@article {156898, title = {Junctional force patterning drives both positional order and planar polarity in the auditory epithelia.}, journal = {Nat Commun}, volume = {16}, year = {2025}, month = {2025 Apr 26}, pages = {3927}, abstract = {

Tissue function depends on the precise organisation of the constituent cells. In the cochlea, the fidelity of hearing depends on mechanosensory hair cells being consistently surrounded by supporting cells. In addition to this positional order, auditory sensitivity depends crucially on planar cell polarity. This is characterised by the alignment of the orientation of eccentrically placed hair bundles on each hair cell. These two levels of order emerge simultaneously despite the cellular fluxes that occur during cochlear development. However, the link between tissue-scale cellular rearrangements and intrinsic cellular mechanisms remains unknown. By combining experimental and theoretical approaches, we find a precise force patterning underpinning positional order and planar cell polarity. This occurs through the modulation of the levels and phospho-type of the regulatory light chain of non-muscle myosin II at specific cell-cell junctions of the auditory epithelium. We propose that the control of junctional mechanics is vital for the organisation of multi-cell-type epithelia.

}, keywords = {Animals, Cell Polarity, Cochlea, Epithelium, Hair Cells, Auditory, Intercellular Junctions, Mice, Myosin Light Chains, Myosin Type II}, issn = {2041-1723}, doi = {10.1038/s41467-025-58557-0}, url = {https://www.nature.com/articles/s41467-025-58557-0}, author = {Prakash, Anubhav and Weninger, Julian and Singh, Nishant and Raman, Sukanya and Rao, Madan and Kruse, Karsten and Ladher, Raj K} } @article {157421, title = {Nonequilibrium asymmetry in the living cell membrane.}, journal = {Faraday Discuss}, year = {2025}, month = {2025 May 08}, abstract = {

We will discuss how sustained nonequilibrium processes operating at the plasma membrane (PM) determine the dynamical organisation (both lateral and transverse) of lipids, their maintenance and control, under physiological conditions. These nonequilibrium processes include active contractile stresses arising from the inevitable interaction of the inner leaflet of the PM with the adjoining actomyosin cortex, and active flipping of specific lipids. Recently, we showed that the inner leaflet phosphatidylserine (PS) interacts with the actomyosin cortex and engages in a strong transbilayer coupling across the leaflets. Here we develop an active Flory-Huggins theory for the mesoscale segregation of liquid-ordered (lo)-liquid-disordered (ld) domains in an asymmetric membrane bilayer, that incorporates both active contractile stresses at the inner leaflet and transbilayer coupling across the leaflets. The interplay between chemical potential gradients, transbilayer coupling and active stresses drives a rich pattern of mesoscale lo domains - static, strongly fluctuating and moving active emulsions - even at temperatures beyond the equilibrium phase transition temperature. We study conditions under which domain registry and slippage could be observed. We end with a discussion on the role of active flippases on PS in maintaining the active mesoscale organisation.

}, issn = {1364-5498}, doi = {10.1039/d4fd00207e}, url = {https://pubmed.ncbi.nlm.nih.gov/40338126/}, author = {Bansal, Ajay Kumar and Rao, Madan} } @article {125204, title = {Cellular compartmentalisation and receptor promiscuity as a strategy for accurate and robust inference of position during morphogenesis. }, journal = {Elife}, year = {2023}, month = {03/2023}, pages = {12:e79257}, abstract = {

Precise spatial patterning of cell fate during morphogenesis requires accurate inference of cellular position. In making such inferences from morphogen profiles, cells must contend with inherent stochasticity in morphogen production, transport, sensing and signalling. Motivated by the multitude of signalling mechanisms in various developmental contexts, we show how cells may utilise multiple tiers of processing (compartmentalisation) and parallel branches (multiple receptor types), together with feedback control, to bring about fidelity in morphogenetic decoding of their positions within a developing tissue. By simultaneously deploying specific and nonspecific receptors, cells achieve a more accurate and robust inference. We explore these ideas in the patterning of Drosophila melanogaster wing imaginal disc by Wingless morphogen signalling, where multiple endocytic pathways participate in decoding the morphogen gradient. The geometry of the inference landscape in the high dimensional space of parameters provides a measure for robustness and delineates stiff and sloppy directions. This distributed information processing at the scale of the cell highlights how local cell autonomous control facilitates global tissue scale design.

}, doi = {10.7554/eLife.79257}, author = {Iyer, Krishnan S and Prabhakara, C and Mayor, Satyajit and Rao, Madan} } @article {129154, title = {A census of actin-associated proteins in humans.}, journal = {Front Cell Dev Biol}, volume = {11}, year = {2023}, month = {2023}, pages = {1168050}, abstract = {

Actin filaments help in maintaining the cell structure and coordinating cellular movements and cargo transport within the cell. Actin participates in the interaction with several proteins and also with itself to form the helical filamentous actin (F-actin). Actin-binding proteins (ABPs) and actin-associated proteins (AAPs) coordinate the actin filament assembly and processing, regulate the flux between globular G-actin and F-actin in the cell, and help maintain the cellular structure and integrity. We have used protein-protein interaction data available through multiple sources (STRING, BioGRID, mentha, and a few others), functional annotation, and classical actin-binding domains to identify actin-binding and actin-associated proteins in the human proteome. Here, we report 2482 AAPs and present an analysis of their structural and sequential domains, functions, evolutionary conservation, cellular localization, abundance, and tissue-specific expression patterns. This analysis provides a base for the characterization of proteins involved in actin dynamics and turnover in the cell.

}, issn = {2296-634X}, doi = {10.3389/fcell.2023.1168050}, author = {Meenakshi S, Iyer and Rao, Madan and Mayor, Satyajit and Sowdhamini, Ramanathan} } @article {129153, title = {Reliable and robust control of nucleus centering is contingent on nonequilibrium force patterns.}, journal = {iScience}, volume = {26}, year = {2023}, month = {2023 May 19}, pages = {106665}, abstract = {

Cell centers their division apparatus to ensure symmetric cell division, a challenging task when the governing dynamics is stochastic. Using fission yeast, we show that the patterning of nonequilibrium polymerization forces of microtubule (MT) bundles the precise localization of spindle pole body (SPB), and hence the division septum, at the onset of mitosis. We define two cellular objectives, , the mean SPB position relative to the geometric center, and , the variance of the SPB position, which are sensitive to genetic perturbations that change cell length, MT bundle number/orientation, and MT dynamics. We show that simultaneous control of reliability and robustness is required to minimize septum positioning error achieved by the wild type (WT). A stochastic model for the MT-based nucleus centering, with parameters measured directly or estimated using Bayesian inference, recapitulates the maximum fidelity of WT. Using this, we perform a sensitivity analysis of the parameters that control nuclear centering.

}, issn = {2589-0042}, doi = {10.1016/j.isci.2023.106665}, author = {Jain, Ishutesh and Rao, Madan and Tran, Phong T} } @article {130545, title = {A view from the President of the Indian Biophysical Society.}, journal = {Biophys Rev}, volume = {15}, year = {2023}, month = {2023 Jun}, pages = {305-306}, abstract = {

This Commentary introduces the readers of Biophysical Reviews to the current president of the Indian Biophysical Society and details a few recent activities of the society in its domestic and international promotion of the biophysics as a scientific discipline.

}, issn = {1867-2450}, doi = {10.1007/s12551-023-01072-7}, author = {Rao, Madan} } @article {115040, title = {Active emulsions in living cell membranes driven by contractile stresses and transbilayer coupling}, journal = {Proc Natl Acad Sci U S A.}, volume = {119}, year = {2022}, month = {07/2022}, pages = {e2123056119}, abstract = {

The spatiotemporal organization 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 glycosylphosphatidylinositol-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 drives the creation of active emulsions, mesoscale liquid order (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 molecular clustering combined with local membrane order, and we 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.

}, doi = {10.1073/pnas.2123056119}, author = {Saha, Suvrajit and Das, A and Patra, C and Anilkumar, AA and Sil, Parijat and Mayor, Satyajit and Rao, Madan} } @article {104421, title = {Active Remodeling of Chromatin and Implications for Folding.}, journal = {J Phys Chem B}, year = {2022}, month = {2021 Dec 24}, abstract = {

Building on the observation that chromatin compaction can be locally modulated by activity, we propose a model of chromatin as an active polymer and study its large scale conformations. In particular, we study an active mechanochemical model of chromosomal folding based on the interplay among polymer elasticity, confinement, topological constraints, and fluctuating active stresses arising from the ATP-dependent action of a variety of chromatin-associated protein machines and chromatin-remodeling proteins and their stochastic turnover. We find that activity drives the chromatin to a nonequilibrium steady state; the statistics of conformations in this nonequilibrium steady state are consistent with recent measurements on intrachromosomal contact probabilities and chromosomal compaction. The contact exponents at steady state show a systematic variation with changes in the nature of activity and the rates of turnover. The steady state configuration of the active chromatin in two dimensions resembles a space-filling Peano curve, which might have implications for the optimization of genome information storage.

}, issn = {1520-5207}, doi = {10.1021/acs.jpcb.1c08655}, author = {Natesan, Ramakrishnan and Gowrishankar, Kripa and Kuttippurathu, Lakshmi and Kumar, P B Sunil and Rao, Madan} } @article {110442, title = {Active segregation dynamics in the living cell}, journal = {INDIAN JOURNAL OF PHYSICS}, year = {2022}, month = {05/2022}, abstract = {

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 works 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 non-reciprocal 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 T-c. 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.

}, doi = {10.1007/s12648-022-02298-z}, author = {Bansal, Ajay and Das, Amit and Rao, Madan} } @article {106556, title = {Glycan processing in the Golgi: optimal information coding and constraints on cisternal number and enzyme specificity.}, journal = {Elife}, volume = {11}, year = {2022}, month = {2022 Feb 17}, abstract = {

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 construct a simplified chemical synthesis model to quantitatively analyse the tradeoffs between the number of cisternae, and the number and specificity of enzymes, required to synthesize a prescribed target glycan distribution of a certain complexity to within a given fidelity. 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 (promiscuity) of enzymes that achieves the target distribution with high fidelity. The geometry of the fidelity landscape in the multidimensional space of the number and specificity of enzymes, inter-cisternal transfer rates, and number of cisternae, provides a measure for robustness and identifies stiff and sloppy directions. Our results show how the complexity of the target glycan distribution and number of glycosylation enzymes places functional constraints on the Golgi cisternal number and enzyme specificity.

}, issn = {2050-084X}, doi = {10.7554/eLife.76757}, author = {Yadav, Alkesh and Vagne, Quentin and Sens, Pierre and Iyengar, Garud and Rao, Madan} } @article {123122, title = {Protein as evolvable functionally constrained amorphous matter.}, journal = {J Biosci}, volume = {47}, year = {2022}, month = {2022}, abstract = {

We explore current ideas around the representation of a protein as an amorphous material, in turn represented by an abstract graph G with edges weighted by elastic stiffnesses. By embedding this graph in physical space, we can map every graph to a spectrum of conformational fluctuations and responses (as a result of, say, ligandbinding). This sets up a {\textquoteright}genotype-phenotype{\textquoteright} map, which we use to evolve the amorphous material to select for fitness. Using this, we study the emergence of allosteric interaction, hinge joint, crack formation and a slide bolt in functional proteins such as adenylate kinase, HSP90, calmodulin and GPCR proteins. We find that these emergent features are associated with specific geometries and mode spectra of floppy or liquid-like regions. Our analysis provides insight into understanding the architectural demands on a protein that enable a prescribed function and its stability to mutations.

}, keywords = {Mutation}, issn = {0973-7138}, author = {Tripathy, Madhusmita and Srivastava, Anand and Sastry, Srikanth and Rao, Madan} } @article {119608, title = {SMC protein RecN drives RecA filament translocation for in~vivo homology search.}, journal = {Proc Natl Acad Sci U S A}, volume = {119}, year = {2022}, month = {2022 Nov 15}, pages = {e2209304119}, abstract = {

While the molecular repertoire of the homologous recombination pathways is well studied, the search mechanism that enables recombination between distant homologous regions is poorly understood. Earlier work suggests that the recombinase RecA, an essential component for homology search, forms an elongated filament, nucleating at the break site. How this RecA structure carries out long-distance search remains unclear. Here, we follow the dynamics of RecA after induction of a single double-strand break on the chromosome. We find that the RecA-nucleoprotein filament, once formed, rapidly translocates in a directional manner in the cell, undergoing several pole-to-pole traversals, until homology search is complete. Concomitant with translocation, we observe dynamic variation in the length of the filament. Importantly in\ vivo, the RecA filament alone is incapable of such long-distance movement; both translocation and associated length variations are contingent on action of structural maintenance of chromosome (SMC)-like protein RecN, via its ATPase cycle. In summary, we have uncovered the three key elements of homology search driven by RecN: mobility of a finite segment of RecA, changes in filament length, and ability to conduct multiple pole-to-pole traversals, which together point to an optimal search strategy.

}, keywords = {Bacterial Proteins, Chromosomes, DNA, Single-Stranded, DNA-Binding Proteins, Rec A Recombinases}, issn = {1091-6490}, doi = {10.1073/pnas.2209304119}, author = {Chimthanawala, Afroze and Parmar, Jyotsana J and Kumar, Sujan and Iyer, Krishnan S and Rao, Madan and Badrinarayanan, Anjana} } @article {115050, title = {Unjamming and emergent nonreciprocity in active ploughing through a compressible viscoelastic fluid.}, journal = {Nat Commun}, volume = {13}, year = {2022}, month = {2022 Aug 04}, pages = {4533}, abstract = {

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 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.

}, issn = {2041-1723}, doi = {10.1038/s41467-022-31984-z}, author = {Banerjee, Jyoti Prasad and Mandal, Rituparno and Banerjee, Deb Sankar and Thutupalli, Shashi and Rao, Madan} } @article {77995, title = {Extreme active matter at high densities.}, journal = {Nat Commun}, volume = {11}, year = {2020}, month = {2020 May 22}, pages = {2581}, abstract = {

We study the remarkable behaviour of dense active matter comprising self-propelled particles at large P{\'e}clet numbers, over a range of persistence times, from τ\ {\textrightarrow}\ 0, when the active fluid undergoes a slowing down of density relaxations leading to a glass transition as the active propulsion force f reduces, to τ\ {\textrightarrow}\ $\infty$, when as f reduces, the fluid jams at a critical point, with stresses along force-chains. For intermediate τ, a decrease in f drives the fluid through an intermittent phase before dynamical arrest at low f. This intermittency is a consequence of periods of jamming followed by bursts of plastic yielding associated with Eshelby deformations. On the other hand, an increase in f leads to an increase in the burst frequency; 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.

}, issn = {2041-1723}, doi = {10.1038/s41467-020-16130-x}, author = {Mandal, Rituparno and Bhuyan, Pranab Jyoti and Chaudhuri, Pinaki and Dasgupta, Chandan and Rao, Madan} } @article {74438, title = {Active morphogenesis of epithelial monolayers.}, journal = {Phys Rev E}, volume = {100}, year = {2019}, month = {2019 Aug}, pages = {022413}, abstract = {

During typical early-stage embryo development, single-cell-thick tissues of tightly bound epithelial cells autonomously generate profound changes in their shape, forming the basis of organism anatomy. We report on a (covariant) active-hydrodynamic theory of such monolayer morphogenesis that is closed under its shape-changing dynamics-i.e., the degrees of freedom that encode monolayer geometry appear properly as broken-symmetry variables. In our theory, the salient physics of tissue-scale deformations emerges from a balance between the displacement and/or shear of a low-Reynolds-number embedding fluid (the "yolk") and cell-autonomous stresses, themselves a result of combining apical contractile stresses with an elastic-like mechanical response under the constraint of constant cell volume. The leading-order hydrodynamic instabilities include both passive constrained-buckling and active deformation, which can be further categorized by cell shape changes that are either "squamous to columnar" or "regular-prism to truncated-pyramid." The deformations resulting from the latter qualitatively reproduce in vivo observations of the onset of both mesoderm and posterior midgut invaginations, which take place during gastrulation in the model organism Drosophila melanogaster.

}, keywords = {Epithelium, Hydrodynamics, Models, Biological, Morphogenesis, Thermodynamics}, issn = {2470-0053}, doi = {10.1103/PhysRevE.100.022413}, author = {Morris, Richard G and Rao, Madan} } @article {72075, title = {Breakdown of effective temperature, power law interactions, and self-propulsion in a momentum-conserving active fluid.}, journal = {Phys Rev E}, volume = {100}, year = {2019}, month = {2019 Dec}, pages = {062602}, abstract = {

The simplest extensions of single-particle dynamics in a momentum-conserving active fluid-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 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.

}, issn = {2470-0053}, doi = {10.1103/PhysRevE.100.062602}, author = {Vishen, Amit Singh and Prost, Jacques and Rao, Madan} } @article {45431, title = {Cascade of transitions in molecular information theory}, journal = {Journal of Statistical Mechanics: Theory and Experiment}, volume = {Art No. 093402}, year = {2018}, month = {10/2018}, abstract = {

Biological organisms are open, adaptive systems that can respond to changes in environment in specific ways. Adaptation and response can be posed as an optimization problem, with a tradeoff between the benefit obtained from a response and the cost of producing environment-specific responses. Using recent results in stochastic thermodynamics, we formulate the cost as the mutual information between the environment and the stochastic response. The problem of designing an optimally performing network now reduces to a problem in rate distortion theory{\textemdash}a branch of information theory that deals with lossy data compression. We find that as the cost of unit information goes down, the system undergoes a sequence of transitions, corresponding to the recruitment of an increasing number of responses, thus improving response specificity as well as the net payoff. We derive formal equations for the transition points and exactly solve them for special cases. The first transition point, also called the coding transition, demarcates the boundary between a passive response and an active decision-making by the system. We study this transition point in detail, and derive three classes of asymptotic behavior, corresponding to the three limiting distributions of the statistics of extreme values. Our work points to the necessity of a union between information theory and the theory of adaptive biomolecular networks, in particular metabolic networks.

}, doi = {10.1088/1742-5468/aaddaa}, author = {Das, S G and Rao, Madan and Iyengar, Garud} } @article {45305, title = {Mechanochemical feedback control of dynamin independent endocytosis modulates membrane tension in adherent cells.}, journal = {Nat Commun}, volume = {9}, year = {2018}, month = {2018 Oct 11}, pages = {4217}, abstract = {

Plasma membrane tension regulates many key cellular processes. It is modulated by, and can modulate, membrane trafficking. However, the cellular pathway(s) involved in this interplay is poorly understood. Here we find that, among a number of endocytic processes operating simultaneously at the cell surface, a dynamin independent pathway, the CLIC/GEEC (CG) pathway, is rapidly and specifically upregulated upon a sudden reduction of tension. Moreover, inhibition (activation) of the CG pathway results in lower (higher) membrane tension. However, alteration in membrane tension does not directly modulate CG endocytosis. This requires vinculin, a mechano-transducer recruited to focal adhesion in adherent cells. Vinculin acts by controlling the levels of a key regulator of the CG pathway, GBF1, at the plasma membrane. Thus, the CG pathway directly regulates membrane tension and is in turn controlled via a mechano-chemical feedback inhibition, potentially leading to homeostatic regulation of membrane tension in adherent cells.

}, issn = {2041-1723}, doi = {10.1038/s41467-018-06738-5}, author = {Thottacherry, Joseph Jose and Kosmalska, Anita Joanna and Kumar, Amit and Vishen, Amit Singh and Elosegui-Artola, Alberto and Pradhan, Susav and Sharma, Sumit and Singh, Parvinder P and Guadamillas, Marta C and Chaudhary, Natasha and Vishwakarma, Ram and Trepat, Xavier and Del Pozo, Miguel A and Parton, Robert G and Rao, Madan and Pullarkat, Pramod and Roca-Cusachs, Pere and Mayor, Satyajit} } @article {39427, title = {A random first-order transition theory for an active glass.}, journal = {Proc Natl Acad Sci U S A}, volume = {115}, year = {2018}, month = {2018 Jul 24}, pages = {7688-7693}, abstract = {

How does nonequilibrium activity modify the approach to a glass? This is an important question, since many experiments reveal the near-glassy nature of the cell interior, remodeled by activity. However, different simulations of dense assemblies of active particles, parametrized by a self-propulsion force, [Formula: see text], and persistence time, [Formula: see text], appear to make contradictory predictions about the influence of activity on characteristic features of glass, such as fragility. This calls for a broad conceptual framework to understand active glasses; here, we extend the random first-order transition (RFOT) theory to a dense assembly of self-propelled particles. We compute the active contribution to the configurational entropy through an effective model of a single particle in a caging potential. This simple active extension of RFOT provides excellent quantitative fits to existing simulation results. We find that whereas [Formula: see text] always inhibits glassiness, the effect of [Formula: see text] is more subtle and depends on the microscopic details of activity. In doing so, the theory automatically resolves the apparent contradiction between the simulation models. The theory also makes several testable predictions, which we verify by both existing and new simulation data, and should be viewed as a step toward a more rigorous analytical treatment of active glass.

}, issn = {1091-6490}, doi = {10.1073/pnas.1721324115}, author = {Nandi, Saroj Kumar and Mandal, Rituparno and Bhuyan, Pranab Jyoti and Dasgupta, Chandan and Rao, Madan and Gov, Nir S} } @article {35146, title = {Soft inclusion in a confined fluctuating active gel.}, journal = {Phys Rev E}, volume = {97}, year = {2018}, month = {2018 Mar}, pages = {032602}, abstract = {

We study stochastic dynamics of a point and extended inclusion within a one-dimensional confined active viscoelastic gel. We show that the dynamics of a point inclusion can be described by a Langevin equation with a confining potential and multiplicative noise. Using a systematic adiabatic elimination over the fast variables, we arrive at an overdamped equation with a proper definition of the multiplicative noise. To highlight various features and to appeal to different biological contexts, we treat the inclusion in turn as a rigid extended element, an elastic element, and a viscoelastic (Kelvin-Voigt) element. The dynamics for the shape and position of the extended inclusion can be described by coupled Langevin equations. Deriving exact expressions for the corresponding steady-state probability distributions, we find that the active noise induces an attraction to the edges of the confining domain. In the presence of a competing centering force, we find that the shape of the probability distribution exhibits a sharp transition upon varying the amplitude of the active noise. Our results could help understanding the positioning and deformability of biological inclusions, e.g., organelles in cells, or nucleus and cells within tissues.

}, issn = {2470-0053}, doi = {10.1103/PhysRevE.97.032602}, author = {Singh Vishen, Amit and Rupprecht, J-F and Shivashankar, G V and Prost, J and Rao, Madan} } @article {25253, title = {Actomyosin pulsation and flows in an active elastomer with turnover and network remodeling.}, journal = {Nat Commun}, volume = {8}, year = {2017}, month = {2017 Oct 24}, pages = {1121}, abstract = {

Tissue remodeling requires cell shape changes associated with pulsation and flow of the actomyosin cytoskeleton. Here we describe the hydrodynamics of actomyosin as a confined active elastomer with turnover of its components. Our treatment is adapted to describe the diversity of contractile dynamical regimes observed in vivo. When myosin-induced contractile stresses are low, the deformations of the active elastomer are affine and exhibit spontaneous oscillations, propagating waves, contractile collapse and spatiotemporal chaos. We study the nucleation, growth and coalescence of actomyosin-dense regions that, beyond a threshold, spontaneously move as a spatially localized traveling front. Large myosin-induced contractile stresses lead to nonaffine deformations due to enhanced actin and crosslinker turnover. This results in a transient actin network that is constantly remodeling and naturally accommodates intranetwork flows of the actomyosin-dense regions. We verify many predictions of our study in Drosophila embryonic epithelial cells undergoing neighbor exchange during germband extension.

}, issn = {2041-1723}, doi = {10.1038/s41467-017-01130-1}, author = {Banerjee, Deb Sankar and Munjal, Akankshi and Lecuit, Thomas and Rao, Madan} } @article {14057, title = {Emergent Structures in an Active Polar Fluid: Dynamics of Shape, Scattering, and Merger.}, journal = {Phys Rev Lett}, volume = {118}, year = {2017}, month = {2017 Feb 17}, pages = {078104}, abstract = {

Spatially localized defect structures emerge spontaneously in a hydrodynamic description of an active polar fluid comprising polar "actin" filaments and "myosin" motor proteins that (un)bind to filaments and exert active contractile stresses. These emergent defect structures are characterized by distinct textures and can be either static or mobile-we derive effective equations of motion for these "extended particles" and analyze their shape, kinetics, interactions, and scattering. Depending on the impact parameter and propulsion speed, these active defects undergo elastic scattering or merger. Our results are relevant for the dynamics of actomyosin-dense structures at the cell cortex, reconstituted actomyosin complexes, and 2D active colloidal gels.

}, issn = {1079-7114}, doi = {10.1103/PhysRevLett.118.078104}, author = {Husain, Kabir and Rao, Madan} } @article {29622, title = {Glassy swirls of active dumbbells.}, journal = {Phys Rev E}, volume = {96}, year = {2017}, month = {2017 Oct}, pages = {042605}, abstract = {

Is an active glass different from a conventional passive glass? To address this, we study the dynamics of a dense binary mixture of soft dumbbells, each subject to an active propulsion force and thermal fluctuations. This dense assembly shows dynamical arrest, first to a translational and then to a rotational glass, as one reduces temperature T or the self-propulsion force f. We monitor the dynamics along an iso-relaxation-time contour in the (T-f) plane. We find dramatic differences both in the fragility and in the nature of dynamical heterogeneity, which characterize the onset of glass formation-the activity-induced glass exhibits large swirls or vortices, whose scale is set by activity, and it appears to diverge as one approaches the glass transition. This large collective swirling movement should have implications for collective cell migration in epithelial layers. We construct continuum hydrodynamic equations for the simulated system, and we show that the observed behavior of this growing dynamic length scale can be understood from these equations.

}, issn = {2470-0053}, doi = {10.1103/PhysRevE.96.042605}, author = {Mandal, Rituparno and Bhuyan, Pranab Jyoti and Chaudhuri, Pinaki and Rao, Madan and Dasgupta, Chandan} } @article {20317, title = {Universal lower bound on the free-energy cost of molecular measurements.}, journal = {Phys Rev E}, volume = {95}, year = {2017}, month = {2017 Jun}, pages = {062410}, abstract = {

The living cell uses a variety of molecular receptors to read and process chemical signals that vary in space and time. We model the dynamics of such molecular level measurements as Markov processes in steady state, with a coupling between the receptor and the signal. We prove exactly that, when the signal dynamics is not perturbed by the receptors, the free energy consumed by the measurement process is lower bounded by a quantity proportional to the mutual information. Our result is completely independent of the receptor architecture and dependent on signal properties alone, and therefore holds as a general principle for molecular information processing.

}, issn = {2470-0053}, doi = {10.1103/PhysRevE.95.062410}, author = {Das, Suman G and Rao, Madan and Iyengar, Garud} } @article {8348, title = {Active fluidization in dense glassy systems.}, journal = {Soft Matter}, volume = {12}, year = {2016}, month = {2016 Jul 20}, pages = {6268-76}, abstract = {

Dense soft glasses show strong collective caging behavior at sufficiently low temperatures. Using molecular dynamics simulations of a model glass former, we show that the incorporation of activity or self-propulsion, f0, can induce cage breaking and fluidization, resulting in the disappearance of the glassy phase beyond a critical f0. The diffusion coefficient crosses over from being strongly to weakly temperature dependent as f0 is increased. In addition, we demonstrate that activity induces a crossover from a fragile to a strong glass and a tendency of active particles to cluster. Our results are of direct relevance to the collective dynamics of dense active colloidal glasses and to recent experiments on tagged particle diffusion in living cells.

}, issn = {1744-6848}, doi = {10.1039/c5sm02950c}, author = {Mandal, Rituparno and Bhuyan, Pranab Jyoti and Rao, Madan and Dasgupta, Chandan} } @article {3546, title = {Actomyosin dynamics drive local membrane component organization in an in vitro active composite layer.}, journal = {Proc Natl Acad Sci U S A}, volume = {113}, year = {2016}, month = {2016 Mar 22}, pages = {E1645-54}, abstract = {

The surface of a living cell provides a platform for receptor signaling, protein sorting, transport, and endocytosis, whose regulation requires the local control of membrane organization. Previous work has revealed a role for dynamic actomyosin in membrane protein and lipid organization, suggesting that the cell surface behaves as an active composite composed of a fluid bilayer and a thin film of active actomyosin. We reconstitute an analogous system in vitro that consists of a fluid lipid bilayer coupled via membrane-associated actin-binding proteins to dynamic actin filaments and myosin motors. Upon complete consumption of ATP, this system settles into distinct phases of actin organization, namely bundled filaments, linked apolar asters, and a lattice of polar asters. These depend on actin concentration, filament length, and actin/myosin ratio. During formation of the polar aster phase, advection of the self-organizing actomyosin network drives transient clustering of actin-associated membrane components. Regeneration of ATP supports a constitutively remodeling actomyosin state, which in turn drives active fluctuations of coupled membrane components, resembling those observed at the cell surface. In a multicomponent membrane bilayer, this remodeling actomyosin layer contributes to changes in the extent and dynamics of phase-segregating domains. These results show how local membrane composition can be driven by active processes arising from actomyosin, highlighting the fundamental basis of the active composite model of the cell surface, and indicate its relevance to the study of membrane organization.

}, issn = {1091-6490}, doi = {10.1073/pnas.1514030113}, author = {K{\"o}ster, Darius Vasco and Husain, Kabir and Iljazi, Elda and Bhat, Abrar and Bieling, Peter and Mullins, R Dyche and Rao, Madan and Mayor, Satyajit} } @article {11587, title = {Nonequilibrium description of de novo biogenesis and transport through Golgi-like cisternae.}, journal = {Sci Rep}, volume = {6}, year = {2016}, month = {2016 Dec 19}, pages = {38840}, abstract = {

A central issue in cell biology is the physico-chemical basis of organelle biogenesis in intracellular trafficking pathways, its most impressive manifestation being the biogenesis of Golgi cisternae. At a basic level, such morphologically and chemically distinct compartments should arise from an interplay between the molecular transport and chemical maturation. Here, we formulate analytically tractable, minimalist models, that incorporate this interplay between transport and chemical progression in physical space, and explore the conditions for de novo biogenesis of distinct cisternae. We propose new quantitative measures that can discriminate between the various models of transport in a qualitative manner-this includes measures of the dynamics in steady state and the dynamical response to perturbations of the kind amenable to live-cell imaging.

}, issn = {2045-2322}, doi = {10.1038/srep38840}, author = {Sachdeva, Himani and Barma, Mustansir and Rao, Madan} } @article {3576, title = {Nonequilibrium phase transitions, fluctuations and correlations in an active contractile polar fluid.}, journal = {Soft Matter}, volume = {12}, year = {2016}, month = {2016 Feb 21}, pages = {2040-6}, abstract = {

We study the patterning, fluctuations and correlations of an active polar fluid consisting of contractile polar filaments on a two-dimensional substrate, using a hydrodynamic description. The steady states generically consist of arrays of inward pointing asters and show a continuous transition from a moving lamellar phase, a moving aster street, to a stationary aster lattice with no net polar order. We next study the effect of spatio-temporal athermal noise, parametrized by an active temperature TA, on the stability of the ordered phases. In contrast to its equilibrium counterpart, we find that the active crystal shows true long range order at low TA. On increasing TA, the asters dynamically remodel, concomitantly we find novel phase transitions characterized by bond-orientational and polar order upon "heating".

}, issn = {1744-6848}, doi = {10.1039/c5sm02527c}, author = {Gowrishankar, Kripa and Rao, Madan} } @article {3574, title = {Phase Segregation of Passive Advective Particles in an Active Medium.}, journal = {Phys Rev Lett}, volume = {116}, year = {2016}, month = {2016 Feb 12}, pages = {068306}, abstract = {

Localized contractile configurations or asters spontaneously appear and disappear as emergent structures in the collective stochastic dynamics of active polar actomyosin filaments. Passive particles which (un)bind to the active filaments get advected into the asters, forming transient clusters. We study the phase segregation of such passive advective scalars in a medium of dynamic asters, as a function of the aster density and the ratio of the rates of aster remodeling to particle diffusion. The dynamics of coarsening shows a violation of Porod behavior; the growing domains have diffuse interfaces and low interfacial tension. The phase-segregated steady state shows strong macroscopic fluctuations characterized by multiscaling and intermittency, signifying rapid reorganization of macroscopic structures. We expect these unique nonequilibrium features to manifest in the actin-dependent molecular clustering at the cell surface.

}, issn = {1079-7114}, doi = {10.1103/PhysRevLett.116.068306}, author = {Das, Amit and Polley, Anirban and Rao, Madan} } @article {1019, title = {Diffusion of GPI-anchored proteins is influenced by the activity of dynamic cortical actin.}, journal = {Mol Biol Cell}, volume = {26}, year = {2015}, month = {2015 Nov 5}, pages = {4033-45}, abstract = {

Molecular diffusion at the surface of living cells is believed to be predominantly driven by thermal kicks. However, there is growing evidence that certain cell surface molecules are driven by the fluctuating dynamics of cortical cytoskeleton. Using fluorescence correlation spectroscopy, we measure the diffusion coefficient of a variety of cell surface molecules over a temperature range of 24-37{\textdegree}C. Exogenously incorporated fluorescent lipids with short acyl chains exhibit the expected increase of diffusion coefficient over this temperature range. In contrast, we find that GPI-anchored proteins exhibit temperature-independent diffusion over this range and revert to temperature-dependent diffusion on cell membrane blebs, in cells depleted of cholesterol, and upon acute perturbation of actin dynamics and myosin activity. A model transmembrane protein with a cytosolic actin-binding domain also exhibits the temperature-independent behavior, directly implicating the role of cortical actin. We show that diffusion of GPI-anchored proteins also becomes temperature dependent when the filamentous dynamic actin nucleator formin is inhibited. However, changes in cortical actin mesh size or perturbation of branched actin nucleator Arp2/3 do not affect this behavior. Thus cell surface diffusion of GPI-anchored proteins and transmembrane proteins that associate with actin is driven by active fluctuations of dynamic cortical actin filaments in addition to thermal fluctuations, consistent with expectations from an "active actin-membrane composite" cell surface.

}, issn = {1939-4586}, doi = {10.1091/mbc.E15-06-0397}, author = {Saha, Suvrajit and Lee, Il-Hyung and Polley, Anirban and Groves, Jay T and Rao, Madan and Mayor, Satyajit} } @article {864, title = {Live cell plasma membranes do not exhibit a miscibility phase transition over a wide range of temperatures.}, journal = {J Phys Chem B}, volume = {119}, year = {2015}, month = {2015 Mar 26}, pages = {4450-9}, abstract = {

Lipid/cholesterol mixtures derived from cell membranes as well as their synthetic reconstitutions exhibit well-defined miscibility phase transitions and critical phenomena near physiological temperatures. This suggests that lipid/cholesterol-mediated phase separation plays a role in the organization of live cell membranes. However, macroscopic lipid-phase separation is not generally observed in cell membranes, and the degree to which properties of isolated lipid mixtures are preserved in the cell membrane remain unknown. A fundamental property of phase transitions is that the variation of tagged particle diffusion with temperature exhibits an abrupt change as the system passes through the transition, even when the two phases are distributed in a nanometer-scale emulsion. We support this using a variety of Monte Carlo and atomistic simulations on model lipid membrane systems. However, temperature-dependent fluorescence correlation spectroscopy of labeled lipids and membrane-anchored proteins in live cell membranes shows a consistently smooth increase in the diffusion coefficient as a function of temperature. We find no evidence of a discrete miscibility phase transition throughout a wide range of temperatures: 14-37 {\textdegree}C. This contrasts the behavior of giant plasma membrane vesicles (GPMVs) blebbed from the same cells, which do exhibit phase transitions and macroscopic phase separation. Fluorescence lifetime analysis of a DiI probe in both cases reveals a significant environmental difference between the live cell and the GPMV. Taken together, these data suggest the live cell membrane may avoid the miscibility phase transition inherent to its lipid constituents by actively regulating physical parameters, such as tension, in the membrane.

}, issn = {1520-5207}, doi = {10.1021/jp512839q}, author = {Lee, Il-Hyung and Saha, Suvrajit and Polley, Anirban and Huang, Hector and Mayor, Satyajit and Rao, Madan and Groves, Jay T} } @article {902, title = {Organelle morphogenesis by active membrane remodeling.}, journal = {Soft Matter}, volume = {11}, year = {2015}, month = {2015 Mar 28}, pages = {2387-93}, abstract = {

Intracellular organelles are subject to a steady flux of lipids and proteins through active, energy consuming transport processes. Active fission and fusion are promoted by GTPases, e.g., Arf-Coatamer and the Rab-Snare complexes, which both sense and generate local membrane curvature. Here we investigate, through Dynamical Triangulation Monte Carlo simulations, the role that these active processes play in determining the morphology and composition segregation in closed membranes. We find that the steady state shapes obtained as a result of such active processes, bear a striking resemblance to the ramified morphologies of organelles in vivo, pointing to the relevance of nonequilibrium fission-fusion in organelle morphogenesis.

}, keywords = {Intracellular Membranes, Membrane Fusion, Models, Biological, Models, Statistical, Monte Carlo Method, Organelles}, issn = {1744-6848}, doi = {10.1039/c4sm02311k}, author = {Ramakrishnan, N and Ipsen, John H and Rao, Madan and Kumar, P B Sunil} } @article {1039, title = {Pre-yield non-affine fluctuations and a hidden critical point in strained crystals.}, journal = {Sci Rep}, volume = {5}, year = {2015}, month = {2015}, pages = {10644}, abstract = {

A crystalline solid exhibits thermally induced localised non-affine droplets in the absence of external stress. Here we show that upon an imposed shear, the size of these droplets grow until they percolate at a critical strain, well below the value at which the solid begins to yield. This critical point does not manifest in most thermodynamic or mechanical properties, but is hidden and reveals itself in the onset of inhomogeneities in elastic moduli, marked changes in the appearance and local properties of non-affine droplets and a sudden enhancement in defect pair concentration. Slow relaxation of stress and an-elasticity appear as observable dynamical consequences of this hidden criticality. Our results may be directly verified in colloidal crystals with video microscopy techniques but are expected to have more general validity.

}, issn = {2045-2322}, doi = {10.1038/srep10644}, author = {Das, Tamoghna and Ganguly, Saswati and Sengupta, Surajit and Rao, Madan} } @article {881, title = {Transbilayer lipid interactions mediate nanoclustering of lipid-anchored proteins.}, journal = {Cell}, volume = {161}, year = {2015}, month = {2015 Apr 23}, pages = {581-94}, abstract = {

Understanding how functional lipid domains in live cell membranes are generated has posed a challenge. Here, we show that transbilayer interactions are necessary for the generation of cholesterol-dependent nanoclusters of GPI-anchored proteins mediated by membrane-adjacent dynamic actin filaments. We find that long saturated acyl-chains are required for forming GPI-anchor nanoclusters. Simultaneously, at the inner leaflet, long acyl-chain-containing phosphatidylserine (PS) is necessary for transbilayer coupling. All-atom molecular dynamics simulations of asymmetric multicomponent-membrane bilayers in a mixed phase provide evidence that immobilization of long saturated acyl-chain lipids at either leaflet stabilizes cholesterol-dependent transbilayer interactions forming local domains with characteristics similar to a liquid-ordered (lo) phase. This is verified by experiments wherein immobilization of long acyl-chain lipids at one leaflet effects transbilayer interactions of corresponding lipids at the opposite leaflet. This suggests a general mechanism for the generation and stabilization of nanoscale cholesterol-dependent and actin-mediated lipid clusters in live cell membranes.

}, keywords = {Actins, Animals, Cell Membrane, CHO Cells, Cricetulus, Glycosylphosphatidylinositols, Lipid-Linked Proteins, Molecular Dynamics Simulation, Phosphatidylserines}, issn = {1097-4172}, doi = {10.1016/j.cell.2015.03.048}, author = {Raghupathy, Riya and Anilkumar, Anupama Ambika and Polley, Anirban and Singh, Parvinder Pal and Yadav, Mahipal and Johnson, Charles and Suryawanshi, Sharad and Saikam, Varma and Sawant, Sanghapal D and Panda, Aniruddha and Guo, Zhongwu and Vishwakarma, Ram A and Rao, Madan and Mayor, Satyajit} }