Efimov-like phase of a three-stranded DNA and the renormalization-group limit cycle Tanmoy Pal, Poulomi Sadhukhan, Somendra M. Bhattacharjee Physical Review E Statistical Nonlinear and Soft Matter Physics, 2015 A three-stranded DNA with short range base pairings only is known to exhibit a classical analog of the quantum Efimov effect, viz., a three-chain bound state at the two-chain melting point where no two are bound. By using a nonperturbative renormalization-group method for a rigid duplex DNA and a flexible third strand, with base pairings and strand exchange, we show that the Efimov-DNA is associated with a limit cycle type behavior of the flow of an effective three-chain interaction. The analysis also shows that thermally generated bubbles play an essential role in producing the effect. A toy model for the flow equations shows the limit cycle in an extended three-dimensional parameter space of the two-chain coupling and a complex three-chain interaction.
Dynamical phase transition of a periodically driven DNA Garima Mishra, Poulomi Sadhukhan, Somendra M. Bhattacharjee, Sanjay Kumar Physical Review E Statistical Nonlinear and Soft Matter Physics, 2013 Replication and transcription are two important processes in living systems. To execute such processes, various proteins work far away from equilibrium in a staggered way. Motivated by this, aspects of hysteresis during unzipping of DNA under a periodic drive are studied. A steady-state phase diagram of a driven DNA is proposed which is experimentally verifiable. As a two-state system, we also compare the results of DNA with that of an Ising magnet under an asymmetrical variation of the magnetic field.
Renormalization group limit cycle for three-stranded DNA Tanmoy Pal, Poulomi Sadhukhan, Somendra M. Bhattacharjee Physical Review Letters, 2013 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 renormalization group 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.
Signature of special behaviours of 1/r 2 interaction in the quantum entanglement entropy Poulomi Sadhukhan, Somendra M Bhattacharjee Journal of Physics A Mathematical and Theoretical, 2012 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.
Entanglement entropy of a quantum unbinding transition and entropy of DNA Poulomi Sadhukhan, Somendra M. Bhattacharjee Epl, 2012 \n 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 counterintuitive, 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 sub-extensive 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.\n
Type II DNA: When the interfacial energy becomes negative Poulomi Sadhukhan, Jaya Maji, Somendra M. Bhattacharjee Epl, 2011 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.
Thermodynamics as a nonequilibrium path integral Poulomi Sadhukhan, Somendra M Bhattacharjee Journal of Physics A Mathematical and Theoretical, 2010 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.
RECENT SCHOLAR PUBLICATIONS
Multiscale Insights of Domain Unfolding in Fibrin Mechanical Response V Sharma, P Sadhukhan arXiv preprint arXiv:2503.24315 , 2025 2025
Developing an unfolding-incorporated coarse-grained polymer model for fibrinogen to study the mechanical behaviour V Sharma, P Sadhukhan arXiv preprint arXiv:2502.15387 , 2025 2025 Citations: 1
Sector-wise analysis of Indian stock market: Long and short-term risk and stability analysis S Sadhukhan, P Sadhukhan arXiv preprint arXiv:2210.09619 , 2022 2022
Efimov-like phase of a three-stranded DNA and the renormalization-group limit cycle T Pal, P Sadhukhan, SM Bhattacharjee Physical Review E 91 (4), 042105 , 2015 2015 Citations: 13
Thermodynamic relations for DNA phase transitions P Sadhukhan, SM Bhattacharjee Indian Journal of Physics 88, 895-904 , 2014 2014 Citations: 14
Elasto-plastic response of reversibly crosslinked biopolymer bundles P Sadhukhan, O Schumann, C Heussinger The European Physical Journal E 37 (6), 1-9 , 2014 2014 Citations: 6
Dynamical phase transition of a periodically driven DNA G Mishra, P Sadhukhan, SM Bhattacharjee, S Kumar Physical Review E—Statistical, Nonlinear, and Soft Matter Physics 87 (2 … , 2013 2013 Citations: 26
Renormalization Group Limit Cycle for Three-Stranded DNA T Pal, P Sadhukhan, SM Bhattacharjee Physical review letters 110 (2), 028105 , 2013 2013 Citations: 29
Signature of special behaviours of interaction in the quantum entanglement entropy P Sadhukhan, SM Bhattacharjee arXiv preprint arXiv:1207.2755 , 2012 2012 Citations: 7
Entanglement entropy of a quantum unbinding transition and entropy of DNA P Sadhukhan, SM Bhattacharjee Europhysics Letters 98 (1), 10008 , 2012 2012 Citations: 10
Negative entanglement entropy, quantum criticality and DNA P Sadhukhan, SM Bhattacharjee 2011
Type II DNA: When the interfacial energy becomes negative P Sadhukhan, J Maji, SM Bhattacharjee Europhysics Letters 95 (4), 48009 , 2011 2011 Citations: 5
Thermodynamics as a nonequilibrium path integral P Sadhukhan, SM Bhattacharjee Journal of Physics A: Mathematical and Theoretical 43 (24), 245001 , 2010 2010 Citations: 13
MOST CITED SCHOLAR PUBLICATIONS
Renormalization Group Limit Cycle for Three-Stranded DNA T Pal, P Sadhukhan, SM Bhattacharjee Physical review letters 110 (2), 028105 , 2013 2013 Citations: 29
Dynamical phase transition of a periodically driven DNA G Mishra, P Sadhukhan, SM Bhattacharjee, S Kumar Physical Review E—Statistical, Nonlinear, and Soft Matter Physics 87 (2 … , 2013 2013 Citations: 26
Thermodynamic relations for DNA phase transitions P Sadhukhan, SM Bhattacharjee Indian Journal of Physics 88, 895-904 , 2014 2014 Citations: 14
Efimov-like phase of a three-stranded DNA and the renormalization-group limit cycle T Pal, P Sadhukhan, SM Bhattacharjee Physical Review E 91 (4), 042105 , 2015 2015 Citations: 13
Thermodynamics as a nonequilibrium path integral P Sadhukhan, SM Bhattacharjee Journal of Physics A: Mathematical and Theoretical 43 (24), 245001 , 2010 2010 Citations: 13
Entanglement entropy of a quantum unbinding transition and entropy of DNA P Sadhukhan, SM Bhattacharjee Europhysics Letters 98 (1), 10008 , 2012 2012 Citations: 10
Signature of special behaviours of interaction in the quantum entanglement entropy P Sadhukhan, SM Bhattacharjee arXiv preprint arXiv:1207.2755 , 2012 2012 Citations: 7
Elasto-plastic response of reversibly crosslinked biopolymer bundles P Sadhukhan, O Schumann, C Heussinger The European Physical Journal E 37 (6), 1-9 , 2014 2014 Citations: 6
Type II DNA: When the interfacial energy becomes negative P Sadhukhan, J Maji, SM Bhattacharjee Europhysics Letters 95 (4), 48009 , 2011 2011 Citations: 5
Developing an unfolding-incorporated coarse-grained polymer model for fibrinogen to study the mechanical behaviour V Sharma, P Sadhukhan arXiv preprint arXiv:2502.15387 , 2025 2025 Citations: 1
Multiscale Insights of Domain Unfolding in Fibrin Mechanical Response V Sharma, P Sadhukhan arXiv preprint arXiv:2503.24315 , 2025 2025
Sector-wise analysis of Indian stock market: Long and short-term risk and stability analysis S Sadhukhan, P Sadhukhan arXiv preprint arXiv:2210.09619 , 2022 2022
Negative entanglement entropy, quantum criticality and DNA P Sadhukhan, SM Bhattacharjee 2011
