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Modeling and Simulation

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https://www.readbyqxmd.com/read/28926929/response-characteristics-and-experimental-study-of-underground-magnetic-resonance-sounding-using-a-small-coil-sensor
#1
Shengwu Qin, Zhongjun Ma, Chuandong Jiang, Jun Lin, Yiguo Xue, Xinlei Shang, Zhiqiang Li
Due to its unique sensitivity to hydrogen protons, magnetic resonance sounding (MRS) is the only geophysical method that directly detects water and can provide nondestructive information on subsurface aquifer properties. The relationship between the surface MRS signal and the location and characteristics of aquifers using large-coil (typically 50-150 m) sensors has been discussed based on forward modelling and experiments. However, few researchers have studied underground MRS using a small-coil sensor. In this paper, a parametric study and a large-scale physical model test were conducted to shed light on the critical response characteristics of underground MRS using a small-coil sensor...
September 15, 2017: Sensors
https://www.readbyqxmd.com/read/28926847/probing-the-stochastic-property-of-endoreduplication-in-cell-size-determination-of-arabidopsis-thaliana-leaf-epidermal-tissue
#2
Kensuke Kawade, Hirokazu Tsukaya
Cell size distribution is highly reproducible, whereas the size of individual cells often varies greatly within a tissue. This is obvious in a population of Arabidopsis thaliana leaf epidermal cells, which ranged from 1,000 to 10,000 μm2 in size. Endoreduplication is a specialized cell cycle in which nuclear genome size (ploidy) is doubled in the absence of cell division. Although epidermal cells require endoreduplication to enhance cellular expansion, the issue of whether this mechanism is sufficient for explaining cell size distribution remains unclear due to a lack of quantitative understanding linking the occurrence of endoreduplication with cell size diversity...
2017: PloS One
https://www.readbyqxmd.com/read/28926766/protonation-of-%C3%AE-lactoglobulin-in-the-presence-of-strong-polyelectrolyte-chains-a-study-using-monte-carlo-simulation
#3
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/28926755/neochordoplasty-versus-leaflet-resection-for-ruptured-mitral-chordae-treatment-virtual-mitral-valve-repair
#4
Ahnryul Choi, David D McPherson, Hyunggun Kim
Degenerative mitral valve (MV) disease involving mitral prolapse is one of the most prevalent MV pathologies. Quadrangular leaflet resection and neochordoplasty demonstrate excellent clinical outcomes for the treatment of posterior leaflet prolapse. We evaluated the functional and biomechanical characteristics of a virtual pathologic MV model suffering from chordal rupture, performed virtual neochordoplasty and quadrangular leaflet resection, and compared the two post-repair MV functions. The pre-repair MV demonstrated severe posterior leaflet prolapse due to the ruptured P2 chordae and excessive stress concentration...
September 13, 2017: Computers in Biology and Medicine
https://www.readbyqxmd.com/read/28926713/phase-separation-kinetics-of-dynamically-self-assembling-nanoparticles-with-toggled-interactions
#5
Zachary M Sherman, Helen Rosenthal, James W Swan
Ordered materials passively self-assembled from dispersions of nanoparticles with steady interactions are subject to thermodynamic constraints on their phase separation kinetics forcing a tradeoff between throughput and quality. Dynamically self-assembling dispersions whose interactions vary in a controlled way with time do not have these constraints and can rapidly form ordered structures while avoiding kinetic arrest. These out-of-equilibrium processes cannot be understood in terms of equilibrium thermodynamics or kinetic models derived from equilibrium thermodynamics, so new theories must be developed before dynamic self-assembly can be used to reliably fabricate nanomaterials...
September 19, 2017: Langmuir: the ACS Journal of Surfaces and Colloids
https://www.readbyqxmd.com/read/28926709/simulating-osmotic-equilibria-a-new-tool-to-calculate-activity-coefficients-in-concentrated-aqueous-salt-solutions
#6
Michael Bley, Magali Duvail, Philippe Guilbaud, Jean-Francois Dufrêche
Herein, a new theoretical method simulating osmotic equilibria and activities is presented, where a bulk liquid and its corresponding vapor phase are simulated with molecular dynamics using polarizable force fields. Time-averaged number density profiles based on the resulting trajectories provide the amount of evaporated molecules present in the vapor phase and consequently the vapor phase density. The activity of the solvent and the corresponding osmotic coefficient are determined by the vapor density at a certain solute concentration with respect to the reference vapor density of the pure solvent...
September 19, 2017: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/28926706/structural-and-kinetic-characterization-of-the-intrinsically-disordered-protein-sev-ntail-through-enhanced-sampling-simulations
#7
Mattia Bernetti, Matteo Masetti, Fabio Pietrucci, Martin Blackledge, Malene Ringkjøbing Jensen, Maurizio Recanatini, Luca Mollica, Andrea Cavalli
Intrinsically disordered proteins (IDPs) are emerging as an important class of the proteome. Being able to interact with different molecular targets, they participate in many physiological and pathological activities. However, due to their intrinsically heterogeneous nature, determining the equilibrium properties of IDPs is still a challenge for biophysics. Herein, we applied state-of-the-art enhanced sampling methods to Sev NTAIL, a test case of IDPs, and constructed a bin-based kinetic model to unveil the underlying kinetics...
September 19, 2017: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/28926566/guidelines-for-the-management-of-a-brain-death-donor-in-the-rhesus-macaque-a-translational-transplant-model
#8
Tiffany J Zens, Juan S Danobeitia, Peter J Chlebeck, Laura J Zitur, Scott Odorico, Kevin Brunner, Jennifer Coonen, Saverio Capuano, Anthony M D'Alessandro, Kristina Matkowskyj, Weixiong Zhong, Jose Torrealba, Luis Fernandez
INTRODUCTION: The development of a translatable brain death animal model has significant potential to advance not only transplant research, but also the understanding of the pathophysiologic changes that occur in brain death and severe traumatic brain injury. The aim of this paper is to describe a rhesus macaque model of brain death designed to simulate the average time and medical management described in the human literature. METHODS: Following approval by the Institutional Animal Care and Use Committee, a brain death model was developed...
2017: PloS One
https://www.readbyqxmd.com/read/28926374/reducing-urban-violence-a-contrast-of-public-health-and-criminal-justice-approaches
#9
Magdalena Cerdá, Melissa Tracy, Katherine M Keyes
BACKGROUND: Cities are investing millions in Cure Violence, a public health approach to reduce urban violence by targeting at-risk youth and redirecting conflict to non-violent responses. The impact of such a program compared to criminal justice responses is unknown because experiments directly comparing criminal justice and public health approaches to violence prevention are infeasible with observational data. We simulated experiments to test the influence of two interventions on violence: a) Cure Violence; and b) directed police patrol in violence hot spots...
September 18, 2017: Epidemiology
https://www.readbyqxmd.com/read/28926372/attrition-bias-related-to-missing-outcome-data-a-longitudinal-simulation-study
#10
Antoine Lewin, Ruben Brondeel, Tarik Benmarhnia, Frédérique Thomas, Basile Chaix
BACKGROUND: Most longitudinal studies do not address potential selection biases due to selective attrition. Using empirical data and simulating additional attrition, we investigated the effectiveness of common approaches to handle missing outcome data from attrition in the association between individual education level and change in body mass index (BMI). METHODS: Using data from the two waves of the French RECORD Cohort Study (N = 7,172), we first examined how inverse probability weighting (IPW) and multiple imputation handled missing outcome data from attrition in the observed data (stage 1)...
September 18, 2017: Epidemiology
https://www.readbyqxmd.com/read/28926200/dual-wavelength-assisted-thermal-hemostasis-for-treatment-of-benign-prostate-hyperplasia
#11
Jiuen Hwang, Hyejin Kim, Truong Van Gia, Jason Xuan, Thomas Hasenberg, Hyun Wook Kang
Laser treatment on a large size of prostate gland often encounters significant bleeding that can prolong the entire procedure and cause urinary complications. The current study investigates the feasibility of dual-wavelength (532 and 980 nm) application to achieve rapid hemostasis for 532-nm laser prostatectomy. Porcine kidney and bleeding phantom models were tested to quantify the degree of the irreversible tissue coagulation and to estimate the time for the complete hemostasis, respectively. The ex vivo kidney testing verifies that the dual-wavelength created up to 40% deeper and 25% wider coagulation regions than a single wavelength does...
September 19, 2017: Journal of Biophotonics
https://www.readbyqxmd.com/read/28926135/a-spatial-approach-to-combatting-wildlife-crime
#12
Sally C Faulkner, Michael C A Stevens, Stephanie S Romañach, Peter A Lindsey, Steven C Le Comber
Poaching can have devastating impacts on animal and plant numbers, and in many countries has reached crisis levels, with illegal hunters employing increasingly sophisticated techniques. Here, we show how geographic profiling - a mathematical technique originally developed in criminology and recently applied to animal foraging and epidemiology - can be adapted for use in investigations of wildlife crime, using data from an eight-year study in Savé Valley Conservancy, Zimbabwe that in total includes more than 10,000 incidents of illegal hunting and the deaths of 6,454 wild animals...
September 19, 2017: Conservation Biology: the Journal of the Society for Conservation Biology
https://www.readbyqxmd.com/read/28926102/in-situ-temperature-relationships-of-biochemical-and-stomatal-controls-of-photosynthesis-in-four-lowland-tropical-tree-species
#13
Martijn Slot, Klaus Winter
Net photosynthetic carbon uptake of Panamanian lowland tropical forest species is typically optimal at 30-32°C. The processes responsible for the decrease in photosynthesis at higher temperatures are not fully understood for tropical trees. We determined temperature responses of maximum rates of RuBP-carboxylation (VCMax ) and RuBP-regeneration (JMax ), stomatal conductance (Gs ) and respiration in the light (RLight ) in situ for four lowland tropical tree species in Panama. Gs had the lowest temperature optimum (TOpt ), similar to that of net photosynthesis, and photosynthesis became increasingly limited by stomatal conductance as temperature increased...
September 19, 2017: Plant, Cell & Environment
https://www.readbyqxmd.com/read/28926100/electrokinetic-motion-of-a-spherical-micro-particle-at-an-oil-water-interface-in-microchannel
#14
Chengfa Wang, Mengqi Li, Yongxin Song, Xinxiang Pan, Dongqing Li
The electrokinetic motion of a negatively charged spherical particle at an oil-water interface in a microchannel is numerically investigated and analyzed in this paper. A three-dimensional (3D) transient numerical model is developed to simulate the particle electrokinetic motion. The channel wall, the surface of the particle and the oil-water interface are all considered negatively charged. The effects of the direct current (DC) electric field, the zeta potentials of the particle-water interface and the oil-water interface, and the dynamic viscosity ratio of oil to water on the velocity of the particle are studied in this paper...
September 19, 2017: Electrophoresis
https://www.readbyqxmd.com/read/28926095/model-based-assessment-using-conventional-bioequivalence-limits-to-ensure-safety-and-efficacy-of-rivaroxaban-in-patients-undergoing-hip-or-knee-replacement
#15
Mario González-Sales, Lanyan Fang, Myong-Jin Kim, Liang Zhao
We evaluated whether the current bioequivalence limit is adequate to ensure safety and efficacy of rivaroxaban in patients under total hip arthroplasty and total knee arthroplasty based on its model informed benefit/risk profile. Clinical data from a total of 7145 patients from 3 phase 2 and 4 phase 3 clinical trials were included in the current model-based exposure-response analysis. The relationships between rivaroxaban exposure measurements (ie, minimum or trough, maximum, average concentration, and area under the concentration-time curve [AUC] at steady state) and clinical outcomes (ie, the probabilities of major bleeding [MB] and venous thromboembolism [VTE]) were modeled using NONMEM 7...
September 19, 2017: Journal of Clinical Pharmacology
https://www.readbyqxmd.com/read/28926071/molecular-dynamics-simulations-of-oligoester-brushes-the-origin-of-unusual-conformations
#16
A D Glova, S V Larin, S G Falkovich, V M Nazarychev, D A Tolmachev, N V Lukasheva, S V Lyulin
We present results from all-atom molecular dynamics simulations for the structural properties of oligomeric lactic acid chains (OLA) grafted to the surface of cellulose nanocrystals (CNCs) and immersed in the melt of polylactic acid (PLA). Earlier, we have found that the distribution of free ends of OLA molecules is bimodal [Glova et al., Polym. Int., 2016, 65(8), 892]. The results cannot be explained within the standard picture of uncharged polymer brushes exposed to the melt of a chemically identical polymer...
September 19, 2017: Soft Matter
https://www.readbyqxmd.com/read/28926061/network-based-modelling-and-percolation-analysis-of-conformational-dynamics-and-activation-in-the-cdk2-and-cdk4-proteins-dynamic-and-energetic-polarization-of-the-kinase-lobes-may-determine-divergence-of-the-regulatory-mechanisms
#17
G M Verkhivker
The overarching goal of delineating molecular principles underlying differentiation of the activation mechanisms in cyclin-dependent kinases (CDKs) is important for understanding regulatory divergences among closely related kinases which can be exploited in drug discovery of targeted and allosteric inhibitors. To systematically characterize dynamic, energetic and network signatures of the activation mechanisms, we combined atomistic simulations and elastic network modeling with the analysis of the residue interaction networks and rigidity decomposition of the CDK2-cyclin A and CDK4-cyclin D1/D3 complexes...
September 19, 2017: Molecular BioSystems
https://www.readbyqxmd.com/read/28926010/economic-assessment-of-an-emerging-disease-the-case-of-schmallenberg-virus-in-france
#18
A Waret-Szkuta, P Alarcon, B Hasler, J Rushton, F Corbière, D Raboisson
Schmallenberg virus (SBV) was first detected in 2011 in Germany and then in France in 2012. This study simulates the production of different ruminant systems in France and estimates, through partial budget analyses, the economic cost of SBV at the farm level, under two disease scenarios (a high-impact and low-impact scenario). A partial budget is used to evaluate the financial effect of incremental changes, and includes only resources or production that will be changed. In the high-impact scenario, the estimated impact of SBV ranged from €23 to €43 per cow per year and €19 to €37 per ewe per year...
April 2017: Revue Scientifique et Technique
https://www.readbyqxmd.com/read/28925991/a-multiscale-imaging-and-modelling-dataset-of-the-human-inner-ear
#19
Nicolas Gerber, Mauricio Reyes, Livia Barazzetti, Hans Martin Kjer, Sergio Vera, Martin Stauber, Pavel Mistrik, Mario Ceresa, Nerea Mangado, Wilhelm Wimmer, Thomas Stark, Rasmus R Paulsen, Stefan Weber, Marco Caversaccio, Miguel A González Ballester
Understanding the human inner ear anatomy and its internal structures is paramount to advance hearing implant technology. While the emergence of imaging devices allowed researchers to improve understanding of intracochlear structures, the difficulties to collect appropriate data has resulted in studies conducted with few samples. To assist the cochlear research community, a large collection of human temporal bone images is being made available. This data descriptor, therefore, describes a rich set of image volumes acquired using cone beam computed tomography and micro-CT modalities, accompanied by manual delineations of the cochlea and sub-compartments, a statistical shape model encoding its anatomical variability, and data for electrode insertion and electrical simulations...
September 19, 2017: Scientific Data
https://www.readbyqxmd.com/read/28925949/a-generic-compliance-modeling-method-for-two-axis-elliptical-arc-filleted-flexure-hinges
#20
Lijian Li, Dan Zhang, Sheng Guo, Haibo Qu
As a kind of important flexible joint, two-axis flexure hinges can realize in-plane and out-of-plane motions and can be used for constructing flexure-based spatial compliant mechanisms. The paper introduces a common two-axis elliptical-arc-filleted flexure hinge that is generated by two different elliptical-arc-filleted cutout profiles and that provides some new hinge types. The analytical compliance equations of both half-segments of the two-axis elliptical-arc flexure hinges are firstly formulated, and then, based on a generic compliance modeling method of a flexure serial chain, the closed-form compliance and precision matrices of two-axis elliptical-arc-filleted flexure hinges are established and validated by the finite element method...
September 19, 2017: Sensors
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