Single polymer gating of channels under a solvent gradient

We study the effect of a gradient of solvent quality on the coil-globule transition for a polymer in a narrow pore. A simple self-attracting self-avoiding walk model of a polymer in solution shows that the variation in the strength of interaction across the pore leads the system to go from one regime (good solvent) to the other (poor solvent) across the channel. This may be thought analogous to thermophoresis, where the polymer goes from the hot region to the cold region under the temperature gradient. The behavior of short chains is studied using exact enumeration whilst the behavior of long chains is studied using transfer matrix techniques. The distribution of the monomer density across the layer suggests that a gate-like effect can be created, with potential applications as a sensor.Comment: 5 Pages, 7 Figures, Accepted in Phys. Rev. E (2013

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.Comment: 18 pages, 9 figures. Accepted in J. Chem. Phys. (2013). arXiv admin note: text overlap with arXiv:1104.305

Quantum oscillator on complex projective space (Lobachewski space) in constant magnetic field and the issue of generic boundary conditions

We perform a 1-parameter family of self-adjoint extensions characterized by the parameter $\omega_0$. This allows us to get generic boundary conditions for the quantum oscillator on $N$ dimensional complex projective space($\mathbb{C}P^N$) and on its non-compact version i.e., Lobachewski space($\mathcal L_N$) in presence of constant magnetic field. As a result, we get a family of energy spectrums for the oscillator. In our formulation the already known result of this oscillator is also belong to the family. We have also obtained energy spectrum which preserve all the symmetry (full hidden symmetry and rotational symmetry) of the oscillator. The method of self-adjoint extensions have been discussed for conic oscillator in presence of constant magnetic field also.Comment: Accepted in Journal of Physics

Quantum-classical correspondence of a field induced KAM-type transition: a QTM approach

A transition from regular to chaotic behaviour in the dynamics of a classical Henon-Heiles oscillator in the presence of an external field is shown to have a similar quantum signature when studied using the pertaining phase portraits and the associated Kolmogorov-Sinai-Lyapunov entropies obtained through the corresponding Bohmian trajectories

Bonding, aromaticity and reactivity patterns in some all-metal and non-metal clusters

Several sandwich-like metal clusters have been studied at the B3LYP/6-311 + G* level of theory. Bonding and reactivity have been analysed through various geometrical parameters and conceptual density functional theory based global reactivity descriptors. Aromaticity patterns have been understood in terms of the associated nucleus independent chemical shift values. Possibility of bond-stretch isomerism in some doped clusters is explored. Preferable sites for electrophilic and nucleophilic attacks have been identified using different local reactivity descriptors