Related papers: Base pair fluctuations in helical models for nucle…
We study the spontaneous nucleation and crystallization of linear and cyclic chains of flexibly connected hard spheres using extensive molecular dynamics simulations. To this end, we present a novel event-driven molecular dynamics…
Recent experiments on unzipping of RNA helix-loop structures by force have shown that about 40-base molecules can undergo kinetic transitions between two well-defined `open' and `closed' states, on a timescale = 1 sec [Liphardt et al.,…
We investigate particle condensation in a driven pair exclusion process on one- and two- dimensional lattices under the periodic boundary condition. The model describes a biased hopping of particles subject to a pair exclusion constraint…
We derive a reduced quasi-one-dimensional theory of geometrically frustrated elastic ribbons. Expressed in terms of geometric properties alone, it applies to ribbons over a wide range of scales, allowing the study of their elastic…
For an understanding of DNA elasticity at high mechanical loads (F > 30 pN), its helical nature needs to be taken into account, in the form of coupling between the twist and stretch degrees of freedom. The prevailing model for DNA…
The theory of mesoscopic fluctuations is applied to inhomogeneous solids consisting of chaotically distributed regions with different crystalline structure. This approach makes it possible to describe statistical properties of such mixture…
The fluctuation exchange (FLEX) approximation is applied to study the Holstein-Hubbard model. Due to the retarded nature of the phonon-mediated electron-electron interaction, neither fast Fourier transform (FFT) nor previously developed NRG…
The escape mechanism of the four hill potential is explored. A thorough numerical investigation takes place in several types of two-dimensional planes and also in a three-dimensional subspace of the entire four-dimensional phase space in…
We study the fluctuational dynamics of a tagged base-pair in double stranded DNA. We calculate the drift force which acts on the tagged base-pair using a potential model that describes interactions at base pairs level and use it to…
The approach for the description of the DNA conformational transformations on the mesoscopic scales in the frame of the double helix is presented. Due to consideration of the joint motions of DNA structural elements along the conformational…
The phase structure of baryonic matter is investigated with focus on the role of fluctuations beyond the mean-field approximation. The prototype test case studied is the chiral nucleon-meson model, with added comments on the chiral…
The ``Brownian bees" model describes an ensemble of $N$ independent branching Brownian particles. When a particle branches into two particles, the particle farthest from the origin is eliminated so as to keep a constant number of particles.…
Helices are a key folding motif in protein structure. The question which factors determine helix stability for a given polypeptide or protein is an ongoing challenge. Here we use van der Waals corrected density-functional theory to address…
The elastic neutron-${}^3\mathrm{H}$ scattering at intermediate energies is studied using rigorous integral equations solved in the momentum-space partial-wave basis. The four-particle transition operators are expanded into…
Mechanical properties of nucleic acids play an important role in many biological processes which often involve physical deformations of these molecules. At sufficiently long length scales (say above $\sim 20-30$ base pairs) the mechanics of…
We study numerically the mechanical stability and elasticity properties of duplex DNA molecules within the frame of a network model incorporating microscopic degrees of freedom related with the arrangement of the base pairs. We pay special…
By exploring a recent model [Palmeri, J., M. Manghi, and N. Destainville. 2007. Phys. Rev. Lett. 99:088103] where DNA bending elasticity, described by the wormlike chain model, is coupled to base-pair denaturation, we demonstrate that small…
We examine the elastic model of short circular DNA. We obtain analytic expressions for configurations, elastic energy, twist and linking number of our solutions. We find the onset of the plectonemic transition. We suggest ways to use our…
Thermal oscillations of base pairs in the Peyrard-Bishop-Holstein model are simulated by stochastic fluctuations of base overlap integrals. Numerical investigation of the model is carried out for a hole transfer in $G_1A_2G_3G_4$ sequence…
We discuss the transient and steady state fluctuation relation for a mechanical system in contact with two deterministic thermostats at different temperatures. The system is a modified Lorentz gas in which the fixed scatterers exchange…