The method of Monte Carlo simulation is a powerful tool to investigate the details of radiation biological damage at the molecular level. In this paper, a Monte Carlo code called NASIC (Nanodosimetry Monte Carlo Simulation Code) was developed. It includes physical module, pre-chemical module, chemical module, geometric module and DNA damage module. The physical module can simulate physical tracks of low-energy electrons in the liquid water event-by-event. More than one set of inelastic cross sections were calculated by applying the dielectric function method of Emfietzoglou's optical-data treatments, with different optical data sets and dispersion models. In the pre-chemical module, the ionised and excited water molecules undergo dissociation processes. In the chemical module, the produced radiolytic chemical species diffuse and react. In the geometric module, an atomic model of 46 chromatin fibres in a spherical nucleus of human lymphocyte was established. In the DNA damage module, the direct damages induced by the energy depositions of the electrons and the indirect damages induced by the radiolytic chemical species were calculated. The parameters should be adjusted to make the simulation results be agreed with the experimental results. In this paper, the influence study of the inelastic cross sections and vibrational excitation reaction on the parameters and the DNA strand break yields were studied. Further work of NASIC is underway.
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http://dx.doi.org/10.1093/rpd/ncv171 | DOI Listing |
Nanomaterials (Basel)
March 2025
Faculty of Physics, St. Petersburg State University, Universitetskaya Emb. 13B, 199034 St. Petersburg, Russia.
The nucleation and growth of surface islands in the pre-coalescence stage has previously been studied by different methods, including the rate equation approach and kinetic Monte Carlo simulations. However, full understanding of island growth kinetics and the scaling properties of their size distributions is still lacking. Here, we investigate rate equations for the irreversible homogeneous growth of islands in the continuum limit, and derive a general island-size distribution whose shape is fully determined by the dynamics of the monomer concentration at a given size dependence of the capture coefficients.
View Article and Find Full Text PDFNanomaterials (Basel)
February 2025
Facultad de Ciencias Básicas, Departamento de Física y Electrónica, Universidad de Córdoba, Monteria 230002, Colombia.
We investigated the hysteresis, pseudo-critical, and compensation behaviors of a quasi-spherical FeCo alloy nanoparticle (2 nm in diameter) using Monte Carlo simulations with thermal bath-type algorithms and a 3D mixed Ising model. The nanostructure was modeled in a body-centered cubic lattice (BCC) through the following configurations: spin S=3/2 for Co and Q=2 for Fe. These simulations reveal that, under the influence of crystal and magnetic fields, the nanoparticle exhibits compensation phenomena, exchange bias, and pseudo-critical temperatures.
View Article and Find Full Text PDFBiom J
April 2025
Department of Mathematics, University of Texas at Arlington, Arlington, Texas, USA.
The mean residual life (MRL) function plays an important role in the summary and analysis of survival data. The main advantage of this function is that it summarizes the information in units of time instead of a probability scale, which requires careful interpretation. Ranked set sampling (RSS) is a sampling technique designed for situations, where obtaining precise measurements of sample units is expensive or difficult, but ranking them without referring to their accurate values is cost-effective or easy.
View Article and Find Full Text PDFJ Exp Bot
March 2025
Graduate School of Integrated Sciences for Life, Hiroshima University, 1-4-3, Kagamiyama, Higashi-Hiroshima 739-8526, Japan.
The leaves of the cycad Encephalartos horridus exhibit a conspicuous glaucous appearance, attributed to the presence of epicuticular wax. However, the molecular and optical bases of this coloration have not been scientifically explained. In this study, we conducted a detailed analysis of the epicuticular wax composition, combined with RNA-Seq and de novo transcriptome assembly, to uncover the molecular mechanisms underlying this phenomenon.
View Article and Find Full Text PDFJ Chem Phys
March 2025
N. D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, 47 Leninsky prosp., Moscow 119991, Russian Federation.
Accurate prediction of polymer properties using molecular dynamics (MD) simulations requires a properly relaxed starting structure. Polymer models built from scratch by specialized algorithms (self-avoiding random walk, Monte Carlo, etc.) are far from relaxed and, moreover, often possess a large number of structural defects: close contacts between atoms, wrong bond distances, voids, unfavorable molecular conformations or packing, etc.
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