Related papers: Water-mediated correlations in DNA-enzyme interact…
A nanocomposite film containing highly polarizable inclusions in a fluid background is explored when an external electric field is applied perpendicular to the planar film. For small electric fields, the induced dipole moments of the…
Treating water as a linearly responding dielectric continuum on molecular length scales allows very simple estimates of solvation structure and thermodynamics for charged and polar solutes. While this approach can successfully account for…
We describe the structure of the time-harmonic electromagnetic field of a vertical Hertzian electric dipole source radiating over an infinite, translation invariant two-dimensional electron system. Our model for the electron flow takes into…
The hydrogen peroxide is present in the living cell at small concentrations that increase under the action of the heavy ion beams in the process of anticancer therapy. The interactions of hydrogen peroxide with DNA, proteins and other…
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…
A model for the motion of ring-shaped DNA in a gel is introduced and studied by numerical simulations and a mean-field approximation. The ring motion is mediated by finger-shaped loops (hernias) that move in an amoeba-like fashion around…
Using a combination of dielectric spectroscopy and solid-state deuteron NMR, the hydration water dynamics of connective tissue proteins is studied at sub-ambient temperatures. In this range, the water dynamics follows an Arrhenius law. A…
The control over DNA elongation in nanofluidic devices holds great potential for large-scale genomic analysis. So far, the manipulation of DNA in nanochannels has been mostly carried out with electrophoresis and seldom with hydrodynamics,…
The bias-dependent transport properties of short poly(G)-poly(C) A-DNA strands attached to Au electrodes are investigated with first principles electronic transport methods. By using the non- equilibrium Green's function approach combined…
Structuring of DNA counterions around the double helix has been studied by the molecular dynamics method. A DNA dodecamer d(CGCGAATTCGCG) in water solution with the alkali metal counterions Na$^{+}$, K$^{+}$, and Cs$^{+}$ has been…
DNA-functionalized particles have great potential for the design of complex self-assembled materials. The major hurdle in realizing crystal structures from DNA-functionalized particles is expected to be kinetic barriers that trap the system…
The design of hydrogels that combine mechanical robustness with dynamic reconfigurability remains a fundamental challenge, as increasing crosslink dissociation rates compromise network integrity. This limitation is addressed through the…
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…
Liquid water, at ambient conditions, has short-range density correlations which are well known in literature. Surprisingly, large scale molecular dynamics simulations reveal an unusually long-distance correlation in `longitudinal' part of…
We report Molecular Dynamics (MD) simulations of a generic hydrophobic nanopore connecting two reservoirs which are initially at different Na+ concentrations, as in a biological cell. The nanopore is impermeable to water under equilibrium…
Microscopy observations show that suspensions of synthetic and natural nano-layered smectite clay particles submitted to a strong external electric field undergo a fast and extended structuring. This structuring results from the interaction…
Urea denatures proteins due to its strong tendency to dehydrate the first solvation shell via urea-residue preferential binding. However, even after extensive experimental and computational investigations, the influence of urea on the…
Gel electrophoresis allows to separate knotted DNA (nicked circular) of equal length according to the knot type. At low electric fields, complex knots being more compact, drift faster than simpler knots. Recent experiments have shown that…
We present an improved model for studying the interactions between dipole moments of water molecules confined in beryl crystals, inspired by recent NMR experiments. Our model is based on a local crystal potential with dihexagonal symmetry…
The water hydration shell has decisive impact on the structural and functional properties of RNA. Changes of RNA structure upon melting and in biochemical processes are accompanied by a change of hydration patterns, a process which is…