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Monte carlo

R Breier, V B Brudanin, P Loaiza, F Piquemal, P P Povinec, E Rukhadze, N Rukhadze, I Štekl
The main limitation in the high-sensitive HPGe gamma-ray spectrometry has been the detector background, even for detectors placed deep underground. Environmental radionuclides such as 40 K and decay products in the 238 U and 232 Th chains have been identified as the most important radioactive contaminants of construction parts of HPGe gamma-ray spectrometers. Monte Carlo simulations have shown that the massive inner and outer lead shields have been the main contributors to the HPGe-detector background, followed by aluminum cryostat, copper cold finger, detector holder and the lead ring with FET...
May 21, 2018: Journal of Environmental Radioactivity
Parvin Eslami Shahrbabki, Bahador Hajimohammadi, Shahram Shoeibi, Mehdi Elmi, Arash Yousefzadeh, Gea Oliveri Conti, Margherita Ferrante, Maryam Amirahmadi, Yadolah Fakhri, Amin Mousavi Khaneghah
A modified "Quick, Easy, Cheap, Effective, Rugged, and Safe" QuEChERS in combination with Ultra-High Performance Liquid Chromatography/tandem mass spectrometry (UHPLC-MS/MS) method was optimized for the determination of acrylamide content in different types of tah-dig (rice, bread, and potato). Also, the non-carcinogenic and carcinogenic risks (target hazard quotient (THQ) and incremental lifetime cancer risk (ILCR)) due to ingestion of acrylamide via tah-dig in the adults and children were assessed by Monte Carlo simulation (MCS) method...
May 21, 2018: Food and Chemical Toxicology
Scott D Bembenek, Gavin Hirst, Taraneh Mirzadegan
We analyzed an extensive data set of 3000 Janssen kinase inhibitors (spanning some 40 therapeutic projects) profiled at 414 kinases in the DiscoverX KINOMEscan to better understand the necessity of using such a full kinase panel versus simply profiling one's compound at a much smaller number of kinases, or mini kinase panel (MKP), to assess its selectivity. To this end, we generated a series of MKPs over a range of sizes, and of varying kinase membership using Monte Carlo simulations. By defining the kinase hit index (KHI), we quantified a compound's selectivity based on the number of kinases it hits...
May 24, 2018: Journal of Chemical Information and Modeling
Xuejiao Zeng, Hao Gao, Xunbin Wei
In the traditional two-step procedure used in intensity-modulated radiation therapy, fluence map optimization (FMO) is performed first, followed by use of a leaf sequencing algorithm (LSA). By contrast, direct aperture optimization (DAO) directly optimizes aperture leaf positions and weights. However, dose calculation using the Monte Carlo (MC) method for DAO is often time-consuming. Therefore, a rapid DAO (RDAO) algorithm is proposed that uses a dose influence matrix based piecewise aperture dose model (DIM-PADM)...
2018: PloS One
Noah R Van Zandt, Mark F Spencer, Michael J Steinbock, Brian M Anderson, Milo W Hyde, Steven T Fiorino
Polychromatic laser light can reduce speckle noise in many wavefront-sensing and imaging applications. To help quantify the achievable reduction in speckle noise, this study investigates the accuracy of three polychromatic wave-optics models under the specific conditions of an unresolved object. Because existing theory assumes a well-resolved object, laboratory experiments are used to evaluate model accuracy. The three models use Monte-Carlo averaging, depth slicing, and spectral slicing, respectively, to simulate the laser-object interaction...
May 20, 2018: Applied Optics
Noah R Van Zandt, Jack E McCrae, Mark F Spencer, Michael J Steinbock, Milo W Hyde, Steven T Fiorino
Polychromatic laser light can reduce speckle noise in wavefront-sensing and imaging applications that use direct-detection schemes. To help quantify the achievable reduction in speckle, this paper investigates the accuracy and numerical efficiency of three separate wave-optics methods. Each method simulates the active illumination of extended objects with polychromatic laser light. In turn, this paper uses the Monte Carlo method, the depth-slicing method, and the spectral-slicing method, respectively, to simulate the laser-object interaction...
May 20, 2018: Applied Optics
Chun-Fang Tong, Yan Zhang, Shou-Qin Lü, Ning Li, Yi-Xin Gong, Hao Yang, Shi-Liang Feng, Yu Du, Dan-Dan Huang, Mian Long
Flowing neutrophils (PMNs) are forced to recruit towards inflamed tissue and adhere on vascular endothelial cells, which is primarily mediated by the binding of β2 -integrins to ICAM-1s. This process is distinct among different organs such as liver and brain, however, the underlying kinetic and mechanical mechanisms regulating tissue-specific recruitment of PMNs remain unclear. Here binding kinetics measurement showed that, ICAM-1 on murine hepatic sinusoidal endothelial cells (LSECs) bound to lymphocyte function-associated antigen-1 (LFA-1) with higher on- and off-rates but lower effective affinity compared to macrophage-1 antigen (Mac-1), while ICAM-1 on cerebral endothelial cells (BMECs or bEnd...
May 23, 2018: American Journal of Physiology. Cell Physiology
Aditya Chattopadhyay, Min Zheng, Mark Paul Waller, U Deva Priyakumar
Knowledge of the structure and dynamics of biomolecules is essential for elucidating the underlying mechanisms of biological processes. Given the stochastic nature of many biological processes, like protein unfolding, it's almost impossible that two independent simulations will generate the exact same sequence of events, which makes direct analysis of simulations difficult. Statistical models like Markov Chains, transition networks etc. help in shedding some light on the mechanistic nature of such processes by predicting long-time dynamics of these systems from short simulations...
May 23, 2018: Journal of Chemical Theory and Computation
Allan K N Alencar, Guilherme C Montes, Daniele G Costa, Luiza V P Mendes, Ananssa M S Silva, Sabrina T Martinez, Margarete M Trachez, Valéria do M N Cunha, Tadeu L Montagnoli, Aline G M Fraga, Hao Wang, Leanne Groban, Carlos A M Fraga, Roberto T Sudo, Gisele Zapata-Sudo
Pulmonary hypertension (PH) is a disease of women (female-to-male ratio 4:1), and is associated with cardiac and skeletal muscle dysfunction. Herein, the activation of a new estrogen receptor (GPER) by the agonist G1 was evaluated in oophorectomized rats with monocrotaline (MCT)-induced PH. Depletion of estrogen was induced by bilateral oophorectomy (OVX) in Wistar rats. Experimental groups included SHAM or OVX rats that received a single intraperitoneal injection of MCT (60 mg/kg) for PH induction. Animals received s...
May 21, 2018: Journals of Gerontology. Series A, Biological Sciences and Medical Sciences
Ladislav Šamaj, Martin Trulsson, Emmanuel Trizac
We study thermal equilibrium of classical pointlike counterions confined between symmetrically charged walls at distance d. At very large couplings when the counterion system is in its crystal phase, a harmonic expansion of particle deviations is made around the bilayer positions, with a free lattice parameter determined from a variational approach. For each of the two walls, the harmonic expansion implies an effective one-body potential at the root of all observables of interest in our Wigner strong-coupling expansion...
May 23, 2018: Soft Matter
Halima Elazhar, Thomas Deschler, Jean Michel Letang, Abdelmjid Nourreddine, Nicolas Arbor
The out-of-field dose in radiation therapy is a growing concern in regards to the late side-effects and secondary cancer induction. In high-energy X-ray therapy, the secondary neutrons generated through photonuclear reactions in the accelerator are part of this secondary dose. The neutron dose is currently not estimated by the treatment planning system (TPS) while it appears to be preponderant for distances greater than 50~cm from the isocenter. Monte Carlo (MC) simulation has become the gold standard for accurately calculating the neutron dose under specific treatment conditions but the method is also known for having a slow statistical convergence, which makes it difficult to be used on a clinical basis...
May 23, 2018: Physics in Medicine and Biology
Steven C Erwin, John L Lyons
Atomistic control over the growth of semiconductor thin films, such as aluminum nitride, is a long-sought goal in materials physics. One promising approach is plasma-assisted atomic layer epitaxy, in which separate reactant precursors are employed to grow the cation and anion layers in alternating deposition steps. The use of a plasma during the growth---most often a hydrogen plasma---is now routine and generally considered critical, but the precise role of the plasma is not well understood. We propose a theoretical atomistic model and elucidate its consequences using analytical rate equations, density-functional theory, and kinetic Monte Carlo statistical simulations...
May 23, 2018: ACS Applied Materials & Interfaces
P Pahari, M Warrier, A D P Rao
Based on the three known proposed pathways for the uni-molecular decomposition of RDX, we have formulated the rate equations. A kinetic Monte Carlo code has been developed and used to simulate the uni-molecular decomposition of RDX based on these equations. The KMC simulations allow one to explore each of the decomposition pathways individually and also the three competing pathways at a specified temperature and pressure. The pressure dependence is incorporated using Lindemann's formalism. The code is validated by reproducing the species evolution along each pathway...
May 22, 2018: Journal of Molecular Modeling
Jorge Luis Benites-Rengifo, Hector Rene Vega-Carrillo
Using Monte Carlos methods, with the MCNP5 code, a gynecological phantom and a vaginal cylinder were modeled. The spatial distribution of absorbed dose rates in Uterine Cervical Cancer treatment through low dose rate brachytherapy was determined. A liquid water gynecology computational phantom, including a vaginal cylinder applicator made of Lucite, was designed. The applicator has a linear array of four radioactive sources of Cesium 137. Around the vaginal cylinder, 13 water spherical cells of 0.5 cm-diameter were modeled to calculate absorbed dose emulating the procedure made by the treatment planning system...
May 19, 2018: Applied Radiation and Isotopes
Shusuke Hirayama, Taeko Matsuura, Ueda Hideaki, Yusuke Fujii, Takaaki Fujii, Seishin Takao, Naoki Miyamoto, Shinichi Shimizu, Rintaro Fujimoto, Kikuo Umegaki, Hiroki Shirato
PURPOSE: To evaluate the biological effects of proton beams as part of daily clinical routine, fast and accurate calculation of dose-averaged linear energy transfer (LETd ) is required. In this study, we have developed the analytical LETd calculation method based on the pencil-beam algorithm (PBA) considering the off-axis enhancement by secondary protons. This algorithm (PBA-dLET) was then validated using Monte Carlo simulation (MCS) results. METHODS: In PBA-dLET, LET values were assigned separately for each individual dose kernel based on the PBA...
May 22, 2018: Medical Physics
S S Fernandes, A Astuto, K C S Patrão, E S Fonseca, W W Pereira, R T Lopes
A long counter detector was manufactured by the Institute of Advanced Studies (IEAV) and was characterised in the neutron low scattering room at Brazilian National Ionising Radiation Metrology Laboratory (LNMRI/IRD) to deploy a secondary Standard for neutron fluence. The effective centre was measured experimentally with 252Cf+D2O, 252Cf, 241AmBe and 238PuBe neutron sources, having average energies from 0.55 to 4.16 MeV. The experimental arrangement and detector construction were carefully reproduced in Monte Carlo simulations, and the computational results were found to be in good agreement with those from experiment...
May 17, 2018: Radiation Protection Dosimetry
Jonathan S Mitchell, Rampal S Etienne, Daniel L Rabosky
Time-calibrated phylogenies of living species have been widely used to study the tempo and mode of species diversification. However, it is increasingly clear that inferences about species diversification - extinction rates in particular - can be unreliable in the absence of paleontological data. We introduce a general framework based on the fossilized birth-death process for studying speciation-extinction dynamics on phylogenies of extant and extinct species. The model assumes that phylogenies can be modeled as a mixture of distinct evolutionary rate regimes and that a hierarchical Poisson process governs the number of such rate regimes across a tree...
May 18, 2018: Systematic Biology
Jason Child, Xinhui Chen, Rakesh D Mistry, Stig Somme, Christine MacBrayne, Peter L Anderson, Ronald N Jones, Sarah K Parker
Background: Metronidazole is traditionally dosed every 6-8 hours even though in adults it has a long half-life, concentration-dependent killing, and 3-hour postantibiotic effect. Based on this logic, some pediatric hospitals adopted once-daily dosing for appendicitis, despite limited pharmacokinetics-pharmacodynamics (PK/PD) in children. We studied pediatric patients with appendicitis given metronidazole once daily to determine whether this dosing would meet target area under the curve (AUC)/minimum inhibitory concentration (MIC) ratio of ≥70 for Bacteroides fragilis...
May 16, 2018: Journal of the Pediatric Infectious Diseases Society
Qiwei Li, Xinlei Wang, Faming Liang, Faliu Yi, Yang Xie, Adi Gazdar, Guanghua Xiao
Digital pathology imaging of tumor tissues, which captures histological details in high resolution, is fast becoming a routine clinical procedure. Recent developments in deep-learning methods have enabled the identification, characterization, and classification of individual cells from pathology images analysis at a large scale. This creates new opportunities to study the spatial patterns of and interactions among different types of cells. Reliable statistical approaches to modeling such spatial patterns and interactions can provide insight into tumor progression and shed light on the biological mechanisms of cancer...
May 18, 2018: Biostatistics
Jan T M Jansen, Paul C Shrimpton, John Richard Holroyd, Sue Edyvean
This is the second paper arising from a project concerning the application of Monte Carlo simulations to provide scanner-specific organ dose coefficients for modern CT scanners. The present focus is centred on the bone dosimetry models that have been developed. Simulations have been performed in photon only transport mode, with the assumption of electron equilibrium. This approximation breaks down for doses to active marrow and endosteum since the target cells are localised within tens of micrometre from bone tissue and dose enhancement functions are necessary to correct for the additional dose from photoelectric electrons created in adjacent material...
May 22, 2018: Physics in Medicine and Biology
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