Related papers: Water-mediated correlations in DNA-enzyme interact…
The formation of polarized signaling domains on cell membranes is a fundamental example of biological pattern formation. While such patterns resemble structures from equilibrium phase separation, they are intrinsically non-equilibrium,…
We evaluate, by means of molecular dynamics simulations employing a realistic DNA coarse-grained model, the phase behaviour and the structural and dynamic properties of tetravalent DNA nanostars, i.e. nanoconstructs completely made of DNA.…
This work constructs an advanced force field, the Completely Multipolar Model (CMM), to quantitatively reproduce each term of an energy decomposition analysis (EDA) for aqueous solvated alkali metal cations and halide anions and their ion…
The absorption of ultraviolet light creates excitations in DNA, which subsequently start moving in the helix. Their fate is important for an understanding of photo damage, and is determined by the interplay of electronic couplings between…
A new classical interaction potential for water simulations is presented. Water is modeled as a fully dissociable set of atoms with a point dipole, determined self-consistently, on every oxygen atom. The oxygen polarizability is not fixed…
We propose a fully ab initio theory to compute the electron density response under the perturbation in the local field. This method is based on our recently developed local dielectric response theory [Phys. Rev. B 92, 241107(R), 2015],…
We present a 2D lattice model of water to study the effects of ion hydration on the properties of water. We map the water molecules as lattice particles consisting of a single Oxygen at the center of a site and two Hydrogen atoms on each…
The interaction of phosphate groups with ions in an aqueous environment has a strong impact on the structure and folding processes of DNA and RNA. The dynamic variety of ionic arrangements, including both contact pairs and water separated…
Broad-band dielectric spectroscopy, heat capacity measurements and molecular dynamic simulations are applied to study excitations of interacting electric dipoles spatially arranged in a network with an inter-dipole distance of 5-10 A. The…
The physics and morphology of biomolecular condensates formed through liquid-liquid phase separation underpin diverse biological processes, exemplified by the nested organization of nucleoli that facilitates ribosome biogenesis. Here, we…
DNA melting and hybridization is a fundamental biological process as well as a crucial step in many modern biotechnology applications. DNA confined on surfaces exhibits different behavior from that in free solutions. The system of…
A mechanism of double strand breaking (DSB) in DNA due to the action of two electrons is considered. These are the electrons produced in the vicinity of DNA molecules due to ionization of water molecules with a consecutive emission of two…
Something about structure of the water shell of DNA and how it can help to design of novel biologically-active molecules and potential drugs with sequence-specific binding to nucleic acids.
This paper aims at a comprehensive understanding on the novel elastic property of double-stranded DNA (dsDNA) discovered very recently through single-molecule manipulation techniques. A general elastic model for double-stranded biopolymers…
The dipole coupling term between a system of N particles with total charge zero and the electromagnetic field is derived in the presence of a weak gravitational field. It is shown that the form of the coupling remains the same as in flat…
We report in situ single-molecule measurements of proton-induced double-strand breaks (DSBs) in DNA immersed in water, using real-time fluorescence tracking along the entire proton path, including the Bragg peak region. By chemically…
We generalize the predictions for attractions between over-all neutral surfaces induced by charge fluctuations/correlations to non-uniform systems that include dielectric discontinuities, as is the case for mixed charged lipid membranes in…
We characterize the role of charge correlations in the adsorption of a short, rod-like anionic polyelectrolyte onto a similarly charged membrane. Our theory reveals two different mechanisms driving the like-charge polyelectrolyte-membrane…
The paper presents an analytical theory and numerical simulations of the dipolar response of hydrated proteins. The effective dielectric constant of the solvated protein, representing the average dipole moment induced at the protein by a…
Molecular biology explains function of molecules by their geometrical and electronical structures that are mainly determined by utilization of quantum effects in chemistry. However, further quantum effects are not thought to play any…