Related papers: Simulation and Experimental Verification of DNA Da…
The processes of interaction of an aqueous solution of methylene blue (MB) organic dye ($C_{16}H_{18}N_{3}SCl$ ) with gamma quanta and electrons have been investigated. A model has been developed, and the passage of electrons with an energy…
Gamma-Ray Bursts (GRBs) are likely to have made a number of significant impacts on the Earth during the last billion years. We have used a two-dimensional atmospheric model to investigate the effects on the Earth's atmosphere of GRBs…
The mechanism allowing a protein to search of a target sequence on DNA is currently described as an intermittent process composed of 3D diffusion in bulk and 1D diffusion along the DNA molecule. Due to the relevant charge of protein and…
This paper presents results of numerical simulations of electron tunneling through water that extend our previous calculations on such systems in several ways. First, a tip-substrate configuration is used; second, calculations are carried…
An efficient approach for the simulation of ion scattering from solids is proposed. For every encountered atom, we take multiple samples of its thermal displacements among those which result in scattering with high probability to finally…
X-ray diffraction microscopy (XDM) is a new form of x-ray imaging that is being practiced at several third-generation synchrotron-radiation x-ray facilities. Although only five years have elapsed since the technique was first introduced, it…
We investigated cellular distribution of a tumor-specific gadolinium chelate in 4T1 and U87 cancer cells with the goal to generate more realistic geometries for Monte Carlo simulations of radiation interaction with nanoparticles in cells.…
The target theory is the most classical hypothesis explaining radiation-induced cell death, the physical or biological nature of the "target" remains ambiguous. This study hypothesizes that the distribution of DNA double-strand breaks…
The European X-ray Free Electron Laser (XFEL) will deliver 30,000 fully coherent, high brilliance X-ray pulses per second each with a duration below 100 fs. This will allow the recording of diffraction patterns of single complex molecules…
All atom molecular dynamics simulations with explicit water were done to study the interaction between two parallel double-stranded DNA molecules in the presence of the multivalent counterions putrescine (2+), spermidine (3+), spermine (4+)…
The melting of a homopolymer double-stranded (ds) deoxyribonucleic acid (DNA) in the dilute limit is studied numerically in the presence of an attractive and impenetrable surface on a simple cubic lattice. The two strands of the DNA are…
We study the static and dynamical properties of DNA in the vicinity of its melting transition, i.e. the separation of the two strands upon heating. The investigation is based on a simple mechanical model which includes the helicoidal…
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…
Low-energy electrons offer a unique possibility for long exposure imaging of individual biomolecules without significant radiation damage. In addition, low-energy electrons exhibit high sensitivity to local potentials and thus can be…
$Objective$. Obtaining the intrinsic dose distributions in particle therapy is a challenging problem that needs to be addressed by imaging algorithms to take advantage of secondary particle detectors. In this work, we investigate the…
Many proteins interact with and deform double-stranded DNA in cells. Single-molecule experiments have studied the elasticity of DNA with helix-deforming proteins, including proteins that bend DNA. These experiments increase the need for…
Gamma-ray bursts (GRBs) are likely to have made a number of significant impacts on the Earth during the last billion years. The gamma radiation from a burst within a few kiloparsecs would quickly deplete much of the Earth's protective ozone…
Strong influence of water molecules on the transport and magnetic properties of DNA, observed in this study, opens up real opportunities for application of DNA in molecular electronics. Interaction of the nucleobases with water molecules…
We study theoretically the in vitro evolution of a DNA sequence by binding to a transcription factor. Using a simple model of protein-DNA binding and available binding constants for the Mnt protein, we perform large-scale, realistic…
Secondary electron cascades can induce significant ionisation in condensed matter due to electron-atom collisions. This is of interest in the context of diffraction and imaging using X-rays, where radiation damage is the main limiting…