arXiv subjects

Sudipto Muhuri

Publications and source records attributed to Sudipto Muhuri.

At least 19 recordsLinked to original sources

arXiv2025

Miniature work-to-work converter engine powered by motor protein

Designing a miniature microscale engine that can override the role of thermal fluctuations has remained elusive and is an important open challenge. Here we provide the design and theoretical framework for a unique information-based engine - a work-to-work converter - comprising a sub-micron size bead and motor protein-microtubule (MT) complex in an optical trap setup. We demonstrate how by implementing a simple motor protein state-dependent feedback protocol of the optical trap stiffness, this engine is able to harness and convert the movement of a motor protein into work output. Unlike other conventional microengines, the fidelity and performance of this engine is determined by the stochasticity of motor (un)binding characteristics. We obtain an analytical form of the work distribution function, average work output and average power output, providing quantitative predictions for engine performance which are validated by stochastic simulations. Remarkably, the average work output per cycle is at least an order of magnitude higher than the thermal fluctuations and supersedes the performance of other microscale engines realized so far.

physics.bio-ph↗

arXiv2025

Active spin model for cell assemblies on 1D substrates

The experimental use of micropatterned quasi-1D substrates has emerged as an useful experimental tool to study the nature of cell-cell interactions and gain insight on collective behaviour of cell colonies. Inspired by these experiments, we propose an active spin model to investigate the emergent properties of the cell assemblies. The lattice gas model incorporates the interplay of self-propulsion, polarity directional switching, intra-cellular attraction, and contact Inhibition Locomotion (CIL). In the absence of vacancies, which corresponds to a confluent cell packing on the substrate, the model reduces to an equilibrium spin model which can be solved exactly. In the presence of vacancies, the clustering is controlled by a dimensionless Peclet Number, Q - the ratio of magnitude of self-propulsion rate and directional switching rate of particles. In the absence of CIL interactions, we invoke a mapping to Katz-Lebowitz-Spohn(KLS) model to determine an exact analytical form of the cluster size distribution in the limit Q << 1. In the limit of Q >> 1, the cluster size distribution exhibits an universal scaling behaviour (in an approximate sense), such that the distribution function can be expressed as a scaled function of Q, particle density and CIL interaction strength. We characterize the phase behaviour of the system in terms of contour plots of average cluster size. The average cluster size exhibit a non-monotonic dependence on CIL interaction strength, attractive interaction strength, and self-propulsion.

cond-mat.soft↗

arXiv2023

Theoretical analysis of cargo transport by catch bonded motors in optical trapping assays

Dynein motors exhibit catch bonding, where the unbinding rate of the motors from microtubule filaments decreases with increasing opposing load. The implications of this catch bond on the transport properties of dynein-driven cargo are yet to be fully understood. In this context, optical trapping assays constitute an important means of accurately measuring the forces generated by molecular motor proteins. We investigate, using theory and stochastic simulations, the transport properties of cargo transported by catch bonded dynein molecular motors - both singly and in teams - in a harmonic potential, which mimics the variable force experienced by cargo in an optical trap. We estimate the biologically relevant measures of first passage time - the time during which the cargo remains bound to the microtubule and detachment force -the force at which the cargo unbinds from the microtubule, using both two-dimensional and one-dimensional force balance frameworks. Our results suggest that even for cargo transported by a single motor, catch bonding may play a role depending on the force scale which marks the onset of the catch bond. By comparing with experimental measurements on single dynein-driven transport, we estimate realistic bounds of this catch bond force scale. Generically, catch bonding results in increased persistent motion, and can also generate non-monotonic behaviour of first passage times. For cargo transported by multiple motors, emergent collective effects due to catch bonding can result in non-trivial re-entrant phenomena wherein average first passage times and detachment forces exhibit non-monotonic behaviour as a function of the stall force and the motor velocity.

physics.bio-ph↗

arXiv2023

Effect of Contact Inhibition Locomotion on confined cellular organization

Experiments performed using micro-patterned one dimensional collision assays have allowed a precise quantitative analysis of the collective manifestation of contact inhibition locomotion (CIL) wherein, individual migrating cells reorient their direction of motion when they come in contact with other cells. Inspired by these experiments, we present a discrete, minimal 1D Active spin model that mimics the CIL interaction between cells in one dimensional channels. We analyze the emergent collective behaviour of migrating cells in such confined geometries, as well as the sensitivity of the emergent patterns to driving forces that couple to cell motion. In the absence of vacancies, akin to dense cell packing, the translation dynamics is arrested and the model reduces to an equilibrium spin model which can be solved exactly. In the presence of vacancies, the interplay of activity-driven translation, cell polarity switching, and CIL results in an exponential steady cluster size distribution. We define a dimensionless Péclet number Q - the ratio of the translation rate and directional switching rate of particles in the absence of CIL. While the average cluster size increases monotonically as a function of Q, it exhibits a non-monotonic dependence on CIL strength, when the Q is sufficiently high. In the high Q limit, an analytical form of average cluster size can be obtained approximately by effectively mapping the system to an equivalent equilibrium process involving clusters of different sizes wherein the cluster size distribution is obtained by minimizing an effective Helmholtz free energy for the system. The resultant prediction of exponential dependence on CIL strength of the average cluster size and Q^{1/2} dependence of the average cluster size is borne out to reasonable accuracy as long as the CIL strength is not very large.

physics.bio-ph↗

arXiv2022

Clustering and finite size effects in a two-species exclusion process

We study the cluster size distribution of particles for a two-species exclusion process which involves totally asymmetric transport process of two oppositely directed species with stochastic directional switching of the species on a 1D lattice. As a function of $Q$ - the ratio of the translation rate and directional switching rate of particles, in the limit of $Q \rightarrow 0$, the probability distribution of the cluster size is an exponentially decaying function of cluster size $m$ and is exactly similar to the cluster size distribution of a TASEP. For $Q>>1$, the model can be mapped to persistent exclusion process (PEP) and the average cluster size, $\langle m \rangle \propto Q^{1/2} $. We obtain an approximate expression for the average cluster size in this limit. For finite system size system of $L$ lattice sites, for a particle number density $ρ$, the probability distribution of cluster sizes exhibits a distinct peak which corresponds to the formation of a single cluster of size $m_s = ρL$. However this peak vanishes in the thermodynamic limit $ L \rightarrow \infty$. Interestingly, the probability of this largest size cluster, $P(m_s)$, exhibits scaling behaviour such that in terms of scaled variable $Q_1 \equiv Q/L^2 ρ(1-ρ)$, data collapse is observed for the probability of this cluster. The statistical features related to clustering observed for this minimal model may also be relevant for understanding clustering characteristics in {\it active } particles systems in confined 1D geometry.

cond-mat.stat-mech↗

arXiv2020

Novel Catchbond mediated oscillations in motor-microtubule complexes

Generation of mechanical oscillation is ubiquitous to wide variety of intracellular processes. We show that catchbonding behaviour of motor proteins provides a generic mechanism of generating spontaneous oscillations in motor-cytoskeletal filament complexes. We obtain the phase diagram to characterize how this novel catch bond mediated mechanism can give rise to bistability and sustained limit cycle oscillations and results in very distinctive stability behaviour, including bistable and non-linearly stabilised in motor-microtubule complexes in biologically relevant regimes. Hitherto, it was thought that the primary functional role of the biological catchbond was to improve surface adhesion of bacteria and cell when subjected to external forces or flow field. Instead our theoretical study shows that the imprint of this catch bond mediated physical mechanism would have ramifications for whole gamut of intracellular processes ranging from oscillations in mitotic spindle oscillations to activity in muscle fibres.

q-bio.SC↗

arXiv2020

Model for growth and morphology of fungal mycelium

We present a minimal driven lattice gas model which generates the morphological characteristics associated with single colony mycelium arising from the growth and branching process of fungal hyphae, which is fed by a single source of nutrients. We first analyze the growth and transport process in the primary hypha modeled as a growing 1-d lattice, which is subject to particle (vesicle) loss due to presence of dynamically created branching sites. We show that the spatial profile of vesicles along the growing lattice is an exponential distribution, while the length grows logarithmically with time. We also find that the probability distribution of length of the hypha tends to a Gaussian distribution function at late times. In contrast, the probability distribution function of the time required for growth to a specific length tends to a broad log-normal distribution. We simulate the resultant 2-d morphology generated by the growing primary hypha, quantifying the motility behavior and morphological characteristics of the colony. Analysis of the temporal behavior and morphological characteristics of the resultant 2-d morphology reveals a wide variability of these characteristics which depend on the input parameters which characterize the branching and elongation dynamics of the hyphae. By calibrating the input parameters for our model, we make some quantitative comparison of the predictions of our model with the observed experimental growth characteristics of fungal hyphae and the morphological characteristics of single colony fungal mycelium.

cond-mat.stat-mech↗

arXiv2020

Clustering in two models of interacting motors

We study a two-species bidirectional exclusion process, and a single species variant, which is motivated by the motion of organelles and vesicles along microtubules. Specifically, we are interested in the clustering of the particles and appearance of a single large cluster as the ratio $Q$ of the translation to switching rates is varied. We find that, although for a finite system, there is a clustering phenomenon in which the probability of finding a single large cluster changes from being negligible to having finite values, the phenomenon shifts to larger $Q$ values as the system size is increased. This suggests that the observed clustering is not a true (nonequilibrium) transition in the thermodynamic sense but rather a finite-size effect.

cond-mat.stat-mech↗

arXiv2019

Dynein catch bond as a mediator of codependent bidirectional cellular transport

Intracellular bidirectional transport of cargo on microtubule filaments is achieved by the collective action of oppositely directed dynein and kinesin motors. Experiments have found that in certain cases, inhibiting the activity of one type of motor results in an overall decline in the motility of the cellular cargo in both directions. This counter-intuitive observation, referred to as {\em paradox of codependence} is inconsistent with the existing paradigm of a mechanistic tug-of-war between oppositely directed motors. Unlike kinesin, dynein motors exhibit catchbonding, wherein the unbinding rates of these motors decrease with increasing force on them. Incorporating this catchbonding behavior of dynein in a theoretical model, we show that the functional divergence of the two motors species manifests itself as an internal regulatory mechanism, and leads to codependent transport behaviour in biologically relevant regimes. Using analytical methods and stochastic simulations, we analyse the processivity characteristics and probability distribution of run times and pause times of transported cellular cargoes. We show that catchbonding can drastically alter the transport characteristics and also provide a plausible resolution of the paradox of codependence.

physics.bio-ph↗

arXiv2018

Stabilization of overlapping biofilaments by passive crosslinkers

The formation, maintenance and reorganization of the cytoskeletal filament network is essential for a number of cellular processes. While the crucial role played by active forces generated by motor proteins has been studied extensively, only recently the importance of passive forces exerted by non-enzymatic crosslinkers has been realized. The interplay between active and passive proteins manifests itself, e.g., during cell division, where the spindle structure formed by overlapping microtubules is subject to both active sliding forces generated by crosslinking motor proteins and passive forces exerted by passive crosslinkers, such as Ase1 and PRC1. We propose a minimal model to describe the stability behaviour of a pair of anti-parallel overlapping microtubules resulting from the competition between active motors and passive crosslinkers. We obtain the stability diagram which characterizes the formation of stable overlap of the MT pair, identify the controlling biological parameters which determine their stability, and study the impact of mutual interactions between motors and passive crosslinkers on the stability of these overlapping filaments.

physics.bio-ph↗

arXiv2017

Bidirectional motion of filaments: Role of motor proteins and passive cross linkers

In eukaryotic cells, motor proteins (MP) bind to cytoskeletal filaments and move along them in a directed manner generating active stresses. During cell division a spindle structure of overlapping antiparallel microtubules (MT) form whose stability and dynamics under the influence of MPs has been studied extensively. Although passive cross linkers (PCL) were known to provide structural stability to filamentous network, consequences of the interplay between ATP dependent active forces of MPs and passive entropic forces of PCLs on MT overlap remains largely unexplored. Here, we formulate and characterize a model to study this, using linear stability analysis and numerical integration. In presence of PCLs, we find dynamic phase transitions with changing activity exhibiting regimes of stable partial overlap with or without oscillations, instability towards complete overlap, and stable limit cycle oscillations that emerge via a supercritical Hopf bifurcation characterized by an oscillation frequency determined by the MP and PCL parameters. We show that the overlap dynamics and stability depend crucially on whether both the MTs of overlapping pair are movable or one is immobilized, having potential implications for in vivo and in vitro studies.

physics.bio-ph↗

arXiv2016

Mechanical stability of bipolar spindle assembly

Assembly and stability of mitotic spindle is governed by the interplay of various intra-cellular forces, e.g. the forces generated by motor proteins by sliding overlapping anti-parallel microtubules (MTs) polymerized from the opposite centrosomes, the interaction of kinetochores with MTs, and the interaction of MTs with the chromosomes arms. We study the mechanical behavior and stability of spindle assembly within the framework of a minimal model which includes all these effects. For this model, we derive a closed--form analytical expression for the force acting between the centrosomes as a function of their separation distance and we show that an effective potential can be associated with the interactions at play. We obtain the stability diagram of spindle formation in terms of parameters characterizing the strength of motor sliding, repulsive forces generated by polymerizing MTs, and the forces arising out of interaction of MTs with kinetochores. The stability diagram helps in quantifying the relative effects of the different interactions and elucidates the role of motor proteins in formation and inhibition of spindle structures during mitotic cell division. We also predict a regime of bistability for certain parameter range, wherein the spindle structure can be stable for two different finite separation distances between centrosomes. This occurrence of bistability also suggests mechanical versatility of such self-assembled spindle structures.

physics.bio-ph↗

arXiv2016

Catch bond mechanism in Dynein motor driven collective transport

Recent experiments have demonstrated that dynein motor exhibits catch bonding behaviour, in which the unbinding rate of a single dynein decreases with increasing force, for a certain range of force. Motivated by these experiments, we propose a model for catch bonding in dynein using a threshold force bond deformation (TFBD) model wherein catch bonding sets in beyond a critical applied load force. We study the effect of catch bonding on unidirectional transport properties of cellular cargo carried by multiple dynein motors within the framework of this model. We find catch bonding can result in dramatic changes in the transport properties, which are in sharp contrast to kinesin driven unidirectional transport, where catch bonding is absent. We predict that, under certain conditions, the average velocity of the cellular cargo can actually increase as applied load is increased. We characterize the transport properties in terms of a velocity profile phase plot in the parameter space of the catch bond strength and the stall force of the motor. This phase plot yields predictions that may be experimentally accessed by suitable modifications of motor transport and binding properties. Our work necessitates a reexamination of existing theories of collective bidirectional transport of cellular cargo where the catch bond effect of dynein described in this paper is expected to play a crucial role.

physics.bio-ph↗

arXiv2015

Driven Transport on open filaments with inter-filament switching processes

We study a two filament driven lattice gas model with oppositely directed species of particles moving on two parallel filaments with filament switching processes and particle inflow and outflow at filament ends. The filament switching process is {\it correlated} such that particles switch filaments with finite probability only when oppositely directed particles meet on the same filament. This model mimics some of the coarse grained features observed in context of microtubule (MT) based intracellular transport, wherein cellular cargo loaded and off-loaded at filament ends are transported on multiple parallel microtubule (MT) filaments and can switch between the parallel microtubule filaments. We focus on a regime where the filaments are weakly coupled, such that filament switching rates scale inversely as the length of the filament. We find that the interplay (off)loading processes at the boundaries and the filament switching process leads to some distinctive features of the system. These features includes occurrence of variety of phases in the system with inhomogeneous density profiles including localized density shocks, density difference across the filaments and bidirectional current flows in the system. We analyze the system by developing a mean field (MF) theory and comparing the results obtained from the MF theory with the Monte Carlo (MC) simulations of the dynamics of the system. We find that the steady state density and current profiles of particles and the phase diagram obtained within the MF picture matches quite well with MC simulation results. These findings maybe useful for studying multi-filament intracellular transport.

cond-mat.soft↗

arXiv2015

Collective transport of weakly interacting molecular motors with Langmuir kinetics

Filament based intracellular transport involves the collective action of molecular motor proteins. Experimental evidences suggest that microtubule (MT) filament bound motor proteins such as {\it kinesins} weakly interact among themselves during transport and with the surrounding cellular environment. Motivated by these observations we study a driven lattice gas model for collective unidirectional transport of molecular motors on open filament, which incorporates the short-range interactions between the motors on filaments and couples the transport process on filament with surrounding cellular environment through adsorption-desorption Langmuir (LK) kinetics of the motors. We analyse this model within the framework of a Mean Field (MF) theory in the limit of {\it weak} interactions between the motors. We point to the mapping of this model with the non-conserved version of Katz-Lebowitz-Spohn (KLS) model. The system exhibits rich phase behavior with variety of inhomogeneous phases including localized shocks in the bulk of the filament. We obtain the steady state density and current profiles and analyse their variation as function of the strength of interaction. We compare these MF results with Monte Carlo simulations and find that the MF analysis shows reasonably good agreement as long as the motors are weakly interacting. We also construct the non-equilibrium MF phase diagram.

cond-mat.soft↗

arXiv2014

Jamming transition in a driven lattice gas

We study a two-lane driven lattice gas model with oppositely directed particles moving on two periodic lanes with correlated lane switching processes, so that particles can switch lanes with finite probability only when oppositely directed particles meet on the same lane. This system exhibits an unique behavior, wherein a phase transition is observed between a homogeneous absorbing phase, characterized by complete segregation of oppositely directed particles between the two lanes, and a jammed phase where each species of particles occupy both the lanes, along with formation of large cluster. This transition is accompanied by a finite drop of current in the lattice, emergence of cluster comprising of both species of particles, and is determined by the interplay of the relative rates of translation of particles on the same lane and their lane switching rates. These findings may have interesting implications for understanding the phenomenon of jamming in microtubule filaments observed in context of axonal transport.

cond-mat.stat-mech↗

arXiv2012

Scale invariant pattern in dynamically extending lattice

We study the implications of coupling Langmuir kinetics (LK) process with the dynamics of an extending lattice. The model that we consider couples dynamically extending exclusion process (DEEP) with the process of random attachment and detachment of particles in the bulk of the lattice. We explore a dynamical regime where the boundary processes of lattice extension and particle input compete with the bulk process of particle attachment and detachment. This competition leads to scale invariant density profile of particles when expressed in terms of the relative position in the growing lattice. It also leads to phase coexistence and shocks in the bulk of the lattice. We use a combination of Mean Field (MF) analysis and Monte Carlo simulations to characterize the density profile in growing lattice and construct a MF phase diagram. This study will have possible implications for transport and patterning in growing fungal filament.

cond-mat.soft↗

arXiv2011

Instrinsic oscillations of treadmilling microtubules in a motor bath

We analyse the dynamics of overlapping antiparallel treadmilling microtubules in the presence of crosslinking processive motor proteins that counterbalance an external force. We show that coupling the force-dependent velocity of motors and the kinetics of motor exchange with a bath in the presence of treadmilling leads generically to oscillatory behavior. In addition we show that coupling the polymerization kinetics to the external force through the kinetics of the crosslinking motors can stabilize the oscillatory instability into finite-amplitude nonlinear oscillations and may lead to other scenarios, including bistability.

cond-mat.soft↗