Related papers: Water-mediated correlations in DNA-enzyme interact…
Complementary DNA strands in solution reliably hybridize to form stable duplexes. We study the kinetics of the hybridization process and the mechanisms by which two initially isolated strands come together to form a stable double helix. We…
In this paper we study the role of topology in DNA gel electrophoresis experiments via molecular dynamics simulations. The gel is modelled as a 3D array of obstacles from which half edges are removed at random with probability p, thereby…
We propose a dynamical model depicting the interactions between DNA and a specific binding protein involving long range transmissions. The dynamics rely on the coupling between Hydrogen bonds formed between DNA and protein and between the…
Binary mixtures of water with lower alcohols display non-linear phase behaviour upon mixing which are attributed to potential cluster formation at molecular level. Unravelling such elusive structures requires the investigation of…
The particles of electrorheological fluids can be modelled as dielectric spheres (DS) immersed in a continuum dielectric. When an external field is applied, polarization charges are induced on the surfaces of the spheres and can be…
We demonstrate that a non-vanishing interaction force exists between pairs of induced dipoles in random, statistically stationary electromagnetic field. This new type of optical binding force leads to long-range interaction between dipolar…
The electric dipole moments of $(H_{2}O)_{n}DCl$ ($n=3-9$) clusters have been measured by the beam deflection method. Reflecting the (dynamical) charge distribution within the system, the dipole moment contributes information about the…
Protein-DNA interactions are vital for many processes in living cells, especially transcriptional regulation and DNA modification. To further our understanding of these important processes on the microscopic level, it is necessary that…
We present a microscopic approach for the coupling of cortical activity, as resulting from proper dipole currents of pyramidal neurons, to the electromagnetic field in extracellular fluid in presence of diffusion and Ohmic conduction. As a…
The effective DNA-DNA interaction force is calculated by computer simulations with explicit tetravalent counterions and monovalent salt. For overcharged DNA molecules, the interaction force shows a double-minimum structure. The positions…
Using molecular dynamics simulations we study the dynamics of a water-like TIP5P model of water in hydrophilic and hydrophobic confinement. We find that in case of extreme nanocofinement such that there is only one molecular layer of water…
DNA supercoiling is central to many fundamental processes of living organisms. Its average level along the chromosome and over time reflects the dynamic equilibrium of opposite activities of topoisomerases, which are required to relax…
In this review, we discuss disruptive decoupled water splitting schemes, in which the concurrent production of hydrogen and oxygen in close proximity to each other in conventional electrolysis is replaced by time- or space-separated…
We discern hydration geometries around the sugar-phosphate-backbone of an RNA double helix at the molecular level. RNA disordering upon melting is connected with a transition from ordered water structures towards local phosphate group…
We show that the dynamics of the surface plasmon in metallic nanoparticles damped by its interaction with particle-hole excitations can be modelled by a single degree of freedom coupled to an environment. In this approach, the fast decrease…
We study theoretically the feasibility of using transverse electronic transport within a nanopore for rapid DNA sequencing. Specifically, we examine the effects of the environment and detection probes on the distinguishability of the DNA…
We consider the electromagnetic field in the presence of polarizable point dipoles. In the corresponding effective Maxwell equation these dipoles are described by three dimensional delta function potentials. We review the approaches…
Electrical forces are the background of all the interactions occurring in biochemical systems. From here and by using a combination of ab-initio and ad-hoc models, we introduce the first description of electric field profiles with intrabond…
We analyze van der Waals interactions between two rigid polymers with sequence-specific, anisotropic polarizabilities along the polymer backbones, so that the dipole moments fluctuate parallel to the polymer backbones. Assuming that each…
Dipole condensates, formed from particle-hole pairs, represent a unique class of charge-neutral quantum fluids that evade conventional vector gauge fields, making their electrodynamic responses difficult to probe in natural materials. Here,…