Related papers: Excited state dynamics in DNA double helices
We call {\it monomer} a B-DNA base-pair and examine, analytically and numerically, electron or hole oscillations in monomer- and dimer-polymers, i.e., periodic sequences with repetition unit made of one or two monomers. We employ a…
A theoretical framework for evaluating the approximate energy and dynamic properties associated with the folding of DNA into nucleosomes and chromatin is presented. For this purpose experimentally determined elastic constants of linear DNA…
Previous theoretical studies have shown that measuring the transverse current across DNA strands while they translocate through a nanopore or channel may provide a statistically distinguishable signature of the DNA bases, and may thus allow…
In this paper a lattice model for the diffusional transport of particles in the interphase cell nucleus is proposed. The dynamic behaviour of single chains on the lattice is investigated and Rouse scaling is verified. Dynamical dense…
Cytosine methylation has been found to play a crucial role in various biological processes, including a number of human diseases. The detection of this small modification remains challenging. In this work, we computationally explore the…
Here we present a systematic study of supercoil formation in DNA minicircles under varying linking number by using molecular dynamics simulations of a two-bead coarse-grained model. Our model is designed with the purpose of simulating long…
We present a detailed analysis of several time-dependent DFT (TD-DFT) methods, including conventional hybrid functionals and two types of non-empirically tuned range-separated functionals, for predicting a diverse set of electronic…
Condensation of hundreds of mega-base-pair-long human chromosomes in a small nuclear volume is a spectacular phenomenon. This process is driven by the formation of chromosome loops. ATP consuming motor, condensin, interacts with chromatin…
We study the dynamics of moving discrete breathers in an interfaced piecewise DNA molecule. This is a DNA chain in which all the base pairs are identical and there exists an interface such that the base pairs dipole moments at each side are…
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…
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 electro-optical properties of most semiconductors and insulators of technological interest are dominated by the presence of electron-hole quasiparticles called excitons. The manipulation of these hydrogen-like quasi-particles in…
A systematic study of electron or hole transfer along DNA dimers, trimers and polymers is presented with a tight-binding approach at the base-pair level, using the relevant on-site energies of the base-pairs and the hopping parameters…
While slowly turning the ends of a single molecule of DNA at constant applied force, a discontinuity was recently observed at the supercoiling transition, when a small plectoneme is suddenly formed. This can be understood as an abrupt…
We study the theory of itinerant-hole photoluminescence of two-dimensional electron systems in the regime of the magnetically induced Wigner crystal. We show that the exciton recombination transition develops structure related to the…
Microtubules are biological protein polymers with critical and diverse functions. Their structures share some similarities with photosynthetic antenna complexes, particularly in the ordered arrangement of photoactive molecules with large…
Short blunt-ended DNA duplexes comprising 6 to 20 base pairs self-assemble into polydisperse semi-flexible chains due to hydrophobic stacking interactions between terminal base pairs. Above a critical concentration, which depends on…
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…
We study the nonlinear dynamics of a completely inhomogeneous DNA chain which is governed by a perturbed sine-Gordon equation. A multiple scale perturbation analysis provides perturbed kink-antikink solitons to represent open state…
Photo-induced dynamics of electronic processes in materials are driven by the coupling between electronic and nuclear degrees of freedom. Here we construct 1D and 2D organic-inorganic tin halides to investigate the functional role of…