arXiv subjects

Poulomi Sadhukhan

Publications and source records attributed to Poulomi Sadhukhan.

12 recordsLinked to original sources

arXiv2025

Multiscale Insights of Domain Unfolding in Fibrin Mechanical Response

Fibrinogen, the monomeric unit of fibrin, the main constituent of blood clot, has a very complex structure. The fibrinogen builds the fibrin fiber and network through the half-staggered packing via knob-hole interaction and the $α$C crosslinkers. Due to its rich structure, the elastic behavior also shows a unique nature of very high stretchability and multiple regimes in stress-strain behaviour, which is not yet fully understood. We develop an Unfolding-incorporated Coarse-Grained Polymer (UCGP) model for fibrinogen to study the effect of domain unfolding on the mechanical behavior of fibrin fiber and network. Our model captures the stretching behavior of fibrinogen as observed in AFM and all-atom simulations. We further extend our model to fibrin fiber to study the effect of molecular unfolding at the fiber and network level. We anticipate that our model will be able to account for the nonlinear mechanical behavior of crosslinked fibrin gel. It is possibly the first model of this sort to consider the precise, controllable knowledge of the effects of domain unfolding in crosslinked proteins. This model can also be used to model systems that have sacrificial bonds.

cond-mat.soft↗

arXiv2025

Developing an unfolding-incorporated coarse-grained polymer model for fibrinogen to study the mechanical behaviour

Fibrinogen is a protein found in blood that forms Fibrin polymer network to build a clot during wound healing process when there is a cut in the blood vessel. The fibrin fiber is highly stretchable and shows a complex mechanical properties. The fibrin monomer, Fibrinogen, has a very complex structure which is responsible for its unusual elastic behaviour. In this work, we focus on mechanism of unfolding of D-domain of Fibrinogen, and study its effect in the mechanical behaviour. We develop a coarse-grained (CG) bead-spring model for Fibrinogen which captures the unfolding of folded D-domains along with other necessary structural properties which affect the mechanical behaviour. The results from our unfolding-incorporated coarse-grained polymer (UCGP) model matches with the experimental results. This model has capacity to serve as the minimal unit to build a large-scale hierarchical structure of fibrin fiber and network to possibly unfold the mystery of fibrin's unusual elastic behaviour. This model can also be used for other polymers having folded domains or sacrificial bonds.

cond-mat.soft↗

arXiv2022

Sector-wise analysis of Indian stock market: Long and short-term risk and stability analysis

This paper, for the first time, focuses on the sector-wise analysis of a stock market through multifractal analysis. We have considered Bombay Stock Exchange, India, and identified two time scales, short ($<200$ days) and long time-scale ($>200$ days) for investment. We infer that long-term investment will be more profitable. For long time scale, sectors can be separated into two categories based on the Hurst exponent values; one corresponds to stable sectors with small fluctuations, and the other with dominance of large fluctuations leading to possible downturns in those sectors.

q-fin.ST↗

arXiv2015

Efimov like phase of a three stranded DNA (Efimov-DNA) and the renormalization group limit cycle

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 non-perturbative 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.

cond-mat.soft↗

arXiv2014

Elasto-plastic response of reversibly crosslinked biopolymer bundles

We study the response of F-actin bundles to driving forces through a simple analytical model. We consider two filaments connected by reversibly bound crosslinks and driven by an external force. Two failure modes under load can be defined. \textit{Brittle failure} is observed when crosslinks suddenly and collectively unbind, leading to catastrophic loss of bundle integrity. During \textit{ductile failure}, on the other hand, bundle integrity is maintained, however at the cost of crosslink reorganization and defect formation. We present phase diagrams for the onset of failure, highlighting the importance of the crosslink stiffness for these processes. Crossing the phase boundaries, force-deflection curves display (frequency-dependent) hysteresis loops, reflecting the first-order character of the failure processes. We evidence how the introduction of defects can lead to complex elasto-plastic relaxation processes, once the force is switched off. Depending on, both, the time-scale for defect motion as well as the crosslink stiffness, bundles can remain in a quasi-permanent plastically deformed state for a very long time.

cond-mat.soft↗

arXiv2014

Thermodynamic relations for DNA phase transitions

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.

cond-mat.soft↗

arXiv2013

Dynamical phase transition of a periodically driven DNA

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 in non-equilibrium conditions 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 magnetic field.

cond-mat.soft↗

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

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

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↗