Related papers: A molecular dynamics simulation of DNA damage indu…
Irradiation- and collision-induced fragmentation studies provide information about geometry, electronic properties and interactions between structural units of various molecular systems. Such knowledge brings insights into…
Charge diffusion through desoxyribonucleic acid (DNA) is a physico-chemical phenomenon that on the one hand is being explored for technological purposes, on the other hand is applied by nature for various informational processes in life.…
Motivated by the wide ranging experimental results on the conductivity of DNA, we have investigated extraordinary configurations and chemical environments in which DNA might become a true molecular wire, perticularly from enhanced…
The interplay between bending of the molecule axis and appearance of disruptions in circular DNA molecules, with $\sim 100$ base pairs, is addressed. Three minicircles with different radii and almost equal content of AT and GC pairs are…
In the present work, we develop a general spatial stochastic model to describe the formation and repair of radiation-induced DNA damage. The model is described mathematically as a measure-valued particle-based stochastic system and extends…
Detonation of a three-dimensional reactive non-isotropic molecular crystal is modeled using molecular dynamics simulations. The detonation process is initiated by an impulse, followed by the creation of a stable fast reactive shock wave.…
We review the study of dissociative recombination and ro-vibrational excitation of diatomic and small polyatomic molecular ions initiating complex organic molecules formation. In particular, we show how Multichannel Quantum Defect Theory…
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…
Dissociative electron attachment, that is, the cleavage of chemical bonds induced by low-energy electrons, is difficult to model with standard quantum-chemical methods because the involved anions are not bound but subject to autodetachment.…
We here examine the nonlinear dynamics of artificial homogeneous DNA chain relying on the plain-base rotator model. It is shown that such dynamics can exhibit kink and antikink solitons of sine-Gordon type. In that respect we propose…
The fragmentation of molecular cations following inner-shell decay processes in molecules containing heavy elements underpins the x-ray damage effects observed in x-ray scattering measurements of biological and chemical materials, as well…
The passage of DNA through a nanopore can be effectively decomposed into two distinct phases, docking and actual translocation. In experiments each phase is characterized by a distinct current signature which allows the discrimination of…
Living cells provide a fluctuating, out-of-equilibrium environment in which genes must coordinate cellular function. DNA looping, which is a common means of regulating transcription, is very much a stochastic process; the loops arise from…
The effective DNA-DNA interaction force is calculated by computer simulations with explicit tetravalent counterions and monovalent salt. For overcharged DNA molecules, the interaction force shows a double-minimum structure. The positions…
We propose a scar model to reproduce how double-strand breaks occur in the telomeric DNA damaged by the effect of the $\beta$-decay of tritium to helium. In this scar model, the two hydrogens bonded to the 5$^\prime$ carbon connecting the…
A low pressure discharge sustained in molecular hydrogen with help of the electron cyclotron resonance heating at a frequency of 2.45 GHz is simulated using a fully electromagnetic implicit charge- and energy-conserving…
Radiation damage is considered to be the major problem that still prevents imaging an individual biological molecule for structural analysis. So far, all known mapping techniques using sufficient short wave-length radiation, be it X-rays or…
Simulating collision cascades and radiation damage poses a long-standing challenge for existing interatomic potentials, both in terms of accuracy and efficiency. Machine-learning based interatomic potentials have shown sufficiently high…
Photoionization modelling allows to follow the transport, the emergence, and the absorption of photons taking into account all important processes in nebular plasmas. Such modelling needs the spatial distribution of density, chemical…
We present a molecular dynamics simulation of shock waves propagating in dense deuterium with the electron force field method [J. T. Su and W. A. Goddard, Phys. Rev. Lett. 99, 185003 (2007)], which explicitly takes the excitation of…