Related papers: Base Pair Openings and Temperature Dependence of D…
Even though the persistence length $L_P$ of double-stranded DNA plays a pivotal role in cell biology and nanotechnologies, its dependence on ionic strength $I$ lacks a consensual description. Using a high-throughput single-molecule…
In the present paper we study the impact of dispersion and nonlinearity on DNA dynamics. We rely on the helicoidal Peyrard-Bishop model and use the fact that nonlinear DNA dynamics represents an interplay between nonlinearity and…
To study temperature dependent elastic constants, a new computational method is proposed by combining continuum elasticity theory and first principles calculations. A Gibbs free energy function with one variable with respect to strain at…
It has been speculated that bubble formation of several base-pairs due to thermal fluctuations is indicatory for biological active sites. Recent evidence, based on experiments and molecular dynamics (MD) simulations using the…
SAXS studies of four 60 base-pair DNA duplexes with sequences closely related to part of the GAGE6 (G-antigen 6) promoter have been performed to study the role of DNA conformations in solution and their potential relationship to DNA-protein…
This paper aims at a comprehensive understanding on the novel elastic property of double-stranded DNA (dsDNA) discovered very recently through single-molecule manipulation techniques. A general elastic model for double-stranded biopolymers…
We study the properties of moving breathers in a bent DNA-related model with short range interaction, due to the stacking of the base pairs, and long range interaction, due to the finite dipole moment of the bonds within each base pair. We…
We analyze a microscopic RNA model, which includes two widely used models as limiting cases, namely it contains terms for bond as well as for stacking energies. We numerically investigate possible changes in the qualitative and quantitative…
We investigate kinetic pathways of the DNA melting transition using variable-range versions of the Poland-Scheraga (PS) and Peyrard-Dauxois-Bishop (PDB) models of DNA. In the PS model, we construct a phi^4-field theory to calculate the…
We consider DNA codes based on the nearest-neighbor (stem) similarity model which adequately reflects the "hybridization potential" of two DNA sequences. Our aim is to present a survey of bounds on the rate of DNA codes with respect to a…
When double-stranded DNA molecules are heated, or exposed to denaturing agents, the two strands get separated. The statistical physics of this process has a long history, and is commonly described in term of the Poland-Scheraga (PS) model.…
A theory is presented for the binding of small molecules such as surfactants to semiflexible polymers. The persistence length is assumed to be large compared to the monomer size but much smaller than the total chain length. Such polymers…
Coarse-grained models have played an important role in the study of the behavior of DNA at length scales beyond a few hundred base pairs. Traditionally, these models have relied on structurally featureless and sequence-independent…
We study the dynamics of overdamped Brownian particles interacting through soft pairwise potentials on a comb-like structure. Within the linearized Dean-Kawasaki framework, we characterize the particle density fluctuations by computing…
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…
The glass-forming ability is an important material property for manufacturing glasses and understanding the long-standing glass transition problem. Because of the nonequilibrium nature, it is difficult to develop the theory for it. Here we…
Allosteric interactions between molecules bound to DNA at distant locations have been known for a long time. The phenomenon has been studied via experiments and numerical simulations, but a comprehensive understanding grounded in a theory…
The temperature dependence of the diffusion coefficient of particles is studied on lattices with disorder. A model is investigated with both trap and barrier disorder that was introduced before by Limoge and Bocquet (1990 Phys. Rev. Lett.…
For short DNA molecules in crowded environments, we evaluate macroscopic parameters such as the average end-to-end distance and the twist conformation by tuning the strength of the site specific confinement driven by the crowders. The…
The temperature dependence of the local structure of PbSe has been investigated using pair distribution function (PDF) analysis of x-ray and neutron powder diffraction data and density functional theory (DFT) calculations. Observation of…