Related papers: A molecular dynamics simulation of DNA damage indu…
Radiation damage induced by ion beams is traditionally treated at different levels of theoretical approaches, for the different scales and mechanisms involved.We present here details of a combined approach that, from a method at a…
The ion-electron coupling properties for a ion impurity in an electron gas and for a two component plasma are carried out on the basis of a regularized electron-ion potential removing the short-range Coulomb divergence. This work is largely…
{\bf Introduction}: To revisit the formulation of the mean chord length in microdosimetry and replace it by the particle mean free path appropriate for modelings in radio-biology. {\bf Methods}: We perform a collision-by-collision following…
Electronic excitations and ionisations produced by electron impact are key processes in the radiation-induced damage mechanisms in materials of biological relevance, underlying important medical and technological applications, including…
In recent years significant attention has been attracted to proposals which utilize DNA for nanotechnological applications. Potential applications of these ideas range from the programmable self-assembly of colloidal crystals, to biosensors…
We solve the orientation recovery of a tumbling protein in the gas phase from single-event measurements of the spatial positions of its ions after an X-ray laser induced explosion. We simulate diffracted X-ray signal and ion dynamics under…
A mechanism of double strand breaking (DSB) in DNA due to the action of two electrons is considered. These are the electrons produced in the vicinity of DNA molecules due to ionization of water molecules with a consecutive emission of two…
Radiation damage is an unavoidable process when performing structural investigations of biological macromolecules with X-ray sources. In crystallography this process can be limited through damage distribution in a crystal, while for single…
DNA is now firmly established as a versatile and robust platform for achieving synthetic nanostructures. While the folding of single molecules into complex structures is routinely achieved through engineering basepair sequences, much less…
We explore the laser-induced ionization dynamics of N2 and CO2 molecules subjected to a few-cycle, linearly polarized, 800\,nm laser pulse using effective two-dimensional single active electron time-dependent quantum simulations. We show…
Context: Acceleration in coronal mass ejection driven shocks is currently considered the primary source of large solar energetic particle events. Aims: The solar wind, which feeds shock-accelerated particles, includes numerous ion…
The spatial organization of DNA involves DNA loop extrusion and the formation of protein-DNA condensates. While the significance of each process is increasingly recognized, their interplay remains unexplored. Using molecular dynamics…
In the present paper we address the general problem of selective electrodynamic interactions between DNA and protein, which is motivated by decades of theoretical study and our very recent experimental findings (M. Lechelon et al,…
We present an integrated modeling framework that combines the Generalized Stochastic Microdosimetric Model (GSM2), used to predict cell survival fractions, with MINAS-TIRITH, a fast and efficient Geant4 DNA-based tool for simulating…
Complex organic molecules (COMs) have been widely observed in molecular clouds and protostellar environments. One of the formation mechanisms of COMs is radical reactions on the icy grain surface driven by UV irradiation. While many…
To characterize the thermodynamical equilibrium of DNA chains interacting with a solution of non-specific binding proteins, a Flory-Huggins free energy model was implemented. We explored the dependence on DNA and protein concentrations of…
Using Langevin Dynamic simulations, we study effects of the shear force on the rupture of a double stranded DNA molecule. The model studied here contains two single diblock copolymers interacting with each other. The elastic constants of…
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.…
In this work, we study the damage in crystalline molybdenum material samples due to neutron bombardment in a primary knock-on atom range of 0.5-10 keV at room temperature. We perform machine learned molecular dynamics (MD) simulations with…
It is well known that the structural deformations (stressed states) of DNA molecule play a crucial role in its biological functions including gene expression. For instance, looping in DNA (often mediated by protein binding) is a crucial…