Thermodynamics as a nonequilibrium path integral

Sadhukhan, Poulomi; Bhattacharjee, Somendra M.

doi:10.1088/1751-8113/43/24/245001

Cited by 11 publications

(17 citation statements)

References 8 publications

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“…For example, an instantaneous change in force would require a work w = xg if the distance remains fixed at x. Then the histogram transformation in statistical mechanics gives us the free energy difference as [51] …”

Section: Thermodynamic Descriptionmentioning

confidence: 99%

Thermodynamic relations for DNA phase transitions

Sadhukhan

Bhattacharjee

2014

Indian J Phys

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The force induced unzipping transition of a double stranded DNA is considered from a purely thermodynamic point of view. This analysis provides us with a set of relations that can be used to test microscopic theories and experiments. The thermodynamic approach is based on the hypothesis of impenetrability of the force in the zipped state. The melting and the unzipping transitions are considered in the same framework and compared with the existing statistical model results. The analysis is then extended to a possible continuous unzipping transition.

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Section: Thermodynamic Descriptionmentioning

confidence: 99%

Thermodynamic relations for DNA phase transitions

Sadhukhan

Bhattacharjee

2014

Indian J Phys

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“…In a recent work [32], Kapri showed that using the work theorem [33], it is possible to extract the equilibrium force-extension curve from the hysteresis loops. In another work, a dy-namical transition has been proposed, where the area of loop changes with the frequency of the applied force from nearly zero to a finite value, similar to the one seen in case of spin systems [34,35].…”

Section: Introductionmentioning

confidence: 99%

Scaling of hysteresis loop of interacting polymers under a periodic force

Mishra

Giri

et al. 2013

The Journal of Chemical Physics

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Using Langevin Dynamics simulations, we study a simple model of interacting-polymer under a periodic force. The force-extension curve strongly depends on the magnitude of the amplitude (F ) and the frequency (ν) of the applied force. In low frequency limit, the system retraces the thermodynamic path. At higher frequencies, response time is greater than the external time scale for change of force, which restrict the biomolecule to explore a smaller region of phase space that results in hysteresis of different shapes and sizes. We show the existence of dynamical transition, where area of hysteresis loop approaches to a large value from nearly zero area with decreasing frequency. The area of hysteresis loop is found to scale as F α ν β for the fixed length. These exponents are found to be the same as of the mean field values for a time dependent hysteretic response to periodic force in case of the isotropic spin.

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“…The bracket · · · denotes average over all possible paths between A and B. Recently, Sadhukhan and Bhattacharjee [14] have given a dynamics-independent nonequilibrium path integral formulation of the JE that can easily be generalized to cases involving parameters like temperature and interactions. The applicability of JE has been questioned for boundary-switching processes.…”

Section: Introductionmentioning

confidence: 99%

Hysteresis and nonequilibrium work theorem for DNA unzipping

Kapri

2012

Phys. Rev. E

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We study by using Monte Carlo simulations the hysteresis in unzipping and rezipping of a double stranded DNA (dsDNA) by pulling its strands in opposite directions in the fixed force ensemble. The force is increased at a constant rate from an initial value g(0) to some maximum value g(m) that lies above the phase boundary and then decreased back again to g(0). We observed hysteresis during a complete cycle of unzipping and rezipping. We obtained probability distributions of work performed over a cycle of unzipping and rezipping for various pulling rates. The mean of the distribution is found to be close (the difference being within 10%, except for very fast pulling) to the area of the hysteresis loop. We extract the equilibrium force versus separation isotherm by using the work theorem on repeated nonequilibrium force measurements. Our method is capable of reproducing the equilibrium and the nonequilibrium force-separation isotherms for the spontaneous rezipping of dsDNA.

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Thermodynamics as a nonequilibrium path integral

Cited by 11 publications

References 8 publications

Thermodynamic relations for DNA phase transitions

Thermodynamic relations for DNA phase transitions

Scaling of hysteresis loop of interacting polymers under a periodic force

Hysteresis and nonequilibrium work theorem for DNA unzipping

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