Related papers: Attraction between DNA molecules mediated by multi…
We investigate knotting probabilities of long double-stranded DNA strands in a coarse-grained Kratky-Porod model for DNA with Monte Carlo simulations. Various ionic conditions are implemented by adjusting the effective diameter of monomers.…
By molecular dynamics simulation, we study the charge inversion phenomenon of a rod macroion in the presence of polyelectrolyte counterions. We simulate electrophoresis of the macroion under an applied electric field. When both counterions…
The Poisson-Boltzmann (PB) theory is extensively used to gain insight on charged colloids and biological systems as well as to elucidate fundamental properties of intermolecular forces. Many works were devoted in the past to study PB…
Ion distributions in dilute polyelectrolyte solutions are studied by means of Langevin dynamics simulations. We show that the distributions depend on the conformation of a chain while the conformation is determined by the chain stiffness…
We calculate the interaction potential between two colloids immersed in an aqueous mixture containing salt near or above the critical temperature. We find an attractive interaction far from the coexistence curve due to the combination of…
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…
Charge migration along DNA molecules has attracted scientific interest for over half a century. Reports on possible high rates of charge transfer between donor and acceptor through the DNA, obtained in the last decade from solution…
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.…
The forces between charged macromolecules, usually given in terms of osmotic pressure, are highly affected by the intervening ionic solution. While in most theoretical studies the solution is treated as a homogeneous structureless…
We present micro-rheological measurments of the drag force on colloids pulled through a solution of lambda-DNA (used here as a monodisperse model polymer) with an optical tweezer. The experiments show a violation of the Stokes-Einstein…
Understanding how soft matter systems, including biological ones, can develop collective electromagnetic phenomena under external fields at ambient conditions remains a central challenge, as thermal fluctuations are generally expected to…
Long-ranged attractions across water between two surfaces that are randomly covered with (mobile) positive and negative charge domains have been attributed to induced correlation of the charges (positive lining up with negative) as the…
Molecular Dynamics simulations of crystallization in a supercooled liquid of Lennard-Jones particles with different range of attractions shows that the inclusion of the attractive forces from the first, second and third coordination shell…
The vibrational dynamics of a DNA molecule with counterions neutralizing the charged phosphate groups have been studied. With the help of elaborated model the conformational vibrations of the DNA double helix with alkaline metal ions have…
The high linear charge density of 20-base-pair oligomers of DNA is shown to lead to a striking non-monotonic dependence of the long-time self-diffusion on the concentration of the DNA in low-salt conditions. This generic non-monotonic…
Electronic and magnetic properties of DNA structures doped by simple and transition d- and f-metal ions (Gd, La, Cu, Zn, Au) are reviewed. Both one- and two dimensional systems are considered. A particular attention is paid to gadolinium…
Experiments using the Surface Force Apparatus (SFA) have found anomalously long-ranged interactions between charged surfaces in concentrated salt solutions. Ion clustering have been suggested as a possible origin of this behaviour. In this…
We investigate quantum transport characteristics of a ladder model, which effectively mimics the topology of a double-stranded DNA molecule. We consider the interaction of tunneling charges with a selected internal vibrational degree of…
The interplay of membrane proteins is vital for many biological processes, such as cellular transport, cell division, and signal transduction between nerve cells. Theoretical considerations have led to the idea that the membrane itself…
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…