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Sumantra Sarkar

Publications and source records attributed to Sumantra Sarkar.

15 recordsLinked to original sources

Interface Fluctuations in a Turbulent Binary Fluid using Data-Driven Methods

Interfacial fluctuations in a two-phase binary fluid mixture reveal signatures of underlying physical processes that occur within each phase and on a range of spatial and temporal scales. In this study, we investigate a model binary fluid system consisting of a single droplet of one phase moving in the background of the second phase. The binary fluid system is subjected to turbulent forcing. We perform extensive direct numerical simulations of the turbulent system to examine how quantities such as interfacial dynamics and droplet acceleration can be systematically decoded. Extensive simulations of binary fluid systems are computationally expensive and time-consuming. In contrast, data-driven models have shown promise in recent times in reducing computational cost. In this work, we build and compare the performances of four interpretable data-driven models, i.e., dynamic mode decomposition (DMD), Hankel DMD, sparse identification of nonlinear dynamics (SINDy), and Stochastic Langevin regression (SLR), each using dimensionality reduction via proper orthogonal decomposition, to identify simplified dynamical equations governing interfacial dynamics and center-of-mass acceleration. We show how these learned models can be generalized to encode physical properties, such as the interfacial surface tension and droplet size. In particular, we show that SLR predicts the underlying dynamical equations of the binary-fluid system with the greatest accuracy over a wide range of interfacial tension values and droplet sizes. In addition, SLR requires fewer terms compared to SINDy to capture the underlying dynamics, and is thus computationally the most efficient among the four methods. These data-driven techniques can be used in many practical applications, such as the dynamics of biological cell membranes, thin films, and other industrial applications.

physics.flu-dyn

Glassy dynamics in active epithelia emerge from an interplay of mechanochemical feedback and crowding

Glassy dynamics in active biological cells remain a subject of debate, as cellular activity rarely slows enough for true glassy features to emerge. In this study, we address this paradox of glassy dynamics in epithelial cells by integrating experimental observations with an active vertex model. We demonstrate that while crowding is essential, it is not sufficient for glassy dynamics to emerge. A mechanochemical feedback loop (MCFL), mediated by cell shape changes through the contractile actomyosin network, is required to drive glass transition in dense epithelial tissues, as revealed via a crosstalk between actin-based cell clustering and dynamic heterogeneity in experiments. Incorporating MCFL into the vertex model reveals contrasting results from those previously predicted by theories -- we show that the MCFL can counteract cell division-induced fluidisation and enable glassy dynamics to emerge through active cell-to-cell communication. Furthermore, our analysis reveals, for the first time, the existence of novel collective mechanochemical oscillations that arise from the crosstalk of two MCFLs. Together, we demonstrate that an interplay between crowding and active mechanochemical feedback enables the emergence of glass-like traits and collective biochemical oscillations in epithelial tissues with active cell-cell contacts.

physics.bio-ph

Symmetry-protected phases in a 1D active solid with mechanochemical feedback

We present a framework for mechanochemical self-organization in active solids where elasticity is reciprocally coupled to Hopf oscillators. Our model reveals a rich landscape of symmetry-protected phases, identified through amplitude equations and group-theoretic analysis. We uncover a universal transition to compression-driven oscillation death (COD), providing a physical basis for localized signaling dampening in biological tissues that resolves inconsistencies in previous models. Our work demonstrates that complex self-organization in active solids can be classified purely through symmetry arguments.

cond-mat.soft

Molecular communication in one-dimensional channels with active transport and crowding

Molecular communication (MC) is a model of information transmission where the signal is transmitted by information-carrying molecules through their physical transport from a transmitter to a receiver through a communication channel. Prior efforts have identified suitable "information molecules" whose efficacy for signal transmission has been studied extensively in diffusive channels (DC). Although easy to implement, DCs are inefficient for distances longer than tens of nanometers. In contrast, molecular motor-driven nonequilibrium or active transport can drastically increase the range of communication and may permit efficient communication up to tens of micrometers. In this paper, we investigate how active transport influences the efficacy of molecular communication, quantified by the mutual information between transmitted and received signals. We consider two specific scenarios: (a) active transport through relays and (b) active transport through a mixture of active and diffusing particles. In each case, we discuss the efficacy of the communication channel and discuss their potential pitfalls.

cond-mat.stat-mech

Self-diffusion is temperature independent on active membranes

Molecular transport maintains cellular structures and functions. For example, lipid and protein diffusion sculpts the dynamic shapes and structures on the cell membrane that perform essential cellular functions, such as cell signaling. Temperature variations in thermal equilibrium rapidly change molecular transport properties. The coefficient of lipid self-diffusion increases exponentially with temperature in thermal equilibrium, for example. Hence, in the noisy cellular environment, where temperatures can fluctuate widely due to local heat generation, maintaining cellular homeostasis through molecular transport is hard in thermal equilibrium. In this paper, using both molecular and lattice-based modeling of membrane transport, we show that the presence of active transport originating from the cell's cytoskeleton can make the self-diffusion of the molecules on the membrane robust to temperature fluctuations. The resultant temperature-independence of self-diffusion keeps the precision of cellular signaling invariant over a broad range of ambient temperatures, allowing cells to make robust decisions. We have also found that the Kawasaki algorithm, the widely used model of lipid transport on lattices, predicts incorrect temperature dependence of lipid self-diffusion in equilibrium. We propose a new algorithm that correctly captures the equilibrium properties of lipid self-diffusion and reproduces experimental observations.

cond-mat.soft

Coarsening of topological defects in 2D polar active matter

We numerically study the coarsening of topological defects in 2D polar active matter and make several interesting observations and predictions. (i) The long time state is characterized by nonzero density of defects, in stark contrast to theoretical expectations. (ii) The kinetics of defect coarsening shows power law decay to steady state, as opposed to exponential decay in thermal equilibrium. (iii) Observations (i) and (ii) together suggest emergent screening of topological charges due to activity. (iv) Nontrivial defect coarsening in the active model leads to nontrivial steady state patterns. We investigate, characterize, and validate these patterns and discuss their biological significance.

cond-mat.soft

Link updating strategies influence consensus decisions as a function of the direction of communication

Consensus decision-making in social groups strongly depends on communication links that determine to whom individuals send, and from whom they receive, information. Here, we ask how consensus decisions are affected by strategic updating of links and how this effect varies with the direction of communication. We quantified the co-evolution of link and opinion dynamics in a large population with binary opinions using mean-field numerical simulations of two voter-like models of opinion dynamics: an Incoming model (where individuals choose who to receive opinions from) and an Outgoing model (where individuals choose who to send opinions to). We show that individuals can bias group-level outcomes in their favor by breaking disagreeing links while receiving opinions (Incoming Model) and retaining disagreeing links while sending opinions (Outgoing Model). Importantly, these biases can help the population avoid stalemates and achieve consensus. However, the role of disagreement avoidance is diluted in the presence of strong preferences - highly stubborn individuals can shape decisions to favor their preferences, giving rise to non-consensus outcomes. We conclude that collectively changing communication structures can bias consensus decisions, as a function of the strength of preferences and the direction of communication.

physics.soc-ph

Efficacy of information transmission in cellular communication

Inter and intra-cellular signaling are essential for individual cells to execute various physiological tasks and accurately respond to changes in their environment. Signaling is carried out via diffusible molecules, the transport of which is often aided by active processes that provide directional advection. How diffusion and advection together impact the accuracy of information transmission during cell signaling remains less studied. To this end, we study a one-dimensional model of cell signaling and compute the mutual information (MI) as a measure of information transmission. We find that the efficacy of the information transmission improves with advection only when the system parameters result in Peclet number greater than one. Intriguingly, MI exhibits nontrivial scaling with the Peclet number, characterized by three distinct regimes. We demonstrate that the observed dependence of MI on the transport properties of signaling molecules has important consequences on cellular communication.

cond-mat.soft

Concentration dependence of diffusion-limited reaction rates and its consequences

Diffusion-limited association reactions are ubiquitous in nature. They are particularly important for biological reactions, where the reaction rates are often determined by the diffusive transport of the molecules on two-dimensional surfaces, such as the cell membrane. The peculiarities of diffusion on two-dimensional surfaces may lead to nontrivial reaction kinetics, such as concentration dependent rate of association between two molecules. However, traditionally, the kinetics of biomolecular association reactions has been modeled using the law of mass action, which assumes that the rate of reaction is a concentration independent constant. In this paper, using multiscale molecular simulation, we investigate the concentration dependence of diffusion-limited association reactions on 2D surfaces. In particular, we quantify the influence of short-ranged pair interactions on the concentration dependence of the reaction rates and codify it in an empirical law. Using this law in a chemical kinetic model, we find that the the steady state behaviors of simple chemical systems are drastically modified by the presence of concentration dependent rates. In particular, we find that it leads to suppression of intrinsic noise in dimerization reaction and destabilizes robust oscillation in Lotka-Volterra predator-prey systems. In fact, we see a transition from robust to fine-tuned behavior in the latter. In addition, we show that concentration dependent reaction rates arise naturally in stochastic predator-prey systems due to intrinsic noise. We comment on the consequences of these results and discuss their implications in the modeling of complex chemical and biological systems. In particular, we comment on the range of validity of the law of mass action, which is a staple in all theoretical modeling of these systems.

cond-mat.soft

Design of conditions for emergence of self-replicators

A self-replicator is usually understood to be an object of definite form that promotes the conversion of materials in its environment into a nearly identical copy of itself. The challenge of engineering novel, micro- or nano-scale self-replicators has attracted keen interest in recent years, both because exponential amplification is an attractive method for generating high yields of specific products, and also because self-reproducing entities have the potential to be optimized or adapted through rounds of iterative selection. Substantial steps forward have been achieved both in the engineering of particular self-replicating molecules, and also in characterizing the physical basis for possible mechanisms of self-replication. At present, however, there is need for a theoretical treatment of what physical conditions are most conducive to the emergence of novel self-replicating structures from a reservoir of building blocks on a desired time-scale. Here we report progress in addressing this need. By analyzing the dynamics of a generic class of heterogeneous particle mixtures whose reaction rates emerge from basic physical interactions, we demonstrate that the spontaneous discovery of self-replication is controlled by relatively generic features of the chemical space, namely: the dispersion in the distribution of reaction timescales and bound-state energies. Based on this analysis, we provide quantitative criteria that may aid experimentalists in designing a system capable of producing self-replicators, and in estimating the likely timescale for exponential growth to start.

cond-mat.soft

Shear-induced rigidity of frictional particles: Analysis of emergent order in stress space

Solids are distinguished from fluids by their ability to resist shear. In traditional solids, the resistance to shear is associated with the emergence of broken translational symmetry as exhibited by a non-uniform density pattern, which results from either minimizing the energy cost or maximizing the entropy or both. In this work, we focus on a class of systems, where this paradigm is challenged. We show that shear-driven jamming in dry granular materials is a collective process controlled solely by the constraints of mechanical equilibrium. We argue that these constraints lead to a broken translational symmetry in a dual space that encodes the statistics of contact forces and the topology of the contact network. The shear-jamming transition is marked by the appearance of this broken symmetry. We extend our earlier work, by comparing and contrasting real space measures of rheology with those obtained from the dual space. We investigate the structure and behavior of the dual space as the system evolves through the rigidity transition in two different shear protocols. We analyze the robustness of the shear-jamming scenario with respect to protocol and packing fraction, and demonstrate that it is possible to define a protocol-independent order parameter in this dual space, which signals the onset of rigidity.

cond-mat.soft

Shear-induced organization of forces in dense suspensions: signatures of discontinuous shear thickening

Dense suspensions can exhibit an abrupt change in their viscosity in response to increasing shear rate. The origin of this discontinuous shear thickening (DST) has been ascribed to the transformation of lubricated contacts to frictional, particle-on-particle contacts. Recent research on the flowing and jamming behavior of dense suspensions has explored the intersection of ideas from granular physics and Stokesian fluid dynamics to better understand this transition from lubricated to frictional rheology. DST is reminiscent of classical phase transitions, and a key question is how interactions between the microscopic constituents give rise to a macroscopic transition. In this paper, we extend a formalism that has proven to be successful in understanding shear jamming of dry grains to dense suspensions. Quantitative analysis of the collective evolution of the contact-force network accompanying the DST transition demonstrates clear changes in the distribution of microscopic variables, and leads to the identification of an "order parameter" characterizing DST.

cond-mat.soft

Shear induced rigidity in athermal materials: a unified statistical framework

Recent studies of athermal systems such as dry grains and dense, non-Brownian suspensions have shown that shear can lead to solidification through the process of shear jamming in grains and discontinuous shear thickening in suspensions. The similarities observed between these two distinct phenomena suggest that the physical processes leading to shear-induced rigidity in athermal materials are universal. We present a non-equilibrium statistical mechanics model, which exhibits the phenomenology of these shear-driven transitions: shear jamming and discontinuous shear thickening in different regions of the predicted phase diagram. Our analysis identifies the crucial physical processes underlying shear-driven rigidity transitions, and clarifies the distinct roles played by shearing forces and the density of grains.

cond-mat.soft

Origin of Rigidity in Dry Granular Solids

Solids are distinguished from fluids by their ability to resist shear. In traditional solids, the resistance to shear is associated with the emergence of broken translational symmetry as exhibited by a non-uniform density pattern. In this work, we focus on the emergence of shear-rigidity in a class of solids where this paradigm is challenged. Dry granular materials have no energetically or entropically preferred density modulations. We show that, in contrast to traditional solids, the emergence of shear rigidity in these granular solids is a collective process, which is controlled solely by boundary forces, the constraints of force and torque balance, and the positivity of the contact forces. We develop a theoretical framework based on these constraints, which connects rigidity to broken translational symmetry in the space of forces, not positions of grains. We apply our theory to experimentally generated shear-jammed (SJ) states and show that these states are indeed characterized by a persistent, non-uniform density modulation in force space, which emerges at the shear-jamming transition.

cond-mat.soft

Broad-tailed force distributions and velocity ordering in a heterogeneous membrane model for collective cell migration

Correlated velocity patterns and associated large length-scale transmission of traction forces have been observed in collective live cell migration as a response to a "wound". We argue that a simple physical model of a force-driven heterogeneous elastic membrane sliding over a viscous substrate can qualitatively explain a few experimentally observed facts: (i) the growth of velocity ordering which spreads from the wound boundary to the interior, (ii) the exponential tails of the traction force distributions, and (iii) the swirling pattern of velocities in the interior of the tissue.

physics.bio-ph