Related papers: Track structure simulation of low energy electron …
A comprehensive analysis of the effects of Geant4 algorithms for condensed transport in detectors is in progress. The first phase of the project focuses on electron multiple scattering, and studies two related observables: the longitudinal…
The complexity of the primary structure of human DNA is explored using methods from nonequilibrium statistical mechanics, dynamical systems theory and information theory. The use of chi-square tests shows that DNA cannot be described as a…
The structure of DNA Binding Proteins enables a strong interaction with their specific target site on DNA. However, recent single molecule experiment reported that proteins can diffuse on DNA. This suggests that the interactions between…
We consider error-correcting coding for deoxyribonucleic acid (DNA)-based storage using nanopore sequencing. We model the DNA storage channel as a sampling noise channel where the input data is chunked into $M$ short DNA strands, which are…
A Geant4-based Python/C++ simulation and coding framework, which has been developed and used in order to aid the R&D efforts for thermal neutron detectors at neutron scattering facilities, is described. Built upon configurable geometry and…
We present a first-principles molecular dynamics (MD) simulation and expound upon a mechanism of oxygen depletion hypothesis to explain the mitigation of normal tissue injury observed in ultra-high-dose-rate (UHDR) FLASH radiotherapy. We…
We investigate the non-equilibrium mechanical motion of double-stranded DNA in a molecular junction under electronic current using Keldysh-Langevin molecular dynamics. Non-equilibrium electronic force reshapes the effective potential energy…
DNA nanocompartment is a typical DNA-based machine whose function is dependent of molecular collective effect. Fundamental properties of the device have been addressed via electrochemical analysis, fluorescent microscopy, and atomic force…
Precision neutrino oscillation experiments of the future---of which DUNE is a prime example---require reliable event generator tools. The 1--4 GeV energy regime, in which DUNE will operate, is marked by the transition from the low-energy…
Accurate knowledge of the response of the detection system is very crucial for unambiguous interpretation of the experimental data. A simulation code has been developed using the Monte Carlo technique involving 3-body kinematics for the…
Based upon the Bonn meson-exchange model for the nucleon-nucleon ($NN$) interaction, we study systematically the charge-symmetry-breaking (CSB) of the $NN$ interaction due to nucleon mass splitting. Particular attention is payed to CSB…
The interaction of energetic ions with the electronic and ionic system of target materials is an interesting but challenging multi-scale problem and understanding of the early stages after impact of heavy, initially charged ions is…
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…
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…
The bias-dependent transport properties of short poly(G)-poly(C) A-DNA strands attached to Au electrodes are investigated with first principles electronic transport methods. By using the non- equilibrium Green's function approach combined…
Monte Carlo simulations have been performed in order to evaluate the efficiencies of several light ions identification techniques. The detection system was composed with layers of scintillating material to measure either the deposited…
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…
Graphite, as a material for high-temperature gas-cooled reactors (HTGR), will be exposed to harsh environment. The stability of graphite structure under irradiation is of a key importance for efficiency, reliability and security of the…
We report the results of a theoretical study of quasielastic electron and neutrino interactions with carbon. Our approach takes into account the effects of final-state interactions between the struck nucleon and the residual nucleus,…
We study sequence dependent complexation between oligonucleotides (single strand DNA) and various generation ethylene diamine (EDA) cored poly amido amide (PAMAM) dendrimers through atomistic molecular dynamics simulations accompanied by…