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Dive into the research topics where Srabanti Chaudhury is active.

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Featured researches published by Srabanti Chaudhury.


Journal of Chemical Physics | 2010

A harmonic transition state approximation for the duration of reactive events in complex molecular rearrangements

Srabanti Chaudhury; Dmitrii E. Makarov

Motivated by recent experimental efforts to measure the time a molecular system spends in transit between the reactants and the products of a chemical reaction, here we study the properties of the distribution of such transit times for the case of conservative dynamics on a multidimensional energy landscape. Unlike reaction rates, transit times are not invariant with respect to the order parameter (a.k.a. the experimental signal) used to monitor the progress of a chemical reaction. Nevertheless, such order parameter dependence turns out to be relatively weak. Moreover, for several model systems we find that the probability distribution of transit times can be estimated analytically, with reasonable accuracy, by assuming that the order parameter coincides with the direction of the unstable normal mode at the transition state. Although this approximation tends to overestimate the actual mean transit time measured using other order parameters, it yields asymptotically correct long-time behavior of the transit time distribution, which is independent of the order parameter.


Journal of Chemical Physics | 2006

Complex chemical kinetics in single enzyme molecules: Kramers's model with fractional Gaussian noise.

Srabanti Chaudhury; Binny J. Cherayil

A model of barrier crossing dynamics governed by fractional Gaussian noise and the generalized Langevin equation is used to study the reaction kinetics of single enzymes subject to conformational fluctuations. The direct application of Kramerss flux-over-population method to this model yields analytic expressions for the time-dependent transmission coefficient and the distribution of waiting times for barrier crossing. These expressions are found to reproduce the observed trends in recent simulations and experiments.


Journal of Physical Chemistry B | 2009

Dynamic Disorder-Driven Substrate Inhibition and Bistability in a Simple Enzymatic Reaction

Srabanti Chaudhury; Oleg A. Igoshin

Conformations and catalytic rates of enzymes (biological catalysts) fluctuate over a wide range of time scales. Recent experimental and theoretical investigations demonstrated case studies where the enzymatic catalysis rate follows the Michaelis-Menten (MM) rate law despite molecular fluctuations. In this paper, we investigate deviations from MM law and their effects on the dynamical behavior of the enzymatic network. We consider a simple kinetic scheme for a single substrate enzymatic reaction in which the product release step is treated explicitly. We examine how conformational fluctuations affect the underlying rate law in the quasi-static limit when conformational dynamics is very slow in one of the states. Our numerical results and analytically solvable model indicate that slow conformational fluctuations of the enzyme-substrate complex lead to non-MM behavior, substrate inhibition, and possible bistability of the reaction network.


Journal of Physical Chemistry B | 2014

Poisson indicator and Fano factor for probing dynamic disorder in single-molecule enzyme inhibition kinetics.

Srabanti Chaudhury

We consider a generic stochastic model to describe the kinetics of single-molecule enzyme inhibition reactions in which the turnover events correspond to conversion of substrate into a product by a single enzyme molecule in the presence of an inhibitor. We observe that slow fluctuations between the active and inhibited state of the enzyme or the enzyme substrate complex can induce dynamic disorder, which is manifested in the measurement of the Poisson indicator and the Fano factor as functions of substrate concentrations for different inhibition reactions. For a single enzyme molecule inhibited by the product, we derive a single-molecule Michaelis-Menten equation for the reaction rate, which shows a dependence on the substrate concentration similar to the ensemble enzymatic catalysis rate as obtained from bulk experimental results. The measurement of Fano factor is shown to be able to discriminate reactions following different inhibition mechanisms and also extract kinetic rates.


Journal of Chemical Physics | 2007

Modulation of electron transfer kinetics by protein conformational fluctuations during early-stage photosynthesis

Srabanti Chaudhury; Binny J. Cherayil

The kinetics of electron transfer during the early stages of the photosynthetic reaction cycle has recently been shown in transient absorption experiments carried out by Wang et al. [Science 316, 747 (2007)] to be strongly influenced by fluctuations in the conformation of the surrounding protein. A model of electron transfer rates in polar solvents developed by Sumi and Marcus using a reaction-diffusion formalism [J. Chem. Phys. 84, 4894 (1986)] was found to be successful in fitting the experimental absorption curves over a roughly 200 ps time interval. The fits were achieved using an empirically determined time-dependent function that described protein conformational relaxation. In the present paper, a microscopic model of this function is suggested, and it is shown that the function can be identified with the dynamic autocorrelation function of intersegment distance fluctuations that occur in a harmonic potential of mean force under the action of fractional Gaussian noise.


Journal of Chemical Physics | 2007

Dynamic disorder in single-molecule Michaelis-Menten kinetics: The reaction-diffusion formalism in the Wilemski-Fixman approximation

Srabanti Chaudhury; Binny J. Cherayil

Single-molecule equations for the Michaelis-Menten [Biochem. Z. 49, 333 (1913)] mechanism of enzyme action are analyzed within the Wilemski-Fixman [J. Chem. Phys. 58, 4009 (1973); 60, 866 (1974)] approximation after the effects of dynamic disorder--modeled by the anomalous diffusion of a particle in a harmonic well--are incorporated into the catalytic step of the reaction. The solution of the Michaelis-Menten equations is used to calculate the distribution of waiting times between successive catalytic turnovers in the enzyme beta-galactosidase. The calculated distribution is found to agree qualitatively with experimental results on this enzyme obtained at four different substrate concentrations. The calculations are also consistent with measurements of correlations in the fluctuations of the fluorescent light emitted during the course of catalysis, and with measurements of the concentration dependence of the randomness parameter.


PLOS ONE | 2012

Spontaneous Clearance of Viral Infections by Mesoscopic Fluctuations

Srabanti Chaudhury; Alan S. Perelson; Nikolai A. Sinitstyn

Spontaneous disease extinction can occur due to a rare stochastic fluctuation. We explore this process, both numerically and theoretically, in two minimal models of stochastic viral infection dynamics. We propose a method that reduces the complexity in models of viral infections so that the remaining dynamics can be studied by previously developed techniques for analyzing epidemiological models. Using this technique, we obtain an expression for the infection clearance time as a function of kinetic parameters. We apply our theoretical results to study stochastic infection clearance for specific stages of HIV and HCV dynamics. Our results show that the typical time for stochastic clearance of a viral infection increases exponentially with the size of the population, but infection still can be cleared spontaneously within a reasonable time interval in a certain population of cells. We also show that the clearance time is exponentially sensitive to the viral decay rate and viral infectivity but only linearly dependent on the lifetime of an infected cell. This suggests that if standard drug therapy fails to clear an infection then intensifying therapy by adding a drug that reduces the rate of cell infection rather than immune modulators that hasten infected cell death may be more useful in ultimately clearing remaining pockets of infection.


Journal of Statistical Mechanics: Theory and Experiment | 2008

Resolving a puzzle concerning fluctuation theorems for forced harmonic oscillators in non-Markovian heat baths

Srabanti Chaudhury; Debarati Chatterjee; Binny J. Cherayil

A harmonic oscillator that evolves under the action of both a systematic time-dependent force and a random time-correlated force can do work w. This work is a random quantity, and Mai and Dhar have recently shown,using the generalized Langevin equation (GLE) for the oscillator’s position x,that it satisfies a fluctuation theorem. In principle, the same result could have been derived from the Fokker–Planck equation (FPE) for the probability density function, P(x,w, t), for the oscillator being at x at time t, having done work w. Although the FPE equivalent to the above GLE is easily constructed and solved, one finds, unexpectedly, that its predictions for the mean and variance of w do not agree with the fluctuation theorem. We show that to resolve this contradiction, it is necessary to construct an FPE that includes the velocity of the oscillator, v, as an additional variable. The FPE for P(x, v,w, t) does indeed yield expressions for the mean and variance of w that agree with the fluctuation theorem.


Journal of Chemical Physics | 2006

Structural relaxation in complex liquids: Non-Markovian dynamics in a bistable potential

Srabanti Chaudhury; Binny J. Cherayil

The time correlation function C(t) identical with of the distance fluctuations of a particle moving in a bistable potential under the action of fractional Gaussian noise (fGn) is calculated from a Smoluchowski-type equation derived from a generalized Langevin equation (GLE). The time derivative of this function, dC(t)dt, is compared with data from optical Kerr effect measurements of liquid crystal dynamics in the vicinity of the isotropic-to-nematic transition, which are related to the time derivative of an orientational correlation function. A number of characteristic features of the experimental decay curves, including short and intermediate time power law behavior and long time exponential relaxation, are qualitatively reproduced by the analytical calculations, even though the latter do not explicitly treat orientational degrees of freedom. The GLE formalism with fGn was, in fact, originally proposed as a model of protein conformational fluctuations, so the present results suggest that it may also serve more generally as a model of structural relaxation in complex condensed phase media.


EPL | 2017

Dynamics of end-pulled polymer translocation through a nanopore

Jalal Sarabadani; Bappa Ghosh; Srabanti Chaudhury; Tapio Ala-Nissila

We consider the translocation dynamics of a polymer chain forced through a nanopore by an external force on its head monomer on the trans side. For a proper theoretical treatment we generalize the iso-flux tension propagation (IFTP) theory to include friction arising from the trans side subchain. The theory reveals a complicated scenario of multiple scaling regimes depending on the configurations of the cis and the trans side subchains. In the limit of high driving forces

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Binny J. Cherayil

Indian Institute of Science

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Divya Singh

Indian Institute of Science

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Bappa Ghosh

Indian Institute of Science Education and Research

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Anusheela Das

Indian Institute of Technology Kharagpur

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Alan S. Perelson

Los Alamos National Laboratory

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Dmitrii E. Makarov

University of Texas at Austin

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Jianshu Cao

Massachusetts Institute of Technology

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