Related papers: Symmetries of Electrostatic Interaction between DN…
We introduce a coarse-grained model of DNA with bases modeled as rigid-body ellipsoids to capture their anisotropic stereochemistry. Interaction potentials are all physicochemical and generated from all-atom simulation/parameterization with…
A mesoscopic model for heterogeneous DNA denaturation is developed in the framework of the path integral formalism. The base pair stretchings are treated as one-dimensional, time dependent paths contributing to the partition function. The…
The effective interaction between two parallel strands of helical bio-molecules, such as deoxyribose nucleic acids (DNA), is calculated using computer simulations of the "primitive" model of electrolytes. In particular we study a simple…
The phase diagram of isospin-symmetric chemically equilibrated mixture of alpha particles and nucleons is studied in the mean-field approximation. Skyrme-like parametrization is used for the mean-field potentials as functions of partial…
We scrutinize the effect of polyvalent ions on polymer-DNA interactions. We extend a recently developed test charge theory to the case of a stiff polymer interacting with a DNA molecule in an electrolyte mixture. The theory accounts for…
Concentrated solutions of short blunt-ended DNA duplexes, down to 6 base pairs, are known to order into the nematic liquid crystal phase. This self-assembly is due to the stacking interactions between the duplex terminals that promotes…
In many biopolymer solutions, attractive interactions that stabilize finite-sized clusters at low concentrations also promote phase separation at high concentrations. Here we study a model biopolymer system that exhibits the opposite…
We predict the existence of a totally new class of phases in weakly coupled, three-dimensional stacks of two-dimensional (2D) XY-models. These ``sliding phases'' behave essentially like decoupled, independent 2D XY-models with precisely…
The interplay between bending of the molecule axis and appearance of disruptions in circular DNA molecules, with $\sim 100$ base pairs, is addressed. Three minicircles with different radii and almost equal content of AT and GC pairs are…
We use coherent states as trial states for a variational approach to study a system of a finite number of three-level atoms interacting in a dipolar approximation with a one-mode electromagnetic field. The atoms are treated as…
Dynamics of the polymorphic A<->B transitions in DNA is compared for two polypurine sequences, poly(dA).poly(dT) and poly(dG).poly(dC), long known to exhibit contrasting properties in experiments. In free molecular dynamics simulations…
We investigate the appearance of pi lapses in the transmission phase theta of a two-level quantum dot with Coulomb interaction U. Using the numerical and functional renormalization group methods we study the entire parameter space for…
We model the electron clouds of nucleic acids in DNA as a chain of coupled quantum harmonic oscillators with dipole-dipole interaction between nearest neighbours resulting in a van der Waals type bonding. Crucial parameters in our model are…
The high linear charge density of 20-base-pair oligomers of DNA is shown to lead to a striking non-monotonic dependence of the long-time self-diffusion on the concentration of the DNA in low-salt conditions. This generic non-monotonic…
Polarizable particle systems, including charged colloids, polarizable ions, biomolecular assemblies, and soft nanomaterials, can exhibit contact electrostatic interactions that depart strongly from Coulomb behavior when dielectric mismatch…
We study the constraints on the CP-violating soft-breaking phases in the minimal supersymmetric standard model using the limits on the chromoelectric dipole moment of the strange quark extracted from the neutron EDM experiment. Our…
The phase diagram of a water solution of DNA and oppositely charged spherical macroions is studied. DNA winds around spheres to form beads-on-a-string complexes resembling the chromatin 10 nm fiber. At small enough concentration of spheres…
In the unconstrained MSSM, we reanalyze the constraints on the phases of supersymmetric flavour conserving couplings that follow from the electron and neutron electric dipole moments (EDM). We find that the constraints become weak if at…
We study interactions of unparticles ${\cal {U}}$ of dimension $d_{\cal {U}}$ due to Georgi with Standard Model (SM) fields through effective operators. The unparticles describe the low energy physics of a non-trivial scale invariant…
A symmetry classification of possible interactions in a diatomic molecular chain is provided. For nonlinear interactions the group of Lie point transformations, leaving the lattice invariant and taking solutions into solutions, is at most…