PubMed · 734018
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W W Rozeboom. 1978. Estimation of cross-validated multiple correlation: a clarification.. https://pubmed.ncbi.nlm.nih.gov/734018/
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Objective.To build and validate a simulation framework to perform single-cell and bulk-cell whole genome sequencing simulation of radiation-exposed Monte Carlo (MC) cell models to assist radiation genomics studies.Approach.Sequencing the genomes of radiation-damaged cells can provide useful insight into radiation action for radiobiology research. However, carrying out post-irradiation sequencing experiments can often be challenging, expensive, and time-consuming. Although computational simulations have the potential to provide solutions to these experimental challenges, and aid in designing optimal experiments, the absence of tools currently limits such application. MC toolkits exist to simulate radiation exposures of cell models but there are no tools to simulate single- and bulk-cell sequencing of cell models containing radiation-damaged DNA. Therefore, we aimed to develop a MC simulation framework to address this gap by designing a tool capable of simulating sequencing processes for radiation-damaged cells. Main results.We developed RadiSeq-a multi-threaded whole-genome DNA sequencing simulator written in C++. RadiSeq can be used to simulate Illumina sequencing of radiation-damaged cell models produced by MC simulations. RadiSeq has been validated through comparative analysis, where simulated data were matched against experimentally obtained data, demonstrating reasonable agreement between the two. Additionally, it comes with numerous features designed to closely resemble actual whole-genome sequencing. RadiSeq is also highly customizable with a single input parameter file.Significance.RadiSeq enables the research community to perform complex simulations of radiation-exposed DNA sequencing, supporting the optimization, planning, and validation of costly and time-intensive radiation biology experiments. This framework provides a powerful tool for advancing radiation genomics research.
The space in the unit cell of a metmyoglobin crystal not occupied by myoglobin atoms was filled with water using Monte Carlo calculations. Independent calculations with different amounts of water have been performed. Structure factors were calculated using the water coordinates thus obtained and the known coordinates of the myoglobin atoms. A comparison with experimental structure factors showed that both the low and the high resolution regime could be well reproduced with 814 Monte Carlo water molecules per unit cell with a B-value of 50 A2. The Monte Carlo water molecules yield a smaller standard R-value (0.166) than using a homogeneous electron density for the simulation of the crystal water (R = 0.212). A reciprocal space refinement of the water and the protein coordinates has been performed. Monte Carlo calculations can be used to obtain information for crystallographically invisible parts of the unit cell and yield better coordinates for the visible part in the refinement.
The Compton scattered photons from a scattering medium can be analyzed in a Compton spectrometer and the primary energy spectrum derived using the Compton equation. Since the reconstruction algorithm assumes that only singly-scattered photons from the scatterer are detected, multiply-scattered photons introduce errors into the measurements unless they can be accurately corrected for. In this work, a Monte Carlo collision density estimator was used to determine the contribution from photons multiply-scattered from a Lucite scatterer in the form of a square rod. The ratio of multiply- to singly-scattered photons was determined for rod thicknesses from 0.5 to 5 mm and photons of energy 20 to 110 keV. The ratio in percent can be well approximated as a linear function of energy with slope 2.2. For thicknesses below 2 mm, the ratio is less than 5% at all energies.