arXiv subjects

Somendra M. Bhattacharjee

Publications and source records attributed to Somendra M. Bhattacharjee.

At least 37 records · Page 2Linked to original sources

arXiv2012

TYPE II DNA: when the interfacial energy becomes negative

An important step in transcription of a DNA base sequence to a protein is the initiation from the exact starting point, called promoter region. We propose a physical mechanism for identification of the promoter region, which relies on a new classification of DNAs into two types, Type-I and Type-II, like superconductors, depending on the sign of the energy of the interface separating the zipped and the unzipped phases. This is determined by the energies of helical ordering and stretching over two independent length scales. The negative interfacial energy in Type II DNA leads to domains of helically ordered state separated by defect regions, or blobs, enclosed by the interfaces. The defect blobs, pinned by non-coding promoter regions, would be physically distinct from all other types of bubbles. We also show that the order of the melting transition under a force is different for Type I and Type II.

cond-mat.stat-mech↗

arXiv2012

Renormalization Group Limit Cycle for Three-Stranded DNA

We show that there exists an Efimov-like three strand DNA bound state at the duplex melting point and it is described by a renormalization group limit cycle. A nonperturbative RG is used to obtain this result in a model involving short range pairing only. Our results suggest that Efimov physics can be tested in polymeric systems.

cond-mat.soft↗

arXiv2012

Efimov effect of triple-stranded DNA: Real-space renormalization group and Zeros of the partition function

We study the melting of three-stranded DNA by using the real-space renormalization group and exact recursion relations. The prediction of an unusual Efimov-analog three-chain bound state, that appears at the critical melting of two-chain DNA, is corroborated by the zeros of the partition function. The distribution of the zeros has been studied in detail for various situations. We show that the Efimov DNA can occur even if the three-chain (i. e., three-monomer) interaction is repulsive in nature. In higher dimensions, a striking result that emerged in this repulsive zone is a continuous transition from the critical state to the Efimov DNA.

cond-mat.stat-mech↗

arXiv2012

Signature of special behaviours of $1/r^2$ interaction in the quantum entanglement entropy

We study the bipartite von Neumann entropy of two particles interacting via a long-range scale-free potential $V(r)\sim -g/r^2$ in three dimensions, close to the unbinding transition. The nature of the quantum phase transition changes from critical ($-3/4<g<1/4$) to first order ($g<-3/4$) with $g=-3/4$ as a multicritical point. Here we show that the entanglement entropy has different behaviours for the critical and the first order regimes. But still there exists an interesting multicritical scaling behaviour for all $g\in (-2<g<1/4)$ controlled by the $g=-3/4$ case.

cond-mat.stat-mech↗

arXiv2012

Entanglement entropy of a quantum unbinding transition and entropy of DNA

Two significant consequences of quantum fluctuations are entanglement and criticality. Entangled states may not be critical but a critical state shows signatures of universality in entanglement. A surprising result found here is that the entanglement entropy may become arbitrarily large and negative near the dissociation of a bound pair of quantum particles. Although apparently counter-intuitive, it is shown to be consistent and essential for the phase transition, by mapping to a classical problem of DNA melting. We associate the entanglement entropy to a subextensive part of the entropy of DNA bubbles, which is responsible for melting. The absence of any extensivity requirement in time makes this negative entropy an inevitable consequence of quantum mechanics in continuum. Our results encompass quantum critical points and first-order transitions in general dimensions.

cond-mat.stat-mech↗

arXiv2010

Dynamic phase transition in the conversion of B-DNA to Z-DNA

The long time dynamics of the conformational transition from B-DNA to Z-DNA is shown to undergo a dynamic phase transition. We obtained the dynamic phase diagram for the stability of the front separating B and Z. The instability in this front results in two split fronts moving with different velocities. Hence, depending on the system parameters a denatured state may develop dynamically eventhough it is thermodynamically forbidden. This resolves the current controversies on the transition mechanism of the B-DNA to Z-DNA.

cond-mat.soft↗

arXiv2010

When a DNA Triple helix melts: An analog of the Efimov state

The base sequences of DNA contain the genetic code and to decode it a double helical DNA has to open its base pairs. Recent studies have shown that one can use a third strand to identify the base sequences without opening the double helix but by forming a triple helix. It is predicted here that such a three chain system exhibits the unusual behaviour of the existence of a three chain bound state in the absence of any two being bound. This phenomenon is analogous to the Efimov state in three particle quantum mechanics. A scaling theory is used to justify the Efimov connection. Real space renormalization group (RG), and exact numerical calculations are used to validate the prediction of a biological Efimov effect.

cond-mat.soft↗

arXiv2010

Thermodynamics as a nonequilibrium path integral

Thermodynamics is a well developed tool to study systems in equilibrium but no such general framework is available for non-equilibrium processes. Only hope for a quantitative description is to fall back upon the equilibrium language as often done in biology. This gap is bridged by the work theorem. By using this theorem we show that the Barkhausen-type non-equilibrium noise in a process, repeated many times, can be combined to construct a special matrix ${\cal S}$ whose principal eigenvector provides the equilibrium distribution. For an interacting system ${\cal S}$, and hence the equilibrium distribution, can be obtained from the free case without any requirement of equilibrium.

cond-mat.stat-mech↗

arXiv2009

Interfacial instability and DNA fork reversal by repair proteins

A repair protein like RecG moves the stalled replication fork in the direction from the zipped to the unzipped state of DNA. It is proposed here that a softening of the zipped-unzipped interface at the fork results in the front propagating towards the unzipped side. In this scenario, an ordinary helicase destabilizes the zipped state locally near the interface and the fork propagates towards the zipped side. The softening of the interface can be produced by the aromatic interaction, predicted from crystal structure, between RecG and the nascent broken base pairs at the Y-fork. A numerical analysis of the model also reveals the possibility of a stop and go type motion.

cond-mat.soft↗

arXiv2008

Manipulating a single adsorbed DNA for a critical endpoint

We show the existence of a critical endpoint in the phase diagram of unzipping of an adsorbed double-stranded (ds) polymer like DNA. The competition of base pairing, adsorption and stretching by an external force leads to the critical end point. From exact results, the location of the critical end point is determined and its classical nature established.

cond-mat.soft↗

arXiv2008

Nonequilibrium tricriticality in one dimension

We show the existence of a nonequilibrium tricritical point induced by a repulsive interaction in one dimensional asymmetric exclusion process. The tricritical point is associated with the particle-hole symmetry breaking introduced by the repulsion. The phase diagram and the crossover in the neighbourhood of the tricritical point for the shock formation at one of the boundaries are determined.

cond-mat.stat-mech↗

arXiv2007

Randomly forced DNA

We study the effect of random forces on a double stranded DNA in unzipping the two strands, analogous to the problem of an adsorbed polymer under a random force. The ground state develops bubbles of various lengths as the random force fluctuation is increased. The unzipping phase diagram is shown to be drastically different from the pure case.

cond-mat.soft↗

arXiv2006

Duality and phase diagram of one dimensional transport

The observation of duality by Mukherji and Mishra in one dimensional transport problems has been used to develop a general approach to classify and characterize the steady state phase diagrams. The phase diagrams are determined by the zeros of a set of coarse-grained functions without the need of detailed knowledge of microscopic dynamics. In the process, a new class of nonequilibrium multicritical points has been identified.

cond-mat.stat-mech↗

arXiv2005

Unzipping DNA by force: thermodynamics and finite size behaviour

We discuss the thermodynamic behaviour near the force induced unzipping transition of a double stranded DNA in two different ensembles. The Y-fork is identified as the coexisting phases in the fixed distance ensemble. From finite size scaling of thermodynamic quantities like the extensibility, the length of the unzipped segment of a Y-fork, the phase diagram can be recovered. We suggest that such procedures could be used to obtain the thermodynamic phase diagram from experiments on finite length DNA.

cond-mat.soft↗

arXiv2005

Unzipping an adsorbed polymer in a dirty or random environment

The phase diagram of unzipping of an adsorbed directed polymer in two dimensions in a random medium has been determined. Both the hard-wall and the soft-wall cases are considered. Exact solutions for the pure problem with different affinities on the two sides are given. The results obtained by the numerical procedure adopted here are shown to agree with the exact results for the pure case. The characteristic exponents for unzipping for the random problem are different from the pure case. The distribution functions for the unzipped length, first bubble, and the spacer are determined.

cond-mat.stat-mech↗

arXiv2005

Is small-world network disordered?

Recent renormalization group results predict non self averaging behaviour at criticality for relevant disorder. However, we find strong self averaging(SA) behaviour in the critical region of a quenched Ising model on an ensemble of small-world networks, despite the relevance of the random bonds at the pure critical point.

cond-mat.dis-nn↗

arXiv2005

Directed polymers and Randomness

The effects of two types of randomness on the behaviour of directed polymers are discussed in this chapter. The first part deals with the effect of randomness in medium so that a directed polymer feels a random external potential. The second part deals with the RANI model of two directed polymers with heterogeneity along the chain such that the interaction is random. The random medium problem is better understood compared to the RANI model.

cond-mat.stat-mech↗

arXiv2005

Nonequilibrium Criticality at Shock Formation in Steady States

The steady state shock formation in processes like nonconserving asymmetric simple exclusion processes in varied situations is shown to be a nonequilibrium critical phenomenon. The diverging length scales and the quantitative description of the transition including the phase boundary are obtained from a few general properties of the dynamics without relying on specific details.

cond-mat.stat-mech↗