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Monte carlo

Baralee Punyawudho, Narukjaporn Thammajaruk, Kiat Ruxrungtham, Anchalee Avihingsanon
There is evidence that Thai patients receiving standard doses of ritonavir (RTV)-boosted atazanavir (ATV/r) have high exposure to atazanavir (ATV) leading to a higher risk of toxicity. A lower dose of ATV/r may provide adequate exposure in this population. However, pharmacokinetic data on ATV/r in Thai patients required for dose adjustment are limited. This study aimed to develop a population pharmacokinetic model of ATV/r and to determine the influence of patient characteristics on ATV pharmacokinetics. Monte Carlo simulations were performed to estimate the proportion of patients achieving target ATV trough concentration (Ctrough) with the standard ATV/r dose of 300/100 mg and a low dose of 200/100 mg once daily (OD)...
January 18, 2017: International Journal of Antimicrobial Agents
E A Ustinov
The paper aims at a comparison of techniques based on the kinetic Monte Carlo (kMC) and the conventional Metropolis Monte Carlo (MC) methods as applied to the hard-sphere (HS) fluid and solid. In the case of the kMC, an alternative representation of the chemical potential is explored [E. A. Ustinov and D. D. Do, J. Colloid Interface Sci. 366, 216 (2012)], which does not require any external procedure like the Widom test particle insertion method. A direct evaluation of the chemical potential of the fluid and solid without thermodynamic integration is achieved by molecular simulation in an elongated box with an external potential imposed on the system in order to reduce the particle density in the vicinity of the box ends...
January 21, 2017: Journal of Chemical Physics
Rocío Rodríguez-Cantano, Massimiliano Bartolomei, Marta I Hernández, José Campos-Martínez, Tomás González-Lezana, Pablo Villarreal, Ricardo Pérez de Tudela, Fernando Pirani, Javier Hernández-Rojas, José Bretón
Clusters formed by the combination of rare gas (RG) atoms of He, Ne, Ar, and Kr on coronene have been investigated by means of a basin-hopping algorithm and path integral Monte Carlo calculations at T = 2 K. Energies and geometries have been obtained and the role played by the specific RG-RG and RG-coronene interactions on the final results is analysed in detail. Signatures of diffuse behavior of the He atoms on the surface of the coronene are in contrast with the localization of the heavier species, Ar and Kr...
January 21, 2017: Journal of Chemical Physics
Fernando Luís Barroso da Silva, Philippe Derreumaux, Samuela Pasquali
A new numerical scheme for RNA (ribonucleic acid) titration based on the Debye-Hückel framework for the salt description is proposed in an effort to reduce the computational costs for further applications to study protein-RNA systems. By means of different sets of Monte Carlo simulations, we demonstrated that this new scheme is able to correctly reproduce the experimental titration behavior and salt pKa shifts. In comparison with other theoretical approaches, similar or even better outcomes are achieved at much lower computational costs...
January 21, 2017: Journal of Chemical Physics
Juan Berenguer, Elena Rodríguez-Castellano, Ana Carrero, Miguel A Von Wichmann, Marta Montero, María J Galindo, Josep Mallolas, Manuel Crespo, María J Téllez, Carmen Quereda, José Sanz, Carlos Barros, Cristina Tural, Ignacio Santos, Federico Pulido, Josep M Guardiola, Rafael Rubio, Enrique Ortega, María L Montes, Juan J Jusdado, Gabriel Gaspar, Herminia Esteban, José M Bellón, Juan González-García
: We assessed non-liver-related non-AIDS-related (NLR-NAR) events and mortality in a cohort of HIV/HCV-coinfected patients treated with interferon and ribavirin between 2000 and 2008. The censoring date was May 31, 2014. Cox regression analysis was performed to assess the adjusted hazard rate (HR) of overall death in responders and non-responders. Fine and Gray regression analysis was conducted to determine the adjusted sub-hazard rate (sHR) of NLR deaths and NLR-NAR events considering death as the competing risk...
January 21, 2017: Hepatology: Official Journal of the American Association for the Study of Liver Diseases
Massimiliano Chiappini, Erika Eiser, Francesco Sciortino
A new gel-forming colloidal system based on a binary mixture of fd-viruses and gold nanoparticles functionalized with complementary DNA single strands has been recently introduced. Upon quenching below the DNA melt temperature, such a system results in a highly porous gel state, that may be developed in a new functional material of tunable porosity. In order to shed light on the gelation mechanism, we introduce a model closely mimicking the experimental one and we explore via Monte Carlo simulations its equilibrium phase diagram...
January 2017: European Physical Journal. E, Soft Matter
P Kapli, S Lutteropp, J Zhang, K Kobert, P Pavlidis, A Stamatakis, T Flouri
MOTIVATION: In recent years, molecular species delimitation has become a routine approach for quantifying and classifying biodiversity. Barcoding methods are of particular importance in large-scale surveys as they promote fast species discovery and biodiversity estimates. Among those, distance-based methods are the most common choice as they scale well with large datasets; however, they are sensitive to similarity threshold parameters and they ignore evolutionary relationships. The recently introduced "Poisson Tree Processes" (PTP) method is a phylogeny-aware approach that does not rely on such thresholds...
January 19, 2017: Bioinformatics
Shaun M Davidson, Paul D Docherty, Rua Murray
Parameter identification is an important and widely used process across the field of biomedical engineering. However, it is susceptible to a number of potential difficulties, such as parameter trade-off, causing premature convergence at non-optimal parameter values. The proposed Dimensional Reduction Method (DRM) addresses this issue by iteratively reducing the dimension of hyperplanes where trade off occurs, and running subsequent identification processes within these hyperplanes. The DRM was validated using clinical data to optimize 4 parameters of the widely used Bergman Minimal Model of glucose and insulin kinetics, as well as in-silico data to optimize 5 parameters of the Pulmonary Recruitment (PR) Model...
January 17, 2017: Mathematical Biosciences
J E Galford
The gamma ray pit at the API Calibration Facility, located on the University of Houston campus, defines the API unit for natural gamma ray logs used throughout the petroleum logging industry. Future use of the facility is uncertain. An alternative method is proposed to preserve the gamma ray API unit definition as an industry standard by using Monte Carlo modeling to obtain accurate counting rate-to-API unit conversion factors for gross-counting and spectral gamma ray tool designs.
January 12, 2017: Applied Radiation and Isotopes
Jakob Ödén, Kjell Eriksson, Iuliana Toma-Dasu
PURPOSE: A constant relative biological effectiveness (RBE) of 1.1 is currently used in proton radiation therapy to account for the increased biological effectiveness compared to photon therapy. However, there is increasing evidence that proton RBE vary with the linear energy transfer (LET), the dose per fraction and the type of the tissue. Therefore, this study aims to evaluate the impact of disregarding variations in RBE when comparing proton and photon dose plans for prostate treatments for various fractionation schedules using published RBE models and several α/β assumptions...
January 20, 2017: Medical Physics
Edoardo Colzani, Alessandro Cassini, Daniel Lewandowski, Marie-Josee J Mangen, Dietrich Plass, Scott A McDonald, Alies van Lier, Juanita A Haagsma, Guido Maringhini, Alessandro Pini, Piotr Kramarz, Mirjam E Kretzschmar
The burden of disease framework facilitates the assessment of the health impact of diseases through the use of summary measures of population health such as Disability-Adjusted Life Years (DALYs). However, calculating, interpreting and communicating the results of studies using this methodology poses a challenge. The aim of the Burden of Communicable Disease in Europe (BCoDE) project is to summarize the impact of communicable disease in the European Union and European Economic Area Member States (EU/EEA MS)...
2017: PloS One
Hao Jiang, Ioannis George Economou, Athanassios Z Panagiotopoulos
Phase equilibria of water/CO2 and water/n-alkane mixtures over a range of temperatures and pressures were obtained from Monte Carlo simulations in the Gibbs ensemble. Three sets of Drude-type polarizable models for water, namely the BK3, GCP, and HBP models, were combined with a polarizable Gaussian charge CO2 (PGC) model to represent the water/CO2 mixture. The HBP water model describes hydrogen bonds between water and CO2 explicitly. All models underestimate CO2 solubility in water if standard combining rules are used for the dispersion interactions between water and CO2 ...
January 20, 2017: Journal of Physical Chemistry. B
Guglielmo Mazzola, Sandro Sorella
We propose an ab initio molecular dynamics method, capable of dramatically reducing the autocorrelation time required for the simulation of classical and quantum particles at finite temperatures. The method is based on an efficient implementation of a first order Langevin dynamics modified by means of a suitable, position dependent acceleration matrix S. Here, we apply this technique to both Lennard-Jones models, to demonstrate the accuracy and speeding-up of the sampling, and within a quantum Monte Carlo based wave function approach, for determining the phase diagram of high-pressure hydrogen with simulations much longer than the autocorrelation time...
January 6, 2017: Physical Review Letters
Suman Majumder, Johannes Zierenberg, Wolfhard Janke
Using state of the art Monte Carlo simulations of a bead-spring model we investigate both the equilibrium and the nonequilibrium behavior of the homopolymer collapse. The equilibrium properties obtained via multicanonical sampling recover the well-known finite-size scaling behavior of collapse for our model polymer. For the nonequilibrium dynamics we study the collapse by quenching the homopolymer from an expanded coiled state into the globular phase. The sequence of events observed during the collapse is independent of the quench depth...
January 20, 2017: Soft Matter
Yongfeng Zhang, Chao Jiang, Xianming Bai
This report presents an accelerated kinetic Monte Carlo (KMC) method to compute the diffusivity of hydrogen in hcp metals and alloys, considering both thermally activated hopping and quantum tunneling. The acceleration is achieved by replacing regular KMC jumps in trapping energy basins formed by neighboring tetrahedral interstitial sites, with analytical solutions for basin exiting time and probability. Parameterized by density functional theory (DFT) calculations, the accelerated KMC method is shown to be capable of efficiently calculating hydrogen diffusivity in α-Zr and Zircaloy, without altering the kinetics of long-range diffusion...
January 20, 2017: Scientific Reports
Daria Kondrashova, Alexander Lauerer, Dirk Mehlhorn, Hervé Jobic, Armin Feldhoff, Matthias Thommes, Dipanjan Chakraborty, Cedric Gommes, Jovana Zecevic, Petra de Jongh, Armin Bunde, Jörg Kärger, Rustem Valiullin
Nanoporous silicon produced by electrochemical etching of highly B-doped p-type silicon wafers can be prepared with tubular pores imbedded in a silicon matrix. Such materials have found many technological applications and provide a useful model system for studying phase transitions under confinement. This paper reports a joint experimental and simulation study of diffusion in such materials, covering displacements from molecular dimensions up to tens of micrometers with carefully selected probe molecules. In addition to mass transfer through the channels, diffusion (at much smaller rates) is also found to occur in directions perpendicular to the channels, thus providing clear evidence of connectivity...
January 20, 2017: Scientific Reports
Henning Huckfeldt, Alexander Gaul, Nicolas Müglich, Dennis Holzinger, Dennis Nissen, Manfred Albrecht, Daniel Emmrich, Andre Beyer, A Goelzhaeuser, Arno Ehresmann
The magnetic modification of exchange bias materials by ���ion bombardment induced magnetic patterning��� has been established more than a decade ago. To understand these experimental findings several theoretical models were introduced. Few investigations, however, did focus on magnetic property modifications caused by effects of ion bombardment in the ferromagnetic layer. In the present study, the structural changes occurring under ion bombardment were investigated by Monte-Carlo simulations and in experiments...
January 20, 2017: Journal of Physics. Condensed Matter: An Institute of Physics Journal
Jared Strydhorst, Thomas Carlier, Arnaud Dieudonné, Maurizio Conti, Irène Buvat
PURPOSE: Accurate reconstruction of the dose delivered by (90) Y microspheres using a postembolization PET scan would permit the establishment of more accurate dose-response relationships for treatment of hepatocellular carcinoma with (90) Y. However, the quality of the PET data obtained is compromised by several factors, including poor count statistics and a very high random fraction. This work uses Monte Carlo simulations to investigate what impact factors other than low count statistics have on the quantification of(90) Y PET...
October 2016: Medical Physics
Kate A Levin, Jill Carson, Emilia Crighton
OBJECTIVE: to measure the impact of the 'My Power of Attorney' media campaign on the number of new power of attorney (POA) registrations in Scotland. SETTING: POA registrations in Scotland processed by the Office of the Public Guardian during January 2010 to June 2015. METHODS: multilevel Poisson models for POA registrations nested by council and annual quarter were run using Markov chain Monte Carlo methods, adjusting for time, campaign (variable ranging between 0 and 5 dependent on intensity of campaign measured by the number of media platforms received) and offset term mid-year population estimate for those aged 25 years+/65 years+...
January 18, 2017: Age and Ageing
Fan Zhang, Patrick Flaherty
BACKGROUND: The detection of rare single nucleotide variants (SNVs) is important for understanding genetic heterogeneity using next-generation sequencing (NGS) data. Various computational algorithms have been proposed to detect variants at the single nucleotide level in mixed samples. Yet, the noise inherent in the biological processes involved in NGS technology necessitates the development of statistically accurate methods to identify true rare variants. RESULTS: We propose a Bayesian statistical model and a variational expectation maximization (EM) algorithm to estimate non-reference allele frequency (NRAF) and identify SNVs in heterogeneous cell populations...
January 19, 2017: BMC Bioinformatics
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