arXiv subjects

Nir S. Gov

Publications and source records attributed to Nir S. Gov.

36 records · Page 2Linked to original sources

arXiv2020

Pair Formation in Insect Swarms Driven by Adaptive Long-Range Interactions

In swarms of flying insects, the motions of individuals are largely uncoordinated with those of their neighbors, unlike the highly ordered motion of bird flocks. However, it has been observed that insects may transiently form pairs with synchronized relative motion while moving through the swarm. The origin of this phenomenon remains an open question. In particular, it is not known if pairing is a new behavioral process or whether it is a natural byproduct of typical swarming behavior. Here, using an "adaptive-gravity" model that proposes that insects interact via long-range gravity-like acoustic attractions that are modulated by the total background sound (via "adaptivity" or fold-change detection) and that reproduces measured features of real swarms, we show that pair formation can indeed occur without the introduction of additional behavioral rules. In the model, pairs form robustly whenever two insects happen to move together from the center of the swarm (where the background sound is high) toward the swarm periphery (where the background sound is low). Due to adaptivity, the attraction between the pair increases as the background sound decreases, thereby forming a bound state since their relative kinetic energy is smaller than their pair-potential energy. When the pair moves into regions of high background sound, however, the process is reversed and the pair may break up. Our results suggest that pairing should appear generally in biological systems with long-range attraction and adaptive sensing, such as during chemotaxis-driven cellular swarming.

physics.bio-ph↗

arXiv2020

One dimensional cell motility patterns

During migration cells exhibit a rich variety of seemingly random migration patterns, which makes unraveling the underlying mechanisms that control cell migration a daunting challenge. For efficient migration cells require a mechanism for polarization, so that traction forces are produced in the direction of motion, while adhesion is released to allow forward migration. To simplify the study of this process cells have been studied when placed along one-dimensional tracks, where single cells exhibit both smooth and stick-slip migration modes. The stick-slip motility mode is characterized by protrusive motion at the cell front, coupled with slow cell elongation, which is followed by rapid retractions of the cell back. In this study, we explore a minimal physical model that couples the force applied on the adhesion bonds to the length variations of the cell and the traction forces applied by the polarized actin retrograde flow. We show that the rich spectrum of cell migration patterns emerges from this model as different \emph{deterministic} dynamical phases. This result suggests a source for the large cell-to-cell variability (CCV) in cell migration patterns observed in single cells over time and within cell populations. The large heterogeneity can arise from small fluctuations in the cellular components that are greatly amplified due to moving the cells' internal state across the dynamical phase transition lines. Temporal noise is shown to drive random changes in the cellular polarization direction, which is enhanced during the stick-slip migration mode. These results offer a new framework to explain experimental observations of migrating cells, resulting from noisy switching between underlying deterministic migration modes.

physics.bio-ph↗

arXiv2020

Excitable solitons: Annihilation, crossover, and nucleation of pulses in mass-conserving activator-inhibitor media

Excitable pulses are among the most widespread dynamical patterns that occur in many different systems, ranging from biological cells to chemical reactions and ecological populations. Traditionally, the mutual annihilation of two colliding pulses is regarded as their prototypical signature. Here we show that colliding excitable pulses may exhibit soliton-like crossover and pulse nucleation if the system obeys a mass conservation constraint. In contrast to previous observations in systems without mass conservation, these alternative collision scenarios are robustly observed over a wide range of parameters. We demonstrate our findings using a model of intracellular actin waves since, on time scales of wave propagations over the cell scale, cells obey the conservation of actin monomers. The results provide a key concept to understand the ubiquitous occurrence of actin waves in cells, suggesting why they are so common, and why their dynamics is robust and long-lived.

nlin.PS↗

arXiv2019

Similarities between Insect Swarms and Isothermal Globular Clusters

Previous work has suggested that disordered swarms of flying insects can be well modeled as self-gravitating systems, as long as the "gravitational" interaction is adaptive. Motivated by this work we compare the predictions of the classic, mean-field King model for isothermal globular clusters to observations of insect swarms. Detailed numerical simulations of regular and adaptive gravity allow us to expose the features of the swarms' density profiles that are captured by the King model phenomenology, and those that are due to adaptivity and short-range repulsion. Our results provide further support for adaptive gravity as a model for swarms.

physics.bio-ph↗

arXiv2019

Dynamics and escape of active particles in a harmonic trap

The dynamics of active particles is of interest at many levels and is the focus of theoretical and experimental research. There have been many attempts to describe the dynamics of particles affected by random active forces in terms of an effective temperature. This kind of description is tempting due to the similarities (or lack thereof) with systems in or near thermal equilibrium. However, the generality and validity of the effective temperature is not yet fully understood. Here, we studied the dynamics of trapped particles subjected to both thermal and active forces. The particles were not overdamped. Expressions for the effective temperature due to the potential and kinetic energies were derived, and they differ from each other. A third possible effective temperature can be derived from the escape time of the particle from the trap, using a Kramers-like expression for the mean escape time. We found that over a large fraction of the parameter space, the potential energy effective temperature is in agreement with the escape temperature, while the kinetic effective temperature only agrees with the former two in the overdamped limit. Moreover, we show that the specific implementation of the random active force, and not only its first two moments and the two point auto-correlation function, affects the escape time distribution.

cond-mat.stat-mech↗

arXiv2018

Signatures of motor susceptibility in the dynamics of a tracer particle in an active gel

We study a model for the motion of a tracer particle inside an active gel, exposing the properties of the van Hove distribution of the particle displacements. Active events of a typical force magnitude give rise to non-Gaussian distributions, having exponential tails or side-peaks. The side-peaks appear when the local bulk elasticity of the gel is large enough and few active sources are dominant. We explain the regimes of the different distributions, and study the structure of the peaks for active sources that are susceptible to the elastic stress that they cause inside the gel. We show how the van Hove distribution is altered by both the duty cycle of the active sources and their susceptibility, and suggest it as a sensitive probe to analyze microrheology data in active systems with restoring elastic forces.

cond-mat.soft↗

arXiv2018

Effective temperature of active fluids and sheared granular matter

The dynamics within active fluids, driven by internal activity of the self-propelled particles, is a subject of intense study in non-equilibrium physics. These systems have been explored using simulations, where the motion of a passive tracer particle is followed. Similar studies have been carried out for passive granular matter that is driven by shearing its boundaries. In both types of systems the non-equilibrium motion have been quantified by defining a set of "effective temperatures", using both the tracer particle kinetic energy and the fluctuation-dissipation relation. We demonstrate that these effective temperatures extracted from the many-body simulations fit analytical expressions that are obtained for a single active particle inside a visco-elastic fluid. This result provides testable predictions and suggests a unified description for the dynamics inside active systems.

physics.bio-ph↗

arXiv2018

Forces in inhomogeneous open active-particle systems

We study the force that non-interacting point-like active particles apply to a symmetric inert object in the presence of a gradient of activity and particle sources and sinks. We consider two simple patterns of sources and sinks that are common in biological systems. We analytically solve a one dimensional model designed to emulate higher dimensional systems, and study a two dimensional model by numerical simulations. We specify when the particle flux due to the creation and annihilation of particles can act to smooth the density profile that is induced by a gradient in the velocity of the active particles, and find the net resultant force due to both the gradient in activity and the particle flux. These results are compared qualitatively to observations of nuclear motion inside the oocyte, that is driven by a gradient in activity of actin-coated vesicles.

cond-mat.stat-mech↗

arXiv2018

Active mechanics reveal molecular-scale force kinetics in living oocytes

Active diffusion of intracellular components is emerging as an important process in cell biology. This process is mediated by complex assemblies of molecular motors and cytoskeletal filaments that drive force generation in the cytoplasm and facilitate enhanced motion. The kinetics of molecular motors have been precisely characterized in-vitro by single molecule approaches, however, their in-vivo behavior remains elusive. Here, we study the active diffusion of vesicles in mouse oocytes, where this process plays a key role in nuclear positioning during development, and combine an experimental and theoretical framework to extract molecular-scale force kinetics (force, power-stroke, and velocity) of the in-vivo active process. Assuming a single dominant process, we find that the nonequilibrium activity induces rapid kicks of duration $τ\sim$ 300 $μ$s resulting in an average force of $F \sim$ 0.4 pN on vesicles in in-vivo oocytes, remarkably similar to the kinetics of in-vitro myosin-V. Our results reveal that measuring in-vivo active fluctuations allows extraction of the molecular-scale activity in agreement with single-molecule studies and demonstrates a mesoscopic framework to access force kinetics.

physics.bio-ph↗

arXiv2017

Generalized Archimedes' principle in active fluids

We show how a gradient in the motility properties of non-interacting point-like active particles can cause a pressure gradient that pushes a large inert object. We calculate the force on an object inside a system of active particles with position dependent motion parameters, in one and two dimensions, and show that a modified Archimedes' principle is satisfied. We characterize the system, both in terms of the model parameters and in terms of experimentally measurable quantities: the spatial profiles of the density, velocity and pressure. This theoretical analysis is motivated by recent experiments, which showed that the nucleus of a mouse oocyte (immature egg cell) moves from the cortex to the center due to a gradient of activity of vesicles propelled by molecular motors; it more generally applies to artificial systems of controlled localized activity.

cond-mat.stat-mech↗

arXiv2017

Nonequilibrium mode-coupling theory for dense active systems of self-propelled particles

The physics of active systems of self-propelled particles, in the regime of a dense liquid state, is an open puzzle of great current interest, both for statistical physics and because such systems appear in many biological contexts. We develop a nonequilibrium mode-coupling theory (MCT) for such systems, where activity is included as a colored noise with the particles having a self-propulsion foce $f_0$ and persistence time $τ_p$. Using the extended MCT and a generalized fluctuation-dissipation theorem, we calculate the effective temperature $T_{eff}$ of the active fluid. The nonequilibrium nature of the systems is manifested through a time-dependent $T_{eff}$ that approaches a constant in the long-time limit, which depends on the activity parameters $f_0$ and $τ_p$. We find, phenomenologically, that this long-time limit is captured by the potential energy of a single, trapped active particle (STAP). Through a scaling analysis close to the MCT glass transition point, we show that $τ_α$, the $α$-relaxation time, behaves as $τ_α\sim f_0^{-2γ}$, where $γ=1.74$ is the MCT exponent for the passive system. $τ_α$ may increase or decrease as a function of $τ_p$ depending on the type of active force correlations, but the behavior is always governed by the same value of the exponent $γ$. Comparison with numerical solution of the nonequilibrium MCT as well as simulation results give excellent agreement with the scaling analysis.

cond-mat.soft↗

arXiv2017

Stable Swarming Using Adaptive Long-range Interactions

Sensory mechanisms in biology, from cells to humans, have the property of adaptivity, whereby the response produced by the sensor is adapted to the overall amplitude of the signal; reducing the sensitivity in the presence of strong stimulus, while increasing it when it is weak. This property is inherently energy consuming and a manifestation of the non-equilibrium nature of living organisms. We explore here how adaptivity affects the effective forces that organisms feel due to others in the context of a uniform swarm, both in two and three dimensions. The interactions between the individuals are taken to be attractive and long-range, of power-law form. We find that the effects of adaptivity inside the swarm are dramatic, where the effective forces decrease (or remain constant) with increasing swarm density. Linear stability analysis demonstrates how this property prevents collapse (Jeans instability), when the forces are adaptive. Adaptivity therefore endows swarms with a natural mechanism for self-stabilization.

physics.bio-ph↗

arXiv2016

Nonequilibrium dissipation in living oocytes

Living organisms are inherently out-of-equilibrium systems. We employ new developments in stochastic energetics and rely on a minimal microscopic model to predict the amount of mechanical energy dissipated by such dynamics. Our model includes complex rheological effects and nonequilibrium stochastic forces. By performing active microrheology and tracking micron-sized vesicles in the cytoplasm of living oocytes, we provide unprecedented measurements of the spectrum of dissipated energy. We show that our model is fully consistent with the experimental data, and we use it to offer predictions for the injection and dissipation energy scales involved in active fluctuations.

q-bio.SC↗

arXiv2015

Long-range Acoustic Interactions in Insect Swarms: An Adaptive Gravity Model

The collective motion of groups of animals emerges from the net effect of the interactions between individual members of the group. In many cases, such as birds, fish, or ungulates, these interactions are mediated by sensory stimuli that predominantly arise from nearby neighbors. But not all stimuli in animal groups are short range. Here, we consider mating swarms of midges, which interact primarily via long-range acoustic stimuli. We exploit the similarity in form between the decay of acoustic and gravitational sources to build a model for swarm behavior. By accounting for the adaptive nature of the midges' acoustic sensing, we show that our "adaptive gravity" model makes mean-field predictions that agree well with experimental observations of laboratory swarms. Our results highlight the role of sensory mechanisms and interaction range in collective animal behavior. The adaptive interactions that we present here open a new class of equations of motion, which may appear in other biological contexts.

physics.bio-ph↗

arXiv2014

Pearling instability of membrane tubes driven by curved proteins and actin polymerization

Membrane deformation inside living cells is crucial for the proper shaping of various intracellular organelles and is necessary during the fission/fusion processes that allow membrane recycling and transport (e.g. endocytosis). Proteins that induce membrane curvature play a key role in such processes, mostly by adsorbing to the membrane and forming a scaffold that deforms the membrane according to the curvature of the proteins. In this paper we explore the possibility of membrane tube destabilisation through a pearling mechanism enabled by the combined effects of the adsorbed curved proteins and the actin polymerization they may recruit. The pearling instability can furthermore serve as the initiation for fission of the tube into vesicles. We find that adsorbed proteins are more likely to stabilise the tubes, while the actin polymerization can provide the additional constrictive force needed for the robust instability. We discuss the relevance of the theoretical results to in-vivo and in-vitro experiments.

physics.bio-ph↗

arXiv2012

Patterning of polar active filaments on a tense cylindrical membrane

We study the dynamics and patterning of polar contractile filaments on the surface of a cylindrical cell using active hydrodynamic equations that incorporate couplings between curvature and filament orientation. Cables and rings spontaneously emerge as steady state configurations on the cylinder, and can be stationary or moving, helical or segments moving along helical trajectories. Contractility induces coalescence of proximal rings. We observe phase transitions in the steady state patterns upon changing cell diameter and make several testable predictions. Our results are relevant to the dynamics and patterning of a variety of active biopolymers in cylindrical cells.

cond-mat.soft↗

arXiv2011

Effective Temperature of Red Blood Cell Membrane Fluctuations

Biologically driven non-equilibrium fluctuations are often characterized by their non-Gaussianity or by an "effective temperature", which is frequency dependent and higher than the ambient temperature. We address these two measures theoretically by examining a randomly kicked "particle", with a variable number of kicking "motors", and show how these two indicators of non-equilibrium behavior can contradict. Our results are compared with new experiments on shape fluctuations of red-blood cell membranes, and demonstrate how the physical nature of the motors in this system can be revealed using these global measures of non-equilibrium.

physics.bio-ph↗

arXiv2007

Packing defects and the width of biopolymer bundles

The formation of bundles composed of actin filaments and cross-linking proteins is an essential process in the maintenance of the cells' cytoskeleton. It has also been recreated by in-vitro experiments, where actin networks are routinely produced to mimic and study the cellular structures. It has long been observed that these bundles seem to have a well defined width distribution, which has not been adequately described theoretically. We propose here that packing defects of the filaments, quenched and random, contribute an effective repulsion that counters the cross-linking adhesion energy and leads to a well defined bundle width. This is a two-dimensional strain-field version of the classic Rayleigh instability of charged droplets.

cond-mat.soft↗