniques do not apply to this system. Furthermore, the system can not be written in a form of gradient flow, which is why recently developed Gamma-convergence techniques also can not be used for the justification of the formal derivation. Such justification is presented in a one-dimensional model problem and it leads to a stability result in a class of 'sharp interface' initial data.

math.AP↗

arXiv2016

Phase-Field Model of Cell Motility: Traveling Waves and Sharp Interface Limit

This letter is concerned with asymptotic analysis of a PDE model for motility of a eukaryotic cell on a substrate. This model was introduced in [1], where it was shown numerically that it successfully reproduces experimentally observed phenomena of cell-motility such as a discontinuous onset of motion and shape oscillations. The model consists of a parabolic PDE for a scalar phase-field function coupled with a vectorial parabolic PDE for the actin filament network (cytoskeleton). We formally derive the sharp interface limit (SIL), which describes the motion of the cell membrane and show that it is a volume preserving curvature driven motion with an additional nonlinear term due to adhesion to the substrate and protrusion by the cytoskeleton. In a 1D model problem we rigorously justify the SIL, and, using numerical simulations, observe some surprising features such as discontinuity of interface velocities and hysteresis. We show that nontrivial traveling wave solutions appear when the key physical parameter exceeds a certain critical value and the potential in the equation for phase field function possesses certain asymmetry.

math.AP↗

arXiv2016

Sharp interface limit in a phase field model of cell motility

We consider a system of two coupled parabolic PDEs introduced in [1] to model motility of eukaryotic cells. We study the asymptotic behavior of solutions in the limit of a small parameter related to the width of the interface in phase field function (sharp interface limit). We formally derive an equation of motion of the interface, which is mean curvature motion with an additional nonlinear term. In a 1D model parabolic problem we rigorously justify the sharp interface limit. To this end, a special form of asymptotic expansion is introduced to reduce analysis to a single nonlinear PDE. Further stability analysis reveals a qualitative change in the behavior of the system for small and large values of the coupling parameter. Using numerical simulations we also show discontinuities of the interface velocity and hysteresis. Also, in the 1D case we establish nontrivial traveling waves when the coupling parameter is large enough.

math.AP↗

arXiv2015

Effective Rheological Properties in Semidilute Bacterial Suspensions

Interactions between swimming bacteria have led to remarkable experimentally observable macroscopic properties such as the reduction of the effective viscosity, enhanced mixing, and diffusion. In this work, we study an individual based model for a suspension of interacting point dipoles representing bacteria in order to gain greater insight into the physical mechanisms responsible for the drastic reduction in the effective viscosity. In particular, asymptotic analysis is carried out on the corresponding kinetic equation governing the distribution of bacteria orientations. This allows one to derive an explicit asymptotic formula for the effective viscosity of the bacterial suspension in the limit of bacterium non-sphericity. The results show good qualitative agreement with numerical simulations and previous experimental observations. Finally, we justify our approach by proving existence, uniqueness, and regularity properties for this kinetic PDE model.

math.AP↗

arXiv2013

Complexity reduction in many particles systems with random initial data

We consider the motion of interacting particles governed by a coupled system of ODEs with random initial conditions. Direct computations for such systems are prohibitively expensive due to a very large number of particles and randomness requiring many realizations in their locations in the presence of strong interactions. While there are several approaches that address the above difficulties, none addresses all three simultaneously. Our goal is to develop such a computational approach in order to capture the experimentally observed emergence of correlations in the collective state (patterns due to strong interactions). Our approach is based on the truncation of the BBGKY hierarchy that allows one to go beyond the classical Mean Field limit and capture correlations while drastically reducing the computational complexity. Finally, we provide an example showing a numerical solution of this nonlinear and non-local system.

physics.comp-ph↗

arXiv2012

Boundary conditions in PDE model of collisions of swimmers

The goal of the paper is to determine boundary conditions in PDE models of collisions of microswimmers in a viscous fluid. We consider two self-propelled spheres (microswimmers) moving towards each other in viscous fluid. We first show that under commonly used no-slip boundary conditions on the fluid-solid interface the microswimmers do not collide which is a generalization of the well-known no-collision paradox for solid bodies (with no self-propulsion) in a viscous fluid. Secondly, we show that the microswimmers do collide when the no-slip boundary conditions are replaced by the Navier boundary conditions which therefore provides an adequate model of microswimmers such as swimming bacteria. The self-propulsion mechanism generates a drag force pulling a bacterium backwards and the collision problem is reduced to the analysis of competition between the drag and self-propulsion. For no-slip this is done by utilizing the Lorentz Reciprocal Theorem and the analytical solution for two solid spheres in the fluid. The analysis for the Navier boundary conditions is based on the variational formulation of Stokes problem. A Poincare type inequality for symmetrized gradient is introduced in this work.

math.AP↗

arXiv2010

A nonlinear transmission problem for a compound plate with thermoelastic part

In this paper we study a nonlinear transmission problem for a plate which consists of thermoelastic and isothermal parts. The problem generates a dynamical system in a suitable Hilbert space. Main result is the proof of the asymptotic smoothness of this dynamical system. Also we prove the existence of a compact global attractor in particular cases when the nonlinearity is of Berger type or scalar.

math.DS↗

arXiv2008

Asymptotic behaviour of thermoviscoelastic Berger plate

System of partial differential equations with a convolution terms and non-local nonlinearity describing oscillations of plate due to Berger approach and with accounting for thermal regime in terms of Coleman-Gurtin and Gurtin-Pipkin law and fading memory of material is considered. The equation is transformed into a dynamical system in a suitable Hilbert space which asymptotic behaviour is analysed. Existence of the compact global attractor in this dynamical system and some of its properties are proved in this article. Main tool in analysis of asymptotic behaviour is stabilizability inequality.

math.DS↗