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Monte Carlo simulation

Babu J N Reddy, Suvranta Tripathy, Michael Vershinin, Marvin Tanenbaum, Jing Xu, Michelle Mattson-Hoss, Karim Arabi, Dail Chapman, Tory Doolin, Changbong Hyeon, Steven P Gross
The kinesin family proteins are often studied as prototypical molecular motors; a deeper understanding of them can illuminate regulation of intracellular transport. It is typically assumed that they function identically. Here we find that this assumption of homogeneous function appears incorrect: variation among motors' velocities in vivo and in vitro is larger than the stochastic variation expected for an ensemble of 'identical" motors. When moving on microtubules, slow and fast motors are persistently slow, and fast, respectively...
July 21, 2017: Traffic
Tomaz Urbic
In this paper we applied analytical theories for the two dimensional chain-forming fluid. Wertheims thermodynamic perturbation theory (TPT) and integral equation theory (IET) for associative liquids were used to study thermodynamical and structural properties of the chain-forming model. The model has polymerizing points at arbitrary position from center of the particles. Calculated analytical results were tested against corresponding results obtained by Monte Carlo computer simulations to check the accuracy of the theories...
July 2017: Journal of Molecular Liquids
Bartłomiej Włodarczyk, Jakub Pietrzak
Here, we present a hybrid approach for simulating an edge illumination X-ray phase-contrast imaging (EIXPCi) set-up using graphics processor units (GPU) with a high degree of accuracy. In this study, the applicability of pixel, mesh and non-uniform rational B-splines (NURBS) objects to carry out realistic maps of X-ray phase-contrast distribution at a human scale is accounted for by using numerical anthropomorphic phantoms and a very fast and robust simulation framework which integrates total interaction probabilities along selected X-ray paths...
July 17, 2017: Physica Medica: PM
Wolfgang Schmickler, Douglas Henderson
The storage of ions in narrow nanotubes is investigated by grand-canonical Monte Carlo simulations. The interaction between the ions is screened by the image charge on the wall of the tube, but at close distances it is still much larger than the thermal energy. Depending on the electrochemical potential imposed by the contact with an electrolyte solution, two different regimes can be distinguished at the potential of zero charge: for low values corresponding to an ionophobic pore the tube is almost empty; for high values - ionophilic pore - a one dimensional salt is formed...
July 20, 2017: Physical Chemistry Chemical Physics: PCCP
Pedro L Esquinas, Carlos F Uribe, M Gonzalez, Cristina Rodríguez-Rodríguez, Urs O Häfeli, Anna Celler
The main applications of (188)Re in radionuclide therapies include trans-arterial liver radioembolization and palliation of painful bone-metastases. In order to optimize (188)Re therapies, the accurate determination of radiation dose delivered to tumors and organs at risk is required. Single photon emission computed tomography (SPECT) can be used to perform such dosimetry calculations. However, the accuracy of dosimetry estimates strongly depends on the accuracy of activity quantification in (188)Re images...
July 20, 2017: Physics in Medicine and Biology
Xue Zhang, Na Li, Hao Wang, Chenyang Yuan, Gaochen Gu, Yajie Zhang, Damian Nieckarz, Paweł Szabelski, Shimin Hou, Boon K Teo, Yongfeng Wang
The self-assembly behavior of a V-shaped bispyridine, 1,3-bi(4-pyridyl)benzene (BPyB), was studied by scanning tunneling microscopy on the (111) surfaces of Cu, Ag, and Au. BPyB molecules coordinately bonded with active Cu adatoms on Cu(111) in the form of complete polygonal rings at low coverages. On Ag(111), BPyB molecules aggregated into two-dimensional islands by relatively weak intermolecular hydrogen bonds. The coexistence of hydrogen bonds and coordination interaction was observed on the BPyB-covered Au(111) substrate...
July 21, 2017: ACS Nano
Cheng Zhan, Cheng Lian, Yu Zhang, Matthew W Thompson, Yu Xie, Jianzhong Wu, Paul R C Kent, Peter T Cummings, De-En Jiang, David J Wesolowski
Supercapacitors such as electric double-layer capacitors (EDLCs) and pseudocapacitors are becoming increasingly important in the field of electrical energy storage. Theoretical study of energy storage in EDLCs focuses on solving for the electric double-layer structure in different electrode geometries and electrolyte components, which can be achieved by molecular simulations such as classical molecular dynamics (MD), classical density functional theory (classical DFT), and Monte-Carlo (MC) methods. In recent years, combining first-principles and classical simulations to investigate the carbon-based EDLCs has shed light on the importance of quantum capacitance in graphene-like 2D systems...
July 2017: Advanced Science (Weinheim, Baden-Wurttemberg, Germany)
Ming-Chien Hsieh, David G Lynn, Martha A Grover
Intermediate dynamic assemblies are increasingly seen as necessary for the initial desolvation and organization of biomaterials to achieve their final crystalline order, and here we present a general peptide assembly model for two-step nucleation. The model predicts the phase transitions and equilibria between different phases by a combination of the Flory-Huggins parameter, the particle growth constant, and the binding energy to the assemblies. Monte Carlo simulations are used to demonstrate how the system evolves from pure solution phases to the final thermodynamic assembly phase via a metastable particle phase...
July 19, 2017: Journal of Physical Chemistry. B
Yoshifumi Oya, Kenji Hata, Tomonori Ohba
We present the structures of NaCl aqueous solution in carbon nanotubes with diameters of 1, 2, and 3 nm based on an analysis performed using X-ray diffraction and canonical ensemble Monte Carlo simulations. Anomalously longer nearest-neighbor distances were observed in the electrolyte for the 1-nm-diameter carbon nanotubes; in contrast, in the 2 and 3 nm carbon nanotubes, the nearest-neighbor distances were shorter than those in the bulk electrolyte. We also observed similar properties for water in carbon nanotubes, which was expected because the main component of the electrolyte was water...
July 19, 2017: Langmuir: the ACS Journal of Surfaces and Colloids
Eyad H Al-Samra, Nicholas J B Green
This work describes stochastic models developed to study the competition between radical scavenging and recombination for simple model systems typical of radiation chemistry, where the reactive particles are tightly clustered and reactions are assumed fully diffusion limited. Three models are developed: a Monte Carlo random flights model with a periodic boundary condition for scavengers, Monte Carlo simulations in which the scavenging rate is calculated from the Smoluchowski theory for diffusion-limited reactions and a modification of the independent reaction times method where the scavengers close to the spur are explicitly included and the scavengers further away are treated as a continuum...
July 19, 2017: Physical Chemistry Chemical Physics: PCCP
Umberto Restelli, Giuliano Rizzardini, Andrea Antinori, Adriano Lazzarin, Marzia Bonfanti, Paolo Bonfanti, Davide Croce
BACKGROUND: In January 2014, the European Medicines Agency issued a marketing authorization for dolutegravir (DTG), a second-generation integrase strand transfer inhibitor for HIV treatment. The study aimed at determining the incremental cost-effectiveness ratio (ICER) of the use of DTG+backbone compared with raltegravir (RAL)+backbone, darunavir (DRV)+ritonavir(r)+backbone and efavirenz/tenofovir/emtricitabine (EFV/TDF/FTC) in HIV-positive treatment-naïve patients and compared with RAL+backbone in treatment-experienced patients, from the Italian National Health Service's point of view...
2017: Therapeutics and Clinical Risk Management
Wei Yu, Jinru Ji, Tingting Xiao, Chaoqun Ying, Jiaheng Fang, Ping Shen, Yonghong Xiao
BACKGROUND: Dicloxacillin, a semisynthetic isoxazolyl penicillin, exhibits antimicrobial activity against a wide variety of Gram-positive bacteria, as well as stability against penicillinases and low level of toxicity. The objective of this study was to obtain optimal dosing regimen of oral administration of dicloxacillin by analyzing the pharmacokinetic (PK) index in healthy volunteers and in vitro antibacterial activity by using Monte Carlo simulation. MATERIALS AND METHODS: A total of 867 clinical isolates from community-onset infections were collected from 31 secondary hospitals in People's Republic of China...
2017: Drug Design, Development and Therapy
Renfeng Li, Luhong Wang, Liangliang Li, Tony Yu, Haiyan Zhao, Karena W Chapman, Yanbin Wang, Mark L Rivers, Peter J Chupas, Ho-Kwang Mao, Haozhe Liu
In situ high energy X-ray pair distribution function (PDF) measurements, microtomography and reverse Monte Carlo simulations were used to characterize the local structure of liquid gallium up to 1.9 GPa. This pressure range includes the well-known solid-solid phase transition from Ga-I to Ga-II at low temperature. In term of previous research, the local structure of liquid gallium within this domain was suggested a mixture of two local structures, Ga I and Ga II, based on fitting experimental PDF to known crystal structure, with a controversy...
July 18, 2017: Scientific Reports
Andrew J Wroe, Grant McAuley, Anthony V Teran, Jeannie Wong, Marco Petasecca, Michael Lerch, James M Slater, Anatoly B Rozenfeld
As technology continues to develop, external beam radiation therapy is being employed, with increased conformity, to treat smaller targets. As this occurs, the dosimetry methods and tools employed to quantify these fields for treatment also have to evolve to provide increased spatial resolution. The team at the University of Wollongong has developed a pixelated silicon detector prototype known as the dose magnifying glass (DMG) for real-time small-field metrology. This device has been tested in photon fields and IMRT...
July 18, 2017: Journal of Applied Clinical Medical Physics
Andreas Franz Resch, Hermann Fuchs, Dietmar Georg
Oxygen (<sup>16</sup>O) ions are a potential alternative to carbon ions in ion beam therapy. Their enhanced linear energy transfer indicates a higher relative biological effectiveness and a reduced oxygen enhancement ratio. Due to the limited availability of <sup>16</sup>O ion beams, Monte Carlo (MC) transport codes are important research tools to investigate their potential. The purpose of this study was to validate GATE/Geant4 for <sup>16</sup>O ion beam therapy on experimental data from literature...
July 18, 2017: Physics in Medicine and Biology
Yan Zhang, Li Wang, Ru-Xin Yao, Xian-Ming Zhang
A fourfold interpenetrated diamond-like topological metal-organic framework (MOF), Ni(pybz)2 [pybz = 4-(4-pyridyl)benzoate] was successfully synthesized and fully characterized. This MOF can serve as coating material in gas chromatographic capillary column for the separation of some low boiling point essential oils. The prepared columns have good recognition ability and excellent selectivity toward a series of organic compounds, including alcohols, aldehydes, ketones, carboxylic acid, ethers, ester, and amines...
July 18, 2017: Inorganic Chemistry
Kannan Sridharan, Gowri Sivaramakrishnan
INTRODUCTION: Patients with trigeminal neuralgia (TN) are often refractory to recommended first-line agents. Due to the absence of a systematic review, we undertook a network meta-analysis to assess various interventions that can be used to manage refractory TN. METHODS: Electronic databases were searched using appropriate strategies to identify randomized controlled clinical trials in patients with refractory TN, evaluating the proportion of patients with a minimum of 50% reduction in pain or a minimum of 2 cm reduction in score in an appropriate pain scale or complete pain relief by subjective pain scales...
July 17, 2017: Clinical Drug Investigation
Solène Desmée, France Mentré, Christine Veyrat-Follet, Bernard Sébastien, Jérémie Guedj
BACKGROUND: Joint models of longitudinal and time-to-event data are increasingly used to perform individual dynamic prediction of a risk of event. However the difficulty to perform inference in nonlinear models and to calculate the distribution of individual parameters has long limited this approach to linear mixed-effect models for the longitudinal part. Here we use a Bayesian algorithm and a nonlinear joint model to calculate individual dynamic predictions. We apply this approach to predict the risk of death in metastatic castration-resistant prostate cancer (mCRPC) patients with frequent Prostate-Specific Antigen (PSA) measurements...
July 17, 2017: BMC Medical Research Methodology
T Joseph Mattingly, Julia F Slejko, C Daniel Mullins
BACKGROUND: Numerous economic models have been published evaluating treatment of chronic hepatitis C virus (HCV) infection, but none provide a comprehensive comparison among new antiviral agents. OBJECTIVE: Evaluate the cost-effectiveness of all recommended therapies for treatment of genotypes 1 and 4 chronic HCV. METHODS: Using data from clinical trials, observational analyses, and drug pricing databases, Markov decision models were developed for HCV genotypes 1 and 4 to compare all recommended drugs from the perspective of the third-party payer over a 5-, 10-, and 50-year time horizon...
July 1, 2017: Annals of Pharmacotherapy
M A Martínez, J Rovira, R Prasad Sharma, M Nadal, M Schuhmacher, V Kumar
Prenatal exposure to Endocrine disruptors (EDs), such as Bisphenol A (BPA) and di (2-ethylhexyl) phthalate (DEHP), has been associated with obesity and diabetes diseases in childhood, as well as reproductive, behavioral and neurodevelopment problems. The aim of this study was to estimate the prenatal exposure to BPA and DEHP through food consumption for pregnant women living in Tarragona County (Spain). Probabilistic calculations of prenatal exposure were estimated by integrated external and internal dosimetry modelling, physiologically based pharmacokinetic (PBPK) model, using a Monte-Carlo simulation...
July 14, 2017: Environmental Research
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