Related papers: Helix untwisting and bubble formation in circular …
In order to understand the possible sequence of transitions from the disordered columnar phase to the helical phase in hexa(hexylthio)triphenylene (HHTT), we study a three-dimensional planar model with octupolar interactions inscribed on a…
Dynamics of DNA bubbles are of interest for both statistical physics and biology. We present exact solutions to the Fokker-Planck equation governing bubble dynamics in the presence of a long-range entropic interaction. The complete meeting…
We introduce a computational method to discover polymorphs in molecular crystals at finite temperature. The method is based on reproducing the crystallization process starting from the liquid and letting the system discover the relevant…
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…
We use a coarse-grained molecular model to study the self-assembly process of complexes of cationic and neutral lipids with DNA molecules ("lipoplexes") - a promising nonviral carrier of DNA for gene therapy. We identify the resulting…
We recently proposed a dynamical mesoscopic model for DNA, which is based, like statistical ones, on site-dependent finite stacking and pairing enthalpies. In the present article, we first describe how the parameters of this model are…
Twisted magnetic fields should be ubiquitous in flare-producing active regions where the magnetic fields are strongly non-potential. It has been shown that reconnection in helical magnetic coronal loops results in plasma heating and…
One-neutron halo nuclei, composed by a weakly-bound particle coupled to a core nucleus, are studied within a particle-plus-core model. A semi-microscopic method to generate the two-body Hamiltonian of such a system, including core…
We propose a nonlinear model derived from first principles, to describe bubble dynamics of DNA. Our model equations include a term derived from the dissipative effect of intermolecular vibrational modes. Such modes are excited by the…
We examine the effects of thermal fluctuations on thin elastic filaments with non-circular cross-section and arbitrary spontaneous curvature and torsion. Analytical expressions for orientational correlation functions and for the persistence…
The formation of bubble defects of the double stranded DNA is treated according to the Lifshits theory of disordered chains. A molecule of the DNA is modelled on a harmonic lattice with nearest neighbour interaction, elastic constants being…
Ring polymers exhibit unique flow properties due to their closed chain topology. Despite recent progress, we have not yet achieved a full understanding of the nonequilibrium flow behavior of rings in nondilute solutions where intermolecular…
The sequence-dependent structural variability and conformational dynamics of DNA play pivotal roles in many biological milieus, such as in the site-specific binding of transcription factors to target regulatory elements. To better…
A general theory of nucleation for colloids and macromolecules in solution is formulated within the context of fluctuating hydrodynamics. A formalism for the determination of nucleation pathways is developed and stochastic differential…
The model of the deformation of DNA macromolecule is developed with the accounting of two types of components of deformation: external and internal. External components describe the bend, twist and stretch of the double helix. The internal…
To explain the differentiation of stem cells in terms of dynamical systems theory, models of interacting cells with intracellular protein expression dynamics are analyzed and simulated. Simulations were carried out for all possible protein…
Bending of DNA from a straight rod to a circular form in presence of any of the mono-, di-, tri- or tetravalent counterions has been simulated in strong Coulomb coupling environment employing a previously developed energy minimization…
By combining analytical and numerical calculations, we investigate the minimal-energy shape of short DNA loops of approximately $100$ base pairs (bp). We show that in these loops the excess twist density oscillates as a response to an…
We introduce a coarse-grained rigid nucleotide model of DNA that reproduces the basic thermodynamics of short strands: duplex hybridization, single-stranded stacking and hairpin formation, and also captures the essential structural…
We predict various detectable mechanical responses to the presence of local DNA defects which are defined as short DNA segments exhibiting mechanical properties obviously different from the 50 nm persistence length based semiflexible…