Dynamical phase transition of a periodically driven DNA

Mishra, Garima; Sadhukhan, Poulomi; Bhattacharjee, Somendra M.; Kumar, Sanjay

doi:10.1103/physreve.87.022718

Cited by 20 publications

(38 citation statements)

References 39 publications

(59 reference statements)

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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]. In low frequency limit, for a short DNA (16 base pairs), the scaling exponents (α and β) are found to be the same as of the isotropic spin system.…”

Section: Introductionmentioning

confidence: 76%

“…For example, if half of a polymer chain is allowed to interact with the other half of a chain, in such a way that the first monomer interacts only with the N th monomer (last one), and the second monomer interacts with the (N − 1) th and so, the ground state conformation resembles a zipped conformation of DNA of N p (= N/2) base pairs as shown in Fig. 1a [34,35,43,48]. Similarly, if any monomer of the chain is allowed to interact with the rest of non-bonded monomers of the polymer chain, the ground state will resemble the globule (collapsed) state of a self-interacting polymer [36].…”

Section: Model and Methodsmentioning

confidence: 99%

“…1. The value of f increases to its maximum value F in m s steps at interval ∆f (= 0.01) and then decreases to 0 in the same way [34,35]. Since, we are interested in the non-equilibrium regime, we allow only n LD time steps (much below the equilibrium time) in each increment of ∆f .…”

Section: Dynamical Transition At Finite Temperaturementioning

confidence: 99%

“…In this context, it is pertinent to mention here that in Ref. [34], modeling of DNA involves a single polymer chain with native interaction (base pairing) as shown in Fig. 1a.…”

Section: Introductionmentioning

confidence: 99%

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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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Section: Introductionmentioning

confidence: 76%

Section: Model and Methodsmentioning

confidence: 99%

Section: Dynamical Transition At Finite Temperaturementioning

confidence: 99%

“…In this context, it is pertinent to mention here that in Ref. [34], modeling of DNA involves a single polymer chain with native interaction (base pairing) as shown in Fig. 1a.…”

Section: Introductionmentioning

confidence: 99%

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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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“…In the case if the mismatch repair system does not work properly cell may die [16]. Mathematically one can model the replication as the force applied on an end of the DNA chain [33]. Physics of opening of chain due to thermal fluctuation and mechanical forces is completely different [34][35][36].…”

Section: Force Induced Transitionsmentioning

confidence: 99%

Pulling short DNA molecules having defects on different locations

Singh

2015

Phys. Rev. E

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We present a study on the role of defects on the stability of short DNA molecules. We consider short DNA molecules (16 base pairs) and investigate the thermal as well as mechanical denaturation of these molecules in the presence of defects that occurs anywhere in the molecule. For the investigation, we consider four different kinds of chains. Not only the ratio of AT to GC different in these molecules but also the distributions of AT and GC along the molecule are different. With suitable modifications in the statistical model to show the defect in a pair, we investigate the denaturation of short DNA molecules in thermal as well as constant force ensemble. In the force ensemble, we pulled the DNA molecule from each end (keeping other end free) and observed some interesting features of opening of the molecule in the presence of defects in the molecule. We calculate the probability of opening of the DNA molecule in the constant force ensemble to explain the opening of base pairs and hence the denaturation of molecules in the presence of defects.

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Differential stability of DNA based on salt concentration

Maity

Singh

2016

Eur Biophys J

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Intracellular positive ions neutralize negative charges on the phosphates of a DNA strand, conferring greater strength on the hydrogen bonds that connect complementary strands into a double helix and so confer enhanced stability. Beyond a certain value of salt concentration, the DNA molecule displays an unstable nature in vivo as well as in vitro. We consider a wide range of salt concentrations and study the stability of the DNA double helix using a statistical model. Through numerical calculations, we attempt to explain the different behavior exhibited by DNA molecules in this range. We compare our results with experimental data and find a close agreement.

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Dynamical phase transition of a periodically driven DNA

Cited by 20 publications

References 39 publications

Scaling of hysteresis loop of interacting polymers under a periodic force

Scaling of hysteresis loop of interacting polymers under a periodic force

Pulling short DNA molecules having defects on different locations

Differential stability of DNA based on salt concentration

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