arXiv subjects

Sanjay Kumar

Publications and source records attributed to Sanjay Kumar.

At least 109 records · Page 6Linked to original sources

arXiv2013

A note on Schwarzian derivatives and normal families

We establish a criterion for local boundedness and hence normality of a family $\F$ of analytic functions on a domain $D$ in the complex plane whose corresponding family of derivatives is locally bounded. Furthermore we investigate the relation between domains of normality of a family $\F$ of meromorphic functions and its corresponding Schwarzian derivative family. We also establish some criterion for the Schwarzian derivative family of a family $\F$ of analytic functions on a domain $D$ in the complex plane to be a normal family.

math.DS↗

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

Effect of shear force on the separation of double stranded DNA

Using the Langevin Dynamics simulation, we have studied the effects of the shear force on the rupture of short double stranded DNA at different temperatures. We show that the rupture force increases linearly with the chain length and approaches to the asymptotic value in accordance with the experiment. The qualitative nature of these curves almost remains same for different temperatures but with a shift in the force. We observe three different regimes in the extension of covalent bonds (back bone) under the shear force.

cond-mat.soft↗

arXiv2012

Escaping Set of e^z-1

We investigate the set I(f) of points that converge to infinity under iteration of the map f(z) = e^z-1 and show that it is the disjoint union of countably many rays and uncountable union of infinite sets whose points escape to infinity through the sets.

math.DS↗

arXiv2012

Stretching force dependent transitions in single stranded DNA

Mechanical properties of DNA, in particular their stretch dependent extension and their loop formation characteristics, have been recognized as an effective probe for understanding the possible biochemical role played by them in a living cell. Single stranded DNA (ssDNA), which, till recently was presumed to be an simple flexible polymer continues to spring surprises. Synthetic ssDNA, like polydA (polydeoxyadenosines) has revealed an intriguing force-extension (FX) behavior exhibiting two plateaus, absent in polydT (polydeoxythymidines) for example. Loop closing time in polydA had also been found to scale exponentially with inverse temperature, unexpected from generic models of homopolymers. Here we present a new model for polydA which incorporates both a helix-coil transition and a over-stretching transition, accounting for the two plateaus. Using transfer matrix calculation and Monte-Carlo simulation we show that the model reproduces different sets of experimental observations, quantitatively. It also predicts interesting reentrant behavior in the temperature-extension characteristics of polydA, which is yet to be verified experimentally.

cond-mat.soft↗

arXiv2010

Shock-driven hydrodynamic instability induced by particle seeding

We report an experimental observation of an instability in gas of constant density (air) with an initial non-uniform seeding of small droplets that develops as a planar shock wave passes through the gas-droplet mix. The seeding non-uniformity is produced by vertical injection of a slow-moving jet of air pre-mixed with glycol droplets into the test section of a shock tube, with the plane of the shock parallel to the axis of the jet. After the shock passage, we observe development of two counter-rotating vortices in the plane normal to that axis. The physical mechanism of the instability we observe is peculiar to multiphase flow, where the shock acceleration causes the second (embedded) phase to move with respect to the embedding medium. With sufficient seeding concentration, this leads to entrainment of the embedding phase that acquires a relative velocity dependent on the initial seeding, resulting in vortex formation in the flow.

physics.flu-dyn↗

arXiv2009

Force induced unfolding of bio-polymers in a cellular environment: A model study

Effect of molecular crowding and confinement experienced by protein in the cell during unfolding has been studied by modeling a linear polymer chain on a percolation cluster. It is known that internal structure of the cell changes in time, however, they do not change significantly from their initial structure. In order to model this we introduce the correlation among the different disorder realizations. It was shown that the force-extension behavior for correlated disorder in both constant force ensemble (CFE) and constant distance ensemble (CDE) is significantly different than the one obtained in absence of molecular crowding.

cond-mat.soft↗

arXiv2009

Stretching of a single-stranded DNA: Evidence for structural transition

Recent experiments have shown that the force-extension (F-x) curve for single-stranded DNA (ssDNA) consisting only of adenine [poly(dA)] is significantly different from thymine [poly(dT)]. Here, we show that the base stacking interaction is not sufficient to describe the F-x curves as seen in the experiments. A reduction in the reaction co-ordinate arising from the formation of helix at low forces and an increase in the distance between consecutive phosphates of unstacked bases in the stretched state at high force in the proposed model, qualitatively reproduces the experimentally observed features. The multi-step plateau in the F-x curve is a signature of structural change in ssDNA.

cond-mat.soft↗

arXiv2009

Effects of Molecular Crowding on stretching of polymers in poor solvent

We consider a linear polymer chain in a disordered environment modeled by percolation clusters on a square lattice. The disordered environment is meant to roughly represent molecular crowding as seen in cells. The model may be viewed as the simplest representation of biopolymers in a cell. We show the existence of intermediate states during stretching arising as a consequence of molecular crowding. In the constant distance ensemble the force-extension curves exhibit oscillations. We observe the emergence of two or more peaks in the probability distribution curves signaling the coexistence of different states and indicating that the transition is discontinuous unlike what is observed in the absence of molecular crowding.

cond-mat.stat-mech↗

arXiv2009

Can re-entrance be observed in force induced transitions?

A large conformational change in the reaction co-ordinate and the role of the solvent in the formation of base-pairing are combined to settle a long standing issue {\it i.e.} prediction of re-entrance in the force induced transition of DNA. A direct way to observe the re-entrance, i.e a strand goes to the closed state from the open state and again to the open state with temperature, appears difficult to be achieved in the laboratory. An experimental protocol (in direct way) in the constant force ensemble is being proposed for the first time that will enable the observation of the re-entrance behavior in the force-temperature plane. Our exact results for small oligonucleotide that forms a hairpin structure provide the evidence that re-entrance can be observed.

cond-mat.soft↗

arXiv2008

Force induced stretched state: Effects of temperature

A model of self avoiding walks with suitable constraint has been developed to study the effect of temperature on a single stranded DNA (ssDNA) in the constant force ensemble. Our exact calculations for small chains show that the extension (reaction co-ordinate) may increase or decrease with the temperature depending upon the applied force. The simple model developed here which incorporates semi-microscopic details of base direction provide an explanation of the force induced transitions in ssDNA as observed in experiments.

cond-mat.stat-mech↗

arXiv2007

Modeling force-induced bio-polymer unfolding

We study the conformations of polymer chains in a poor solvent, with and without bending rigidity, by means of a simple statistical mechanics model. This model can be exactly solved for chains of length up to N=55 using exact enumeration techniques. We analyze in details the differences between the constant force and constant distance ensembles for large but finite N. At low temperatures, and in the constant force ensemble, the force-extension curve shows multiple plateaus (intermediate states), in contrast with the abrupt transition to an extended state prevailing in the $N \to \infty$ limit. In the constant distance ensemble, the same curve provides a unified response to pulling and compressing forces, and agrees qualitatively with recent experimental results. We identify a cross-over length, proportional to $N$, below which the critical force of unfolding decreases with temperature, while above, it increases wiyh temperature. Finally, the force-extension curve for stiff chains exhibits "saw-tooth" like behavior, as observed in protein unfolding experiments.

cond-mat.stat-mech↗

arXiv2007

Weighted composition operators on weighted Bergman spaces of bounded symmetric domains

In this paper, we study the weighted compositon operators on weighted Bergman spaces of bounded symmetric domains. The necessary and sufficient conditions for a weighted composition operator $W_{ϕ,ψ}$ to be bounded and compact are studied by using the Carleson measure techniques. In the last section, we study the Schatten p-class weighted composition operators.

math.FA↗

arXiv2007

Force induced conformational transition in a system of interacting stiff polymer: Application to unfolding

We consider a stiff polymer chain in poor solvent and apply a force at one end of the chain. We find that by varying the stiffness parameter, polymer undergoes a transition from the globule state to the folded like state. The conformation of folded state mimics the $β$-sheet as seen in titin molecule. Using exact enumeration technique, we study the extension-force and force-temperature diagrams of such a system. Force-temperature diagram shows the re-entrance behaviour for flexible chain. However, for stiff chain this re-entrance behaviour is absent and there is an enhancement in $θ$-temperature with the rise of stiffness. We further propose that the internal information about the frozen structure of polymer can be read from the distribution of end-to-end distance which shows saw-tooth like behaviour.

cond-mat.soft↗

arXiv2007

Effects of Eye-phase in DNA unzipping

The onset of an "eye-phase" and its role during the DNA unzipping is studied when a force is applied to the interior of the chain. The directionality of the hydrogen bond introduced here shows oscillations in force-extension curve similar to a "saw-tooth" kind of oscillations seen in the protein unfolding experiments. The effects of intermediates (hairpins) and stacking energies on the melting profile have also been discussed.

cond-mat.soft↗

arXiv2007

Role of conformational entropy in force-induced bio-polymer unfolding

A statistical mechanical description of flexible and semi-flexible polymer chains in a poor solvent is developed in the constant force and constant distance ensembles. We predict the existence of many intermediate states at low temperatures stabilized by the force. A unified response to pulling and compressing forces has been obtained in the constant distance ensemble. We show the signature of a cross-over length which increases linearly with the chain length. Below this cross-over length, the critical force of unfolding decreases with temperature, while above, it increases with temperature. For stiff chains, we report for the first time "saw-tooth" like behavior in the force-extension curves which has been seen earlier in the case of protein unfolding.

cond-mat.soft↗

arXiv2007

Does changing the pulling direction give better insight into biomolecules?

Single molecule manipulation techniques reveal that the mechanical resistance of a protein depends on the direction of the applied force. Using a lattice model of polymers, we show that changing the pulling direction leads to different phase diagrams. The simple model proposed here indicates that in one case the system undergoes a transition akin to the unzipping of a $β$ sheet, while in the other case the transition is of a shearing (slippage) nature. Our results are qualitatively similar to experimental results. This demonstrates the importance of varying the pulling direction since this may yield enhanced insights into the molecular interactions responsible for the stability of biomolecules.

cond-mat.stat-mech↗

arXiv2007

Collapse Transition of Two-Dimensional Flexible and Semiflexible Polymers

The nature of the globule-coil transition of surface-confined polymers has been an issue of debate. Here this 2D collapse transition is studied through a partially directed lattice model. In the general case of polymers with positive bending stiffness ($Δ>0$), the collapse transition is {\em first-order}; it becomes {\em second-order} only in the limiting case of zero bending stiffness ($Δ\equiv 0$). These analytical results are confirmed by Monte Carlo simulations. We also suggest some possible future experiments.

cond-mat.soft↗