Related papers: Multivalent ion-mediated nucleic acid helix-helix …
Recent results connected to nuclear collision dynamics, from low up to relativistic energies, are reviewed. Heavy ion reactions offer the unique opportunity to probe the complex nuclear many-body dynamics and to explore, in laboratory…
Molecular dynamics (MD) simulation, which is considered an important tool for studying physical and chemical processes at the atomic scale, requires accurate calculations of energies and forces. Although reliable energies and forces can be…
Knowledge of the behavior of hydrogen in metal hydrides is the key for understanding their electronic properties. So far, no experimental methods exist to access these properties beyond 100 GPa, where high-Tc superconductivity emerges.…
The binding of proteins onto DNA contributes to the shaping and packaging of genome as well as to the expression of specific genetic messages. With a view to understanding the interplay between the presence of proteins and the deformation…
Within the Time Dependent Hartree Fock (TDHF) approach, we investigate the impact of several ingredients of the nuclear effective interaction, such as incompressibility, symmetry energy, effective mass, derivative of the Lane potential and…
Force-induced structural transitions both in relatively random and in designed single-stranded DNA (ssDNA) chains are studied theoretically. At high salt conditions, ssDNA forms compacted hairpin patterns stabilized by base-pairing and…
The folding of biological macromolecules is a fundamental process of which we lack a full comprehension. Mostly studied in proteins and RNA, single-stranded DNA (ssDNA) also folds, at physiological salt conditions, by forming non-specific…
Urea titration of RNA by urea is an effective approach to investigate the forces stabilizing this biologically important molecule. We used all atom molecular dynamics simulations using two urea force fields and two RNA constructs to…
In the present work, we investigate the ionization of molecules of biological interest by the impact of multicharged ions in the intermediate to high energy range. We performed full non-perturbative distorted-wave calculations (CDW) for…
Recent experiments on unzipping of RNA helix-loop structures by force have shown that about 40-base molecules can undergo kinetic transitions between two well-defined `open' and `closed' states, on a timescale = 1 sec [Liphardt et al.,…
We discuss how a balance can be established between the force acting to eject DNA from viral capsids and the force resisting its entry into a colloidal suspension which mimics the host cell cytoplasm. The ejection force arises from the…
In this work we propose a model for DNA double helix within the tight-binding framework that incorporates the helicity of the molecules. We have studied localization properties of three DNAsequences,the periodic poly(dG)-poly(dC) and…
The morphology of DNA is strongly influenced by its surrounding environment, including factors such as pH, salt type and valency, and the presence of polymers. Inorganic salts are known to reduce the DNA chain length through mechanisms like…
Even though the persistence length $L_P$ of double-stranded DNA plays a pivotal role in cell biology and nanotechnologies, its dependence on ionic strength $I$ lacks a consensual description. Using a high-throughput single-molecule…
Our understanding of magnetic reconnection (MR) under chromospheric conditions remains limited. Recent observations have demonstrated the important role of ion-neutral interactions in the dynamics of the chromosphere. Furthermore, the…
Helicase opening of double-stranded nucleic acids may be "active" (the helicase directly destabilizes the dsNA to promote opening) or "passive" (the helicase binds ssNA available due to a thermal fluctuation which opens part of the dsNA).…
Deep Inelastic Scattering (DIS) experiments at the planned Electron-Ion Collider will be affected by details of the hadron formation inside the nuclear volume. Besides semi-inclusive particle production experiments decays of the target…
Microscopic studies of nuclear matter under diverse conditions of density and asymmetry are of great contemporary interest. Concerning terrestrial applications, they relate to future experimental facilities that will make it possible to…
The structure of DNA Binding Proteins enables a strong interaction with their specific target site on DNA. However, recent single molecule experiment reported that proteins can diffuse on DNA. This suggests that the interactions between…
One of the most progressive methods of cancer treatment is ion beam therapy. The simulations of water radiolysis show that in the cell medium the most long-living species are hydrogen peroxide (H$_2$O$_2$) molecules. But up to the present…