arXiv subjects

Sutapa Mukherji

Publications and source records attributed to Sutapa Mukherji.

At least 19 recordsLinked to original sources

arXiv2023

Modelling cargo transport in crowded environments: effect of motor association to cargos

In intracellular transports, motor proteins transport macromolecules as cargos to desired locations by moving on biopolymers such as microtubules. Recent experiments suggest that cargos that can associate motor proteins during their translocation have larger run-length, association time and can overcome the motor traffic on microtubule tracks. Here, we model the dynamics of a cargo that can associate at the most m free motors present on the track as obstacles to its motion. The proposed models display competing effects of association and crowding, leading to a peak in the run-length with the free motor density. This result is consistent with past experimental observations. For m=2 and 3, we show that this feature is governed by the largest eigenvalue of the transition matrix describing the cargo dynamics. In all the above cases, free motors are assumed to be present as stalled obstacles. We finally compare simulation results for the run-length for general scenarios where the free motors undergo processive motion in addition to binding and unbinding to or from the microtubule.

physics.bio-ph↗

arXiv2019

Small RNA driven feed-forward loop: Fine-tuning of protein synthesis through sRNA mediated cross-talk

Often in bacterial regulatory networks, small noncoding RNAs (sRNA) interact with several mRNA species. The competition among mRNAs for binding to the same pool of sRNA might lead to crosstalk between the mRNAs. This is similar to the competing endogenous RNA (ceRNA) effect wherein the competition to bind to the same pool of miRNA in Eukaryotes leads to miRNA mediated crosstalk resulting in subtle and complex gene regulation with stabilised gene expression. We study an sRNA-driven feedforward loop (sFFL) where the top-tier regulator, an sRNA (RprA), translationally activates the target protein (RicI) directly and also, indirectly, via up-regulation of its transcriptional activator (RpoS/sigma^s). We show that the sRNA-mediated crosstalk between the two mRNA species leads to maximum target protein synthesis for low synthesis rates of RpoS-mRNA. This indicates the possibility of an optimal target protein synthesis with efficient utilisation of RpoS-mRNA which is typically associated with various other stress response activities inside the cell. Since gene expression is inherently stochastic due to the probabilistic nature of various molecular interactions associated with it, we next quantify the fluctuations in the target protein level using generating function-based approach and stochastic simulations. The coefficient of variation that provides a measure of fluctuations in the concentration shows a minimum under conditions that also correspond to optimal target protein synthesis. This prompts us to conclude that, in sFFL, the crosstalk leads to optimal target protein synthesis with minimal noise and efficient utilisation of RpoS-mRNA.

q-bio.MN↗

arXiv2019

Small RNA driven feed-forward loop: critical role of sRNA in noise filtering

A feed-forward loop (FFL) is a common gene-regulatory motif in which usually the upstream regulator is a protein, a transcription factor, that regulates the expression of the target protein in two parallel pathways. Here, we study a distinct sRNA-driven FFL (sFFL) discovered recently in Salmonella enterica. Unlike previously studied transcriptional FFLs (tFFL) and sRNA-mediated FFLs (smFFL), here the upstream regulator is an sRNA that activates the target protein and its transcriptional activator. Such sFFL has not been subjected to rigorous analysis. We, therefore, set out to understand two aspects. First is a quantitative comparison of the regulatory response of sFFL with tFFL and smFFL using a differential equation framework. Since the process of gene expression is inherently stochastic, the second objective is to find how the noise affects the functionality of sFFL. We find the response of sFFLto be stronger, faster, and more sensitive to the initial concentration of the upstream regulator than tFFL and smFFL. Further, a generating function based analysis and stochastic simulations lead to a non-trivial prediction that an optimal noise filtration can be attained depending on the synthesis rate of the sRNA and the degradation rate of the transcriptional activator. We conclude that in sFFL, sRNA plays a critical role not only in driving a rapid and strong response, but also a reliable response that depends critically on its concentration. Given the advantages of sFFL brought out in this work, it should not be surprising if future work reveals their employment in different biological contexts.

q-bio.MN↗

arXiv2018

Global Density Profile for Asymmetric Simple Exclusion Process from Renormalization Group Flows

The totally asymmetric simple exclusion process along with particle adsorption and evaporation kinetics is a model of boundary-induced nonequilibrium phase transition. In the continuum limit, the average particle density across the system is described by a singular differential equation involving multiple scales which lead to the formation of boundary layers (BL) or shocks. A renormalization group analysis is developed here by using the location and the width of the BL as the renormalization parameters. It not only allows us to cure the large distance divergences in the perturbative solution for the BL but also generates, from the BL solution, an analytical form for the global density profile. The predicted scaling form is checked against numerical solutions for finite systems.

cond-mat.stat-mech↗

arXiv2018

Threshold response and bistability in gene regulation by small noncoding RNA

In this paper, we study through mathematical modelling the combined effect of transcriptional and translational regulation by proteins and small noncoding RNAs (sRNA) in a genetic feedback motif that has an important role in the survival of E.coli under stress associated with oxygen and energy availability. We show that subtle changes in this motif can bring in drastically different effects on the gene expression. In particular, we show that a threshold response in the gene expression changes to a bistable response as the regulation on sRNA synthesis or degradation is altered. These results are obtained under deterministic conditions. Next, we study how the gene expression is altered by additive and multiplicative noise which might arise due to probabilistic occurrences of different biochemical events. Using the Fokker-Planck formulation, we obtain steady state probability distributions for sRNA concentration for the network motifs displaying bistability. The probability distributions are found to be bimodal with two peaks at low and high concentrations of sRNAs. We further study the variations in the probability distributions under different values of noise strength and correlations. The results presented here might be of interest for designing synthetic network for artificial control.

q-bio.MN↗

arXiv2017

Renormalization group analysis for an asymmetric simple exclusion process

A perturbative renormalization group method is used to obtain steady-state density profiles of a particle non-conserving asymmetric simple exclusion process. This method allows us to obtain a globally valid solution for the density profile without the asymptotic matching of bulk and boundary layer solutions. In addition, we show a nontrivial scaling of the boundary layer width with the system size close to specific phase boundaries.

cond-mat.stat-mech↗

arXiv2016

Transcriptional and translational regulation in Arc protein network of Escherichia coli's stress response

Recently, there has been a lot of effort in understanding sRNA mediated regulation of gene expression and how this mode of regulation differs from transcriptional regulation.In E.coli, in the presence of oxidative stress, the synthesis of sigma^s is regulated through an interesting mechanism involving both transcriptional and sRNA-mediated translational regulation. The key regulatory factors involved in transcriptional and translational regulation are ArcA and ArcB proteins and ArcZ sRNA, respectively. Phosphorylated ArcA, in a feedforward mechanism, represses the transcriptions sigma^s and ArcZ sRNA with the latter being a post-transcriptional activator for sigma^s. Through a feedback mechanisms, ArcZ sRNA destabilises ArcB mRNA and regulates the level of ArcB protein, a kinase that phosphorylates ArcA. The oxygen and energy availability is expected to influence the ArcA phosphorylation rate and, as a consequence, in equilibrium, the system is likely to be in either a high ArcB (low ArcZ) or a low ArcB (high ArcZ) state. Kinetic modelling studies suggest that the rate of destabilisation of ArcB mRNA by ArcZ sRNA must be appropriately tuned for achieving the desired state. In particular, for a high phosphorylation rate, the transition from a low to a high ArcZ synthesis regime with the increase in sRNA-mRNA interaction is similar to the threshold-linear response observed earlier. Further, we show that the mRNA destabilisation by sRNA might be, in particular, beneficial in the low phosphorylation state for having the right concentration levels of ArcZ and ArcB. Stochastic simulation results suggest that as the ArcZ-ArcB binding affinity is increased, the probability distribution for the number of ArcZ molecules becomes flatter indicating frequently occurring transcriptional bursts of varying strengths.

q-bio.MN↗

arXiv2016

Entropy production and large deviation function for systems with microscopically irreversible transitions

We obtain the large deviation function for entropy production of the medium and its distribution function for two-site totally asymmetric simple exclusion process(TASEP) and three-state unicyclic network. Since such systems are described through microscopic irreversible transitions, we obtain time-dependent transition rates by sampling the states of these systems at a regular short time interval $τ$. These transition rates are used to derive the large deviation function for the entropy production in the nonequilibrium steady state and its asymptotic distribution function. The shapes of the large deviation function and the distribution function depend on the value of the mean entropy production rate which has a non-trivial dependence on the particle injection and withdrawal rates in case of TASEP. Further, it is argued that in case of a TASEP, the distribution function tends to be like a Poisson distribution for smaller values of particle injection and withdrawal rates.

cond-mat.stat-mech↗

arXiv2015

Work distribution function for a Brownian particle driven by a nonconservative force

We derive the distribution function of work performed by a harmonic force acting on a uniformly dragged Brownian particle subjected to a rotational torque. Following the Onsager and Machlup's functional integral approach, we obtain the transition probability of finding the Brownian particle at a particular position at time $t$ given that it started the journey from a specific location at an earlier time. The difference between the forward and the time-reversed form of the generalized Onsager-Machlup's Lagrangian is identified as the rate of medium entropy production which further helps us develop the stochastic thermodynamics formalism for our model. The probability distribution for the work done by the harmonic trap is evaluated for an equilibrium initial condition. Although this distribution has a Gaussian form, it is found that the distribution does not satisfy the conventional work fluctuation theorem.

cond-mat.stat-mech↗

arXiv2014

Work and heat distributions for a Brownian particle subjected to an oscillatory drive

Using the Onsager-Machlup functional integral approach, we obtain the work distribution function and the distribution of the dissipated heat of a Brownian particle subjected to a confining harmonic potential and an oscillatory driving force. In the long time limit, the width of the work distribution function initially increases with the frequency of the driving force and finally saturates to a fixed value for large values of the angular frequency. Using the results from the work distribution part, we next obtain the distribution of the dissipated heat for the equilibrium initial condition. Using the method of steepest descent, we obtain a Gaussian distribution for small fluctuations in the large time limit. The distribution function, for a fixed time has been obtained numerically. It is shown that the heat distribution, in general, does not satisfy the transient fluctuation theorem.

cond-mat.stat-mech↗

arXiv2013

Coupling driven exclusion and diffusion processes on parallel lanes: boundary induced phase transitions and boundary layers

We study a driven many particle system comprising of two identical lanes of finite lengths. On one lane, particles hop diffusively with a bias in a specific direction. On the other lane, particles hop in a specific direction obeying mutual exclusion rule. In addition, the two lanes are connected with each other through exchange of particles with certain rules. The system, at its two ends, is in contact with particle reservoirs which maintain specific particle densities at the two ends. In this paper, we study boundary-induced phase transitions exhibited by this system and predict the phase diagram using the technique of fixed point based boundary layer analysis. An interesting manifestation of the interplay of two density variables associated with two lanes is found in the shock phase in which the particle density profile across the lane with unidirectional hopping shows a jump discontinuity (shock) from a low- to a high-density region. The density profile on the diffusion-lane never exhibits a shock. However, the shock in the other lane gives rise to a discontinuity in the slope of the diffusion-lane density profile. We show how an approximate solution for the slope can be obtained in the boundary layer analysis framework.

cond-mat.stat-mech↗

arXiv2012

Phase-plane analysis of driven multi-lane exclusion models

We show how a fixed point based boundary-layer analysis technique can be used to obtain the steady-state particle density profiles of driven exclusion processes on two-lane systems with open boundaries. We have considered two distinct two-lane systems. In the first, particles hop on the lanes in one direction obeying exclusion principle and there is no exchange of particles between the lanes. The hopping on one lane is affected by the particle occupancies on the other, which thereby introduces an indirect interaction among the lanes. Through a phase plane analysis of the boundary layer equation, we show why the bulk density undergoes a sharp change as the interaction between the lanes is increased. The second system involves one lane with driven exclusion process and the other with biased diffusion of particles. In contrast to the previous model, here there is a direct interaction between the lanes due to particle exchange between them. In this model, we have looked at two possible scenarios with constant (flat) and non-constant bulk profiles. The fixed point based boundary layer method provides a new perspective on several aspects including those related to maximal/minimal current phases, possibilities of shocks under very restricted boundary conditions for the flat profile but over a wide range of boundary conditions for the non-constant profile.

cond-mat.stat-mech↗

arXiv2012

Length-dependent dynamics of microtubules

Certain regulatory proteins influence the polymerization dynamics of microtubules by inducing catastrophe with a rate that depends on the microtubule length. Using a discrete formulation, here we show that, for a catastrophe rate proportional to the microtubule length, the steady-state probability distributions of length decay much faster with length than an exponential decay as seen in the absence of these proteins.

physics.bio-ph↗

arXiv2010

Multi-shocks in asymmetric simple exclusions processes: Insights from fixed-point analysis of the boundary-layers

The boundary-induced phase transitions in an asymmetric simple exclusion process with inter-particle repulsion and bulk non-conservation are analyzed through the fixed points of the boundary layers. This system is known to have phases in which particle density profiles have different kinds of shocks. We show how this boundary-layer fixed-point method allows us to gain physical insights on the nature of the phases and also to obtain several quantitative results on the density profiles especially on the nature of the boundary-layers and shocks.

cond-mat.stat-mech↗

arXiv2009

Fixed points and boundary layers in exclusion processes

In this paper, we show how a fixed point based boundary layer analysis can be used to understand phases and phase transitions in asymmetric simple exclusion processes (ASEPs) with open boundaries. In order to illustrate this method, we choose a two-species ASEP which has interesting phase transitions not seen in the one-species case. We also apply this method to the single species problem where the analysis is simple but nevertheless quite insightful.

cond-mat.stat-mech↗

arXiv2008

Shocks in asymmetric simple exclusion processes of interacting particles

In this paper, we study shocks and related transitions in asymmetric simple exclusion processes of particles with nearest neighbor interactions. We consider two kinds of inter-particle interactions. In one case, the particle-hole symmetry is broken due to the interaction. In the other case, particles have an effective repulsion due to which the particle-current-density drops down near the half filling. These interacting particles move on a one dimensional lattice which is open at both the ends with injection of particles at one end and withdrawal of particles at the other. In addition to this, there are possibilities of attachments or detachments of particles to or from the lattice with certain rates. The hydrodynamic equation that involves the exact particle current-density of the particle conserving system and additional terms taking care of the attachment-detachment kinetics is studied using the techniques of boundary layer analysis.

cond-mat.stat-mech↗

arXiv2008

Model for the unidirectional motion of a dynein molecule

Cytoplasmic dyneins transport cellular organelles by moving on a microtubule filament. It has been found recently that depending on the applied force and the concentration of the adenosine triphosphate (ATP) molecules, dynein's step size varies. Based on these studies, we propose a simple model for dynein's unidirectional motion taking into account the variations in its step size. We study how the average velocity and the relative dispersion in the displacement vary with the applied load. The model is amenable to further extensions by inclusion of details associated with the structure and the processivity of the molecule.

cond-mat.stat-mech↗

arXiv2007

Dynamic instability of microtubules: effect of catastrophe-suppressing drugs

Microtubules are stiff filamentary proteins that constitute an important component of the cytoskeleton of cells. These are known to exhibit a dynamic instability. A steadily growing microtubule can suddenly start depolymerizing very rapidly; this phenomenon is known as ``catastrophe''. However, often a shrinking microtubule is ``rescued'' and starts polymerizing again. Here we develope a model for the polymerization-depolymerization dynamics of microtubules in the presence of {\it catastrophe-suppressing drugs}. Solving the dynamical equations in the steady-state, we derive exact analytical expressions for the length distributions of the microtubules tipped with drug-bound tubulin subunits as well as those of the microtubules, in the growing and shrinking phases, tipped with drug-free pure tubulin subunits. We also examine the stability of the steady-state solutions.

cond-mat.stat-mech↗