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Moumita Das

Publications and source records attributed to Moumita Das.

At least 19 recordsLinked to original sources

Recursive Gaussian Processes and the Bayesian Brain

Predictive coding offers a powerful framework for cortical computation, yet scalable implementations that respect both Bayesian exactness and neurobiological constraints remain scarce. We bridge this gap by formally connecting predictive coding to Recursive Gaussian Processes (RGPs). RGPs employ a single Gaussian process \( g(t, \cdot) \) indexed by layer index and input value, preventing the representational collapse of standard deep Gaussian processes while allowing learnable cross-layer dependence via \( r_{1g} \). We demonstrate that RGPs intrinsically implement hierarchical Bayesian inference, uncertainty propagation, and precision-weighted prediction error. Critically, we map RGP components---the shared GP, spike-and-slab variable selection, and MCMC dynamics---onto the canonical cortical microcircuit, providing a neurobiological substrate for these computations. Drawing on the free energy principle, we show that RGP inference minimizes variational free energy, formally linking Bayesian mechanics to neuronal dynamics. Our synthesis positions RGPs as both a principled computational tool and a candidate model for the brain's predictive machinery, generating testable predictions for laminar-specific dynamics and spectral asymmetries between feedforward and feedback processing.

q-bio.NC

Pinned Boundaries Delay Contraction and Shape Stress Relaxation in Active Gels

Cells dynamically generate, transmit, and dissipate stress. Central to these processes is the actomyosin cortex, an active contractile material that drives cellular mechanical behavior. While prior studies have focused on freely contracting actomyosin systems, the role of mechanical constraints such as adhesion to boundaries remains less explored. To address this, we employ reconstituted actomyosin gels to investigate cellular contractility. We study contraction dynamics under pinned boundary conditions, where the gel is adhered transversely to two opposing surfaces, mimicking supracellular actomyosin networks in tissues and embryos. We find that pinned contraction leads to stress buildup, delaying contraction, producing intermittent dynamics, and generating spatially nonuniform strain fields. Stress is relieved through several pathways, including active-stress-driven symmetric constriction and defect-driven processes such as boundary detachment and internal rupture. We develop a hydrodynamic model incorporating elastic, viscous, and active stress contributions that distinguishes between stress-accumulation and stress-release phases and links variations in active stress to the observed intermittent dynamics. The model predicts distinct energy relaxation rates before and after detachment events, providing insight into stress dissipation. We compare experiments with numerical simulations, which reproduce the observed behavior and reveal how internal energy is generated and dissipated during stress buildup and relaxation. Together, our results demonstrate how boundary conditions and spatial heterogeneity govern the mechanical behavior of contractile active gels. These findings provide insight into stress regulation in cellular and tissue-scale systems and may inform the design of adaptive soft materials and bioinspired robotic systems.

cond-mat.soft

Stability analysis of action potential generation using Markov models of voltage-gated sodium channel isoforms

We investigate a conductance-based neuron model to explore how voltage-gated ion channel isoforms influence action-potential generation. The model combines a six-state Markov representation of NaV channels with a first-order KV3.1 model, allowing us to vary maximal sodium and potassium conductances and compare nine NaV isoforms. Using bifurcation theory and local stability analysis, we map regions of stable limit cycles and visualize excitability landscapes via heatmap-based diagrams. These analyses show that isoforms NaV1.3, NaV1.4 and NaV1.6 support broad excitable regimes, while isoforms NaV1.7 and NaV1.9 exhibit minimal oscillatory behavior. Our findings provide insights into the role of channel heterogeneity in neuronal dynamics and may help to guide the design of synthetic excitable systems by narrowing the parameter space needed for robust action-potential trains.

q-bio.NC

BARCODE: Biomaterial Activity Readouts to Categorize, Optimize, Design and Engineer for high throughput screening and characterization of dynamically restructuring soft materials

Active, responsive, nonequilibrium materials, at the forefront of materials engineering, offer dynamical restructuring, mobility and other complex life-like properties. Yet, this enhanced functionality comes with significant amplification of the size and complexity of the datasets needed to characterize their properties, thereby challenging conventional approaches to analysis. To meet this need, we present BARCODE (Biomaterial Activity Readouts to Categorize, Optimize, Design and Engineer), an open-access software that automates high throughput screening of microscopy video data to enable nonequilibrium material optimization and discovery. BARCODE produces a unique fingerprint or barcode of performance metrics that visually and quantitatively encodes dynamic material properties with minimal file size. Using three complementary material agnostic analysis branches, BARCODE significantly reduces data dimensionality and size, while providing rich, multiparametric outputs and rapid tractable characterization of activity and structure. We analyze a series of datasets of cytoskeleton networks and cell monolayers to demonstrate the ability of BARCODE to accelerate and streamline screening and analysis, reveal unexpected correlations and emergence, and enable broad non-expert data access, comparison, and sharing.

cond-mat.soft

Active and passive crosslinking of cytoskeleton scaffolds tune the effects of cell inclusions on composite structure

Incorporating cells within active biomaterial scaffolds is a promising strategy to develop forefront materials that can autonomously sense, respond, and alter the scaffold in response to environmental cues or internal cell circuitry. Using dynamic biocompatible scaffolds that can self-alter their properties via crosslinking and motor-driven force-generation opens even greater avenues for actuation and control. However, the design principles associated with engineering active scaffolds embedded with cells are not well established. To address this challenge, we design a dynamic scaffold material of bacteria cells embedded within a composite cytoskeletal network of actin and microtubules that can be passively or actively crosslinked by either biotin-streptavidin or multimeric kinesin motors. Using quantitative microscopy, we demonstrate the ability to embed cells of volume fractions 0.4 to 2% throughout the network without compromising the structural integrity of the network or inhibiting crosslinking or motor-driven dynamics. Our findings suggest that both passive and active crosslinking promote entrainment of cells within the network, while depletion interactions play a more important role in uncrosslinked networks. Moreover, we show that large-scale structures emerge with the addition of cell fractions as low as 0.4%, but these structures do not influence the microscale structural lengthscale of the materials. Our work highlights the potential of our composite biomaterial in designing autonomous materials controlled by cells, and provides a roadmap for effectively coupling cells to complex composite materials with an eye towards using cells as in situ factories to program material modifications.

physics.bio-ph

Probing quantum correlations in non-degenerate hyper-Raman process

Possibilities of observing single mode and intermodal quantum correlations (e.g., antibunching, steering and entanglement) are studied for a probed-hyper-Raman system with specific attention on the impact of a probe on the single and multi-mode quantum correlations generated in a hyper-Raman active system. The physical system studied here considers that the probe interacts continuously with the non-degenerate pump modes in the hyper-Raman active system via a nonlinear coupling. The investigation has revealed that quantum correlations in the Raman systems can be controlled using the probe. Further, it is observed that the quantum steering between the pump and anti-Stokes modes can be influenced significantly by controlling the interaction between the system and the probe. Unlike steering, probe could neither deteriorate the nonclassical correlations, namely intermodal entanglement and photon antibunching, nor induce them. Though the witness of the corresponding nonclassical effect depends on the initial state of the probe as well as the coupling strength

quant-ph

Rigidity transitions in anisotropic networks happen in multiple steps

We study how the rigidity transition in a triangular lattice changes as a function of anisotropy by preferentially filling bonds on the lattice in one direction. We discover that the onset of rigidity in anisotropic spring networks arises in at least two steps, reminiscent of the two-step melting transition in two dimensional crystals. In particular, our simulations demonstrate that the percolation of stress-supporting bonds happens at different critical volume fractions along different directions. By examining each independent component of the elasticity tensor, we determine universal exponents and develop universal scaling functions to analyze isotropic rigidity percolation as a multicritical point. We expect that these results will be important for elucidating the underlying mechanical phase transitions governing the properties of biological materials ranging from the cytoskeletons of cells to the extracellular networks of tissues such as tendon where the networks are often preferentially aligned.

cond-mat.soft

Introducing antiferromagnetic ordering on the surface states of Bi2Se3 topological insulator by Europium doping

Topological insulators (TIs) are materials with an insulating bulk characterized by a gapped band structure, along with gapless metallic surface states having a Dirac cone with a helical spin structure in momentum space. The helical spin--momentum locking of the surface states arises from intrinsic spin--orbit coupling (SOC) and provides topological protection to the surface states against scattering from external perturbations, like defects and non-magnetic impurities. Breaking the topological protection of surface states of topological insulators is an essential prerequisite for exploring their applications. Rare-earth ions typically exhibit larger magnetic moments than transition-metal ions and thus promise the opening of a wider exchange gap in the Dirac surface states of topological insulators. Bi$_2$Se$_3$ is an interesting material; on the one hand, it has semiconducting properties when it is thin sheets; on the other hand, it's a topological insulator when the structure has a minimum of six quintuple layers (QLs), with diverse applications in photothermal, thermoelectric, and optical properties. Here, we have developed a controlled colloidal synthesis with low temperature and a cost-effective process for the synthesis of undoped and Eu-doped 2D layered Bi$_2$Se$_3$ nanosheets. Scanning tunneling spectroscopy measurements demonstrated a correlation between the shift of Dirac point position and the dopant content, which has been theoretically established by the band structure calculation. At low temperatures below 10K, for the 10\% Eu-doped sample, magnetic data suggests an antiferromagnetic ordering in the sample, which may be the contribution of the mixed valence state of Europium. Our results support that antiferromagnetic exchange interaction can exist in topological surface states in rare-earth Eu-doped Bi$_2$Se$_3$, which can open a new window to novel quantum phenomena.

cond-mat.mtrl-sci

Morphological Control of Bundled Actin Networks Subject to Fixed-Mass Depletion

Depletion interactions are thought to significantly contribute to the organization of intracellular structures in the crowded cytosol. The strength of depletion interactions depends on physical parameters like the depletant number density and the depletant size ratio. Cells are known to dynamically regulate these two parameters by varying the copy number of proteins of a wide distribution of sizes. However, mammalian cells are also known to keep the total protein mass density remarkably constant, to within 0.5% throughout the cell cycle. We thus ask how the strength of depletion interactions varies when the total depletant mass is held fixed, a.k.a. fixed-mass depletion. We answer this question via scaling arguments, as well as by studying depletion effects on networks of reconstituted semiflexible actin $\textit{in silico}$ and $\textit{in vitro}$. We examine the maximum strength of the depletion interaction potential $U^*$ as a function of $q$, the size ratio between the depletant and the matter being depleted. We uncover a scaling relation $U^* \sim q^{-\zeta}$ for two cases: fixed volume fraction $\phi$ and fixed mass density $\rho$. For fixed volume fraction, we report $\zeta < 0$. For the fixed mass density case, we report $\zeta > 0$, which suggests the depletion interaction strength increases as the depletant size ratio is increased. To test this prediction, we prepared our filament networks at fixed mass concentrations with varying sizes of the depletant molecule poly(ethylene glycol) (PEG). We characterize the depletion interaction strength in our simulations via the mesh size. In experiments, we observe two distinct actin network morphologies, which we call weakly bundled and strongly bundled. We identify a mass concentration where different PEG depletant sizes leads to weakly bundled or strongly bundled morphologies...[more in main text].

cond-mat.soft

Quantum Zeno and anti-Zeno effects in the dynamics of non-degenerate hyper-Raman processes coupled to two linear waveguides

The effect of the presence of two probe waveguides on the dynamics of hyper-Raman processes is studied in terms of quantum Zeno and anti-Zeno effects. Specifically, the enhancement (diminution) of the evolution of the hyper-Raman processes due to interaction with the probe waveguides via evanescent waves is viewed as quantum Zeno (anti-Zeno) effect. We considered the two probe waveguides interacting with only one of the optical modes at a time. For instance, as a specific scenario, it is considered that the two non-degenerate pump modes interact with each probe waveguide linearly while Stokes and anti-Stokes modes do not interact with the probes. Similarly, in another scenario, we assumed both the probe waveguides interact with Stokes (anti-Stokes) mode simultaneously. The present results show that quantum Zeno (anti-Zeno) effect is associated with phase-matching (mismatching). However, we did not find any relation between the presence of the quantum Zeno effect and antibunching in the bosonic modes present in the hyper-Raman processes.

quant-ph

Timed material self-assembly controlled by circadian clock proteins

Active biological molecules present a powerful, yet largely untapped, opportunity to impart autonomous regulation to materials. Because these systems can function robustly to regulate when and where chemical reactions occur, they have the ability to bring complex, life-like behavior to synthetic materials. Here, we achieve this design feat by using functionalized circadian clock proteins, KaiB and KaiC, to engineer time-dependent crosslinking of colloids. The resulting material self-assembles with programmable kinetics, producing macroscopic changes in material properties, via molecular assembly of KaiB-KaiC complexes. We show that colloid crosslinking depends strictly on the phosphorylation state of KaiC, with kinetics that are synced with KaiB-KaiC complexing. Our microscopic image analyses and computational models indicate that the stability of colloidal super-structures depends sensitively on the number of Kai complexes per colloid connection. Consistent with our model predictions, a high concentration stabilizes the material against dissolution after a robust self-assembly phase, while a low concentration allows circadian oscillation of material structure. This work introduces the concept of harnessing biological timers to control synthetic materials; and, more generally, opens the door to using protein-based reaction networks to endow synthetic systems with life-like functional properties.

cond-mat.soft

Active restructuring of cytoskeleton composites leads to increased mechanical stiffness, memory, and heterogeneity

The composite cytoskeleton, comprising interacting networks of semiflexible actin and rigid microtubules, actively generates forces and restructures using motor proteins such as myosins to enable key mechanical processes including cell motility and mitosis. Yet, how motor-driven activity alters the mechanics of cytoskeleton composites remains an open challenge. Here, we perform optical tweezers microrheology on actin-microtubule composites driven by myosin II motors to show that motor activity increases the linear viscoelasticity and elastic storage of the composite by active restructuring to a network of tightly-packed filament clusters and bundles. Our nonlinear microrheology measurements performed hours after cessation of activity show that the motor-contracted structure is stable and robust to nonlinear forcing. Unique features of the nonlinear response include increased mechanical stiffness, memory and heterogeneity, coupled with suppressed filament bending following motor-driven restructuring. Our results shed important new light onto the interplay between viscoelasticity and non-equilibrium dynamics in active polymer composites such as the cytoskeleton.

cond-mat.soft

Depletion-Driven Morphological Control of Bundled Actin Networks

The actin cytoskeleton is a semiflexible biopolymer network whose morphology is controlled by a wide range of biochemical and physical factors. Actin is known to undergo a phase transition from a single-filament state to a bundled state by the addition of polyethylene glycol (PEG) molecules in sufficient concentration. While the depletion interaction experienced by these biopolymers is well-known, the effect of changing the molecular weight of the depletant is less well understood. Here, we experimentally identify a phase transition in solutions of actin from networks of filaments to networks of bundles by varying the molecular weight of PEG polymers, while holding the concentration of these PEG polymers constant. We examine the states straddling the phase transition in terms of micro and macroscale properties. We find that the mesh size, bundle diameter, persistence length, and intra-bundle spacing between filaments across the line of criticality do not show significant differences, while the relaxation time, storage modulus, and degree of bundling change between the two states do show significant differences. Our results demonstrate the ability to tune actin network morphology and mechanics by controlling depletant size, a property which could be exploited to develop actin-based materials with switchable rigidity.

cond-mat.soft

Reentrant Rigidity Percolation in Structurally Correlated Filamentous Networks

Many biological tissues feature a heterogeneous network of fibers whose tensile and bending rigidity contribute substantially to these tissues' elastic properties. Rigidity percolation has emerged as a important paradigm for relating these filamentous tissues' mechanics to the concentrations of their constituents. Past studies have generally considered tuning of networks by spatially homogeneous variation in concentration, while ignoring structural correlation. We here introduce a model in which dilute fiber networks are built in a correlated manner that produces alternating sparse and dense regions. Our simulations indicate that structural correlation consistently allows tissues to attain rigidity with less material. We further find that the percolation threshold varies non-monotonically with the degree of correlation, such that it decreases with moderate correlation and once more increases for high correlation. We explain the eventual reentrance in the dependence of the rigidity percolation threshold on correlation as the consequence of large, stiff clusters that are too poorly coupled to transmit forces across the network. Our study offers deeper understanding of how spatial heterogeneity may enable tissues to robustly adapt to different mechanical contexts.

cond-mat.soft

Motor antagonism dictates emergent dynamics in active double networks tuned by crosslinkers

The cytoskeleton relies on diverse populations of motors, filaments, and binding proteins acting in concert to enable non-equilibrium processes ranging from mitosis to chemotaxis. Its versatile reconfigurability, programmed by interactions between its constituents, make the cytoskeleton foundational active matter. Yet, current active matter endeavors are limited largely to single force-generating components acting on a single substrate, far from the composite cytoskeleton in cells. Here, we engineer actin-microtubule double-networks, driven by kinesin and myosin motors and tuned by crosslinkers, to ballistically restructure and flow with speeds that span three orders of magnitude depending on the composite formulation and time relative to the onset of motor activity. Differential dynamic microscopy analyses reveal that kinesin and myosin compete to delay the onset of acceleration and suppress discrete restructuring events, while passive crosslinking of either actin or microtubules has an opposite effect. Our minimal advection-diffusion model and spatial correlation analyses correlate these dynamics to structure, with motor antagonism suppressing reconfiguration and de-mixing, while crosslinking enhances clustering. Despite the rich formulation space and emergent formulation-dependent structures, the non-equilibrium dynamics across all networks and timescales can be organized into three classes: slow isotropic reorientation, fast directional flow, and multimode restructuring. Moreover, our mathematical model demonstrates that diverse structural motifs can arise simply from the interplay between motor-driven advection and frictional drag. These general features of our platform facilitate applicability to other active matter systems, and shed light on diverse ways that cytoskeletal components can cooperate or compete to enable wide-ranging cellular processes.

physics.bio-ph

Sustained Order-Disorder Transitions in a Model Colloidal System Driven by Rhythmic Crosslinking

Biological systems have the unique ability to self-organize and generate autonomous motion and work. Motivated by this, we investigate a 2D model colloidal network that can repeatedly transition between disordered states of low connectivity and ordered states of high connectivity via rhythmic binding and unbinding of biomimetic crosslinkers. We use Langevin dynamics to investigate the time-dependent changes in structure and collective properties of this system as a function of colloidal packing fractions and crosslinker oscillation periods and characterize the degree of order in the system by using network connectivity, bond length distributions, and collective motion. Our simulations suggest that we can achieve distinct states of this colloidal system with pronounced differences in microstructural order and large residence times in the ordered state when crosslinker kinetics and lifetimes depend directly on the oscillation period and this oscillation period is much larger than the colloidal diffusion time. Our results will provide insights into the rational design of smart active materials that can independently cycle between ordered and disordered states with desired material properties on a programmed schedule.

cond-mat.soft

Structural Origins of Cartilage Shear Mechanics

Healthy cartilage is a remarkable tissue, able to withstand tens of millions of loading cycles with minimal damage. While much is known about the structural origins of its compressive mechanics, how composition determines its mechanical behavior in shear, a major mode of failure, is poorly understood. Through a combination of microscale structure-function experiments and modeling, we develop a rigidity percolation framework to explain the structural origins of cartilage shear mechanics. This framework provides a new quantitative understanding for how the known degradative events in osteoarthritis determine the mechanical changes that are a hallmark of this disease. As such, this work provides a road map for understanding disease progression and in combination with non-invasive techniques such as MRI will enable more effective diagnosis and treatment.

physics.bio-ph

Fast Falsification of Neural Networks using Property Directed Testing

Neural networks are now extensively used in perception, prediction and control of autonomous systems. Their deployment in safety-critical systems brings forth the need for verification techniques for such networks. As an alternative to exhaustive and costly verification algorithms, lightweight falsification algorithms have been heavily used to search for an input to the system that produces an unsafe output, i.e., a counterexample to the safety of the system. In this work, we propose a falsification algorithm for neural networks that directs the search for a counterexample, guided by a safety property specification. Our algorithm uses a derivative-free sampling-based optimization method. We evaluate our algorithm on 45 trained neural network benchmarks of the ACAS Xu system against 10 safety properties. We show that our falsification procedure detects all the unsafe instances that other verification tools also report as unsafe. Moreover, in terms of performance, our falsification procedure identifies most of the unsafe instances faster, in comparison to the state-of-the-art verification tools for feed-forward neural networks such as NNENUM and Neurify and in many instances, by orders of magnitude.

cs.AI