Related papers: A Simulation Approach for Determining the Spectrum…
In solution, DNA is a highly charged macromolecule which bears a unit of negative charge on each phosphate of its sugar-phosphate backbone. Although partially compensated by counterions adsorbed at or condensed near it, DNA still produces a…
A detailed description of the conformational plasticity of double stranded DNA (ds) is a necessary framework for understanding protein-DNA interactions. Until now, however structure and kinetics of the transition from the basic conformation…
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…
The interaction of heavy charged particles with DNA is of interest for several areas, from hadrontherapy to aero-space industry. In this paper, a TD-DFT study on the interaction of a 4 keV proton with an isolated DNA base pair was carried…
A version of Geant4 has been developed to treat high-energy proton radiography. This article presents the results of calculations simulating the effects of nuclear elastic scattering for various test step wedges. Comparisons with…
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…
230 MeV proton beam out of a cyclotron was delivered into a Zebra multi layered IC detector (IBA) calibrated in terms of penetration range in water. The analysis of the measured Bragg peak determines penetration range in water which can be…
A theory of the unzipping of double-stranded (ds) DNA is presented, and is compared to recent micromanipulation experiments. It is shown that the interactions which stabilize the double helix and the elastic rigidity of single strands (ss)…
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…
To overcome the problem of inefficient computing time and unreliable results in MCNP5 calculation, a two-step method is adopted to calculate the energy deposition of prompt gamma-rays in detectors for depleted uranium spherical shells under…
The results of measurements and computer simulations of radioactivities and dose rates as functions of decay time are presented for Pb-nat and Bi-209 irradiated by 1.5-GeV protons, Co-59, Cu-63, and Cu-65 irradiated by 0.13- and 1.2-GeV…
Single molecule experiments on B-DNA stretching have revealed one or two structural transitions, when increasing the external force. They are characterized by a sudden increase of DNA contour length and a decrease of the bending rigidity.…
Cytosine methylation has been found to play a crucial role in various biological processes, including a number of human diseases. The detection of this small modification remains challenging. In this work, we computationally explore the…
Proton therapy has been rapidly advancing due to its excellent conformal index, but its relatively low relative biological effect (RBE) has somewhat limited its therapeutic efficacy for certain tumors. To address this, we previously…
Interactions of protons with nuclei are modeled in a form that is suitable for Monte Carlo simulation of proton transport. The differential cross section (DCS) for elastic collisions of protons with neutral atoms is expressed as the product…
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…
We investigate knotting probabilities of long double-stranded DNA strands in a coarse-grained Kratky-Porod model for DNA with Monte Carlo simulations. Various ionic conditions are implemented by adjusting the effective diameter of monomers.…
Gamma-ray spectroscopy provides diagnostics of particle acceleration in solar flares, but care must be taken when interpreting the spectra due to effects of the angular distribution of the accelerated particles (such as relativistic…
1D and 2D supernova simulations for stars between 11 and 25 solar masses are presented, making use of the Prometheus/Vertex neutrino-hydrodynamics code, which employs a full spectral treatment of the neutrino transport. Multi-dimensional…
Charge transfer in a DNA duplex chain is studied by constructing a system with virtual electrodes connected at the ends of each DNA strand. The systeym is described by the tight-binding model and its transport is analyzed by the transfer…