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Tunneling and over-barrier ionization are the primary processes of strong-field ionization of atoms and molecules. While the dynamics of tunneling ionization have been extensively studied, exploration of over-barrier ionization dynamics has…
Ion-induced DNA damage is an important effect underlying ion-beam cancer therapy. This paper introduces the methodology of modeling DNA damage induced by a shock wave caused by a projectile ion. Specifically, it is demonstrated how single-…
Bending of DNA from a straight rod to a circular form in presence of any of the mono-, di-, tri- or tetravalent counterions has been simulated in strong Coulomb coupling environment employing a previously developed energy minimization…
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…
Gene regulation is one of the most important fundamental biological processes in living cells. It involves multiple protein molecules that locate specific sites on DNA and assemble gene initiation or gene repression multi-molecular…
Accurate knowledge of the thermodynamic properties of nucleic acids is crucial to predicting their structure and stability. To date most measurements of base-pair free energies in DNA are obtained in thermal denaturation experiments, which…
Structural changes in giant DNA induced by the addition of the flexible polymer PEG were examined by the method of single-DNA observation. In dilute DNA conditions, individual DNA assumes a compact state via a discrete coil-globule…
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 rapid worldwide spread of severe viral infections, often involving novel modifications of viruses, poses major challenges to our health care systems. This means that tools that can efficiently and specifically diagnose viruses are much…
The mechanism of threshold elongation (overstretching) of DNA macromolecules under the action of external force is studied within the framework of phenomenological approach. When considering the task it is taken into account that…
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…
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…
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…
We propose a simple model for the kinetics of packaging of viral DNA in to a capsid against an external force trying to prevent it. The model leads to a Butler-Volmer type dependence of the rate of packaging on the pulling force F.
Chiral-induced-spin-selectivity of electron transport and its interplay with DNA's mechanical motion is explored in a double stranded DNA helix with spin-orbit-coupling. The mechanical degree of freedom is treated as a stochastic classical…
By resorting to the thick-chain model we discuss how the stretching response of a polymer is influenced by the self-avoidance entailed by its finite thickness. The characterization of the force versus extension curve for a thick chain is…
The bacterial flagellar motor is an ion-powered transmembrane protein complex which drives swimming in many bacterial species. The motor consists of a cytoplasmic 'rotor' ring and a number of 'stator' units, which are bound to the cell wall…
The mechanical model based on beads and springs, which we recently proposed to study non-specific DNA-protein interactions [J. Chem. Phys. 130, 015103 (2009)], was improved by describing proteins as sets of interconnected beads instead of…
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…
We investigate the ionic current modulation in DNA nanopore translocation setups by numerically solving the electrokinetic mean-field equations for an idealized model. Specifically, we study the dependence of the ionic current on the…