Related papers: Partition function of a bubble formed in double st…
A double stranded DNA molecule when pulled with a force acting on one end of the molecule can become either partially or completely unzipped depending on the magnitude of the force F. For a random DNA sequence, the number M of unzipped base…
Let $W_N(\beta) = \mathrm{E}_0\left[e^{ \sum_{n=1}^N \beta\omega(n,S_n) - N\beta^2/2}\right]$ be the partition function of a two-dimensional directed polymer in a random environment, where $\omega(i,x), i\in \mathbb{Z}_+, x\in \mathbb{Z}^2$…
Many single-stranded (ss) RNA viruses self assemble from capsid protein subunits and the nucleic acid to form an infectious virion. It is believed that the electrostatic interactions between the negatively charged RNA and the positively…
The harmonic oscillator with dissipation is studied within the framework of the Lindblad theory for open quantum systems. By using the Wang-Uhlenbeck method, the Fokker-Planck equation, obtained from the master equation for the density…
Motivated by the wide range of applicability of the fluctuation and dissipation phenomena in non-equilibrium systems, we provide a universal study scheme for the dissipation of the energy and the corresponding Brownian motion analysis of…
Experiments have revealed correlation-driven behavior of DNA in charged solutions, including charge inversion and condensation. This paper presents calculations of a lattice-gas model of charge inversion for the adsorption of charged dimers…
Nanochannels provide means for detailed experiments on the effect of confinement on biomacromolecules, such as DNA. We here introduce a model for the complete unfolding of DNA from the circular to linear configuration. Two main ingredients…
We study the Type IIA NS five-brane wrapped on a Calabi-Yau manifold X in a double-scaled decoupling limit. We calculate the euclidean partition function in the presence of a flat RR 3-form field. The classical contribution is given by a…
In order to study the rotating strongly coupled Bose-Einstein condensations(BEC), a holographic model defined in an AdS black hole that duals to a coupled two-component condensations in global $U(1)$ symmetry broken phase with…
Several properties of trapped hard sphere bosons are evaluated using variational Monte Carlo techniques. A trial wave function composed of a renormalized single particle Gaussian and a hard sphere Jastrow function for pair correlations is…
The recently introduced nested sampling algorithm allows the direct and efficient calculation of the partition function of atomistic systems. We demonstrate its applicability to condensed phase systems with periodic boundary conditions by…
A simple model of a circularly closed dsDNA in a poor solvent is considered as an example of a semi-flexible polymer with self-attraction. To find the ground states, the conformational energy is computed as a sum of the bending and…
Recently, it has been shown that entropy can be used to sort Brownian particles according to their size. In particular, a combination of a static and a time-dependent force applied on differently sized particles which are confined in an…
The role of thermal pressure fluctuations in the ejection of tightly packaged DNA from protein capsid shells is discussed in a model calculation. At equilibrium before ejection we assume the DNA is folded many times into a bundle of…
Most binary superlattices created using DNA functionalization or other approaches rely on particle size differences to achieve compositional order and structural diversity. Here we study two-dimensional (2D) assembly of DNA-functionalized…
We investigate the fragmentation dynamics of an atomic chain under tensile stress. We have classified the location, stability type (indices) and energy of all equilibria for the general $n$-particle chain, and have highlighted the…
We perform the quantitative evaluation of the entanglement dynamics in scattering events between two insistinguishable electrons interacting via Coulomb potential in 1D and 2D semiconductor nanostructures. We apply a criterion based on the…
While the statistical mechanical description of DNA has a long tradition, renewed interest in DNA melting from a physics perspective is nourished by measurements of the fluctuation dynamics of local denaturation bubbles by single molecule…
We study the tensor structure function $b_1\xq$ in deep inelastic scattering (DIS) of an electron from a polarized deuteron target. We model the electron-nucleon cross section at the starting point for $Q^2$ evolution by…
Translocation of a single stranded DNA (ssDNA) through an alpha-hemolysin channel in a lipid membrane driven by applied transmembrane voltage V was extensively studied recently. While the bare charge of the ssDNA piece inside the channel is…