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"Validation" simulation model

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https://www.readbyqxmd.com/read/28330175/exploration-of-the-binding-modes-of-l-asparaginase-complexed-with-its-amino-acid-substrates-by-molecular-docking-dynamics-and-simulation
#1
Erva Rajeswara Reddy, Rajulapati Satish Babu, Potla Durthi Chandrasai, Pola Madhuri
Acute lymphocytic leukemia (ALL) is an outrageous disease worldwide. L-Asparagine (L-Asn) and L-glutamine (L-Gln) deamination plays crucial role in ALL treatment. Role of Erwinaze(®) (L-asparaginase from Erwinia chrysanthemi) in regulation of L-Asn and L-Gln has been confirmed by the experimental studies. Therapeutic research against ALL remained elusive with the lack of structural information on Erwinaze(®) enzyme. In this present study, homology model of the Erwinaze(®) was developed using MODELLER and the same was validated by various quality indexing tools...
June 2016: 3 Biotech
https://www.readbyqxmd.com/read/28328501/monte-carlo-simulations-of-diffusion-weighted-mri-in-myocardium-validation-and-sensitivity-analysis
#2
Joanne Bates, Darryl McClymont, Irvin Teh, Peter Kohl, Jurgen Schneider, Vicente Grau
A model of cardiac microstructure and diffusion MRI is presented, and compared with experimental data from ex vivo rat hearts. The model includes a simplified representation of individual cells, with physiologically correct cell size and orientation, as well as intra- to extracellular volume ratio. Diffusion MRI is simulated using a Monte Carlo model and realistic MRI sequences. The results show good correspondence between the simulated and experimental MRI signals. Similar patterns are observed in the eigenvalues of the diffusion tensor, the mean diffusivity (MD) and the fractional anisotropy (FA)...
March 10, 2017: IEEE Transactions on Medical Imaging
https://www.readbyqxmd.com/read/28328281/educational-role-for-an-advanced-suturing-task-in-the-pediatric-laparoscopic-surgery-simulator
#3
Maeve O'Neill Trudeau, Brian Carrillo, Ahmed Nasr, Justin T Gerstle, Georges Azzie
BACKGROUND: Laparoscopic models are recognized as important training tools. Lower fidelity systems are used mainly for simpler tasks; an advanced suturing task may allow for additional training of experts. The purpose of this study was to explore the educational role of an advanced suturing task using motion analysis and establish the task's construct validity. METHODS: The pediatric laparoscopic surgery (PLS) simulator was customized with motion-tracking hardware and software...
March 22, 2017: Journal of Laparoendoscopic & Advanced Surgical Techniques. Part A
https://www.readbyqxmd.com/read/28327499/a-fast-measuring-method-for-the-inner-diameter-of-coaxial-holes
#4
Lei Wang, Fangyun Yang, Luhua Fu, Zhong Wang, Tongyu Yang, Changjie Liu
A new method for fast diameter measurement of coaxial holes is studied. The paper describes a multi-layer measuring rod that installs a single laser displacement sensor (LDS) on each layer. This method is easy to implement by rotating the measuring rod, and immune from detecting the measuring rod's rotation angles, so all diameters of coaxial holes can be calculated by sensors' values. While revolving, the changing angles of each sensor's laser beams are approximately equal in the rod's radial direction so that the over-determined nonlinear equations of multi-layer holes for fitting circles can be established...
March 22, 2017: Sensors
https://www.readbyqxmd.com/read/28327436/investigating-the-affinity-of-bde154-and-3oh-bde154-with-hsa-experimental-and-simulation-validation
#5
Wu Yang, Lulu Yang, Zhongsheng Yi, Zhiwei Wu, Jinfang Nie, Aiqian Zhang
The physicochemical properties of polybrominated diphenyl ethers are important for modeling their transport, but these data are often missing. Here, satisfactory bioactivity results were obtained using human serum albumin as the carrier, 2,2',4,4',5,6'-hexabromodiphenyl ether (BDE154) and 3-hydroxy-2,2',4,4', 5,6'-hexabromodiphenyl ether (3OH-BDE154) as the ligands, using UV-visible absorbance, fluorescence, circular dichroism, molecular docking, and molecular dynamics methods. The interactions between human serum albumin and BDE154 or 3OH-BDE154 were verified, consistent with the static quenching procedure...
March 6, 2017: Environmental Toxicology and Pharmacology
https://www.readbyqxmd.com/read/28326347/the-insufficiencies-of-risk-analysis-of-impending-pathological-fractures-in-patients-with-femoral-metastases-a-literature-review
#6
Emir Benca, Janina M Patsch, Winfried Mayr, Dieter H Pahr, Reinhard Windhager
PURPOSE: Pathologic fractures in patients with bone metastases are a common problem in clinical orthopaedic routine. On one hand recognition of metastatic lesions, which are at a high risk of fracture, is essential for timely prophylactic fixation, while on the other hand patients with a low risk of pathologic fractures should be spared from overtreatment. The purpose of this review is to identify all methods for fracture risk evaluation in patients with femoral metastases in the literature and to evaluate their predictive values in clinical applications...
December 2016: Bone Reports
https://www.readbyqxmd.com/read/28326241/modeling-of-the-growth-of-gaas-algaas-core-shell-nanowires
#7
Qian Zhang, Peter W Voorhees, Stephen H Davis
Heterostructured GaAs-AlGaAs core-shell nanowires with have attracted much attention because of their significant advantages and great potential for creating high performance nanophotonics and nanoelectronics. The spontaneous formation of Al-rich stripes along certain crystallographic directions and quantum dots near the apexes of the shell are observed in AlGaAs shells. Controlling the formation of these core-shell heterostructures remains challenging. A two-dimensional model valid on the wire cross section, that accounts for capillarity in the faceted surface limit and deposition has been developed for the evolution of the shell morphology and concentration in Al x Ga1-x As alloys...
2017: Beilstein Journal of Nanotechnology
https://www.readbyqxmd.com/read/28325911/theoretical-and-computational-validation-of-the-kuhn-barrier-friction-mechanism-in-unfolded-proteins
#8
Stanislav M Avdoshenko, Atanu Das, Rohit Satija, Garegin A Papoian, Dmitrii E Makarov
A long time ago, Kuhn predicted that long polymers should approach a limit where their global motion is controlled by solvent friction alone, with ruggedness of their energy landscapes having no consequences for their dynamics. In contrast, internal friction effects are important for polymers of modest length. Internal friction in proteins, in particular, affects how fast they fold or find their binding targets and, as such, has attracted much recent attention. Here we explore the molecular origins of internal friction in unfolded proteins using atomistic simulations, coarse-grained models and analytic theory...
March 21, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28325006/a-simplified-state-space-model-of-biventricular-assist-device-cardiovascular-system-interaction
#9
Vivian C A Koh, Einly Lim, Boon Chiang Ng, Yong Kuen Ho, Nigel H Lovell
A simplified state-space model of biventricular assist device (BiVAD)-cardiovascular system (CVS) interaction is presented. The state-space equations includes a six-compartments CVS model incorporating the ventricles, the pulmonary and systemic circulations as well as the non-linear behavior of the valve flow, together with a left ventricular assist device (LVAD) and a right ventricular assist device (RVAD) component. The left and right pump speeds serve as the input variables for the state-space model. The model is simulated with three operational modes, i...
August 2016: Conference Proceedings: Annual International Conference of the IEEE Engineering in Medicine and Biology Society
https://www.readbyqxmd.com/read/28324776/microstructural-evolution-of-ti6al4v-in-ultrasonically-assisted-cutting-numerical-modelling-and-experimental-analysis
#10
Wei Bai, Ronglei Sun, Jürgen Leopold, Vadim V Silberschmidt
This paper aims to elucidate the effect of ultrasonically assisted cutting (UAC) on microstructure in a machined surface and a chip of Ti6Al4V alloy. To investigate microstructural evolution, a FE-based cutting model with an enhanced material formulation and temperature dependent material properties was developed. A Johnson-Mehl-Avrami-Kolmogorov (JMAK) model for the Ti6Al4V alloy was employed to simulate dynamic recrystallization and predict a resultant grain size. Due to a specific thermomechanical load in UAC, the distributions of strains, strain rates and temperatures in a workpiece in the machining process were investigated...
March 9, 2017: Ultrasonics
https://www.readbyqxmd.com/read/28323867/understanding-and-coping-with-extremism-in-an-online-collaborative-environment-a-data-driven-modeling
#11
Csilla Rudas, Olivér Surányi, Taha Yasseri, János Török
The Internet has provided us with great opportunities for large scale collaborative public good projects. Wikipedia is a predominant example of such projects where conflicts emerge and get resolved through bottom-up mechanisms leading to the emergence of the largest encyclopedia in human history. Disaccord arises whenever editors with different opinions try to produce an article reflecting a consensual view. The debates are mainly heated by editors with extreme views. Using a model of common value production, we show that the consensus can only be reached if groups with extreme views can actively take part in the discussion and if their views are also represented in the common outcome, at least temporarily...
2017: PloS One
https://www.readbyqxmd.com/read/28323703/biomechanical-effects-of-human-lumbar-discography-in-vitro-experiments-and-their-finite-element-validation
#12
Kristen E Lipscomb, Nesrin Sarigul-Klijn, Eric Klineberg, Vivek Mohan
STUDY DESIGN: An experimental and computational finite element analysis of human lumbar spine discography and its resulting effects on disk biomechanics. OBJECTIVE: To characterize the changes in stress and displacement of the human lumbar spine disks after puncture due to discography. SUMMARY OF BACKGROUND DATA: Discography of the intervertebral disk (IVD) may be used to diagnose pathology of the disk and determine whether it may be a source for chronic back pain...
April 2017: Clinical Spine Surgery
https://www.readbyqxmd.com/read/28323442/an-investigation-of-human-body-model-morphing-for-the-assessment-of-abdomen-responses-to-impact-against-a-population-of-test-subjects
#13
Philippe Beillas, Fabien Berthet
OBJECTIVE: Human Body Models have the potential to better describe the human anatomy and variability than dummies. However, datasets available to verify the human response to impact are typically limited in numbers, and they are not size or gender specific. The objective of the study was to investigate the use of model morphing methodologies within that context. METHODS: In the current study, a simple human model scaling methodology was developed to morph two detailed human models (Global Human Body Model Consortium models 50(th) male, M50 and 5(th) female F05) to the dimensions of Post Mortem Human Surrogates (PMHS) used in published literature...
March 21, 2017: Traffic Injury Prevention
https://www.readbyqxmd.com/read/28322433/a-9-pool-metabolic-structured-kinetic-model-describing-days-to-seconds-dynamics-of-growth-and-product-formation-by-penicillium-chrysogenum
#14
Wenjun Tang, Amit T Deshmukh, Cees Haringa, Guan Wang, Walter van Gulik, Wouter van Winden, Matthias Reuss, Joseph J Heijnen, Jianye Xia, Ju Chu, Henk J Noorman
A powerful approach for the optimization of industrial bioprocesses is to perform detailed simulations integrating large scale computational fluid dynamics (CFD) and cellular reaction dynamics (CRD). However, complex metabolic kinetic models containing a large number of equations pose formidable challenges in CFD-CRD coupling and computation time afterward. This necessitates to formulate a relatively simple but yet representative model structure. Such a kinetic model should be able to reproduce metabolic responses for short-term (mixing time scale of tens of seconds) and long-term (fed-batch cultivation of hours/days) dynamics in industrial bioprocesses...
March 21, 2017: Biotechnology and Bioengineering
https://www.readbyqxmd.com/read/28320982/comparison-of-three-acute-stress-models-for-simulating-the-pathophysiology-of-stress-related-mucosal-disease
#15
Bhagawati Saxena, Sanjay Singh
Stress-related mucosal disease (SRMD) is highly prevalent in intensive care patients leading to increasing treatment cost and mortality. SRMD is a disease elusive of ideal treatment. Evaluation of drugs is very pertinent for the efficient and safe treatment of SRMD. It relies mainly on in vivo screening models. There are various stress models, and till date, none of them is validated for simulating the SRMD pathophysiology. The present study aims to choose the best model, which reproduce pathophysiology of SRMD, among previously established stress models...
March 19, 2017: Drug Discoveries & Therapeutics
https://www.readbyqxmd.com/read/28320660/experimental-validation-of-a-fast-forward-model-for-guided-wave-tomography-of-pipe-elbows
#16
Alexander J Brath, Francesco Simonetti, Peter B Nagy, Geir Instanes
Ultrasonic guided wave tomography (GWT) methods for the detection of corrosion and erosion damage in straight pipe sections are now well advanced. However, successful application of GWT to pipe bends has not yet been demonstrated due to the computational burden associated with the complex forward model required to simulate guided wave propagation through the bend. In a previous paper [Brath et al., IEEE Trans. Ultrason. Ferroelectr. Freq. Contr., vol. 61, pp. 815-829, 2014] we have shown that the speed of the forward model can be increased by replacing the three-dimensional pipe bend with a two-dimensional rectangular domain in which guided wave propagation is formulated based on an artificially inhomogeneous and elliptically anisotropic (INELAN) acoustic model...
March 15, 2017: IEEE Transactions on Ultrasonics, Ferroelectrics, and Frequency Control
https://www.readbyqxmd.com/read/28319851/-31-p-dephased-13-c-detected-redor-for-nmr-crystallography-at-natural-isotopic-abundance
#17
Alexander I Greenwood, Mary C Clay, Chad M Rienstra
Typically, the process of NMR-based structure determination relies on accurately measuring a large number of internuclear distances to serve as restraints for simulated annealing calculations. In solids, the rotational-echo double-resonance (REDOR) experiment is a widely used approach to determine heteronuclear dipolar couplings corresponding to distances usually in the range of 1.5-8Å. A challenge in the interpretation of REDOR data is the degeneracy of symmetric subunits in an oligomer or equivalent molecules in a crystal lattice, which produce REDOR trajectories that depend explicitly on two or more distances instead of one...
February 28, 2017: Journal of Magnetic Resonance
https://www.readbyqxmd.com/read/28319661/atomistic-insights-into-nucleation-and-formation-of-hexagonal-boron-nitride-on-ni-from-first-principles-based-reactive-molecular-dynamics-simulations
#18
Song Liu, Adri C T van Duin, Diana M van Duin, Bin Liu, James H Edgar
Atomistic-scale insights into the growth of a continuous, atomically thin hexagonal boron nitride (hBN) lattice from elemental boron and nitrogen on Ni substrates were obtained from multi-scale modeling combining density functional theory (DFT) and reactive molecular dynamics (rMD). The quantum mechanical calculations focused on the adsorption and reaction energetics for the hBN building-block species, i.e., atomic B, N, BxNy (x, y = 1-2), on Ni(111) and Ni(211), and the diffusion pathways of elemental B and N on these slab model surfaces and in the sublayer...
March 20, 2017: ACS Nano
https://www.readbyqxmd.com/read/28319451/a-best-example-of-channel-structure-annotation-by-molecular-simulation
#19
Shanlin Rao, Gianni Klesse, Phillip J Stansfeld, Stephen J Tucker, Mark S P Sansom
An increasing number of ion channel structures are being determined. This generates a need for computational tools to enable functional annotation of channel structures. However, a number of studies of ion channel and model pores have indicated that the physical dimensions of a pore are not always a reliable indicator of its conductive status. This is due to the unusual behavior of water within nano-confined spaces, resulting in a phenomenon referred to as 'hydrophobic gating'. We have recently demonstrated how simulating the behavior of water within an ion channel pore can be used to predict its conductive status...
March 20, 2017: Channels
https://www.readbyqxmd.com/read/28319199/a-computational-analysis-of-in-vivo-vegfr-activation-by-multiple-co-expressed-ligands
#20
Lindsay E Clegg, Feilim Mac Gabhann
The splice isoforms of vascular endothelial growth A (VEGF) each have different affinities for the extracellular matrix (ECM) and the coreceptor NRP1, which leads to distinct vascular phenotypes in model systems expressing only a single VEGF isoform. ECM-immobilized VEGF can bind to and activate VEGF receptor 2 (VEGFR2) directly, with a different pattern of site-specific phosphorylation than diffusible VEGF. To date, the way in which ECM binding alters the distribution of isoforms of VEGF and of the related placental growth factor (PlGF) in the body and resulting angiogenic signaling is not well-understood...
March 20, 2017: PLoS Computational Biology
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