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"Validation" simulation model

Pingkeng Wu, Alex Nikolov, Darsh Wasan
Capillary dynamics is a ubiquitous everyday phenomenon. It has practical applications in diverse fields, including ink-jet printing, lab-on-a-chip, biotechnology, and coating. Understanding capillary dynamics requires essential knowledge on the molecular level of how fluid molecules interact with a solid substrate (the wall). Recent studies conducted with the surface force apparatus (SFA), atomic force microscope (AFM), and statistical mechanics simulation revealed that molecules/nanoparticles confined into the film/wall surfaces tend to self-layer into 2D layer/s and even 2D in-layer with increased confinement and fluid volume fraction...
February 10, 2017: Advances in Colloid and Interface Science
Arkadiusz Jędrzejewski
We investigate the q-voter model with stochastic noise arising from independence on complex networks. Using the pair approximation, we provide a comprehensive, mathematical description of its behavior and derive a formula for the critical point. The analytical results are validated by carrying out Monte Carlo experiments. The pair approximation prediction exhibits substantial agreement with simulations, especially for networks with weak clustering and large average degree. Nonetheless, for the average degree close to q, some discrepancies originate...
January 2017: Physical Review. E
Ilya Rips
Decay of the metastable state is analyzed within the quantum Kramers model in the weak-to-intermediate dissipation regime. The decay kinetics in this regime is determined by energy exchange between the unstable mode and the stable modes of thermal bath. In our previous paper [Phys. Rev. A 42, 4427 (1990)PLRAAN1050-294710.1103/PhysRevA.42.4427], Grabert's perturbative approach to well dynamics in the case of the discrete bath [Phys. Rev. Lett. 61, 1683 (1988)PRLTAO0031-900710.1103/PhysRevLett.61.1683] has been extended to account for the second order terms in the classical equations of motion (EOM) for the stable modes...
January 2017: Physical Review. E
Esther M Vicente, Martin A Lodge, Steven P Rowe, Richard L Wahl, Eric C Frey
PURPOSE: We investigated the feasibility of using simpler methods than manual whole-organ volume-of-interest (VOI) definition to estimate the organ activity concentration in single photon emission computed tomography (SPECT) in cases where the activity in the organ can be assumed to be uniformly distributed on the scale of the voxel size. In particular, we investigated an anatomic region-of-interest (ROI) defined in a single transaxial slice, and a single sphere placed inside the organ boundaries...
February 16, 2017: Medical Physics
Luca Luschi, Giuseppe Iannaccone, Francesco Pieri
We present a new approach to the temperature compensation of MEMS Lamé resonators, based on the combined effect of the doping concentration and of the geometry of etch holes on the equivalent temperature coefficients of silicon. To this purpose, we develop and validate an analytical model which describes the effect of etch holes on the temperature stability of Lamé resonators through comparison with experiments available in the literature and FEM simulations. We show that two interesting regions of the design space for Lamé resonators exist, where a cancellation of the first-order temperature coefficient of the resonance frequency is possible: [100]-oriented silicon with n-doping of 2...
February 9, 2017: IEEE Transactions on Ultrasonics, Ferroelectrics, and Frequency Control
S Le Dizès, C Aulagnier, D Maro, M Rozet, F Vermorel, D Hébert, C Voiseux, L Solier, C Godinot, B Fievet, P Laguionie, O Connan, O Cazimajou, M Morillon
In this paper, a dynamic compartment model with a high temporal resolution has been investigated to describe tritium transfer in grassland ecosystems exposed to atmospheric (3)H releases from nuclear facilities under normal operating or accidental conditions. TOCATTA-χ model belongs to the larger framework of the SYMBIOSE modelling and simulation platform that aims to assess the fate and transport of a wide range of radionuclides in various environmental systems. In this context, the conceptual and mathematical models of TOCATTA-χ have been designed to be relatively simple, minimizing the number of compartments and input parameters required...
February 12, 2017: Journal of Environmental Radioactivity
Y Bian, J B Holland
Genome-wide association mapping using dense marker sets has identified some nucleotide variants affecting complex traits that have been validated with fine-mapping and functional analysis. However, many sequence variants associated with complex traits in maize have small effects and low repeatability. In contrast to genome-wide association study (GWAS), genomic prediction (GP) is typically based on models incorporating information from all available markers, rather than modeling effects of individual loci. We considered methods to integrate results of GWASs into GP models in the context of multiple interconnected families...
February 15, 2017: Heredity
Yufeng Zhang, Xiaohan Du, Yurong Shi
The design characteristics of street canyons were investigated in Guangzhou in the hot-humid area of China, and the effects of the design factors and their interactions on pedestrian thermal comfort were studied by numerical simulations. The ENVI-met V4.0 (BASIC) model was validated by field observations and used to simulate the micrometeorological conditions and the standard effective temperature (SET) at pedestrian level of the street canyons for a typical summer day of Guangzhou. The results show that the micrometeorological parameters of mean radiant temperature (MRT) and wind speed play key roles in pedestrian thermal comfort...
February 14, 2017: International Journal of Biometeorology
Tom Mingasson, Tanguy Duval, Nikola Stikov, Julien Cohen-Adad
HIGHLIGHTS AxonPacking: Open-source software for simulating white matter microstructure.Validation on a theoretical disk packing problem.Reproducible and stable for various densities and diameter distributions.Can be used to study interplay between myelin/fiber density and restricted fraction. Quantitative Magnetic Resonance Imaging (MRI) can provide parameters that describe white matter microstructure, such as the fiber volume fraction (FVF), the myelin volume fraction (MVF) or the axon volume fraction (AVF) via the fraction of restricted water (fr)...
2017: Frontiers in Neuroinformatics
H M T Boer, S T Butler, C Stötzel, M F W Te Pas, R F Veerkamp, H Woelders
A recently developed mechanistic mathematical model of the bovine estrous cycle was parameterized to fit empirical data sets collected during one estrous cycle of 31 individual cows, with the main objective to further validate the model. The a priori criteria for validation were (1) the resulting model can simulate the measured data correctly (i.e. goodness of fit), and (2) this is achieved without needing extreme, probably non-physiological parameter values. We used a least squares optimization procedure to identify parameter configurations for the mathematical model to fit the empirical in vivo measurements of follicle and corpus luteum sizes, and the plasma concentrations of progesterone, estradiol, FSH and LH for each cow...
February 15, 2017: Animal: An International Journal of Animal Bioscience
Jason R Determann, James E Fleischli, Donald F D'Alessandro, Dana P Piasecki
An important consideration for the successful use of fresh osteochondral allografts for the patellofemoral joint is selection of appropriately sized donor allografts. This is particularly challenging for matching grafts to the patella because of the substantial variability in articular contour that exists. At present, selection of donor patellae is based only on the width of the proximal tibia, with no established means of quantifying basic patellar size, facet configuration, or articular contour. We hypothesized that using a combination of standard radiographic measurements to generate an accurate profile of the recipients native patella would result in a more accurate donor graft...
February 14, 2017: Journal of Knee Surgery
Giovani Fiore, Erik Anderson, C Spencer Garborg, Mark Murray, Mark Johnson, Michael J Moore, Laurens Howle, K Alex Shorter
Bio-logging tags are an important tool for the study of cetaceans, but superficial tags inevitably increase hydrodynamic loading. Substantial forces can be generated by tags on fast-swimming animals, potentially affecting behavior and energetics or promoting early tag removal. Streamlined forms have been used to reduce loading, but these designs can accelerate flow over the top of the tag. This non-axisymmetric flow results in large lift forces (normal to the animal) that become the dominant force component at high speeds...
2017: PloS One
Hans J Lee, Briana Coleman, Andrew D Lerner, David Feller-Kopman, Roy Semaan, Bernice Frimpong, Lonny Yarmus
BACKGROUND: Procedural learning requires both didactic knowledge and motor skills. Optimal teaching styles and techniques remain to be defined for pulmonary procedural learning. We investigated the preferences of learners at 2 different points in a pulmonary career; as pulmonary fellows and as clinical practitioners. METHODS: A perception survey was conducted among pulmonary fellows and practitioners from multiple institutions throughout the United States. Fellows and practitioners were immediately surveyed on procedural learning factors after completing a procedural learning course using low/high-fidelity and/or cadaver simulators...
February 10, 2017: Journal of Bronchology & Interventional Pulmonology
Azimeh N V Dehkordi, Alireza Kamali-Asl, James R Ewing, Ning Wen, Indrin J Chetty, Hassan Bagher-Ebadian
Extravascular extracellular space (ve ) is a key parameter to characterize the tissue of cerebral tumors. This study introduces an artificial neural network (ANN) as a fast, direct, and accurate estimator of ve from a time trace of the longitudinal relaxation rate, ΔR1 (R1  = 1/T1 ), in DCE-MRI studies. Using the extended Tofts equation, a set of ΔR1 profiles was simulated in the presence of eight different signal to noise ratios. A set of gain- and noise-insensitive features was generated from the simulated ΔR1 profiles and used as the ANN training set...
February 14, 2017: NMR in Biomedicine
Andreas Ipsen
The mass peak centroid is a quantity that is at the core of mass spectrometry (MS). However, despite its central status in the field, models of its statistical distribution are often chosen quite arbitrarily and without attempts at establishing a proper theoretical justification for their use. Recent work has demonstrated that for mass spectrometers employing analog-to-digital converters (ADCs) and electron multipliers, the statistical distribution of the mass peak intensity can be described via a relatively simple model derived essentially from first principles...
February 3, 2017: Analytical Chemistry
Amine M Samoudi, Stefan Kampusch, Emmeric Tanghe, Jozsef C Széles, Luc Martens, Eugenijus Kaniusas, Wout Joseph
OBJECTIVE: Percutaneous stimulation of the auricular branch of the vagus nerve (pVNS) by miniaturized needle electrodes in the auricle gained importance as a treatment for acute and chronic pain. The objective is to establish a realistic numerical model of pVNS and investigate the effects of stimulation waveform, electrodes' depth, and electrodes' position on nerve excitation threshold and the percentage of stimulated nerves. METHODS: Simulations were performed with Sim4Life...
February 13, 2017: Medical & Biological Engineering & Computing
Reza Drikvandi
Nonlinear mixed-effects models are frequently used for pharmacokinetic data analysis, and they account for inter-subject variability in pharmacokinetic parameters by incorporating subject-specific random effects into the model. The random effects are often assumed to follow a (multivariate) normal distribution. However, many articles have shown that misspecifying the random-effects distribution can introduce bias in the estimates of parameters and affect inferences about the random effects themselves, such as estimation of the inter-subject variability...
February 13, 2017: Journal of Pharmacokinetics and Pharmacodynamics
Navid Nezafat, Mahboobeh Eslami, Manica Negahdaripour, Mohammad Reza Rahbar, Younes Ghasemi
Helicobacter pylori is the cunning bacterium that can live in the stomachs of many people without any symptoms, but gradually can lead to gastric cancer. Due to various obstacles, which are related to anti-H. pylori antibiotic therapy, recently developing an anti-H. pylori vaccine has attracted more attention. In this study, different immunoinformatics and computational vaccinology approaches were employed to design an efficient multi-epitope oral vaccine against H. pylori. Our multi-epitope vaccine is composed of heat labile enterotoxin IIc B (LT-IIc) that is used as a mucosal adjuvant to enhance vaccine immunogenicity for oral immunization, cartilage oligomeric matrix protein (COMP) to increase vaccine stability in acidic pH of gut, one experimentally protective antigen, OipA, and two hypothetical protective antigens, HP0487 and HP0906, and "CTGKSC" peptide motif that target epithelial microfold cells (M cells) to enhance vaccine uptake from the gut barrier...
February 14, 2017: Molecular BioSystems
Jonasz Słomka, Jörn Dunkel
Classical turbulence theory assumes that energy transport in a 3D turbulent flow proceeds through a Richardson cascade whereby larger vortices successively decay into smaller ones. By contrast, an additional inverse cascade characterized by vortex growth exists in 2D fluids and gases, with profound implications for meteorological flows and fluid mixing. The possibility of a helicity-driven inverse cascade in 3D fluids had been rejected in the 1970s based on equilibrium-thermodynamic arguments. Recently, however, it was proposed that certain symmetry-breaking processes could potentially trigger a 3D inverse cascade, but no physical system exhibiting this phenomenon has been identified to date...
February 13, 2017: Proceedings of the National Academy of Sciences of the United States of America
Ingrid Keupers, Patrick Willems
Modern, model based river quality management strongly relies on river water quality models to simulate the temporal and spatial evolution of pollutant concentrations in the water body. Such models are typically constructed by extending detailed hydrodynamic models with a component describing the advection-diffusion and water quality transformation processes in a detailed, physically based way. This approach is too computational time demanding, especially when simulating long time periods that are needed for statistical analysis of the results or when model sensitivity analysis, calibration and validation require a large number of model runs...
February 1, 2017: Water Research
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