Related papers: Simulation and Experimental Verification of DNA Da…
The resolution of X-ray diffraction microscopy is limited by the maximum dose that can be delivered prior to sample damage. In the proposed Serial Crystallography method, the damage problem is addressed by distributing the total dose over…
The paper discusses some 3D simulations to compute the ionizing radiation dose during laser-plasma experiments leading to the generation of accelerated protons and electrons. Also, we suggest a new method to increase the measurement…
This proceeding discusses the impact of XUV/X-ray irradiation on materials, and how their response is affected by temperature, size, and structure. When materials are exposed to intense XUV/X-ray irradiation, they undergo a series of…
The present work introduces a rigorous stochastic model, named Generalized Stochastic Microdosimetric Model (GSM2), to describe biological damage induced by ionizing radiation. Starting from microdosimetric spectra of energy deposition in…
The highly energetic electrons in a transmission electron microscope (TEM) can alter or even completely destroy the structure of samples before sufficient information can be obtained. This is especially problematic in the case of zeolites,…
The passage of energetic ions through tissue initiates a series of physico-chemical events, which lead to biodamage. The study of this scenario using a multiscale approach brought about the theoretical prediction of shock waves initiated by…
The distance-resolved effective interaction potential between two parallel DNA molecules is calculated by computer simulations with explicit tetravalent counterions and monovalent salt. Adding counterions first yields an attractive minimum…
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 used a multiscale model to study the damage caused by swift heavy ions in GaN. The model combines Monte Carlo and molecular dynamics simulations to analyze the material response to the excitation initiated by a projectile. We found that…
Single molecule DNA experiments often generate data from force versus extension measurements involving the tethering of a microsphere to one end of a single DNA molecule while the other is attached to a substrate. We show that the…
Free-electron lasers (FELs) opened a new window on imaging the motion of atoms and molecules. At SLAC, FEL experiments are performed at LCLS using 120 Hz pulses with 10^12 to 10^13 photons in 10 fs (billions of times brighter than at the…
Secondary electron cascades are responsible for significant ionizations in macroscopic samples during irradiation with X-rays. A quantitative analysis of these cascades is needed, e.g. for assessing damage in optical components at X-ray…
Electroporation is a physical method to induce the uptake of therapeutic drugs and DNA, by eukaryotic cells and tissues. The phenomena behind electro-mediated membrane permeabilization to plasmid DNA have been shown to be significantly more…
The problem of DNA-DNA interaction mediated by divalent counterions is studied using computer simulation. Although divalent counterions cannot condense free DNA molecules in solution, we show that if DNA configurational entropy is…
Energetic ions lose their energy in tissue mainly by ionising its molecules. This produces secondary electrons which transport this energy radially away from the ion path. The ranges of most of these electrons do not exceed a few…
The oxDNA model of DNA has been applied widely to systems in biology, biophysics and nanotechnology. It is currently available via two independent open source packages. Here we present a set of clearly-documented exemplar simulations that…
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 sequence-dependent structural variability and conformational dynamics of DNA play pivotal roles in many biological milieus, such as in the site-specific binding of transcription factors to target regulatory elements. To better…
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…
Recent theoretical predictions on DNA mechanical separation induced by pulling forces are numerically tested within a model in which self-avoidance for DNA strands is fully taken into account. DNA strands are described by interacting pairs…