Related papers: Water-mediated correlations in DNA-enzyme interact…
The problem of DNA-DNA interaction mediated by divalent counterions is studied using computer simulation. Although divalent counterions cannot condense free DNA molecules in solution, we show that if DNA configurational entropy is…
Water mediates electrostatic interactions via the orientation of its dipoles around ions, molecules, and interfaces. This induced water polarization consequently influences multiple phenomena. In particular, water polarization modulated by…
We show that the electric dipole-dipole interaction between a pair of polar molecules undergoes an all-out transformation when superimposed by a far-off resonant optical field. The combined interaction potential becomes tunable by variation…
Trapping, linearization, and imaging of single molecule DNA is of broad interest to both biophysicists who study polymer physics and engineers who build nucleic acid analyzing methods such as optical mapping. In this study, single DNA…
Intermolecular polarization interactions in water are determined using a minimal atomic multipole model constructed with distributed polarizabilities. Hydrogen bonding and other properties of water-water interactions are reproduced to fine…
We consider the effect of spatial correlations on sources of polarized electromagnetic radiation. The sources, assumed to be monochromatic, are constructed out of dipoles aligned along a line such that their orientation is correlated with…
Positions of protons in DNA hydrogen bonds are fundamental for the fidelity of the replication process. Because the hydrogen bond is partially covalent the electronic structure of DNA plays an important role in the replication process.…
There is a long-standing question about the molecular configuration of interfacial water molecules in the proximity of solid surfaces, particularly carbon atoms which play a crucial role in electrochemistry and biology. In this study, the…
We investigate the impact of dielectric boundary forces on the translocation process of charged rigid DNA segments through solid neutral nanopores. We assess the electrostatic contribution to the translocation free energy barrier of a model…
The phase diagram of a water solution of DNA and oppositely charged spherical macroions is studied. DNA winds around spheres to form beads-on-a-string complexes resembling the chromatin 10 nm fiber. At small enough concentration of spheres…
We probe the electrostatic cost associated with the approach phase of DNA translocation events. Within an analytical theory at the Debye-Huckel level, we calculate the electrostatic free energy of a rigid DNA molecule interacting with a…
Electrochemical phenomena in biology often unfold in confined geometries where micrometer- to millimeter-scale domains coexist with nanometer-scale interfacial diffuse charge layers. We analyze a model lipid membrane-electrolyte system…
Inspired by recent experiments on chromosomal dynamics, we introduce an exactly solvable model for the interaction between a flexible polymer and a set of motor-like enzymes. The enzymes can bind and unbind to specific sites of the polymer…
Using computer simulations, we study a membrane of parallel narrow pores filled with one-dimensional wires of hydrogen-bonded water molecules. We show that such a membrane is equivalent to a system of effective charges located at opposite…
Over the last decade, an increasing body of evidence has emerged, supporting the existence of a metastable liquid-liquid critical point in supercooled water, whereby two distinct liquid phases of different densities coexist. Analysing long…
An effective Hamiltonian and equations of motion for treating both the resonant dipole-dipole interaction between two-level atoms and the resonant atom-field interaction are derived, which can suitably be used for studying the influence of…
Molecular recognition between two double stranded (ds) DNA with homologous sequences may not seem compatible with the B-DNA structure because the sequence information is hidden when it is used for joining the two strands. Nevertheless, it…
We study energy levels of two heteronuclear molecules moving in a spherically symmetric harmonic trap. A role of electric dipole interactions is compared and contrasted with our earlier results (https://arxiv.org/abs/1512.00631) for two…
We investigate diffusion-limited reactions between a diffusing particle and a target site on a semiflexible polymer, a key factor determining the kinetics of DNA-protein binding and polymerization of cytoskeletal filaments. Our theory…
As a key molecule of Life, Deoxyribonucleic acid (DNA) is the focus of numbers of investigations with the help of biological, chemical and physical techniques. From a physical point of view, both experimental and theoretical works have…