Related papers: Dynamics of K$^+$ counterions around DNA double he…
The model of the deformation of DNA macromolecule is developed with the accounting of two types of components of deformation: external and internal. External components describe the bend, twist and stretch of the double helix. The internal…
Ionic behaviors, including ion distributions and hydration characteristics at solid-liquid interfaces, are important research interests in many important applications, such as electric double-layer capacitors and water lubrication. Here, we…
We studied the electrical conductivity of DNA molecules with conducting atomic force microscopy as a function of the chemical nature of the substrate surfaces, the nature of the electrical contact, and the number of DNA molecules (from a…
We study the electrokinetics of a single polyelectrolyte chain in salt solution using hydrodynamic simulations. The salt-dependent chain mobility compares well with experimental DNA data. The mobility of condensed counterions exhibits a…
We have performed molecular dynamics simulations to study the effect of an external electric field on a macroion in the solution of multivalent Z:1 salt. To obtain plausible hydrodynamics of the medium, we explicitly make the simulation of…
Ion-mediated interaction is critical to the structure and stability of nucleic acids. Recent experiments suggest that the multivalent ion-induced aggregation of double-stranded (ds) RNAs and DNAs may strongly depend on the topological…
The electrostatic contribution to twist rigidity of DNA is studied, and it is shown that the Coulomb self-energy of the double-helical sugar-phosphate backbone contributes considerably to twist rigidity of DNA--the electrostatic twist…
The conformational vibrations of Z-DNA with counterions are studied in framework of phenomenological model developed. The structure of left-handed double helix with counterions neutralizing the negatively charged phosphate groups of DNA is…
Molecular dynamics simulations are used to study the equilibrium distribution of monovalent ions in a nanopore connecting two water reservoirs separated by a membrane, both for the empty pore and that with a single stranded DNA molecule…
We investigate the non-equilibrium mechanical motion of double-stranded DNA in a molecular junction under electronic current using Keldysh-Langevin molecular dynamics. Non-equilibrium electronic force reshapes the effective potential energy…
We study numerically the mechanical stability and elasticity properties of duplex DNA molecules within the frame of a network model incorporating microscopic degrees of freedom related with the arrangement of the base pairs. We pay special…
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…
We study the role of cations on the stability of double stranded DNA (dsDNA) molecules.It is known that the two strands of double stranded DNA(dsDNA) have negative charge due to phosphate group. Cations in the form of salt in the solution,…
Strongly correlated electrostatics of DNA systems has drawn the interest of many groups, especially the condensation and overcharging of DNA by multivalent counterions. By adding counterions of different valencies and shapes, one can…
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…
The effective force between two parallel DNA molecules is calculated as a function of their mutual separation for different valencies of counter- and salt ions and different salt concentrations. Computer simulations of the primitive model…
The sequence-dependent structural variability and conformational dynamics of DNA play pivotal roles in many biological milieus, such as in the site-specific binding of transcription factors to target regulatory elements. To better…
DNA molecules spin-coated on amorphous quartz substrates are shown to form stable films. Electron density profiles (EDPs) along the film depth show that film prepared from aqueous solution of DNA exhibits layering of the molecules in three…
We develop an analytical theory that accounts for the image and surface charge interactions between a charged dielectric membrane and a DNA molecule translocating through the membrane. Translocation events through neutral carbon-based…
Water near detonation nanodiamonds (DNDs) forms a Hydrogen Bond (HB) network, whose strength influences DNDs' fluorescence intensity and colloidal stability in aqueous suspensions. However, effects of dissolved ions and DND's surface…