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Nucleosomes organize the folding of DNA into chromatin and significantly influence transcription, replication, regulation and repair. All atom molecular dynamics simulations of a nucleosome and of its 146 basepairs of DNA free in solution…
We simulate the dynamics of a quantum dot coupled to the single resonating mode of a metal nano-particle. Systems like this are known as metamolecules. In this study, we consider a time-dependent driving field acting onto the metamolecule.…
DNA is a flexible molecule, but the degree of its flexibility is subject to debate. The commonly-accepted persistence length of $l_p \approx 500\,$\AA\ is inconsistent with recent studies on short-chain DNA that show much greater…
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…
Single x-ray photons can be resonantly scattered and stored with the help of suitable transitions in the atomic nucleus. Here, we investigate theoretically means of mechanical-free modulation for the frequency spectra of such x-ray photons…
Relativistic AGN jets exhibit multi-timescale variability and a broadband non-thermal spectrum extending from radio to gamma-rays. These highly magnetized jets are prone to undergo several Magneto-hydrodynamic (MHD) instabilities during…
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…
The twisting deformation of mechanically stretched DNA molecules is studied by a coarse grained Hamiltonian model incorporating the fundamental interactions that stabilize the double helix and accounting for the radial and angular base pair…
The double-helical structure of DNA results from canonical base pairing and stacking interactions. However, variations from steady-state conformations result from mechanical perturbations in cells. These different topologies have…
Heat-induced mobility of nucleosomes along DNA is an experimentally well-studied phenomenon. A recent experiment shows that the repositioning is modified in the presence of minor-groove binding DNA ligands. We present here a stochastic…
Most of the DNA that composes a complex organism is non-coding and defined as junk. Even the coding part is composed of genes that affect the phenotype differently. Therefore, a random mutation has an effect on the specimen fitness that…
Despite the significance of the high flexibility exhibited by short DNAs, there remains an incomplete understanding of their anomalous persistence length. In this study, we propose a novel approach wherein each fundamental characteristic of…
Cell signaling, gene expression, and metabolism are affected by cell-cell heterogeneity and random changes in the environment. The effects of such fluctuations on cell signaling and gene expression have recently been studied intensively…
We study scattering resonances of finite one-dimensional systems of high-contrast resonators beyond the subwavelength regime. Introducing a novel tridiagonal frequency-dependent capacitance matrix, we derive quantitative asymptotic…
Nematic drops suspended in the isotropic phase of the same substance were subjected to alternating electrical fields of varying frequency. The system was carefully kept in the isotropic-nematic coexistance region, which was broadened due to…
A discrete nonlinear Schrodinger (NLS) model with long-range dispersive interactions describing the dynamical structure of DNA is proposed. Dispersive interactions of two types: the power dependence $r^{-s}$ and the exponential dependence…
The percentage and sequence of AT and GC base pairs and charges on the DNA backbone contribute significantly to the stiffness of DNA. This elastic property of DNA also changes with small interacting ligands. The single-molecule force…
We study the effects of the sequence on the propagation of nonlinear excitations in simple models of DNA, and how those effects are modified by noise. Starting from previous results on soliton dynamics on lattices defined by aperiodic…
We study the electric properties of single-stranded DNA molecules with hairpin-like shapes in the presence of a magnetic flux. It is shown that the current amplitude can be modulated by the applied field. The details of the electric…
We introduce a sequence-dependent parametrization for a coarse-grained DNA model [T. E. Ouldridge, A. A. Louis, and J. P. K. Doye, J. Chem. Phys. 134, 085101 (2011)] originally designed to reproduce the properties of DNA molecules with…