Related papers: Water-mediated correlations in DNA-enzyme interact…
We study sequence dependent complexation between oligonucleotides (single strand DNA) and various generation ethylene diamine (EDA) cored poly amido amide (PAMAM) dendrimers through atomistic molecular dynamics simulations accompanied by…
The behavior of long DNA molecules in a cell-sized confined space was investigated. We prepared water-in-oil droplets covered by phospholipids, which mimic the inner space of a cell, following the encapsulation of DNA molecules with…
The dielectrophoresis method for trapping and attaching nanoscale double-stranded DNA between nanoelectrodes was developed. The method gives a high yield of trapping single or a few molecules only which enables transport measurements at the…
An external electric field changes the physical properties of polar-liquids due to the reorientation of their permanent dipoles. For example it should affect significantly the physical properties of water confined in a nanochannel. The…
A polarizable environment, prominently the solvent, responds to electronic changes in biomolecules rapidly. The knowledge of conformational relaxation of the biomolecule itself, however, may be scarce or missing. In this work, we describe…
The dependence of DNA assemblies conductance on relative humidity is investigated theoretically. Following earlier suggestions, we consider the ionic conductivity through the layers of water adsorbed by DNA molecules. The increase in…
The structure and dynamics of aqueous solvation of ethanol and ethylene are studied by DFT-based Car-Parrinello molecular dynamics. We did not find an enhancement of the structure of the hydrogen bonded network of hydrating water molecules.…
The existence of water dimers in equilibrium water vapor at room temperature and their anomalous properties revealed by recent studies suggest the benchmark role of water dimer in both experiment and theory. However, there has been a…
In two nearby atoms, the dipole-dipole interaction can couple transitions with orthogonal dipole moments. This orthogonal coupling accounts for a number of interesting effects, but strongly depends on the geometry of the setup. Here, we…
When the DNA double helix is subjected to external forces it can stretch elastically to elongations reaching 100% of its natural length. These distortions, imposed at the mesoscopic or macroscopic scales, have a dramatic effect on…
We suggest that the DNA molecules could form the cholesteric phase owing to an interaction mediated by the network of the hydrogen bonds (H-network) in the solvent. The model admits of the dependence of the optical activity of the solution…
Motivated by DNA electrophoresis near a nanopore, we consider the flow field around an "elongated jet", a long thin source which injects momentum into a liquid. This solution qualitatively describes the electro-osmotic flow around a long…
Arrays of optically trapped nanoparticles have emerged as a promising platform for the study of complex non-equilibrium phenomena. Analogous to atomic many-body systems, one of the crucial ingredients is the ability to precisely control the…
Despite the ubiquity of aqueous electrolytes, the effect of salt on water organization remains controversial. We introduce a nonlocal and nonlinear field theory for the nanoscale polarization of ions and water and derive the electrolyte…
The lack of molecular-level understanding for the electronic excitation response of DNA to charged particle radiation, such as high-energy protons, remains a fundamental scientific bottleneck in advancing proton and other ion beam cancer…
We present analysis of a system of three two-level atoms interacting with each other through the dipole-dipole interaction. The interaction manifests between excited state of one of the atoms and the ground state of its nearest neighbour.…
Here we reveal details of the interaction between human lysozyme proteins, both native and fibrils, and their water environment by intense terahertz time domain spectroscopy. With the aid of a rigorous dielectric model, we determine the…
Motivated by the implications of the complex and dynamic modular geometry of an enzyme on its motion, we investigate the effect of combining long-range internal and external hydrodynamic interactions due to thermal fluctuations with…
Motivated by the wide ranging experimental results on the conductivity of DNA, we have investigated extraordinary configurations and chemical environments in which DNA might become a true molecular wire, perticularly from enhanced…
Using both theoretical modeling and computer simulations we study a model system for DNA interactions in the vicinity of charged membranes. We focus on the polarization of the mobile charges in the membranes due to the nearby charged rods…