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Monte carlo

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https://www.readbyqxmd.com/read/28926766/protonation-of-%C3%AE-lactoglobulin-in-the-presence-of-strong-polyelectrolyte-chains-a-study-using-monte-carlo-simulation
#1
Paola Torres, Luciano Bojanich, Fabricio Sanchez-Varretti, Antonio Jose Ramirez-Pastor, Evelina Quiroga, Valeria Boeris, Claudio F Narambuena
In this work, the molecular interaction between the protein β-lactoglobulin and strong polyelectrolyte chains was studied using Monte Carlo simulations. Different coarse-grained models were used to represent the system components. Both net charge and protonation of the isolated dimeric protein were analyzed as a function of pH. The acid-base equilibrium of each titratable group was distinctively modified by the presence of polyanion or polycation chains. The complexation on the wrong side of pI was more evident with the polycation than with the polyanion...
September 8, 2017: Colloids and Surfaces. B, Biointerfaces
https://www.readbyqxmd.com/read/28926734/a-quality-by-design-based-approach-to-a-capillary-electrokinetic-assay-for-the-determination-of-dextromepromazine-and-levomepromazine-sulfoxide-as-impurities-of-levomepromazine
#2
Stephan Niedermeier, Gerhard K E Scriba
Using a quality by design approach, a capillary electrophoresis method for the simultaneous determination of dextromepromazine and the oxidation product levomepromazine sulfoxide in levomepromazine was developed. The analytical target profile was defined that the method should be able to quantify 0.1% of both impurities with a precision of  ≤10%. Hydroxypropyl-γ-cyclodextrin was used as chiral selector. The critical process parameters cyclodextrin concentration, buffer pH and concentration as well as temperature and applied voltage were studied using a fractional factorial resolution V+ design for defining the knowledge space...
September 8, 2017: Journal of Pharmaceutical and Biomedical Analysis
https://www.readbyqxmd.com/read/28926253/understanding-the-role-of-dna-topology-in-target-search-dynamics-of-proteins
#3
Anupam Mondal, Arnab Bhattacherjee
A wide range of cellular processes initiates upon recognising and binding of proteins to specific DNA sites. Typically, the recognition process is incredibly fast owing to a complex mechanism that combines different 3D and 1D modes of translocation of the protein. While few studies performed on selected DNA topologies suggested that the DNA topology might alter the balance between these two modes and therefore the target search kinetics, its detail role in target search mechanism remains unclear. Here, we present a discrete-state stochastic approach that allows us to incorporate the topological information of DNA molecule explicitly and predict its role during the process when proteins search for their specific binding sites on DNA...
September 19, 2017: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/28925682/role-of-proton-diffusion-in-the-nonexponential-kinetics-of-proton-coupled-electron-transfer-from-photoreduced-zno-nanocrystals
#4
Soumya Ghosh, Alexander V Soudackov, Sharon Hammes-Schiffer
Experiments have suggested that photoreduced ZnO nanocrystals transfer an electron and a proton to organic radicals through a concerted proton-coupled electron transfer (PCET) mechanism. The kinetics of this process was studied by monitoring the decay of the absorbance that reflects the concentration of electrons in the conduction bands of the nanocrystals. Interestingly, this absorbance exhibited nonexponential decay kinetics that could not be explained by heterogeneities of the nanoparticles or electron content...
September 19, 2017: ACS Nano
https://www.readbyqxmd.com/read/28925088/comparison-of-a-quantum-random-number-generator-with-pseudorandom-number-generators-for-their-use-in-molecular-monte-carlo-simulations
#5
Dario Ghersi, Abhishek Parakh, Mihaly Mezei
Four pseudorandom number generators were compared with a physical, quantum-based random number generator using the NIST suite of statistical tests, which only the quantum-based random number generator could successfully pass. We then measured the effect of the five random number generators on various calculated properties in different Markov-chain Monte Carlo simulations. Two types of systems were tested: conformational sampling of a small molecule in aqueous solution and liquid methanol under constant temperature and pressure...
September 18, 2017: Journal of Computational Chemistry
https://www.readbyqxmd.com/read/28923301/clinical-pharmacokinetics-and-pharmacodynamic-target-attainment-of-pazufloxacin-in-prostate-tissue-dosing-considerations-for-prostatitis
#6
Kogenta Nakamura, Kazuro Ikawa, Genya Nishikawa, Ikuo Kobayashi, Masahiro Narushima, Hiroyuki Muramatsu, Shingo Morinaga, Keishi Kajikawa, Yoshiharu Kato, Masahito Watanabe, Kenji Zennami, Kent Kanao, Norifumi Morikawa, Makoto Sumitomo
The present study examined the clinical pharmacokinetics of pazufloxacin in prostate tissue and estimated the probability of target attainment for tissue-specific pharmacodynamic goals related to treating prostatitis using various intravenous dosing regimens. Patients with prostatic hypertrophy received prophylactic infusions of pazufloxacin (500 mg, n = 23; 1000 mg, n = 25) for 0.5 h prior to transurethral prostate resection. Drug concentrations in plasma (0.5-5 h) and prostate tissue (0.5-1.5 h) were measured by high-performance liquid chromatography and used for subsequent noncompartmental and three-compartmental analysis...
September 8, 2017: Journal of Infection and Chemotherapy: Official Journal of the Japan Society of Chemotherapy
https://www.readbyqxmd.com/read/28923171/potential-early-biomarkers-of-sarcopenia-among-independent-older-adults
#7
Ana Coto Montes, José Antonio Boga, Carlos Bermejo Millo, Adrián Rubio González, Yaiza Potes Ochoa, Ignacio Vega Naredo, Marta Martínez Reig, Luis Romero Rizos, Pedro Manuel Sánchez Jurado, Juan Jose Solano, Pedro Abizanda, Beatriz Caballero
OBJECTIVES: There are no tools or biomarkers for a quantitative analysis of sarcopenia. STUDY DESIGN: Cross-sectional study of the diagnosis of sarcopenia in 200 independent adults aged 70 years or over. MAIN OUTCOME MEASURES: Sarcopenia was defined as loss of muscle mass together with low strength and/or loss of physical performance. We considered different clinical parameters and assayed potential blood biomarkers (cell energetic metabolism, muscle performance, inflammation, infection and oxidative stress)...
October 2017: Maturitas
https://www.readbyqxmd.com/read/28922807/tedizolid-is-highly-bactericidal-in-the-treatment-of-pulmonary-mycobacterium-avium-complex-disease
#8
Devyani Deshpande, Shashikant Srivastava, Jotam G Pasipanodya, Pooi S Lee, Tawanda Gumbo
Objectives: To determine if tedizolid is effective for pulmonary Mycobacterium avium complex (MAC) disease, and to use pharmacokinetics/pharmacodynamics to design optimal doses. Methods: We performed an exposure-response experiment in the hollow-fibre system model of intracellular MAC (HFS-MAC). We mimicked the tedizolid concentration-time profiles achieved in the lungs of patients treated once daily for 28 days. The HFS-MAC was sampled at intervals to determine the tedizolid pharmacokinetics and MAC intracellular burden...
September 1, 2017: Journal of Antimicrobial Chemotherapy
https://www.readbyqxmd.com/read/28922806/linezolid-as-treatment-for-pulmonary-mycobacterium-avium-disease
#9
Devyani Deshpande, Shashikant Srivastava, Jotam G Pasipanodya, Tawanda Gumbo
Objectives: To identify the pharmacokinetic/pharmacodynamic parameters and exposures of linezolid in the treatment of pulmonary Mycobacterium avium complex (MAC) disease. Methods: Human-derived monocytes infected with MAC were inoculated into hollow-fibre systems for dose-effect and dose-scheduling studies. We mimicked linezolid concentration-time profiles achieved in adult human lungs treated for 28 days. Sampling to confirm that the intended linezolid pharmacokinetics had been achieved, and for enumeration of MAC colony-forming units, was performed based on repetitive sampling from each system over the 28 days...
September 1, 2017: Journal of Antimicrobial Chemotherapy
https://www.readbyqxmd.com/read/28922140/a-point-kernel-algorithm-for-microbeam-radiation-therapy
#10
Charlotte Debus, Uwe Oelfke, Stefan Bartzsch
Microbeam Radiation Therapy (MRT) is a treatment approach in radiation therapy where the treatment field is spatially fractionated into arrays of a few tens of micrometre wide planar beams of unusually high peak doses separated by low dose regions of several hundred micrometre width. In preclinical studies, this treatment approach has proven to spare normal tissue more effectively than conventional radiation therapy, while being equally efficient in tumour control. So far dose calculations in MRT, a prerequisite for future clinical applications are based on Monte Carlo simulations...
September 18, 2017: Physics in Medicine and Biology
https://www.readbyqxmd.com/read/28921881/use-of-a-radial-projection-to-reduce-the-statistical-uncertainty-of-spot-lateral-profiles-generated-by-monte-carlo-simulation
#11
Xiaoning Ding, Wei Liu, Jiajian Shen, Aman Anand, Joshua B Stoker, Yanle Hu, Martin Bues
Monte Carlo (MC) simulation has been used to generate commissioning data for the beam modeling of treatment planning system (TPS). We have developed a method called radial projection (RP) for postprocessing of MC-simulation-generated data. We used the RP method to reduce the statistical uncertainty of the lateral profile of proton pencil beams with axial symmetry. The RP method takes advantage of the axial symmetry of dose distribution to use the mean value of multiple independent scores as the representative score...
September 18, 2017: Journal of Applied Clinical Medical Physics
https://www.readbyqxmd.com/read/28921613/voxel-based-multi-model-fitting-method-for-modelling-time-activity-curves-in-spect-images
#12
David Sarrut, Adrien Halty, Jean-Noel Badel, Ludovic Ferrer, Manuel Bardiès
PURPOSE: Estimating the biodistribution and the pharmacokinetics from timesequence SPECT images on a per-voxel basis is useful for studying activity nonuniformity or computing absorbed dose distributions by convolution of voxel kernels or Monte-Carlo radiation transport. Current approaches are either region-based, thus assuming uniform activity within the region, or voxel-based but using the same fitting model for all voxels. METHODS: We propose a voxel-based multi-model fitting method (VoMM) that estimates a fitting function for each voxel by automatically selecting the most appropriate model among a predetermined set with Akaike criteria...
September 17, 2017: Medical Physics
https://www.readbyqxmd.com/read/28921536/technical-note-a-simulation-study-on-the-feasibility-of-radiotherapy-dose-enhancement-with-calcium-tungstate-and-hafnium-oxide-nano-and-microparticles
#13
Nicholas J Sherck, You-Yeon Won
PURPOSE: To assess the radiotherapy dose enhancement (RDE) potential of calcium tungstate (CaWO4 ) and hafnium oxide (HfO2 ) nano- and microparticles (NPs). A Monte Carlo simulation study was conducted to gauge their respective RDE potentials relative to that of the broadly studied gold (Au) NP. The study was warranted due to the promising clinical and preclinical studies involving both CaWO4 and HfO2 NPs as RDE agents in the treatment of various types of cancers. The study provides a baseline RDE to which future experimental RDE trends can be compared to...
September 18, 2017: Medical Physics
https://www.readbyqxmd.com/read/28921448/assessment-of-dose-uniformity-around-high-dose-rate-192-ir-and-60-co-stepping-sources
#14
Bagher Farhood, Mahdi Ghorbani
This study aimed to evaluate dose uniformity for (192)Ir and (60)Co stepping sources. High dose rate (192)Ir and (60)Co stepping sources were simulated by the MCNPX Monte Carlo code. To investigate dose uniformity, treatment lengths of 30, 50, 100, and 150 mm with stepping distances of 3, 5, 7, and 10 mm were considered. Finally, dose uniformity for the (192)Ir and (60)Co stepping sources with increasing distances from the source were assessed at these treatment lengths and steps. The findings showed that the dose distribution was non-uniform for regions in close vicinity of the source, especially in the high source steps, but for most points at distances >10 mm from the center of the source, the dose distribution was uniform...
September 18, 2017: Radiological Physics and Technology
https://www.readbyqxmd.com/read/28921104/development-of-constant-ph-simulation-methods-in-implicit-solvent-and-applications-in-biomolecular-systems
#15
REVIEW
Fernando Luís Barroso daSilva, Luis Gustavo Dias
pH is a critical parameter for biological and technological systems directly related with electrical charges. It can give rise to peculiar electrostatic phenomena, which also makes them more challenging. Due to the quantum nature of the process, involving the forming and breaking of chemical bonds, quantum methods should ideally by employed. Nevertheless, due to the very large number of ionizable sites, different macromolecular conformations, salt conditions, and all other charged species, the CPU time cost simply becomes prohibitive for computer simulations, making this a quite complex problem...
September 18, 2017: Biophysical Reviews
https://www.readbyqxmd.com/read/28920937/resolving-ultrafast-exciton-migration-in-organic-solids-at-the-nanoscale
#16
Samuel B Penwell, Lucas D S Ginsberg, Rodrigo Noriega, Naomi S Ginsberg
Effectiveness of molecular-based light harvesting relies on transport of excitons to charge-transfer sites. Measuring exciton migration, however, has been challenging because of the mismatch between nanoscale migration lengths and the diffraction limit. Instead of using bulk substrate quenching methods, here we define quenching boundaries all-optically with sub-diffraction resolution, thus characterizing spatiotemporal exciton migration on its native nanometre and picosecond scales. By transforming stimulated emission depletion microscopy into a time-resolved ultrafast approach, we measure a 16-nm migration length in poly(2,5-di(hexyloxy)cyanoterephthalylidene) conjugated polymer films...
September 18, 2017: Nature Materials
https://www.readbyqxmd.com/read/28919325/the-influence-of-lifestyle-on-airborne-particle-surface-area-doses-received-by-different-western-populations
#17
A Pacitto, L Stabile, T Moreno, P Kumar, A Wierzbicka, L Morawska, G Buonanno
In the present study, the daily dose in terms of particle surface area received by citizens living in five cities in Western countries, characterized by different lifestyle, culture, climate and built-up environment, was evaluated and compared. For this purpose, the exposure to sub-micron particle concentration levels of the population living in Barcelona (Spain), Cassino (Italy), Guilford (United Kingdom), Lund (Sweden), and Brisbane (Australia) was measured through a direct exposure assessment approach. In particular, measurements of the exposure at a personal scale were performed by volunteers (15 per each population) that used a personal particle counter for different days in order to obtain exposure data in microenvironments/activities they resided/performed...
September 14, 2017: Environmental Pollution
https://www.readbyqxmd.com/read/28918765/three-dimensional-3d-nanometrology-based-on-scanning-electron-microscope-sem-stereophotogrammetry
#18
Vipin N Tondare, John S Villarrubia, András E Vlada R
Three-dimensional (3D) reconstruction of a sample surface from scanning electron microscope (SEM) images taken at two perspectives has been known for decades. Nowadays, there exist several commercially available stereophotogrammetry software packages. For testing these software packages, in this study we used Monte Carlo simulated SEM images of virtual samples. A virtual sample is a model in a computer, and its true dimensions are known exactly, which is impossible for real SEM samples due to measurement uncertainty...
September 18, 2017: Microscopy and Microanalysis
https://www.readbyqxmd.com/read/28918522/simulations-and-experimental-investigations-of-the-competitive-adsorption-of-ch4-and-co2-on-low-rank-coal-vitrinite
#19
Song Yu, Jiang Bo, Li Jiahong
The mechanism for the competitive adsorption of CH4 and CO2 on coal vitrinite (DV-8, maximum vitrinite reflectance R o,max = 0.58%) was revealed through simulation and experimental methods. A saturated state was reached after absorbing 17 CH4 or 22 CO2 molecules per DV-8 molecule. The functional groups (FGs) on the surface of the vitrinite can be ranked in order of decreasing CH4 and CO2 adsorption ability as follows: [-CH3] > [-C=O] > [-C-O-C-] > [-COOH] and [-C-O-C-] > [-C=O] > [-CH3] > [-COOH]...
September 16, 2017: Journal of Molecular Modeling
https://www.readbyqxmd.com/read/28916394/a-useful-strategy-based-on-chromatographic-data-combined-with-quality-by-design-approach-for-food-analysis-applications-the-case-study-of-furanic-derivatives-in-sugarcane-honey
#20
Pedro Silva, Catarina L Silva, Rosa Perestrelo, Fernando M Nunes, José S Câmara
Sugarcane honey (SCH) is one of the Madeira Island products par excellence and it is now popular worldwide. Its sui generis and peculiar sensory properties, explained by a variety of volatile compounds including furanic derivatives (FDs), arise mainly from manufacturing and storage conditions. A simple high-throughput approach based on semi-automatic microextraction by packed sorbent (MEPS) combined with ultra-high performance liquid chromatography (UHPLC) was developed and validated for identification and quantification of target FDs in sugarcane honey...
September 8, 2017: Journal of Chromatography. A
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