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Monte Carlo simulation

Jonathon Van Schelt, Daniel Smith, Nicholas Fong, Dolla Toomeh, Patricia A Sponseller, Derek W Brown, Meghan W Macomber, Nina A Mayr, Shilpen Patel, Adam Shulman, G V Subrahmanyam, K Govindarajan, Eric C Ford
PURPOSE: We propose a novel compensator-based IMRT system designed to provide a simple, reliable, and cost-effective adjunct technology, with the goal of expanding global access to advanced radiotherapy techniques. The system would employ easily-reusable tungsten bead compensators that operate independent of a gantry (e.g. mounted in a ring around the patient). Thereby the system can be retrofitted to existing linac and cobalt teletherapy units. This study explores the quality of treatment plans from the proposed system and the dependence on associated design parameters...
May 19, 2018: Medical Physics
Sara Gholampourkashi, Joanna E Cygler, Bernie Lavigne, Emily Heath
PURPOSE: To verify the accuracy of 4D Monte Carlo (MC) simulations, using the 4DdefDOSXYZnrc user code, in a deforming anatomy. We developed a tissue-equivalent and reproducible deformable lung phantom and evaluated 4D simulations of delivered dose to the phantom by comparing calculations against measurements. METHODS: A novel deformable phantom consisting of flexible foam, emulating lung tissue, inside a Lucite external body was constructed. A removable plug, containing an elastic tumor that can hold film and other dosimeters, was inserted in the phantom...
May 15, 2018: Physica Medica: PM
Alireza Mashaghi, Abolfazl Ramezanpour
We study a diagnostic strategy which is based on the anticipation of the diagnostic process by simulation of the dynamical process starting from the initial findings. We show that such a strategy could result in more accurate diagnoses compared to a strategy that is solely based on the direct implications of the initial observations. We demonstrate this by employing the mean-field approximation of statistical physics to compute the posterior disease probabilities for a given subset of observed signs (symptoms) in a probabilistic model of signs and diseases...
March 2018: Physical Review. E
Benjamin Steinegger, Alessio Cardillo, Paolo De Los Rios, Jesús Gómez-Gardeñes, Alex Arenas
The containment of epidemic spreading is a major challenge in science. Vaccination, whenever available, is the best way to prevent the spreading, because it eventually immunizes individuals. However, vaccines are not perfect, and total immunization is not guaranteed. Imperfect immunization has driven the emergence of antivaccine movements that totally alter the predictions about the epidemic incidence. Here, we propose a mathematically solvable mean-field vaccination model to mimic the spontaneous adoption of vaccines against influenzalike diseases and the expected epidemic incidence...
March 2018: Physical Review. E
Christopher Amey, Jonathan Machta
Population annealing is an easily parallelizable sequential Monte Carlo algorithm that is well suited for simulating the equilibrium properties of systems with rough free-energy landscapes. In this work we seek to understand and improve the performance of population annealing. We derive several useful relations between quantities that describe the performance of population annealing and use these relations to suggest methods to optimize the algorithm. These optimization methods were tested by performing large-scale simulations of the three-dimensional (3D) Edwards-Anderson (Ising) spin glass and measuring several observables...
March 2018: Physical Review. E
Dipanjan Mandal, Trisha Nath, R Rajesh
We study the different phases and the phase transitions in a system of Y-shaped particles, examples of which include immunoglobulin-G and trinaphthylene molecules, on a triangular lattice interacting exclusively through excluded volume interactions. Each particle consists of a central site and three of its six nearest neighbors chosen alternately, such that there are two types of particles which are mirror images of each other. We study the equilibrium properties of the system using grand canonical Monte Carlo simulations that implement an algorithm with cluster moves that is able to equilibrate the system at densities close to full packing...
March 2018: Physical Review. E
N C Costa, T Blommel, W-T Chiu, G Batrouni, R T Scalettar
The Holstein model describes the interaction between fermions and a collection of local (dispersionless) phonon modes. In the dilute limit, the phonon degrees of freedom dress the fermions, giving rise to polaron and bipolaron formation. At higher densities, the phonons mediate collective superconducting (SC) and charge-density wave (CDW) phases. Quantum Monte Carlo (QMC) simulations have considered both these limits but have not yet focused on the physics of more general phonon spectra. Here we report QMC studies of the role of phonon dispersion on SC and CDW order in such models...
May 4, 2018: Physical Review Letters
Aleksander Kubica, Michael E Beverland, Fernando Brandão, John Preskill, Krysta M Svore
Three-dimensional (3D) color codes have advantages for fault-tolerant quantum computing, such as protected quantum gates with relatively low overhead and robustness against imperfect measurement of error syndromes. Here we investigate the storage threshold error rates for bit-flip and phase-flip noise in the 3D color code (3DCC) on the body-centered cubic lattice, assuming perfect syndrome measurements. In particular, by exploiting a connection between error correction and statistical mechanics, we estimate the threshold for 1D stringlike and 2D sheetlike logical operators to be p_{3DCC}^{(1)}≃1...
May 4, 2018: Physical Review Letters
Daniele Coslovich, Misaki Ozawa, Walter Kob
The physical behavior of glass-forming liquids presents complex features of both dynamic and thermodynamic nature. Some studies indicate the presence of thermodynamic anomalies and of crossovers in the dynamic properties, but their origin and degree of universality is difficult to assess. Moreover, conventional simulations are barely able to cover the range of temperatures at which these crossovers usually occur. To address these issues, we simulate the Kob-Andersen Lennard-Jones mixture using efficient protocols based on multi-CPU and multi-GPU parallel tempering...
May 17, 2018: European Physical Journal. E, Soft Matter
Mohanad F Abdulhameed, Ihab Habib, Suzan A Al-Azizz, Ian Robertson
Cystic echinococcosis (CE) is a highly endemic parasitic zoonosis in Iraq with substantial impacts on livestock productivity and human health. The objectives of this study were to study the abattoir-based occurrence of CE in marketed offal of sheep in Basrah province, Iraq, and to estimate, using a probabilistic modelling approach, the direct economic losses due to hydatid cysts. Based on detailed visual meat inspection, results from an active abattoir survey in this study revealed detection of hydatid cysts in 7...
February 2018: Parasite Epidemiology and Control
Abbas Alloul, Ramon Ganigue, Marc Spiller, Francis A Meerburg, Cristina Cagnetta, Korneel Rabaey, Siegfried E Vlaeminck
This critical review outlines a roadmap for the conversion of chemical oxygen demand (COD) contained in sewage to commodities based on three-steps: capture COD as sludge, ferment it to volatile fatty acids (VFA), and upgrade VFA to products. The article analyzes the state-of-the-art of this three-step approach and discusses the bottlenecks and challenges. The potential of this approach is illustrated for the European Union's 28 member states (EU-28) through Monte Carlo simulations. High-rate contact stabilization captures the highest amount of COD (66-86 gCOD person equivalent-1 day-1 in 60% of the iterations)...
May 17, 2018: Environmental Science & Technology
Kazuhiko Hayakawa
Many previous studies report simulation evidence that the goodness-of-fit test in covariance structure analysis or structural equation modeling suffers from the overrejection problem when the number of manifest variables is large compared with the sample size. In this study, we demonstrate that one of the tests considered in Browne (1974) can address this long-standing problem. We also propose a simple modification of Satorra and Bentler's mean and variance adjusted test for non-normal data. A Monte Carlo simulation is carried out to investigate the performance of the corrected tests in the context of a confirmatory factor model, a panel autoregressive model, and a cross-lagged panel (panel vector autoregressive) model...
May 17, 2018: Psychological Methods
Casey L Cazer, Lucas Ducrot, Victoriya V Volkova, Yrjö T Gröhn
[This corrects the article on p. 1753 in vol. 8, PMID: 29033901.].
2018: Frontiers in Microbiology
Christopher W Baugh, Pawan Suri, Christopher G Caspers, Michael A Granovsky, Keith Neal, Michael A Ross
BACKGROUND: Outpatients receive observation services to determine the need for inpatient admission. These services are usually provided without the use of condition-specific protocols and in an unstructured manner, scattered throughout a hospital in areas typically designated for inpatient care. Emergency department observation units (EDOUs) use protocolized care to offer an efficient alternative with shorter lengths of stay, lower costs and higher patient satisfaction. EDOU growth is limited by existing policy barriers that prevent a "two-service" model of separate professional billing for both emergency and observation services...
May 16, 2018: Academic Emergency Medicine: Official Journal of the Society for Academic Emergency Medicine
C Caranica, A Al-Omari, Z Deng, J Griffith, R Nilsen, L Mao, J Arnold, H-B Schüttler
A major challenge in systems biology is to infer the parameters of regulatory networks that operate in a noisy environment, such as in a single cell. In a stochastic regime it is hard to distinguish noise from the real signal and to infer the noise contribution to the dynamical behavior. When the genetic network displays oscillatory dynamics, it is even harder to infer the parameters that produce the oscillations. To address this issue we introduce a new estimation method built on a combination of stochastic simulations, mass action kinetics and ensemble network simulations in which we match the average periodogram and phase of the model to that of the data...
2018: PloS One
Pablo Martínez-Camblor, Sonia Pérez-Fernández, Norberto Corral
Receiver operating-characteristic curve is a popular graphical method frequently used in order to study the diagnostic capacity of continuous (bio)markers. In spite of the existence of a huge number of papers devoted to both theoretical and practical aspects of this topic, the construction of confidence bands has had little impact in the specialized literature. As far as the authors know, in the CRAN there are only three R packages providing receiver operating-characteristic curve confidence regions: plotROC, pROC and fbroc...
June 2018: Statistical Methods in Medical Research
Yun Xie, Zhanchao Li, Jian Zhou
The Hamiltonian replica exchange Monte Carlo (H-REMC) algorithm was applied to study protein adsorption and its performance was compared with that of the temperature replica exchange Monte Carlo (T-REMC). Comparisons indicate that the simulation results are consistent but the computational efficiency is improved for H-REMC. H-REMC could accurately and efficiently identify the preferred orientations of glucose oxidase (GOx) on charged surfaces; different preferential GOx orientations on different surfaces and solution conditions could be spotted with a much fewer number of simulation runs...
May 16, 2018: Physical Chemistry Chemical Physics: PCCP
A Fogliata, F De Rose, A Stravato, G Reggiori, S Tomatis, M Scorsetti, L Cozzi
BACKGROUND: Monte Carlo simulations were run to estimate the dose variations generated by thedifference arising from the chemical composition of the tissues. METHODS: CT datasets of five breast cancer patients were selected. Mammary gland was delineated as clinical target volume CTV, as well as CTV_lob and CTV_fat, being the lobular and fat fractions of the entire mammary gland. Patients were planned for volumetric modulated arc therapy technique, optimized in the Varian Eclipse treatment planning system...
May 15, 2018: Radiation Oncology
Alessandro Esposito, Sofia Silva, Jorge Oliveira, Joana Lencart, João Santos
BACKGROUND: IMRT provides higher dose conformation to the target and dose sparing to surrounding tissues than 3DCRT. Monte Carlo method in Medical Physics is not a novelty to approach dosimetric problems. A new PENELOPE based code named PRIMO recently was published. The most intriguing features of PRIMO are the user-friendly approach, the stand-alone property and the built-in definition of different linear accelerators models. Nevertheless, IMRT simulations are not yet implemented. METHODS: A Varian Trilogy with a Millennium120 MLC and a Varian Novalis with 120HD MLC were studied...
May 15, 2018: Radiation Oncology
Isla Zhang, Rattachai Pinchaipat, Nigel B Wilding, Malcolm A Faers, Paul Bartlett, Robert Evans, C Patrick Royall
Understanding the phase behaviour of mixtures continues to pose challenges, even for systems that might be considered "simple." Here, we consider a very simple mixture of two colloidal and one non-adsorbing polymer species, which can be simplified even further to a size-asymmetrical binary mixture, in which the effective colloid-colloid interactions depend on the polymer concentration. We show that this basic system exhibits surprisingly rich phase behaviour. In particular, we enquire whether such a system features only a liquid-vapor phase separation (as in one-component colloid-polymer mixtures) or whether, additionally, liquid-liquid demixing of two colloidal phases can occur...
May 14, 2018: Journal of Chemical Physics
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