arXiv subjects

Madan Rao

Publications and source records attributed to Madan Rao.

At least 19 recordsLinked to original sources

arXiv2026

Building and maintaining a System of Intracellular Compartments

Organelle patterning and its heritability remain central mysteries in cell biology, highlighting the fundamental tension between genetic inheritance and self-assembly. Here, we explore the nonequilibrium assembly and emdedded size control of the Golgi cisternae and endosomes, amid a continuous flux of membrane traffic, within a stochastic framework of mechanochemical fusion-fission cycles that violate detailed balance. Using a dynamical systems approach, we identify distinct, robust regimes, ranging from fixed points to limit cycles with definite phase relations between cisternae. We identify these dynamical regimes with diverse phenotypes, from stable cisternae to periodic, cell-cycle-dependent dissolution/reassembly of cisternae to cisternal progression. We analyse its dynamic response to systematic perturbations or driving protocols and make definite predictions that may be tested experimentally. Our analysis reveals that the two competing models of Golgi organization - vesicular transport and cisternal progression - are, in fact, two phases of the same underlying nonequilibrium process. We see that cisternal size homeostasis is brought about by a size-dependent embedded control system driven by fusion-fission kernels. Finally, our framework offers a strategy for controlling cisternal number and chemical identity by modulating the interplay between glycosylation enzymes and membrane fission-fusion dynamics.

cond-mat.soft↗

arXiv2025

Activity-driven sorting, approach to criticality and turbulent flows in dense persistent active fluids

We show that dense active fluids comprising interacting particles with persistent self-propulsion are driven to a non-equilibrium steady state consisting of co-moving particles with co-aligned active forces. This velocity and force sorting appears to be associated with a critical state where the length scales associated with spatial correlations of the velocity and the propulsive force grow with system size. At large system sizes, these growing velocity domains are accompanied by the appearance of dynamic macroscopic voids in the steady state, associated with large density fluctuations. The dynamics of the macroscopic voids drives a new kind of turbulent state.

cond-mat.soft↗

arXiv2025

Excitability and travelling waves in renewable active matter

Activity and renewability are distinctive features of living matter, and constitute a new class of materials that we term renewable active matter. A striking example is the cell cytoskeleton, where myosin filaments bind to the actin meshwork, apply contractile stresses and undergo continual stress/strain dependent turnover, thus acting as both force generators and sensors. As a consequence of nonreciprocity, arising from the independence of action and response, such living matter exhibits unusual mechanical properties like, segregation without attraction, fragility and force chains. Here we show that the interplay between activity and turnover gives rise to mechanical excitability in the form of travelling waves and pulses, and spatiotemporal chaos. We provide a systematic study of the nucleation, movement and shape of the travelling pulse, and present a boundary layer analysis to establish the existence of homoclinic orbits. Our analytical results are supported by detailed numerical analysis of the governing partial differential equations. This study has implications for the observed mechanical excitability in a variety of cellular contexts such as in isolated adherent cells and confluent cells within tissues.

cond-mat.soft↗

arXiv2025

Active drive towards elastic spinodals

Active matter, exemplified by adaptive living materials such as the actomyosin cytoskeleton, can navigate material parameter space dynamically, leading to unconventional mechanical responses. In particular, it can self-drive toward elastic spinodal regimes, where inhomogeneous floppy modes induce elastic degeneracy and enable a controlled interplay between rigidity loss and recovery. Proximity to such marginal states leads to stress localization and the formation of force chains that can be actively assembled and disassembled. Here, we extend the classical notion of spinodal states to active solids and demonstrate how these extreme mechanical regimes can be actively accessed. Moreover, we show that in a nonlinear setting, crossing elastic spinodals generates new energy wells and makes force channeling an intrinsic feature of the emerging microstructure.

cond-mat.soft↗

arXiv2025

Emergence of Tension Chains and Active Force Patterning

Viewed under a fluorescence microscope, the actomyosin cytoskeleton presents vivid streaks of lines together with persistent oscillatory waves. Using an active hydrodynamic approach, we show how a uniform distribution of single or mixture of contractile stresslets spontaneously segregate, followed by the formation of singular structures of high contractility (tension chains) in finite time. Simultaneously, the collection of stresslets exhibit travelling waves and swapping as a consequence of nonreciprocity. In the finite geometry of the cell, the collection of active tension chains can form an active web held together by specific anchoring at the cell boundary. On the other hand, preferential wetting at the cell boundary can reinforce active segregation in a mixture of stresslets leading to stratification.

cond-mat.soft↗

arXiv2025

Segregation, Finite Time Elastic Singularities and Coarsening in Renewable Active Matter

Material renewability in active living systems, such as in cells and tissues, can drive the large-scale patterning of forces, with distinctive phenotypic consequences. This is especially significant in the cell cytoskeleton, where multiple species of myosin bound to actin, apply differential contractile stresses and undergo differential turnover, giving rise to patterned force channeling. Here we study the dynamical patterning of stresses that emerge in a hydrodynamic description of a renewable active actomyosin elastomer comprising two myosin species. Our analytical framework also holds for an actomyosin elastomer with a single myosin species. We find that a uniform active contractile elastomer spontaneously segregates into spinodal stress patterns, followed by a finite-time collapse into tension carrying singular structures that display self-similar scaling and caustics. Our numerical analysis carried out in 1D, shows that these singular structures move and merge, and gradually result in a slow coarsening dynamics. We discuss the implications of our findings to the emergence of stress fibers and the spatial patterning of actomyosin. Our study suggests, that with state-dependent turnover of crosslinkers and myosin, the in vivo cytoskeleton can navigate through the space of material parameters to achieve a variety of functional phenotypes.

cond-mat.soft↗

arXiv2024

Active morphodynamics of intracellular organelles in the trafficking pathway

From the Golgi apparatus to endosomes, organelles in the endomembrane system exhibit complex and varied morphologies that are often related to their function. Such membrane-bound organelles operate far from equilibrium due to directed fluxes of smaller trafficking vesicles; the physical principles governing the emergence and maintenance of these structures have thus remained elusive. By understanding individual fission and fusion events in terms of active mechano-chemical cycles, we show how such trafficking manifests at the hydrodynamic scale, resulting not only in fluxes of material -- such as membrane area and encapsulated volume -- but also in active stresses that drive momentum transfer between an organelle and its cytosolic environment. Due to the fluid and deformable nature of the bounding membrane, this gives rise to novel physics, coupling nonequilibrium forces to organelle composition, morphology and hydrodynamic flows. We demonstrate how both stable compartment drift and ramified sac-like morphologies, each reminiscent of Golgi-cisternae, emerge naturally from the same underlying nonequilibrium dynamics of fission and fusion.

cond-mat.soft↗

arXiv2024

A correspondence between Hebbian unlearning and steady states generated by nonequilibrium dynamics

The classic paradigms for learning and memory recall focus on strengths of synaptic couplings and how these can be modulated to encode memories. In a previous paper [A. K. Behera, M. Rao, S. Sastry, and S. Vaikuntanathan, Physical Review X 13, 041043 (2023)], we demonstrated how a specific non-equilibrium modification of the dynamics of an associative memory system can lead to increase in storage capacity. In this work, using analytical theory and computational inference schemes, we show that the dynamical steady state accessed is in fact similar to those accessed after the operation of a classic unsupervised scheme for improving memory recall, Hebbian unlearning or ``dreaming". Together, our work suggests how nonequilibrium dynamics can provide an alternative route for controlling the memory encoding and recall properties of a variety of synthetic (neuromorphic) and biological systems.

cond-mat.dis-nn↗

arXiv2024

Stochastic nanoswimmer: a multistate model for enzyme self-propulsion and enhanced diffusion

Several enzymes exhibit enhanced diffusion in the presence of a substrate. One explanation of this enhancement arises from fluctuating dimer models, which suggest that enzymes have a higher diffusion constant when interacting with substrates compared to when they are free. Another possible mechanism, suggested in both experimental and theoretical studies, is that enzymes act as nanoswimmers. However, existing nanoswimmer models have struggled to account for the exceptionally high self-propulsion speeds observed in experiments, with estimated increases in diffusion due to self-propulsion found to be minimal. In this study, we model enzymes as dimers with fluctuating mobility. We show that even dimers can exhibit run-and-tumble motion when transitioning between states of varying mobility within the enzymatic cycle. By exploring a three-state enzymatic cycle, we identify the conditions under which self-propulsion speeds and increases in diffusion rate consistent with experimental observations can be achieved.

cond-mat.soft↗

arXiv2022

Robust Molecular Computation by Active Mechanics

The living cell expends energetic and material resources to reliably process information from its environment. To do so, it utilises unreliable molecular circuitry that is subject to thermal and other fluctuations. Here, we argue that active, physical processes can provide error correcting mechanisms for information processing. We analyse a model in which fluctuating receptor activation induces contractile stresses that recruit further receptors, dynamically controlling resource usage and accuracy. We show that this active scheme can outperform passive, static clusters (as formed, for instance, by protein crosslinking). We consider simple binary environments, informative decision trees, and chemical computations; in each case, active stresses serve to contextually build signalling platforms that dynamically suppress error and allows for robust cellular computation.

cond-mat.soft↗

arXiv2022

Active emulsions in living cell membranes driven by contractile stresses and transbilayer coupling

The spatiotemporal organisation of proteins and lipids on the cell surface has direct functional consequences for signaling, sorting and endocytosis. Earlier studies have shown that multiple types of membrane proteins including transmembrane proteins that have cytoplasmic actin binding capacity and lipid-tethered GPI-anchored proteins (GPI-APs) form nanoscale clusters driven by active contractile flows generated by the actin cortex. To gain insight into the role of lipids in organizing membrane domains in living cells, we study the molecular interactions that promote the actively generated nanoclusters of GPI-APs and transmembrane proteins. This motivates a theoretical description, wherein a combination of active contractile stresses and transbilayer coupling drive the creation of active emulsions, mesoscale liquid ordered (lo) domains of the GPI-APs and lipids, at temperatures greater than equilibrium lipid-phase segregation. To test these ideas we use spatial imaging of homo-FRET combined with local membrane order and demonstrate that mesoscopic domains enriched in nanoclusters of GPI-APs are maintained by cortical actin activity and transbilayer interactions, and exhibit significant lipid order, consistent with predictions of the active composite model.

cond-mat.soft↗

arXiv2022

Enhancing associative memory recall in non-equilibrium materials through activity

Associative memory, a form of content-addressable memory, facilitates information storage and retrieval in many biological and physical systems. In statistical mechanics models, associative memory at equilibrium is represented through attractor basins in the free energy landscape. Here, we use the Hopfield model, a paradigmatic model to describe associate memory, to investigate the effect of non-equilibrium activity on memory retention and recall. We introduce activity into the system as gaussian-colored noise which breaks detailed balance and forces the system out of equilibrium. We observe that, under these non-equilibrium conditions, the Hopfield network has a higher storage capacity than that allowed at equilibrium. Using analytical and numerical techniques, we show that the rate of entropy production modifies the energy landscape and helps the system to access memory regions which were previously inaccessible.

cond-mat.dis-nn↗

arXiv2021

Active Segregation Dynamics in the Living Cell

In this paper, we bring together our efforts in identifying and understanding nonequilibrium phase segregation driven by active processes in the living cell, with special focus on the segregation of cell membrane components driven by active contractile stresses arising from cortical actomyosin. This also has implications for active segregation dynamics in membraneless regions within the cytoplasm and nucleus (3d). We formulate an active version of the Flory-Huggins theory that incorporates a contribution from fluctuating active stresses. Apart from knitting together some of our past theoretical work in a comprehensive narrative, we highlight some new results, and establish a correspondence with recent studies on Active Model B/B+. We point to the many unusual aspects of the dynamics of active phase segregation, such as (i) anomalous growth dynamics, (ii) coarsening accompanied by propulsion and coalescence of domains that exhibit nonreciprocal effects, (iii) segregation into mesoscale domains, (iv) emergence of a nonequilibrium phase segregated steady state characterised by strong macroscopic fluctuations (fluctuation dominated phase ordering (FDPO)), and (v) mesoscale segregation even above the equilibrium Tc. Apart from its implications for actively driven segregation of binary fluids, these ideas are at the heart of an Active Emulsion description of the lateral organisation of molecules on the plasma membrane of living cells, whose full molecular elaboration appears elsewhere.

cond-mat.soft↗

arXiv2021

Active ploughing through a compressible viscoelastic fluid: Unjamming and emergent nonreciprocity

A dilute suspension of active Brownian particles in a dense compressible viscoelastic fluid, forms a natural setting to study the emergence of nonreciprocity during a dynamical phase transition. At these densities, the transport of active particles is strongly influenced by the passive medium and shows a dynamical jamming transition as a function of activity and medium density. In the process, the compressible medium is actively churned up -for low activity, the active particle gets self-trapped in a spherical cavity of its own making, while for large activity, the active particle ploughs through the medium, either accompanied by a moving anisotropic wake, or leaving a porous trail. A hydrodynamic approach makes it evident that the active particle generates a long range density wake which breaks fore-aft symmetry, consistent with the simulations. Accounting for the back reaction of the compressible medium leads to (i) dynamical jamming of the active particle, and (ii) a dynamical non-reciprocal attraction between two active particles moving along the same direction, with the trailing particle catching up with the leading one in finite time. We emphasize that these nonreciprocal effects appear only when the active particles are moving and so manifest in the vicinity of the jamming-unjamming transition.

cond-mat.soft↗

arXiv2021

Stratification, multivalency and turnover of the active cortical machinery are required for steady active contractile flows at the cell surface

Many cell membrane proteins that bind to actin form dynamic clusters driven by contractile flows generated by the actomyosin machinery at the cell cortex. Recent evidence suggests that a necessary condition for the generation of these protein clusters on the membrane is the stratified organization of the active agents -formin-nucleated actin, myosin-II minifilaments, and ARP2/3-nucleated actin mesh -within the cortex. Further, the observation that these clusters dynamically remodel, requires that the components of this active machinery undergo turnover. Here we develop a coarse-grained agent-based Brownian dynamics simulation that incorporates the effects of stratification, binding of myosin minifilaments to multiple actin filaments and their turnover. We show that these three features of the active cortical machinery -stratification, multivalency and turnover -are critical for the realisation of a nonequilibrium steady state characterised by contractile flows and dynamic orientational patterning. We show that this nonequilibrium steady state enabled by the above features of the cortex, can facilitate multi-particle encounters of membrane proteins that profoundly influence the kinetics of bimolecular reactions at the cell surface.

cond-mat.soft↗

arXiv2020

Glycan processing in the Golgi -- optimal information coding and constraints on cisternal number and enzyme specificity

Many proteins that undergo sequential enzymatic modification in the Golgi cisternae are displayed at the plasma membrane as cell identity markers. The modified proteins, called glycans, represent a molecular code. The fidelity of this glycan code is measured by how accurately the glycan synthesis machinery realises the desired target glycan distribution for a particular cell type and niche. In this paper, we quantitatively analyse the tradeoffs between the number of cisternae and the number and specificity of enzymes, in order to synthesize a prescribed target glycan distribution of a certain complexity. We find that to synthesize complex distributions, such as those observed in real cells, one needs to have multiple cisternae and precise enzyme partitioning in the Golgi. Additionally, for fixed number of enzymes and cisternae, there is an optimal level of specificity of enzymes that achieves the target distribution with high fidelity. Our results show how the complexity of the target glycan distribution places functional constraints on the Golgi cisternal number and enzyme specificity.

q-bio.SC↗

arXiv2019

Breakdown of effective temperature, power law interactions and self-propulsion in a momentum conserving active fluid

Simplest extensions of single particle dynamics in momentum conserving active fluid - that of an active suspension of two colloidal particles or a single particle confined by a wall - exhibit strong departures from Boltzmann behavior, resulting in either a breakdown of an effective temperature description or a steady state with nonzero entropy production rate. This is a consequence of hydrodynamic interactions that introduce multiplicative noise in the stochastic description of the particle positions. This results in fluctuation induced interactions that depend on distance as a power law. We find that the dynamics of activated colloids in a passive fluid, with stochastic forcing localized on the particle, is different from that of passive colloids in an active fluctuating fluid.

cond-mat.soft↗

arXiv2019

Extreme active matter at high densities

Extreme active matter, an assembly of self-propelled particles with large persistence time $τ_p$ and high Péclet number, exhibits remarkable behaviour at high densities. As $τ_p\to 0$, the assembly undergoes a gradual slowing down of density relaxations, as one reduces the active propulsion force $f$, until at the glass transition, the relaxation times diverge. In the other limit, $τ_p \to \infty$, the fluid jams on lowering $f$, at a critical threshold $f^*(\infty)$, with stresses concentrated along force-chains. As one moves away from this jamming threshold, the force-chains dynamically remodel, and the lifetime of the force-balanced configurations diverges as one approaches $f^*(\infty)$, by tuning $τ_p$. In between these limits, the approach to dynamical arrest at low $f$, goes through a phase characterised by intermittency in the kinetic energy. This intermittency is a consequence of long periods of jamming followed by bursts of plastic yielding associated with Eshelby deformations, akin to the response of dense amorphous solids to an externally imposed shear. The frequency of these plastic bursts increases as one moves towards the intermittent phase-fluid boundary, where the correlated plastic events result in large scale vorticity and turbulence. Dense extreme active matter brings together the physics of glass, jamming, plasticity and turbulence, in a new state of driven classical matter.

cond-mat.soft↗