arXiv subjects

D. Giri

Publications and source records attributed to D. Giri.

10 recordsLinked to original sources

arXiv2015

On the rupture of DNA molecule

Using Langevin Dynamic simulations, we study effects of the shear force on the rupture of a double stranded DNA molecule. The model studied here contains two single diblock copolymers interacting with each other. The elastic constants of individual segments of the diblock copolymer are considered to be different. We showed that the magnitude of the rupture force depends on whether the force is applied at $3'-3'-$ends or $5'-5'-$ends. Distributions of extension in hydrogen bonds and covalent bonds along the chain show the striking differences. Motivated by recent experiments, we have also calculated the variation of rupture force for different chain lengths. Results obtained from simulations have been validated with the analytical calculation based on the ladder model of DNA.

cond-mat.soft↗

arXiv2013

Statistical Mechanics of DNA Rupture: Theory and Simulations

We study the effects of the shear force on the rupture mechanism on a double stranded DNA. Motivated by recent experiments, we perform the atomistic simulations with explicit solvent to obtain the distributions of extension in hydrogen and covalent bonds below the rupture force. We obtain a significant difference between the atomistic simulations and the existing results in the iterature based on the coarse-grained models (theory and simulations). We discuss the possible reasons and improve the coarse-grained model by incorporating the consequences of semi-microscopic details of the nucleotides in its description. The distributions obtained by the modified model (simulations and theoretical) are qualitatively similar to the one obtained using atomistic simulations.

cond-mat.soft↗

arXiv2011

Role of loop entropy in the force induced melting of DNA hairpin

Dynamics of a single stranded DNA, which can form a hairpin have been studied in the constant force ensemble. Using Langevin dynamics simulations, we obtained the force-temperature diagram, which differs from the theoretical prediction based on the lattice model. Probability analysis of the extreme bases of the stem revealed that at high temperature, the hairpin to coil transition is entropy dominated and the loop contributes significantly in its opening. However, at low temperature, the transition is force driven and the hairpin opens from the stem side. It is shown that the elastic energy plays a crucial role at high force. As a result, the phase diagram differs significantly with the theoretical prediction.

cond-mat.soft↗

arXiv2009

Force induced melting of the constrained DNA

We develop a simple model to study the effects of an applied force on the melting of a double stranded DNA (dsDNA). Using this model, we could study the stretching, unzipping, rupture and slippage like transition in a dsDNA. We show that in absence of an applied force, the melting temperature and the melting profile of dsDNA strongly depend on the constrained imposed on the ends of dsDNA. The nature of the phase boundary which separates the zipped and the open state for the shearing like transition is remarkably different than the DNA unzipping

cond-mat.soft↗

arXiv2008

Role of pulling direction in understanding the energy landscape of proteins

Single molecule force spectroscopy provide details of the underlying energy surfaces of proteins which are essential to the understanding of their unfolding process. Recently, it has been observed experimentally that by pulling proteins in different directions relative to their secondary structure, one can gain a better understanding of the shape of the energy landscape. We consider simple lattice models which are anisotropic in nature to study the response of a force in unfolding of a polymer. Our analytical solution of the model, supported by extensive numerical calculations, reveal that the force temperature diagrams are very different depending on the direction of the applied force. We find that either unzipping or shearing kind transitions dominate the dynamics of the unfolding process depending solely on the direction of the applied force.

cond-mat.stat-mech↗

arXiv2002

Does a surface attached globule phase exist ?

A long flexible neutral polymer chain immersed in a poor solvent and interacting with an impenetrable attractive surface exhibits a phase known as surface attached globule ({\bf SAG}) in addition to other adsorbed and desorbed phases. In the thermodynamic limit, the {\bf SAG} phase has the same free energy per monomer as the globular phase, and the transition between them is a surface transition. We have investigated the phase diagrams of such a chain in both two- and three- dimensions and calculated the distribution of monomers in different domains of the phase diagram.

cond-mat.stat-mech↗

arXiv2000

Multifractal Behaviour of n-Simplex Lattice

We study the asymptotic behaviour of resistance scaling and fluctuation of resistance that give rise to flicker noise in an {\em n}-simplex lattice. We propose a simple method to calculate the resistance scaling and give a closed-form formula to calculate the exponent, $β_L$, associated with resistance scaling, for any n. Using current cumulant method we calculate the exact noise exponent for n-simplex lattices.

cond-mat.stat-mech↗

arXiv1997

Sandpile Model with Activity Inhibition

A new sandpile model is studied in which bonds of the system are inhibited for activity after a certain number of transmission of grains. This condition impels an unstable sand column to distribute grains only to those neighbours which have toppled less than m times. In this non-Abelian model grains effectively move faster than the ordinary diffusion (super-diffusion). A novel system size dependent cross-over from Abelian sandpile behaviour to a new critical behaviour is observed for all values of the parameter m.

cond-mat.stat-mech↗

arXiv1996

Evolution of the electronic structure of cyclic polythiophene upon bipolaron doping

Electronic structures of undoped and doped cyclic polythiophene (PT) are studied using modified $σ$-bond compressibility model. Cyclic PT doped with odd number of bipolarons creates an aromatic polyene backbone containing (4$n$+2) $π$-electrons and the system is driven towards the quinoid form. Consequently, we find an insulator-metal transition for dopant concentration $\geq$ 14 mol $\%$ and a $\sim$ 0.8 eV redshift in Fermi energy at 30 mol$\%$. For even number of bipolarons, we propose here that the form having two singly occupied degenerate orbitals will be stable in a sufficiently large cyclic PT.

cond-mat↗

arXiv1996

A study of one dimensional correlated disordered systems using invariant measure method

The behavior of electronic states of one dimensional correlated disordered systems which are modelled by a tight binding Hamiltonian is studied analytically using the invariant measure method. The approach of Bovier is generalized to include the possibility of different site energies and nearest neighbor hopping integrals inside the correlated sites or the cluster. The process is further elaborated by applying to the symmetric random trimer model which contains in it many hitherto known models of this category. An alternative mathematical definition of the exceptional energy ($E_S$) from the invariant measure density along with physical arguments substantiating it is presented. Furthermore, the procedure for obtaining exceptional energies is outlined and applied to the symmetric random trimer model to derive conditions for obtaining doubly degenerate exceptional energies. The Lyapunov exponent ($γ(E)$) or the inverse localization length of states around the exceptional energy is found to vary as $\sim (E - E_S)^{2n}$ in the leading order. $n$ denotes the degeneracy of the exceptional energy. The density of states at the exceptional energies are calculated. We further propose that one dimensional correlated disordered systems can be mapped to a Lloyd model in which the width of the distribution of site energies is determined by the reflection coefficient of the cluster embedded in the lattice of the another constituent. The importance of our results is discussed.

cond-mat↗