Related papers: Multivalent ion-mediated nucleic acid helix-helix …
We probe the electrostatic cost associated with the approach phase of DNA translocation events. Within an analytical theory at the Debye-Huckel level, we calculate the electrostatic free energy of a rigid DNA molecule interacting with a…
The twisting deformation of mechanically stretched DNA molecules is studied by a coarse grained Hamiltonian model incorporating the fundamental interactions that stabilize the double helix and accounting for the radial and angular base pair…
Hard processes in nucleus-nucleus interactions at relativistic energies are reviewed with emphasis on recent PHENIX results from the first run of the Relativistic Heavy-Ion Collider at BNL. The observed suppression of moderately high $p_T$…
We construct a theoretical model for the dynamics of a microscale colloidal particle, modeled as an interval, moving horizontally on a DNA-coated surface, modelled as a line coated with springs that can stick to the interval. Averaging over…
Although DNA is often bent in vivo, it is unclear how DNA-bending forces modulate DNA-protein binding affinity. Here, we report how a range of DNA-bending forces modulates the binding of the Integration Host Factor (IHF) protein to various…
We present a general theory for predicting the interaction potentials between DNA-coated colloids, and more broadly, any particles that interact via valence-limited ligand-receptor binding. Our theory correctly incorporates the…
Ions interacting with hydrated RNA play a central role in defining its secondary and tertiary structure. While spatial arrangements of ions, water molecules, and phosphate groups have been inferred from X-ray studies, the role of…
In the following we stress the advantages of the NICA research programme in the context of studying the spectator-induced electromagnetic phenomena present in proton-nucleus and heavy ion collisions. We point at the specific interest of…
We use X-ray scattering and molecular simulations to investigate the structural properties of complexes of multivalent cationic lipids and DNA molecules. At low mole fraction of neutral lipids (NLs), $\Phi_{\rm NL}$, the complexes show…
In many organisms, homologous (or repetitive) chromosomal regions can associate or/and undergo concerted epigenetic changes in the absence of DNA breakage and recombination. The direct specific pairing of DNA duplexes with similar…
While the thermodynamics of DNA hybridization is well understood, much less is known about the kinetics of this classic system. Filling this gap in our understanding has new urgency because DNA nanotechnology often depends critically on…
Adsorption of monovalent and multivalent cat- and anions on a deoxyribose nucleic acid (DNA) molecule from a salt solution is investigated by computer simulation. The ions are modelled as charged hard spheres, the DNA molecule as a point…
We present a molecular dynamics study of the effects of carbon- and iron-ion induced shock waves in DNA duplexes in liquid water. We use the CHARMM force field implemented within the MBN Explorer simulation package to optimize and…
Dynamics of the polymorphic A<->B transitions in DNA is compared for two polypurine sequences, poly(dA).poly(dT) and poly(dG).poly(dC), long known to exhibit contrasting properties in experiments. In free molecular dynamics simulations…
The double folding (DF) approach is one of the widely used methods for finding nucleus-nucleus interaction potential. In the present work, the influence of the nuclear matter density on the DF potential and on the Coulomb barrier parameters…
We present a multi-scale simulation of early stage of DNA damages by the indirect action of hydroxyl ($^\bullet$OH) free radicals generated by electrons and protons. The computational method comprises of interfacing the Geant4-DNA Monte…
Collisions between heavy nuclei at the Relativistic Heavy Ion Collider liberate from the nuclear wavefunction of order 10,000 gluons, quarks and antiquarks. The system is dominated by gluons and up and down (anti) quarks. Heavy quarks,…
The density decreases exponentially with height in the solar gravitationally stratified atmosphere, therefore the collisional coupling between the ionized plasma and the neutrals also decreases. Here, we investigate the role of collisions…
With the recent availability of state-of-the-art heavy-ion stable and radioactive beams, there has been a renew interest in the investigation of nuclear reactions with heavy ions. I first present the role of inelastic and transfer channel…
The formation of nanoscale domains (NDs) in correlated liquids and the emerging collective magnetic properties have been suggested as key mechanisms governing ion transport under external magnetic fields (eMFs). However, the molecular-level…