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Monte Carlo simulation

Sven Dirkmann, Mirko Hansen, Martin Ziegler, Hermann Kohlstedt, Thomas Mussenbrock
In this work we report on the role of ion transport for the dynamic behavior of a double barrier quantum mechanical Al/Al2O3/NbxOy/Au memristive device based on numerical simulations in conjunction with experimental measurements. The device consists of an ultra-thin NbxOy solid state electrolyte between an Al2O3 tunnel barrier and a semiconductor metal interface at an Au electrode. It is shown that the device provides a number of interesting features such as an intrinsic current compliance, a relatively long retention time, and no need for an initialization step...
October 20, 2016: Scientific Reports
Jeffrey A Walker
BACKGROUND: Self-contained tests estimate and test the association between a phenotype and mean expression level in a gene set defined a priori. Many self-contained gene set analysis methods have been developed but the performance of these methods for phenotypes that are continuous rather than discrete and with multiple nuisance covariates has not been well studied. Here, I use Monte Carlo simulation to evaluate the performance of both novel and previously published (and readily available via R) methods for inferring effects of a continuous predictor on mean expression in the presence of nuisance covariates...
2016: PeerJ
Hideki Kato, Keita Sakai, Mizuki Uchiyama, Kentaro Suzuki
The diagnostic reference levels (DRLs) of the general X-ray radiography are defined by the absorbed dose of air at the entrance surface with backscattered radiation from a scattering medium. Generally, the entrance surface dose of the general X-ray radiography is calculated from measured air kerma of primary X-ray multiplied by a backscatter factor (BSF). However, the BSF data employed at present used water for scattering medium, and was calculated based on the water-absorbed dose by incident primary photons and backscattered photons from the scattering medium...
2016: Nihon Hoshasen Gijutsu Gakkai Zasshi
Uwe Schneider, Fabiano Vasi, Jürgen Besserer
BACKGROUND AND PURPOSE: When fractionation schemes for hypofractionation and stereotactic body radiotherapy are considered, a reliable cell survival model at high dose is needed for calculating doses of similar biological effectiveness. An alternative to the LQ-model is the track-event theory which is based on the probabilities for one- and two two-track events. A one-track-event (OTE) is always represented by at least two simultaneous double strand breaks. A two-track-event (TTE) results in one double strand break...
2016: PloS One
Jianfei Yang, Dirk H J Poot, Matthan W A Caan, Tanja Su, Charles B L M Majoie, Lucas J van Vliet, Frans M Vos
PURPOSE: This paper presents and studies a framework for reliable modeling of diffusion MRI using a data-acquisition adaptive prior. METHODS: Automated relevance determination estimates the mean of the posterior distribution of a rank-2 dual tensor model exploiting Jeffreys prior (JARD). This data-acquisition prior is based on the Fisher information matrix and enables the assessment whether two tensors are mandatory to describe the data. The method is compared to Maximum Likelihood Estimation (MLE) of the dual tensor model and to FSL's ball-and-stick approach...
2016: PloS One
Peter Brommesson, Uno Wennergren, Tom Lindström
The structure of contacts that mediate transmission has a pronounced effect on the outbreak dynamics of infectious disease and simulation models are powerful tools to inform policy decisions. Most simulation models of livestock disease spread rely to some degree on predictions of animal movement between holdings. Typically, movements are more common between nearby farms than between those located far away from each other. Here, we assessed spatiotemporal variation in such distance dependence of animal movement contacts from an epidemiological perspective...
2016: PloS One
Vahid Sokhanvaran, Saeid Yeganegi
The quantum mechanics (QM) method and Grand Canonical Monte Carlo (GCMC) simulations were performed to study the effect of lithium cation doping on the adsorption and separation of CO2, CH4 and H2 on 2-fold interwoven metal-organic framework (MOF) Zn2(NDC)2(diPyNI). The second order Moller-Plesset (MP2) calculations on the (Li+-diPyNI) cluster model showed that the energetically most favorable lithium binding site is above the pyridine ring side and at a distance of 1.817 Å from the oxygen atom. The results revealed that the adsorption capacity of Zn2(NDC)2(diPyNI) for carbon dioxide is higher than that of hydrogen and methane at room temperature...
October 19, 2016: Chemphyschem: a European Journal of Chemical Physics and Physical Chemistry
Heewon Park, Atsushi Niida, Seiya Imoto, Satoru Miyano
Driver gene selection is crucial to understand the heterogeneous system of cancer. To identity cancer driver genes, various statistical strategies have been proposed, especially the L1-type regularization methods have drawn a large amount of attention. However, the statistical approaches have been developed purely from algorithmic and statistical point, and the existing studies have applied the statistical approaches to genomic data analysis without consideration of biological knowledge. We consider a statistical strategy incorporating biological knowledge to identify cancer driver gene...
October 19, 2016: Journal of Computational Biology: a Journal of Computational Molecular Cell Biology
Claudia Baumung, Jürgen Rehm, Heike Franke, Dirk W Lachenmeier
Nicotine was not included in previous efforts to identify the most important toxicants of tobacco smoke. A health risk assessment of nicotine for smokers of cigarettes was conducted using the margin of exposure (MOE) approach and results were compared to literature MOEs of various other tobacco toxicants. The MOE is defined as ratio between toxicological threshold (benchmark dose) and estimated human intake. Dose-response modelling of human and animal data was used to derive the benchmark dose. The MOE was calculated using probabilistic Monte Carlo simulations for daily cigarette smokers...
October 19, 2016: Scientific Reports
Xue Rui, Yannan Jin, Paul F FitzGerald, Mingye Wu, Adam M Alessio, Paul E Kinahan, Bruno De Man
Computed tomography (CT) has been used for a variety of applications, two of which include diagnostic imaging and attenuation correction for PET or SPECT imaging. Ideally, the x-ray tube spectrum should be optimized for the specific application to minimize the patient radiation dose while still providing the necessary information. In this study, we proposed a projection-based analytic approach for the analysis of contrast, noise, and bias. Dose normalized contrast to noise ratio (CNRD), inverse noise normalized by dose (IND) and bias are used as evaluation metrics to determine the optimal x-ray spectrum...
November 7, 2016: Physics in Medicine and Biology
H Behar, N Brenner, G Ariel, Y Louzoun
Cooperative interactions between individuals in a population and their stability properties are central to population dynamics and evolution. We introduce a generic class of nonlinear dynamical systems describing such interactions between producers and non-producers of a rapidly equilibrating common resource extracted from a finite environment. In the deterministic mean field approximation, fast-growing non-producers drive the entire population to extinction. However, the presence of arbitrarily small perturbations destabilizes this fixed point into a stochastic attractor where both phenotypes can survive...
October 18, 2016: Physical Biology
Gabriel L S Rodrigues, Willian Ricardo Rocha
In this article Density Functional Theory in conjunction with Monte Carlo statistical mechanical simulation were used to investigate the electronic structure, reduction potential, solvation and solvent effects on the electronic spectra of nitrosyl ammine complexes, using [Ru(NH3)5(NO)]2+/3+ as model compounds. In addition, ligand exchange reactions with solvent water molecules were also investigated. It is shown that the complexes are involved in strong hydrogen bonds in aqueous solution, with mean average energies of (-13...
October 18, 2016: Journal of Physical Chemistry. B
Saijie Pan, Niels Boon, Monica Olvera de la Cruz
Epitaxial growth of DNA functionalized nanoparticles is used to grow extended superlattices with a preferred orientation for optimizing the physical properties of meta-materials for real applications. Like any solid in nature, superlattices can contain different kinds of structural defects, which significantly alter their physical properties. Further development of these materials requires a deeper understanding of, as well as precise control over, structural defect formation. Here we use Monte Carlo simulations to conduct a systematic study of the equilibrium structures of the adsorbed nanoparticle monolayers by changing the binding energies of different attachment sites...
October 18, 2016: ACS Nano
Iris K Minichmayr, André Schaeftlein, Joseph L Kuti, Markus Zeitlinger, Charlotte Kloft
OBJECTIVES: We aimed to assess linezolid pharmacokinetics in the plasma and interstitial space fluid (ISF) of patients with sepsis, diabetic foot infections or cystic fibrosis and healthy volunteers. The impacts of joint characteristics and disease on plasma and target-site exposure were to be identified together with the benefit of dose intensification in critically ill patients. METHODS: Rich plasma (n = 1598) and ISF concentrations in subcutaneous adipose (n = 1430) and muscle tissue (n = 1089) measured by microdialysis were pooled from three clinical trials with 51 individuals receiving 600 mg of intravenous and oral linezolid...
October 17, 2016: Clinical Pharmacokinetics
Lipeng Ning, Evren Özarslan, Carl-Fredrik Westin, Yogesh Rathi
Inferring the microstructure of complex media from the diffusive motion of molecules is a challenging problem in diffusion physics. In this paper, we introduce a novel representation of diffusion MRI (dMRI) signal from tissue with spatially-varying diffusivity using a diffusion disturbance function. This disturbance function contains information about the (intra-voxel) spatial fluctuations in diffusivity due to restrictions, hindrances and tissue heterogeneity of the underlying tissue substrate. We derive the short- and long-range disturbance coefficients from this disturbance function to characterize the tissue structure and organization...
October 14, 2016: NeuroImage
Drishti Shah, Vamshi Ruthwik Anupindi, Varun Vaidya
Chronic back pain is an extremely common health problem. The largest category for pain therapy costs includes nonsteroidal anti-inflammatory drugs (NSAIDs) and opioids. However, there has been limited evidence outlining their effectiveness in terms of quality of life for the treatment of chronic back pain. The authors performed a comparative pharmacoeconomic analysis of chronic back pain patients using NSAIDs versus those using opioids alone or combination opioid analgesics. This pharmacoeconomic evaluation was conducted using the Medical Expenditure Panel Survey (MEPS)...
October 17, 2016: Journal of Pain & Palliative Care Pharmacotherapy
Shenli Zhang, Maria Perez-Page, Kelly Guan, Erick Yu, Joseph W Tringe, Ricardo H R Castro, Roland Faller, Pieter Stroeve
Molecular Dynamics (MD) and Monte Carlo (MC) simulations were applied together for the first time to reveal the porous structure transformation mechanisms of mesoporous silica MCM-41 subjected to temperatures up to 2885 K. Silica was experimentally characterized to inform the models and enable prediction of changes in gas adsorption/separation properties. MD simulations suggest that the pore closure process is activated by a collective diffusion of matrix atoms into the porous region, accompanied by bond reformation at the surface...
October 17, 2016: Langmuir: the ACS Journal of Surfaces and Colloids
Amanda A Koepke, Ira M Longini, M Elizabeth Halloran, Jon Wakefield, Vladimir N Minin
Despite seasonal cholera outbreaks in Bangladesh, little is known about the relationship between environmental conditions and cholera cases. We seek to develop a predictive model for cholera outbreaks in Bangladesh based on environmental predictors. To do this, we estimate the contribution of environmental variables, such as water depth and water temperature, to cholera outbreaks in the context of a disease transmission model. We implement a method which simultaneously accounts for disease dynamics and environmental variables in a Susceptible-Infected-Recovered-Susceptible (SIRS) model...
June 2016: Annals of Applied Statistics
Samuel J Blake, Zhangkai Cheng, Shaghik Atakaramians, Steven Meikle, Minghui Lu, Philip Vial, Zdenka Kuncic
PURPOSE: A Geant4 model of a novel, water-equivalent electronic portal imaging device (EPID) prototype for radiotherapy imaging and dosimetry utilising an array of plastic scintillating fibres (PSFs) has been developed. Monte Carlo (MC) simulations were performed to quantify the PSF-EPID imaging performance and to investigate design aspects affecting performance for optimisation. METHODS: Using the Geant4 model, the PSF-EPID's imaging performance for 6 MV photon beams was quantified in terms of its modulation transfer function (MTF), noise power spectrum (NPS) and detective quantum efficiency (DQE)...
October 13, 2016: Physica Medica: PM
J J Bailey, A S Kadyrov, I B Abdurakhmanov, D V Fursa, I Bray
Stopping powers of H, He, H2, and H2O targets for antiprotons have been calculated using a convergent close-coupling method. For He and H2 targets electron-electron correlations are fully accounted for using a multiconfiguration approximation. Two-electron processes are included using an independent-event model. The water molecule is described using a neon-like structure model with a pseudo-spherical potential. Results are tabulated for the purpose of Monte Carlo simulations to model antiproton transport through matter for radiation therapy...
October 11, 2016: Physica Medica: PM
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