arXiv subjects

Shubhadeep Sadhukhan

Publications and source records attributed to Shubhadeep Sadhukhan.

14 recordsLinked to original sources

arXiv2026

From biting to engulfment: Target mechanics determines modes of phagocytosis through curvature--actin coupling

Phagocytosis is a core innate immune process that clears targets spanning a wide range of mechanical properties, yet the role of target mechanics in recognition and engulfment remains unclear. Here, we combine theoretical modeling and experiments to reveal how target stiffness governs distinct modes of phagocyte--target interaction. We develop a membrane-based simulation framework in which both the engulfing cell and its target are deformable and undergo large shape changes, while actin-driven protrusions are regulated by curvature-sensitive membrane complexes. The model predicts three mechanical regimes with increasing target stiffness: (i) biting (trogocytosis), where part of the target is extracted; (ii) pushing, where the target is displaced rather than engulfed; and (iii) complete engulfment. We validate these predictions in epithelial clearance of apoptotic targets in vivo and macrophage engulfment of Giant Unilamellar Vesicles (GUVs) and lymphoma cells. Together, our results identify target mechanics as a key regulator of clearance and cell--cell interactions.

cond-mat.soft↗

arXiv2024

Modelling how lamellipodia-driven cells maintain persistent migration and interact with external barriers

Cell motility is fundamental to many biological processes, and cells exhibit a variety of migration patterns. Many motile cell types follow a universal law that connects their speed and persistency, a property that can originate from the intracellular transport of polarity cues due to the global actin retrograde flow. This mechanism was termed the ``Universal Coupling between cell Speed and Persistency"(UCSP). Here we implemented a simplified version of the UCSP mechanism in a coarse-grained ``minimal-cell" model, which is composed of a three-dimensional vesicle that contains curved active proteins. This model spontaneously forms a lamellipodia-like motile cell shape, which is however sensitive and can depolarize into a non-motile form due to random fluctuations or when interacting with external obstacles. The UCSP implementation introduces long-range inhibition, which stabilizes the motile phenotype. This allows our model to describe the robust polarity observed in cells and explain a large variety of cellular dynamics, such as the relation between cell speed and aspect ratio, cell-barrier scattering, and cellular oscillations in different types of geometric confinements.

physics.bio-ph↗

arXiv2023

Repeated quantum game as a stochastic game: Effects of the shadow of the future and entanglement

We present a systematic investigation of the quantum games, constructed using a novel repeated game protocol, when played repeatedly ad infinitum. We focus on establishing that such repeated games -- by virtue of inherent quantum-mechanical randomness -- can be mapped to the paradigm of stochastic games. Subsequently, using the setup of two-player--two-action games, we explore the pure reactive strategies belonging to the set of reactive strategies, whose support in the quantum games is no longer countably finite but rather non-denumerably infinite. We find that how two pure strategies fare against each other is crucially dependent on the discount factor (the probability of occurrence of every subsequent round) and how much entangled the quantum states of the players are. We contrast the results obtained with the corresponding results in the classical setup and find fundamental differences between them: e.g, when the underlying game is the prisoner's dilemma, in the quantum game setup, always-defect strategy can be beaten by the tit-for-tat strategy for high enough discount factor.

quant-ph↗

arXiv2023

Modelling how curved active proteins and shear flow pattern cellular shape and motility

Cell spreading and motility on an adhesive substrate are driven by the active physical forces generated by the actin cytoskeleton. We have recently shown that coupling curved membrane complexes to protrusive forces, exerted by the actin polymerization that they recruit, provides a mechanism that can give rise to spontaneous membrane shapes and patterns. In the presence of an adhesive substrate, this model was shown to give rise to an emergent motile phenotype, resembling a motile cell. Here, we utilize this ``minimal-cell" model to explore the impact of external shear flow on the cell shape and migration on a uniform adhesive flat substrate. We find that in the presence of shear the motile cell reorients such that its leading edge, where the curved active proteins aggregate, faces the shear flow. The flow-facing configuration is found to minimize the adhesion energy by allowing the cell to spread more efficiently over the substrate. For the non-motile vesicle shapes, we find that they mostly slide and roll with the shear flow. We compare these theoretical results with experimental observations, and suggest that the tendency of many cell types to move against the flow may arise from the very general, and non-cell-type-specific mechanism predicted by our model.

cond-mat.soft↗

arXiv2021

Subduing always defecting mutants by multiplayer reactive strategies: Non-reciprocity versus generosity

A completely non-generous and reciprocal population of players can create a robust cooperating state that cannot be invaded by always defecting free riders if the interactions among players are repeated for long enough. However, strict non-generosity and strict reciprocity are ideal concepts, and may not even be desirable sometimes. Therefore, to what extent generosity or non-reciprocity can be allowed while still not be swamped by the mutants, is a natural question. In this paper, we not only ask this question but furthermore ask how generosity comparatively fares against non-reciprocity in this context. For mathematical concreteness, we work within the framework of multiplayer repeated prisoner's dilemma game with reactive strategies in a finite and an infinite population; and explore the aforementioned questions through the effects of the benefit to cost ratio, the interaction group size, and the population size.

q-bio.PE↗

arXiv2021

Amplitude death in coupled replicator map lattice: averting migration dilemma

Populations composed of a collection of subpopulations (demes) with random migration between them are quite common occurrences. The emergence and sustenance of cooperation in such a population is a highly researched topic in the evolutionary game theory. If the individuals in every deme are considered to be either cooperators or defectors, the migration dilemma can be envisaged: The cooperators would not want to migrate to a defector-rich deme as they fear of facing exploitation; but without migration, cooperation can not be established throughout the network of demes. With a view to studying the aforementioned scenario, in this paper, we set up a theoretical model consisting of a coupled map lattice of replicator maps based on two-player--two-strategy games. The replicator map considered is capable of showing a variety of evolutionary outcomes, like convergent (fixed point) outcomes and nonconvergent (periodic and chaotic) outcomes. Furthermore, this coupled network of the replicator maps undergoes the phenomenon of amplitude death leading to non-oscillatory stable synchronized states. We specifically explore the effect of (i) the nature of coupling that models migration between the maps, (ii) the heterogenous demes (in the sense that not all the demes have same game being played by the individuals), (iii) the degree of the network, and (iv) the cost associated with the migration. In the course of investigation, we are intrigued by the effectiveness of the random migration in sustaining a uniform cooperator fraction across a population irrespective of the details of the replicator dynamics and the interaction among the demes.

physics.soc-ph↗

arXiv2021

Effect of chaotic agent dynamics on coevolution of cooperation and synchronization

The effect of the chaotic dynamical states of the agents on the coevolution of cooperation and synchronization in a structured population of the agents remains unexplored. With a view to gaining insights into this problem, we construct a coupled map lattice of the paradigmatic chaotic logistic map by adopting the Watts--Strogatz network algorithm. The map models the agent's chaotic state dynamics. In the model, an agent benefits by synchronizing with its neighbours and in the process of doing so, it pays a cost. The agents update their strategies (cooperation or defection) by using either a stochastic or a deterministic rule in an attempt to fetch themselves higher payoffs than what they already have. Among some other interesting results, we find that beyond a critical coupling strength, that increases with the rewiring probability parameter of the Watts--Strogatz model, the coupled map lattice is spatiotemporally synchronized regardless of the rewiring probability. Moreover, we observe that the population does not desynchronize completely -- and hence finite level of cooperation is sustained -- even when the average degree of the coupled map lattice is very high. These results are at odds with how a population of the non-chaotic Kuramoto oscillators as agents would behave. Our model also brings forth the possibility of the emergence of cooperation through synchronization onto a dynamical state that is a periodic orbit attractor.

nlin.AO↗

arXiv2021

Cooperators overcome migration dilemma through synchronization

Synchronization, cooperation, and chaos are ubiquitous phenomena in nature. In a population composed of many distinct groups of individuals playing the prisoner's dilemma game, there exists a migration dilemma: No cooperator would migrate to a group playing the prisoner's dilemma game lest it should be exploited by a defector; but unless the migration takes place, there is no chance of the entire population's cooperator-fraction to increase. Employing a randomly rewired coupled map lattice of chaotic replicator maps, modelling replication-selection evolutionary game dynamics, we demonstrate that the cooperators -- evolving in synchrony -- overcome the migration dilemma to proliferate across the population when altruism is mildly incentivized making few of the demes play the leader game.

q-bio.PE↗

arXiv2020

Enstrophy transfers in helical turbulence

In this paper we study the enstrophy transers in helical turbulence using direct numerical simulation. We observe that the helicity injection does not have significant effects on the inertial-range energy and helicity spectra ($\sim k^{-5/3}$) and fluxes (constants). We also calculate the separate contributions to enstrophy transfers via velocity to vorticity and vorticity to vorticity channels. There are four different enstrophy fluxes associated with the former channel or vorticity stretching, and one flux associated with the latter channel or vorticity advection. In the inertial range, the fluxes due to vorticity stretching are larger than that due to advection. These transfers too are insensitive to helicity injection.

physics.flu-dyn↗

arXiv2019

Similarities between the structure functions of thermal convection and hydrodynamic turbulence

In this paper, we analyze the scaling of velocity structure functions of turbulent thermal convection. Using high-resolution numerical simulations, we show that the structure functions scale similar to those of hydrodynamic turbulence, with the scaling exponents in agreement with She and Leveque's predictions [Phys. Rev. Lett. 72, 336-339 (1994)]. The probability distribution functions of velocity increments are non-Gaussian with wide tails in the dissipative scales and become close to Gaussian in the inertial range. The tails of the probability distribution follow a stretched exponential. We also show that in thermal convection, the energy flux in the inertial range is less than the viscous dissipation rate. This is unlike in hydrodynamic turbulence where the energy flux and the dissipation rate are equal.

physics.flu-dyn↗

arXiv2019

Energy and enstrophy spectra and fluxes for the inertial-dissipation range of two-dimensional turbulence

In this paper, using Pao's conjecture [Y.-H. Pao, Phys. Fluids 11, 1371 (1968)], we derive expressions for the spectra and fluxes of kinetic energy and enstrophy for two-dimensional (2D) forced turbulence that extend beyond the inertial range. In these expressions, the fluxes and the spectra contain additional factors of the exponential form. To validate these model predictions, we perform numerical simulations of 2D turbulence with an external force applied at $k=k_f$ in the intermediate range. The numerical results match with the model predictions, except for the energy and enstrophy fluxes for $k<k_f$, where the fluxes exhibit significant fluctuations. We show that these fluctuations arise due to the unsteady nature of the flow at small wavenumbers. For the $k<k_f$, the shell-to-shell energy transfers computed using numerical data show forward energy transfers among the neighbouring shells, but backward energy transfers for other shells.

physics.flu-dyn↗

arXiv2017

Effect of Composition Gradient on Magnetothermal Instability Modified by Shear and Rotation

We model the intracluster medium as a weakly collisional plasma that is a binary mixture of the hydrogen and the helium ions, along with free electrons. When, owing to the helium sedimentation, the gradient of the mean molecular weight (or equivalently, composition or helium ions' concentration) of the plasma is not negligible, it can have appreciable influence on the stability criteria of the thermal convective instabilities, e.g., the heat-flux-buoyancy instability and the magnetothermal instability (MTI). These instabilities are consequences of the anisotropic heat conduction occurring preferentially along the magnetic field lines. In this paper, without ignoring the magnetic tension, we first present the mathematical criterion for the onset of composition gradient modified MTI. Subsequently, we relax the commonly adopted equilibrium state in which the plasma is at rest, and assume that the plasma is in a sheared state which may be due to differential rotation. We discuss how the concentration gradient affects the coupling between the Kelvin--Helmholtz instability and the MTI in rendering the plasma unstable or stable. We derive exact stability criterion by working with the sharp boundary case in which the physical variables---temperature, mean molecular weight, density, and magnetic field---change discontinuously from one constant value to another on crossing the boundary. Finally, we perform the linear stability analysis for the case of the differentially rotating plasma that is thermally and compositionally stratified as well. By assuming axisymmetric perturbations, we find the corresponding dispersion relation and the explicit mathematical expression determining the onset of the modified MTI.

astro-ph.GA↗

arXiv2017

On the Helium fingers in the intracluster medium

In this paper we investigate the convection phenomenon in the intracluster medium (the weakly-collisional magnetized inhomogeneous plasma permeating galaxy clusters) where the concentration gradient of the Helium ions is not ignorable. To this end, we build upon the general machinery employed to study the salt finger instability found in the oceans. The salt finger instability is a form of double diffusive convection where the diffusions of two physical quantities---heat and salt concentrations---occur with different diffusion rates. The analogous instability in the intracluster medium may result owing to the magnetic field mediated anisotropic diffusions of the heat and the Helium ions (in the sea of the Hydrogen ions and the free electrons). These two diffusions have inherently different diffusion rates. Hence the convection caused by the onset of this instability is an example of double diffusive convection in the astrophysical settings. A consequence of this instability is the formation of the vertical filamentary structures having more concentration of the Helium ions with respect to the immediate neighbourhoods of the filaments. We term these structures as Helium fingers in analogy with the salt fingers found in the case of the salt finger instability. Here we show that the width of a Helium finger scales as one-fourth power of the radius of the inner region of the intracluster medium in the supercritical regime. We also determine the explicit mathematical expression of the criterion for the onset of the heat-flux-driven buoyancy instability modified by the presence of inhomogeneously distributed Helium ions.

astro-ph.GA↗

arXiv2016

Stability of Rotating Self-Gravitating Filaments:Stability of Rotating Self-Gravitating Filaments: Effects of Magnetic Field

We have performed systemmatic local linear stability analysis on a radially stratified infinite self-gravitating cylinder of rotating plasma under the influence of magnetic field. In order to render the system analytically tractable, we have focussed solely on the axisymmetric modes of perturbations. Using cylindrical coordinate system, we have derived the critical linear mass density of a non-rotating filament required for gravitational collapse to ensue in the presence of azimuthal magnetic field. Moreover, for such filaments threaded by axial magnetic field, we show that the growth rates of the modes having non-zero radial wavenumber are reduced more strongly by the magnetic field than that of the modes having zero radial wavenumber. More importantly, our study contributes to the understanding of the stability property of rotating astrophysical filaments that are more often than not influenced by magnetic fields. In addition to complementing many relevant numerical studies reported the literature, our results on filaments under the influence of magnetic field generalize some of the very recent analytical works (e.g.,~\citet{jog2014}, etc.). For example, here we prove that even a weak magnetic field can play a dominant role in determining stability of the filament when the rotation timescale is larger than the free fall timescale. A filamentary structure with faster rotation is, however, comparatively more stable for the same magnetic field. The results reported herein, due to strong locality assumption, are strictly valid for the modes for which one can ignore the radial variations in the density and the magnetic field profiles.

astro-ph.GA↗