arXiv subjects

Rajarshi Chakrabarti

Publications and source records attributed to Rajarshi Chakrabarti.

41 records · Page 3Linked to original sources

arXiv2011

Dynamics of diffusion controlled chain closure: flexible chain in presence of hydrodynamic interaction

Based on the Wilemski-Fixman approach (J. Chem. Phys. 60, 866 (1974)) we showed that for a flexible chain in theta solvent hydrodynamic interaction treated with an pre-averaging approximation makes ring closing faster if the chain is not very short. Only for a very short chain the ring closing is slower with hydrodynamic interaction on. We have also shown that the ring closing time for a chain with hydrodynamic interaction in theta solvent scales with the chain length (N) as N^(1.527), in good agreement with previous renormalization group calculation based prediction by Freidman et al. (Phys. Rev. A. 40, 5950 (1989)).

cond-mat.soft↗

arXiv2010

Bubble dynamics in double stranded DNA : A Rouse chain based approach

We propose a model for the fluctuation dynamics of the local denaturation zones (bubbles) in double-stranded DNA. In our formulation, the DNA strand is model as a one dimensional Rouse chain confined at both the ends. The bubble is formed when the transverse displacement of the chain attains a critical value. This simple model effectively reproduces the autocorrelation function for the tagged base pair in the DNA strand as measured in the seminal single molecule experiment by Altan-Bonnet et. al (Phys. Rev. Lett. 90, 138101 (2003)). Although our model is mathematically similar to the one proposed by Chatterjee et al. (J. Chem. Phys. 127, 155104 (2007)) it goes beyond a single reaction coordinate description by incorporating the chain dynamics through a confined Rouse chain and thus considers the collective nature of the dynamics. Our model also shows that the autocorrelation function is very sensitive to the relaxation times of the normal modes of the chain, which is obvious since the fluctuation dynamics of the bubble has the contribution from the different normal modes of the chain.

cond-mat.soft↗

arXiv2008

Transient State Work Fluctuation Theorem for a Driven Classical System

We derive the nonequilibrium transient state work fluctuation theorem and also the Jarzynski equality for a classical harmonic oscillator linearly coupled to a harmonic heat bath, which is dragged by an external agent. Coupling with the bath makes the dynamics not only dissipative but also non-Markovian in general. Since we do not assume anything about the spectral nature of the harmonic bath the derivation is not only restricted to the Markovian bath rather it is more general, for a non-Markovian bath.

cond-mat.stat-mech↗

arXiv2007

Diffusion of Macromolecules across the Nuclear Pore Complex

Nuclear pore complexes (NPCs) are very selective filters that monitor the transport between the cytoplasm and the nucleoplasm. Two models have been suggested for the plug of the NPC. They are (i) it is a reversible hydrogel or (ii) it is a polymer brush. We propose a mesoscopic model for the transport of a protein through the plug, that is general enough to cover both. The protein stretches the plug and creates a local deformation. The bubble so created (prtoein+deformation) executes random walk in the plug. We find that for faster relaxation of the gel, the diffusion of the bubble is greater. Further, on using parameters appropriate for the brush, we find that the diffusion coefficient is much lower. Hence the gel model seems to be more likely explanation for the workings of the plug.

cond-mat.soft↗

arXiv2007

Exact analytical evaluation of time dependent transmission coefficient from the method of reactive flux for an inverted parabolic barrier

In this paper we derive a general expression for the transmission coefficient using the method of reactive flux for a particle coupled to a harmonic bath surmounting a one dimensional inverted parabolic barrier. Unlike Kohen and Tannor [J. Chem. Phys. 103, 6013 (1995)] we use a normal mode analysis where the unstable and the other modes have a complete physical meaning. Importantly our approach results a very general expression for the time dependent transmission coefficient not restricted to overdamped limit. Once the spectral density for the problem is know one can use our formula to evaluate the time dependent transmission coefficient. We have done the calculations with time dependent friction used by Xie [Phys. Rev. Lett 93, 180603 (2004)] and also the one used by Kohen and Tannor [J. Chem. Phys. 103, 6013 (1995)]. Like the formula of Kohen and Tannor our formula also reproduces the results of transition state theory as well as the Kramers theory in the limits t->0 and t->infinity respectively.

cond-mat.stat-mech↗