Related papers: Water-mediated correlations in DNA-enzyme interact…
Motivated by recent experiments we have studied the optical conductivity of DNA in its natural environment containing water molecules and counter ions. Our density functional theory calculations (using SIESTA) for four base pair B-DNA with…
The pair interaction between two stiff parallel linear DNA molecules depends not only on the distance between their axes but on their azimuthal orientation. The positional and orientational order in columnar B-DNA assemblies in solution is…
Understanding and controlling the rheology of polymeric complex fluids that are pushed out-of-equilibrium is a fundamental problem in both industry and biology. For example, to package, repair, and replicate DNA, cells use enzymes to…
In many organisms, homologous (or repetitive) chromosomal regions can associate or/and undergo concerted epigenetic changes in the absence of DNA breakage and recombination. The direct specific pairing of DNA duplexes with similar…
Electroporation is a physical method to induce the uptake of therapeutic drugs and DNA, by eukaryotic cells and tissues. The phenomena behind electro-mediated membrane permeabilization to plasmid DNA have been shown to be significantly more…
In solution, DNA is a highly charged macromolecule which bears a unit of negative charge on each phosphate of its sugar-phosphate backbone. Although partially compensated by counterions adsorbed at or condensed near it, DNA still produces a…
The work presents the detailed analysis of the water dimer properties. Their parameters are investigated on the basis of a multipole interaction potential extended up to the quadrupole--quadrupole and dipole--octupole terms. All main…
The goal of this work is to propose a simple continuous model that captures the dielectric properties of water at the nanometric scale. We write an electrostatic energy as a functional of the polarisation field containing a term in $P^4$…
We scrutinize the effect of polyvalent ions on polymer-DNA interactions. We extend a recently developed test charge theory to the case of a stiff polymer interacting with a DNA molecule in an electrolyte mixture. The theory accounts for…
The intermolecular interaction between a water molecule and the electrons in aromatic {\pi} systems--the water-{\pi} bond--lies at the heart of many chemical processes, yet its properties remain challenging to measure experimentally and…
DNA is now firmly established as a versatile and robust platform for achieving synthetic nanostructures. While the folding of single molecules into complex structures is routinely achieved through engineering basepair sequences, much less…
Gel electrophoresis is a powerful experimental method to probe the topology of DNA and other biopolymers. While there is a large body of experimental work which allows us to accurately separate different topoisomers of a molecule, a full…
We present an improved version of the Stillinger--David polarization potential of the intermolecular interaction in water. A clear algorithm of construction of a function describing the oxygen-hydrogen interaction in water molecules is…
We propose a new method for electrophoretic separation of DNA in which adsorbed polymers are driven over a disordered two-dimensional substrate which contains attractive sites for the polymers. Using simulations of a model for long polymer…
The experiment that the high spin selectivity and the length-dependent spin polarization are observed in double-stranded DNA [Science ${\bf 331}$, 894 (2011)], is elucidated by considering the combination of the spin-orbit coupling, the…
Can we avoid molecular dynamics simulations to estimate the electrostatic interaction between charged objects separated by a nanometric distance in water? To answer this question, we develop a continuous model for the dielectric properties…
DNA is an essential molecule central to the survival and propagation of life, it was imperative to investigate possible electromagnetic properties inherent to it, such as the existence of any non-trivial interactions of this molecule with…
DNA-spools, structures in which DNA is wrapped and helically coiled onto itself or onto a protein core are ubiquitous in nature. We develop a general theory describing the non-equilibrium behavior of DNA-spools under linear tension. Two…
Mechanochemically active enzymes change their shapes within every turnover cycle. Therefore, they induce circulating flows in the solvent around them and behave as oscillating hydrodynamic force dipoles. Because of non-equilibrium…
We present a short review of various experiments that measure charge transfer and charge transport in DNA. Some general comments are made on the possible connection between 'chemistry-style' charge transfer experiments that probe…