arXiv subjects

Ramin Golestanian

Publications and source records attributed to Ramin Golestanian.

At least 109 records · Page 6Linked to original sources

arXiv2020

Nonequilibrium polarity-induced mechanism for chemotaxis: emergent Galilean symmetry and exact scaling exponents

A generically observed mechanism that drives the self-organization of living systems is interaction via chemical signals among the individual elements -- which may represent cells, bacteria, or even enzymes. Here we propose a novel mechanism for such interactions, in the context of chemotaxis, which originates from the polarity of the particles and which generalizes the well-known Keller--Segel interaction term. We study the resulting large-scale dynamical properties of a system of such chemotactic particles using the exact stochastic formulation of Dean and Kawasaki along with dynamical renormalization group analysis of the critical state of the system. At this critical point, an emergent "Galilean" symmetry is identified, which allows us to obtain the dynamical scaling exponents exactly; these exponents reveal superdiffusive density fluctuations and non-Poissonian number fluctuations. We expect our results to shed light on how molecular regulation of chemotactic circuits can determine large-scale behavior of cell colonies and tissues.

cond-mat.stat-mech↗

arXiv2020

Stochastic effects on the dynamics of an epidemic due to population subdivision

Using a stochastic Susceptible-Infected-Removed (SIR) meta-population model of disease transmission, we present analytical calculations and numerical simulations dissecting the interplay between stochasticity and the division of a population into mutually independent sub-populations. We show that subdivision activates two stochastic effects---extinction and desynchronization---diminishing the overall impact of the outbreak, even when the total population has already left the stochastic regime and the basic reproduction number is not altered by the subdivision. Both effects are quantitatively captured by our theoretical estimates, allowing us to determine their individual contributions to the observed reduction of the peak of the epidemic.

q-bio.PE↗

arXiv2020

Optimal navigation strategies for microswimmers on curved manifolds

Finding the fastest path to a desired destination is a vitally important task for microorganisms moving in a fluid flow. We study this problem by building an analytical formalism for overdamped microswimmers on curved manifolds and arbitrary flows. We show that the solution corresponds to the geodesics of a Randers metric, which is an asymmetric Finsler metric that reflects the irreversible character of the problem. Using the example of a spherical surface, we demonstrate that the swimmer performance that follows this "Randers policy" always beats a more direct policy. A study of the shape of isochrones reveals features such as self-intersections, cusps, and abrupt nonlinear effects. Our work provides a link between microswimmer physics and geodesics in generalizations of general relativity.

physics.bio-ph↗

arXiv2020

Magnetic microswimmers exhibit Bose-Einstein-like condensation

We study an active matter system comprised of magnetic microswimmers confined in a microfluidic channel and show that it exhibits a new type of self-organized behavior. Combining analytical techniques and Brownian dynamics simulations, we demonstrate how the interplay of non-equilibrium activity, external driving, and magnetic interactions leads to the condensation of swimmers at the center of the channel via a non-equilibrium phase transition that is formally akin to Bose-Einstein condensation. We find that the effective dynamics of the microswimmers can be mapped onto a diffusivity-edge problem, and use the mapping to build a generalized thermodynamic framework, which is verified by a parameter-free comparison with our simulations. Our work reveals how driven active matter has the potential to generate exotic classical non-equilibrium phases of matter with traits that are analogous to those observed in quantum systems.

cond-mat.stat-mech↗

arXiv2020

Exact axisymmetric interaction of phoretically active Janus particles

We study the axisymmetric interaction of two chemically active Janus particles. By relying on the linearity of the field equations and symmetry arguments, we derive a generic solution for the relative velocity of the particles. We show that regardless of the chemical properties of the system, the relative velocity can be written as a linear summation of geometrical functions which only depend on the gap size between the particles. We evaluate these functions via an exact approach which accounts for the full chemical and hydrodynamic interactions. Using the obtained solution, we expose the role of each compartment in the relative motion, and also discuss the contribution of different interactions. We then show that the dynamical system describing the relative motion of two Janus particles can have up to three fixed points. These fixed points can be stable or unstable, indicating that a system of two Janus particles can exhibit a variety of nontrivial behaviour depending on their initial gap size, and their chemical properties. We also look at the specific case of Janus particles in which one compartment is inert, and present regime diagrams for their relative behaviour in the activity-mobility parameter space.

cond-mat.soft↗

arXiv2020

Quantifying configurational information for a stochastic particle in a flow-field

Flow-fields are ubiquitous systems that are able to transport vital signalling molecules necessary for system function. While information regarding the location and transport of such particles is often crucial, it is not well-understood how to quantify the information in such stochastic systems. Using the framework of nonequilibrium statistical physics, we develop theoretical tools to address this question. We observe that rotation in a flow-field does not explicitly appear in the generalized potential that governs the rate of system entropy production. Specifically, in the neighborhood of a flow-field, rotation contributes to the information content only in the presence of strain -- and then with a comparatively weaker contribution than strain and at higher orders in time. Indeed, strain and especially the flow divergence, contribute most strongly to transport properties such as particle residence time and the rate of information change. These results shed light on how information can be analyzed and controlled in complex artificial and living flow-based systems.

cond-mat.stat-mech↗

arXiv2020

Scalar Active Mixtures: The Non-Reciprocal Cahn-Hilliard Model

Pair interactions between active particles need not follow Newton's third law. In this work we propose a continuum model of pattern formation due to non-reciprocal interaction between multiple species of scalar active matter. The classical Cahn-Hilliard model is minimally modified by supplementing the equilibrium Ginzburg-Landau dynamics with particle number conserving currents which cannot be derived from a free energy, reflecting the microscopic departure from action-reaction symmetry. The strength of the asymmetry in the interaction determines whether the steady state exhibits a macroscopic phase separation or a traveling density wave displaying global polar order. The latter structure, which is equivalent to an active self-propelled smectic phase, coarsens via annihilation of defects, whereas the former structure undergoes Ostwald ripening. The emergence of traveling density waves, which is a clear signature of broken time-reversal symmetry in this active system, is a generic feature of any multi-component mixture with microscopic non-reciprocal interactions.

cond-mat.stat-mech↗

arXiv2020

Wrinkling instability in 3D active nematics

In nature interactions between biopolymers and motor proteins give rise to biologically essential emergent behaviours. Besides cytoskeleton mechanics, active nematics arise from such interactions. Here we present a study on 3D active nematics made of microtubules, kinesin motors and depleting agent. It shows a rich behaviour evolving from a nematically ordered space-filling distribution of microtubule bundles toward a flattened and contracted 2D ribbon that undergoes a wrinkling instability and subsequently transitions into a 3D active turbulent state. The wrinkle wavelength is independent of the ATP concentration and our theoretical model describes its relation with the appearance time. We compare the experimental results with a numerical simulation that confirms the key role of kinesin motors in cross-linking and sliding the microtubules. Our results on the active contraction of the network and the independence of wrinkle wavelength on ATP concentration are important steps forward for the understanding of these 3D systems.

cond-mat.soft↗

arXiv2020

Exact phoretic interaction of two chemically-active particles

We study the nonequilibrium interaction of two isotropic chemically-active particles taking into account the exact near-field chemical interactions as well as hydrodynamic interactions. We identify regions in the parameter space wherein the dynamical system describing the two particles can have a fixed-point---a phenomenon that cannot be captured under the far-field approximation. We find that due to near-field effects, the particles may reach a stable equilibrium at a nonzero gap size, or make a complex that can dissociate in the presence of sufficiently strong noise. We explicitly show that the near-field effects are originated from a self-generated neighbor-reflected chemical gradient, similar to interactions of a self-propelling phoretic particle and a flat substrate.

physics.flu-dyn↗

arXiv2020

Cooperatively enhanced reactivity and 'stabilitaxis' of dissociating oligomeric proteins

Many functional units in biology, such as enzymes or molecular motors, are composed of several subunits that can reversibly assemble and disassemble. This includes oligomeric proteins composed of several smaller monomers, as well as protein complexes assembled from a few proteins. By studying the generic spatial transport properties of such proteins, we investigate here whether their ability to reversibly associate and dissociate may confer them a functional advantage with respect to non-dissociating proteins. In uniform environments with position-independent association-dissociation, we find that enhanced diffusion in the monomeric state coupled to reassociation into the functional oligomeric form leads to enhanced reactivity with distant targets. In non-uniform environments with position-dependent association-dissociation, caused e.g. by spatial gradients of an inhibiting chemical, we find that dissociating proteins generically tend to accumulate in regions where they are most stable, a process that we term 'stabilitaxis'.

physics.chem-ph↗

arXiv2020

Bose-Einstein-like Condensation due to Diffusivity Edge under Periodic Confinement

A generic class of scalar active matter, characterized at the mean field level by the diffusivity vanishing above some threshold density, was recently introduced [Golestanian R 2019 Phys. Rev. E 100 010601(R)]. In the presence of harmonic confinement, such 'diffusivity edge' was shown to lead to condensation in the ground state, with the associated transition exhibiting formal similarities with Bose-Einstein condensation (BEC). In this work, the effect of a diffusivity edge is addressed in a periodic potential in arbitrary dimensions, where the system exhibits coexistence between many condensates. Using a generalized thermodynamic description of the system, it is found that the overall phenomenology of BEC holds even for finite energy barriers separating each neighbouring pair of condensates. Shallow potentials are shown to quantitatively affect the transition, and introduce non-universality in the values of the scaling exponents.

cond-mat.stat-mech↗

arXiv2020

Degenerate states, emergent dynamics and fluid mixing by magnetic rotors

We investigate the collective motion of magnetic rotors suspended in a viscous fluid under an uniform rotating magnetic field. The rotors are positioned on a square lattice, and low Reynolds hydrodynamics is assumed. For a $3 \times 3$ array of magnets, we observe three characteristic dynamical patterns as the external field strength is varied: a synchronized pattern, an oscillating pattern, and a chessboard pattern. The relative stability of these depends on the competition between the energy due to the external magnetic field and the energy of the magnetic dipole-dipole interactions among the rotors. We argue that the chessboard pattern can be understood as an alternation in the stability of two degenerate states, characterized by striped and spin-ice configurations, as the applied magnetic field rotates. For larger arrays, we observe propagation of slip waves that are similar to metachronal waves. The rotor arrays have potential as microfluidic devices that can mix fluids and create vortices of different sizes.

cond-mat.soft↗

arXiv2019

The 2019 Motile Active Matter Roadmap

Activity and autonomous motion are fundamental in living and engineering systems. This has stimulated the new field of active matter in recent years, which focuses on the physical aspects of propulsion mechanisms, and on motility-induced emergent collective behavior of a larger number of identical agents. The scale of agents ranges from nanomotors and microswimmers, to cells, fish, birds, and people. Inspired by biological microswimmers, various designs of autonomous synthetic nano- and micromachines have been proposed. Such machines provide the basis for multifunctional, highly responsive, intelligent (artificial) active materials, which exhibit emergent behavior and the ability to perform tasks in response to external stimuli. A major challenge for understanding and designing active matter is their inherent nonequilibrium nature due to persistent energy consumption, which invalidates equilibrium concepts such as free energy, detailed balance, and time-reversal symmetry. Unraveling, predicting, and controlling the behavior of active matter is a truly interdisciplinary endeavor at the interface of biology, chemistry, ecology, engineering, mathematics, and physics. The vast complexity of phenomena and mechanisms involved in the self-organization and dynamics of motile active matter comprises a major challenge. Hence, to advance, and eventually reach a comprehensive understanding, this important research area requires a concerted, synergetic approach of the various disciplines.

cond-mat.soft↗

arXiv2019

Open-Boundary Hamiltonian adaptive resolution. From grand canonical to non-equilibrium molecular dynamics simulations

We propose an open-boundary molecular dynamics method in which an atomistic system is in contact with an infinite particle reservoir at constant temperature, volume and chemical potential. In practice, following the Hamiltonian adaptive resolution strategy, the system is partitioned into a domain of interest and a reservoir of non-interacting, ideal gas, particles. An external potential, applied only in the interfacial region, balances the excess chemical potential of the system. To ensure that the size of the reservoir is infinite, we introduce a particle insertion/deletion algorithm to control the density in the ideal gas region. We show that it is possible to study non-equilibrium phenomena with this open-boundary molecular dynamics method. To this aim, we consider a prototypical confined liquid under the influence of an external constant density gradient. The resulting pressure-driven flow across the atomistic system exhibits a velocity profile consistent with the corresponding solution of the Navier-Stokes equation. In contrast to available computational methods in which external forces drive the system far from equilibrium, this approach conserves momentum and closely resembles experimental conditions. The presented method can be used to study various direct and indirect out-of-equilibrium conditions in complex molecular systems.

cond-mat.stat-mech↗

arXiv2019

Phoretic Active Matter

These notes are an account of a series of lectures given at the Les Houches Summer School "Active Matter and Non-equilibrium Statistical Physics" during August and September 2018. The lectures can be viewed online at [http://www.ds.mpg.de/lmp/lectures/les-houches-2018].

cond-mat.soft↗

arXiv2019

Diffusion and steady state distributions of flexible chemotactic enzymes

Many experiments in recent years have reported that, when exposed to their corresponding substrate, catalytic enzymes undergo enhanced diffusion as well as chemotaxis (biased motion in the direction of a substrate gradient). Among other possible mechanisms, in a number of recent works we have explored several passive mechanisms for enhanced diffusion and chemotaxis, in the sense that they require only binding and unbinding of the enzyme to the substrate rather than the catalytic reaction itself. These mechanisms rely on conformational changes of the enzyme due to binding, as well as on phoresis due to non-contact interactions between enzyme and substrate. Here, after reviewing and generalizing our previous findings, we extend them in two different ways. In the case of enhanced diffusion, we show that an exact result for the long-time diffusion coefficient of the enzyme can be obtained using generalized Taylor dispersion theory, which results in much simpler and transparent analytical expressions for the diffusion enhancement. In the case of chemotaxis, we show that the competition between phoresis and binding-induced changes in diffusion results in non-trivial steady state distributions for the enzyme, which can either accumulate in or be depleted from regions with a specific substrate concentration.

cond-mat.soft↗

arXiv2019

Active phase separation in mixtures of chemically interacting particles

We theoretically study mixtures of chemically-interacting particles, which produce or consume a chemical to which they are attracted or repelled, in the most general case of many coexisting species. We find a new class of active phase separation phenomena in which the nonequilibrium chemical interactions between particles, which break action-reaction symmetry, can lead to separation into phases with distinct density and stoichiometry. Due to the generic nature of our minimal model, our results shed light on the underlying fundamental principles behind nonequilibrium self-organization of cells and bacteria, catalytic enzymes, or phoretic colloids.

cond-mat.soft↗

arXiv2019

Efficiency limits of the three-sphere swimmer

We consider a swimmer consisting of a collinear assembly of three spheres connected by two slender rods. This swimmer can propel itself forward by varying the lengths of the rods in a way that is not invariant under time reversal. Although any non-reciprocal strokes of the arms can lead to a net displacement, the energetic efficiency of the swimmer is strongly dependent on the details and sequences of these strokes, and also the sizes of the spheres. We define the efficiency of the swimmer using Lighthill's criterion, i.e., the power that is needed to pull the swimmer by an external force at a certain speed, divided by the power needed for active swimming with the same average speed. Here, we determine numerically the optimal stroke sequences and the optimal size ratio of the spheres, while limiting the maximum extension of the rods. Our calculation takes into account both far-field and near-field hydrodynamic interactions. We show that, surprisingly, the three-sphere swimmer with unequal spheres can be more efficient than the equally-sized case. We also show that the variations of efficiency with size ratio is not monotonic and there exists a specific size ratio at which the swimmer has the highest efficiency. We find that the swimming efficiency initially rises by increasing the maximum allowable extension of the rods, and then converges to a maximum value. We calculate this upper limit analytically and report the highest value of efficiency that the three-sphere swimmer can reach.

physics.flu-dyn↗