Related papers: A Simulation Approach for Determining the Spectrum…
The limits of previous methods promote us to design a new approach (named PRESTAGE) to predict proton single event effect (SEE) cross-sections using heavy-ion test data. To more realistically simulate the SEE mechanisms, we adopt Geant4 and…
Employing a recently-developed dispersive optical model (DOM) which allows a complete description of experimental data both above (up to 200 MeV) and below the Fermi energy in $^{40}$Ca, we demonstrate that elastic nucleon-nucleus…
Formation of random network of DNA strands is simulated on a two-dimensional triangular lattice. We investigate the size distribution of pores in the network. The results are interpreted within theory of percolation on Bethe lattice.
Motivated by recent experiments we have studied the optical conductivity of DNA in its natural environment containing water molecules and counter ions. Our density functional theory calculations (using SIESTA) for four base pair B-DNA with…
Within a covariant effective one-boson exchange model for the $T$ matrix of $NN$ interactions we present detailed calculations of bremsstrahlung cross sections for proton - proton and proton - neutron reactions at beam energies in the 1 GeV…
We present in detail and validate an effective Monte Carlo approach for the calculation of the nuclear vibrational densities via integration of molecular eigenfunctions that we have preliminary employed to calculate the densities of the…
A unique feature of generalised parton distributions is their relation to the QCD energy-momentum tensor. In particular, they provide access to the mechanical properties of the proton i.e. the distributions of pressure and shear stress…
To elucidate the possible role of structural waters in stabilizing bent DNA, various conformations of AT-containing decamers, (A5T5)2 and A10:T10, were studied by Monte Carlo simulations. The duplexes were constrained to reproduce the NMR…
{\bf Purpose}: To develop a first principle and multi-scale model for normal tissue complication probability (NTCP) as a function of dose and LET for proton and in general for particle therapy with a goal of incorporating nano-scale…
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…
To improve the quality of cancer treatment with protons, a translation of X-ray Computed Tomography (CT) images into a map of the proton stopping powers needs to be more accurate. Proton stopping powers determined from CT images have…
We present the first proof-of-concept simulations of detectors using biomaterials to detect particle interactions. The essential idea behind a "DNA detector" involves the attachment of a forest of precisely-sequenced single or…
A deep convolutional neural network (CNN) is developed to study symmetry energy $E_{\rm sym}(\rho)$ effects by learning the mapping between the symmetry energy and the two-dimensional (transverse momentum and rapidity) distributions of…
Low-energy electrons (LEEs) are known to be effective in causing strand breaks in DNA. Recent experiments show that an important direct source of LEEs is the intermolecular Coulombic decay (ICD) process. Here we propose a new cascade…
We develop a simple model to study the effects of an applied force on the melting of a double stranded DNA (dsDNA). Using this model, we could study the stretching, unzipping, rupture and slippage like transition in a dsDNA. We show that in…
In this work, we report a novel strategy to construct molecular diodes with a record tunable rectification ratio of as high as 10^6 using oxidatively damaged DNA molecules. Being exposed to several endogenous and exogenous events, DNA…
We report model calculations on DNA single strands which describe the equilibrium dynamics and kinetics of hairpin formation and melting. Modeling is at the level of single bases. Strand rigidity is described in terms of simple polymer…
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 distribution of bubble lengths in double-stranded DNA is presented for segments of varying guanine-cytosine (GC) content, obtained with Monte Carlo simulations using the Peyrard-Bishop-Dauxois model at 310 K. An analytical description…
Correlation length exponent $\nu$ for long linear DNA molecules was determined by direct measurement of the average end-to-end distance as a function of the contour length $s$ by means of atomic force microscopy (AFM). Linear DNA, up to…