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Sample records for 3d qsar analysis

  1. 3D QSAR Analysis on Oxadiazole Derivatives as Anticancer Agents

    Sanmati K. Jain

    2011-07-01

    Full Text Available Three dimensional quantitative structure activity relationship (3D QSAR study by means of partial least square regression (PLSR method was performed on a series of 3-(Aryl-N-(Aryl-1, 2, 4-Oxadiazol-5-amines as antiproliferative agents using molecular design suite (VLifeMDS. This study was performed with 20 compounds (data set using sphere exclusion (SE algorithm and manual selection method used for the division of the data set into training and test set. PLSR methodology with stepwise (SW forward-backward variable selection method was used for building the QSAR models. Five predictive models were generated with sphere exclusion and two with manual data selection methods using PLSR. The most significant model is having correlation coefficient 0.9334 (squared correlation coefficient r2 = 0.8713 indicating noteworthy correlation between biological activity and descriptors. The model has internal predictivity 74.45% (q2 = 0.7445 and highest external predictivity 81.09 % (pred_r2 = 0.8109 and lowest error term for predictive correlation coefficient (pred_r2se = 0.1321. Model showed that steric (S_1278, S_751 and electrostatic (E_307 interactions play important role in determining antiproliferative activity. The molecular field analysis (MFA contour plots provided further understanding of the relationship between structural features of substituted oxadiazole derivatives and their activities which should be applicable to design newer potential antiproliferative agents.

  2. 3D-QSAR studies on glycogen phosphorylase inhibitors by flexible comparative molecular field analysis

    2007-01-01

    Canceling grids accommodating probes in comparative molecular field analysis (CoMFA), the idea of flexibleness is introduced into the CoMFA, and in combination with swarm intelligent algorithm which attempts to optimize distributions of diverse probes around drug molecules, a new 3D-QSAR method is proposed in this context as flexible comparative molecular field analysis (FCoMFA). In preliminary at-tempts to performing QSAR studies on 47 glycogen phosphorylase inhibitors, FCoMFA is employed and confirmed to be potent to exploring ligand-receptor interaction manners at active positions and thus to generating stable and predictable models. Simultaneously by an intuitive graphics regarding probe distribution patterns, impacts of different substituted groups on activities is also given an insight into.

  3. 3D-QSAR Investigation of Synthetic Antioxidant Chromone Derivatives by Molecular Field Analysis

    Jiraporn Ungwitayatorn

    2008-02-01

    Full Text Available A series of 7-hydroxy, 8-hydroxy and 7,8-dihydroxy synthetic chromone derivatives was evaluated for their DPPH free radical scavenging activities. A training set of 30 synthetic chromone derivatives was subject to three-dimensional quantitative structure-activity relationship (3D-QSAR studies using molecular field analysis (MFA. The substitutional requirements for favorable antioxidant activity were investigated and a predictive model that could be used for the design of novel antioxidants was derived. Regression analysis was carried out using genetic partial least squares (G/PLS method. A highly predictive and statistically significant model was generated. The predictive ability of the developed model was assessed using a test set of 5 compounds (r2pred = 0.924. The analyzed MFA model demonstrated a good fit, having r2 value of 0.868 and crossvalidated coefficient r2cv value of 0.771.

  4. Molecular determinants of juvenile hormone action as revealed by 3D QSAR analysis in Drosophila.

    Denisa Liszeková

    Full Text Available BACKGROUND: Postembryonic development, including metamorphosis, of many animals is under control of hormones. In Drosophila and other insects these developmental transitions are regulated by the coordinate action of two principal hormones, the steroid ecdysone and the sesquiterpenoid juvenile hormone (JH. While the mode of ecdysone action is relatively well understood, the molecular mode of JH action remains elusive. METHODOLOGY/PRINCIPAL FINDINGS: To gain more insights into the molecular mechanism of JH action, we have tested the biological activity of 86 structurally diverse JH agonists in Drosophila melanogaster. The results were evaluated using 3D QSAR analyses involving CoMFA and CoMSIA procedures. Using this approach we have generated both computer-aided and species-specific pharmacophore fingerprints of JH and its agonists, which revealed that the most active compounds must possess an electronegative atom (oxygen or nitrogen at both ends of the molecule. When either of these electronegative atoms are replaced by carbon or the distance between them is shorter than 11.5 A or longer than 13.5 A, their biological activity is dramatically decreased. The presence of an electron-deficient moiety in the middle of the JH agonist is also essential for high activity. CONCLUSIONS/SIGNIFICANCE: The information from 3D QSAR provides guidelines and mechanistic scope for identification of steric and electrostatic properties as well as donor and acceptor hydrogen-bonding that are important features of the ligand-binding cavity of a JH target protein. In order to refine the pharmacophore analysis and evaluate the outcomes of the CoMFA and CoMSIA study we used pseudoreceptor modeling software PrGen to generate a putative binding site surrogate that is composed of eight amino acid residues corresponding to the defined molecular interactions.

  5. Combinatorial Pharmacophore-Based 3D-QSAR Analysis and Virtual Screening of FGFR1 Inhibitors

    Nannan Zhou

    2015-06-01

    Full Text Available The fibroblast growth factor/fibroblast growth factor receptor (FGF/FGFR signaling pathway plays crucial roles in cell proliferation, angiogenesis, migration, and survival. Aberration in FGFRs correlates with several malignancies and disorders. FGFRs have proved to be attractive targets for therapeutic intervention in cancer, and it is of high interest to find FGFR inhibitors with novel scaffolds. In this study, a combinatorial three-dimensional quantitative structure-activity relationship (3D-QSAR model was developed based on previously reported FGFR1 inhibitors with diverse structural skeletons. This model was evaluated for its prediction performance on a diverse test set containing 232 FGFR inhibitors, and it yielded a SD value of 0.75 pIC50 units from measured inhibition affinities and a Pearson’s correlation coefficient R2 of 0.53. This result suggests that the combinatorial 3D-QSAR model could be used to search for new FGFR1 hit structures and predict their potential activity. To further evaluate the performance of the model, a decoy set validation was used to measure the efficiency of the model by calculating EF (enrichment factor. Based on the combinatorial pharmacophore model, a virtual screening against SPECS database was performed. Nineteen novel active compounds were successfully identified, which provide new chemical starting points for further structural optimization of FGFR1 inhibitors.

  6. 3-PHENYLQUINOLINYLCHALCONE DERIVATIVES: PHARMACOPHORE MODELLING, 3D-QSAR ANALYSIS AND DOCKING STUDIES AS ANTI-CANCER AGENTS

    2014-01-01

    Certain 3-Phenylquinolinylchalcone derivatives were evaluated for their anti-proliferative activities and found to exhibit anti-cancer and anti-inflammatory activities. 3D-QSAR and molecular docking approaches were performed on 3-Phenylquinolinylchalcone derivatives to understand their structural requisites and binding mode of the best fitted ligand for cancer inhibitory activity. Among them, (E)-3-(3-(4-methoxyphenyl)quinolin-2-yl)-1-phenylprop-2-en-1-one (6a) was the most active compound ag...

  7. 3-PHENYLQUINOLINYLCHALCONE DERIVATIVES: PHARMACOPHORE MODELLING, 3D-QSAR ANALYSIS AND DOCKING STUDIES AS ANTI-CANCER AGENTS

    Manoj Kumar Mahto

    2014-02-01

    Full Text Available Certain 3-Phenylquinolinylchalcone derivatives were evaluated for their anti-proliferative activities and found to exhibit anti-cancer and anti-inflammatory activities. 3D-QSAR and molecular docking approaches were performed on 3-Phenylquinolinylchalcone derivatives to understand their structural requisites and binding mode of the best fitted ligand for cancer inhibitory activity. Among them, (E-3-(3-(4-methoxyphenylquinolin-2-yl-1-phenylprop-2-en-1-one (6a was the most active compound against the growth of  H460, MCF-7, MDA-MB-231 and SKBR-3 cancer cell line respectively. Four featured hypothesis  AHRR.521 of  H460 was considered to be the best hypothesis which yielded a statistically significant 3D-QSAR model built with PLS values 3, Regression coefficient (R2 = 0.8986, Cross validation coefficient (Q2 = 0.9542, Root Mean Square Deviation (RMSD = 0.0067, Pearson-R = 1. Interestingly, the result of docking was found to correlate with the pharmacophore study where this compound was active against all six oncoproteins p53, Raf Kinase, Aurora-A-Kinase, CDK-2, Resveratrol and HSP90. The results provide detailed insights of 6a compound which can afford guidance for rational drug design of novel potent anti-cancer agents

  8. Comparison of steroid substrates and inhibitors of P-glycoprotein by 3D-QSAR analysis

    Li, Yan; Wang, Yong-Hua; Yang, Ling; Zhang, Shu-Wei; Liu, Chang-Hou; Yang, Sheng-Li

    2005-01-01

    Steroid derivatives show a complex interaction with P-glycoprotein (Pgp). To determine the essential structural requirements of a series of structurally related and functionally diverse steroids for Pgp-mediated transport or inhibition, a three-dimensional quantitative structure activity relationship study was performed by comparative similarity index analysis modeling. Twelve models have been explored to well correlate the physiochemical features with their biological functions with Pgp on basis of substrate and inhibitor datasets, in which the best predictive model for substrate gave cross-validated q2=0.720, non-cross-validated r2=0.998, standard error of estimate SEE=0.012, F=257.955, and the best predictive model for inhibitor gave q2=0.536, r2=0.950, SEE=1.761 and F=45.800. The predictive ability of all models was validated by a set of compounds that were not included in the training set. The physiochemical similarities and differences of steroids as Pgp substrate and inhibitor, respectively, were analyzed to be helpful in developing new steroid-like compounds.

  9. Binding affinity prediction of novel estrogen receptor ligands using receptor-based 3-D QSAR methods.

    Sippl, Wolfgang

    2002-12-01

    We have recently reported the development of a 3-D QSAR model for estrogen receptor ligands showing a significant correlation between calculated molecular interaction fields and experimentally measured binding affinity. The ligand alignment obtained from docking simulations was taken as basis for a comparative field analysis applying the GRID/GOLPE program. Using the interaction field derived with a water probe and applying the smart region definition (SRD) variable selection procedure, a significant and robust model was obtained (q(2)(LOO)=0.921, SDEP=0.345). To further analyze the robustness and the predictivity of the established model several recently developed estrogen receptor ligands were selected as external test set. An excellent agreement between predicted and experimental binding data was obtained indicated by an external SDEP of 0.531. Two other traditionally used prediction techniques were applied in order to check the performance of the receptor-based 3-D QSAR procedure. The interaction energies calculated on the basis of receptor-ligand complexes were correlated with experimentally observed affinities. Also ligand-based 3-D QSAR models were generated using program FlexS. The interaction energy-based model, as well as the ligand-based 3-D QSAR models yielded models with lower predictivity. The comparison with the interaction energy-based model and with the ligand-based 3-D QSAR models, respectively, indicates that the combination of receptor-based and 3-D QSAR methods is able to improve the quality of prediction. PMID:12413831

  10. Integrated Computational Tools for Identification of CCR5 Antagonists as Potential HIV-1 Entry Inhibitors: Homology Modeling, Virtual Screening, Molecular Dynamics Simulations and 3D QSAR Analysis

    Suri Moonsamy

    2014-04-01

    Full Text Available Using integrated in-silico computational techniques, including homology modeling, structure-based and pharmacophore-based virtual screening, molecular dynamic simulations, per-residue energy decomposition analysis and atom-based 3D-QSAR analysis, we proposed ten novel compounds as potential CCR5-dependent HIV-1 entry inhibitors. Via validated docking calculations, binding free energies revealed that novel leads demonstrated better binding affinities with CCR5 compared to maraviroc, an FDA-approved HIV-1 entry inhibitor and in clinical use. Per-residue interaction energy decomposition analysis on the averaged MD structure showed that hydrophobic active residues Trp86, Tyr89 and Tyr108 contributed the most to inhibitor binding. The validated 3D-QSAR model showed a high cross-validated rcv2 value of 0.84 using three principal components and non-cross-validated r2 value of 0.941. It was also revealed that almost all compounds in the test set and training set yielded a good predicted value. Information gained from this study could shed light on the activity of a new series of lead compounds as potential HIV entry inhibitors and serve as a powerful tool in the drug design and development machinery.

  11. Automatic generation of alignments for 3D QSAR analyses.

    Jewell, N E; Turner, D B; Willett, P; Sexton, G J

    2001-01-01

    Many 3D QSAR methods require the alignment of the molecules in a dataset, which can require a fair amount of manual effort in deciding upon a rational basis for the superposition. This paper describes the use of FBSS, a program for field-based similarity searching in chemical databases, for generating such alignments automatically. The CoMFA and CoMSIA experiments with several literature datasets show that the QSAR models resulting from the FBSS alignments are broadly comparable in predictive performance with the models resulting from manual alignments. PMID:11774998

  12. Automatic generation of alignments for 3D QSAR analyses

    Jewell, N.E.; D.B. Turner; Willett, P.; Sexton, G.J.

    2001-01-01

    Many 3D QSAR methods require the alignment of the molecules in a dataset, which can require a fair amount of manual effort in deciding upon a rational basis for the superposition. This paper describes the use of FBSS, a pro-ram for field-based similarity searching in chemical databases, for generating such alignments automatically. The CoMFA and CoMSIA experiments with several literature datasets show that the QSAR models resulting from the FBSS alignments are broadly comparable in predictive...

  13. 3D QSAR Study on Alpha Keto Amide Derivatives as gp120-CD4 Inhibitors

    Vinayak D. More

    2012-01-01

    Full Text Available The present communication deals with 3D QDAR analysis on series of Alpha keto amide derivatives some for the designing of new GP120-CD4 inhibitors with anti HIV activity. The four different QSAR models are generated using data set of 32 molecules as gp120-CD4 inhibitors from literature studies. The 3D QSAR result gives insights for understanding of the relationship between structural features of substituted alpha keto amide derivatives and their activities which should be useful to design newer potential anti-HIV agents.

  14. Synthesis, antifeedant activity against Coleoptera and 3D QSAR study of alpha-asarone derivatives.

    Łozowicka, B; Kaczyński, P; Magdziarz, T; Dubis, A T

    2014-01-01

    For the first time, a set of 56 compounds representing structural derivatives of naturally occurring alpha-asarone as an antifeedants against stored product pests Sitophilus granarius L., Trogoderma granarium Ev., and Tribolium confusum Duv., were subjected to the 3D QSAR studies. Three-dimensional quantitative structure-activity relationships (3D-QSAR) for 56 compounds, including 15 newly synthesized, were performed using comparative molecular field analysis s-CoMFA and SOM-CoMSA techniques. QSAR was conducted based on a combination of biological activity (against Coleoptera larvae and beetles) and various geometrical, topological, quantum-mechanical, electronic, and chromatographic descriptors. The CoMSA formalism coupled with IVE (CoMSA-IVE) allowed us to obtain highly predictive models for Trogoderma granarium Ev. larvae. We have found that this novel method indicates a clear molecular basis for activity and lipophilicity. This investigation will facilitate optimization of the design of new potential antifeedants. PMID:24601760

  15. Ligand-based pharmacophore modeling; atom-based 3D-QSAR analysis and molecular docking studies of phosphoinositide-dependent kinase-1 inhibitors

    P Kirubakaran

    2012-01-01

    Full Text Available Phosphoinositide-dependent kinase-1 plays a vital role in the PI3-kinase signaling pathway that regulates gene expression, cell cycle growth and proliferation. The common human cancers include lung, breast, blood and prostate possess over stimulation of the phosphoinositide-dependent kinase-1 signaling and making phosphoinositide-dependent kinase-1 an interesting therapeutic target in oncology. A ligand-based pharmacophore and atom-based 3D-QSAR studies were carried out on a set of 82 inhibitors of PDK1. A six point pharmacophore with two hydrogen bond acceptors (A, three hydrogen bond donors (D and one hydrophobic group (H was obtained. The pharmacophore hypothesis yielded a 3D-QSAR model with good partial least square statistics results. The training set correlation is characterized by partial least square factors (R2 = 0.9557, SD = 0.2334, F = 215.5, P = 1.407e-32. The test set correlation is characterized by partial least square factors (Q2 ext = 0.7510, RMSE = 0.5225, Pearson-R =0.8676. The external validation indicated that our QSAR model possess high predictive power with good value of 0.99 and value of 0.88. The docking results show the binding orientations of these inhibitors at active site amino acid residues (Ala162, Thr222, Glu209 and Glu166 of phosphoinositide-dependent kinase-1 protein. The binding free energy interactions of protein-ligand complex have been calculated, which plays an important role in molecular recognition and drug design approach.

  16. Molecular docking, MM/GBSA and 3D-QSAR studies on EGFR inhibitors

    RAJU BATHINI; SREE KANTH SIVAN; SABIHA FATIMA; VIJJULATHA MANGA

    2016-07-01

    Epidermal growth factor receptor (EGFR) is the first growth factor receptor proposed as a target for cancer therapy. Molecular modeling protocols like molecular docking, molecular mechanics/generalized born surface area (MM/GBSA) calculations and three dimensional-quantitative structure activity relationship(3D-QSAR) studies were performed on 45 molecules to understand the structural requirements for EGFR tyrosine kinase inhibitors. Conformation for all the molecules obtained from molecular docking were used as is for 3D-QSAR analysis. Comparative molecular field analysis (CoMFA) and comparative molecular similarityindices analysis (CoMSIA) models were obtained by performing partial least square analysis on 35 training molecules and these models were validated using 10 test moleucles. The models showed good statistical results in terms of r², q² loo and r² pred values. Information rendered from 3D-QSAR model and sitemap analysis was used to optimize lead molecule to design prospective inhibitors. Improvement in EGFR binding affinity can be achieved by substitutional modification on phenyl ring attached to alkynyl group with bulkier hydrogen bond donor and acceptor substituents that can increase favourable interaction with the receptor.

  17. Residue-Ligand Interaction Energy (ReLIE on a Receptor-Dependent 3D-QSAR Analysis of S- and NH-DABOs as Non-Nucleoside Reverse Transcriptase Inhibitors

    Monique Araújo de Brito

    2012-06-01

    Full Text Available A series of 74 dihydroalkoxybenzyloxopyrimidines (DABOs, a class of highly potent non-nucleoside reverse transcriptase inhibitors (NNRTIs, was retrieved from the literature and studied by receptor-dependent (RD three-dimensional quantitative structure-activity relationship (3D-QSAR analysis to derive RD-3D-QSAR models. The descriptors in this new method are the steric and electrostatic interaction energies of the protein-ligand complexes (per residue simulated by molecular dynamics, an approach named Residue-Ligand Interaction Energy (ReLIE. This study was performed using a training set of 59 compounds and the MKC-442/RT complex structure as reference. The ReLIE-3D-QSAR models were constructed and evaluated by genetic algorithm (GA and partial least squares (PLS. In the best equations, at least one term is related to one of the amino acid residues of the p51 subunit: Asn136, Asn137, Glu138, and Thr139. This fact implies the importance of interchain interaction (p66-p51 in the equations that best describe the structure-activity relationship for this class of compounds. The best equation shows q2 = 0.660, SEcv = 0.500, r2 = 0.930, and SEE = 0.226. The external predictive ability of this best model was evaluated using a test set of 15 compounds. In order to design more potent DABO analogues as anti-HIV/AIDS agents, substituents capable of interactions with residues like Ile94, Lys101, Tyr181, and Tyr188 should be selected. Also, given the importance of the conserved Asn136, this residue could become an attractive target for the design of novel NNRTIs with improved potency and increased ability to avoid the development of drug-resistant viruses.

  18. 3D-QSAR studies on Plasmodium falciparam proteins: a mini-review.

    Divakar, Selva; Hariharan, Sivaram

    2015-01-01

    3D-QSAR has become a very important tool in the field of Drug Discovery, especially in important areas like malarial research. The 3D-QSAR is principally a ligand-based drug design but the bioactive conformation of the ligand can also be taken into account in constructing a 3D-QSAR model. The induction of receptor-based 3D-QSAR has been proven to give more robust statistical models. In this review, we have discussed the various 3D-QSAR works done so far which were aimed at combating malaria caused by Plasmodium falciparam. We have also discussed the various enzymes/receptors (targets) in Plasmodium falciparam for which the 3D-QSAR had been generated. The enzymes - wild and mutated dihydrofolate reductase, enoyl acyl protein carrier protein reductase, farnesyltransferase, cytochrome bc1, and falcipains were the major targets for pharmacophore-based drug design. Apart from the above-mentioned targets there were many scaffolds for which the target macromolecule was undefined and could have single/multiple targets. The generated 3D-QSAR model can be used to identify hits by screening the pharmacophore against a chemical library. In this review, the hits identified against various targets of plasmodium falciparam that have been discussed along with their basic scaffold. The various software programs and chemical databases that have been used in the generation of 3D-QSAR and screening were given. From this review, we understand that there is a considerable need to develop novel scaffolds that are different from the existing ligands to overcome cross-resistance. PMID:25543683

  19. Estudos de QSAR 3D para um conjunto de inibidores de butirilcolinesterase humana QSAR 3D studies of a series of human butyrylcholinesterase inhibitors

    Humberto F. Freitas

    2009-01-01

    Full Text Available Alzheimer's disease (AD is considered the main cause of cognitive decline in adults. The available therapies for AD treatment seek to maintain the activity of cholinergic system through the inhibition of the enzyme acetylcholinesterase. However, butyrylcholinesterase (BuChE can be considered an alternative target for AD treatment. Aiming at developing new BuChE inhibitors, robust QSAR 3D models with high predictive power were developed. The best model presents a good fit (r²=0.82, q²=0.76, with two PCs and high predictive power (r²predict=0.88. Analysis of regression vector shows that steric properties have considerable importance to the inhibition of the BuChE.

  20. The continuous molecular fields approach to building 3D-QSAR models.

    Baskin, Igor I; Zhokhova, Nelly I

    2013-05-01

    The continuous molecular fields (CMF) approach is based on the application of continuous functions for the description of molecular fields instead of finite sets of molecular descriptors (such as interaction energies computed at grid nodes) commonly used for this purpose. These functions can be encapsulated into kernels and combined with kernel-based machine learning algorithms to provide a variety of novel methods for building classification and regression structure-activity models, visualizing chemical datasets and conducting virtual screening. In this article, the CMF approach is applied to building 3D-QSAR models for 8 datasets through the use of five types of molecular fields (the electrostatic, steric, hydrophobic, hydrogen-bond acceptor and donor ones), the linear convolution molecular kernel with the contribution of each atom approximated with a single isotropic Gaussian function, and the kernel ridge regression data analysis technique. It is shown that the CMF approach even in this simplest form provides either comparable or enhanced predictive performance in comparison with state-of-the-art 3D-QSAR methods. PMID:23719959

  1. Receptor-based 3D QSAR analysis of estrogen receptor ligands--merging the accuracy of receptor-based alignments with the computational efficiency of ligand-based methods.

    Sippl, W

    2000-08-01

    One of the major challenges in computational approaches to drug design is the accurate prediction of binding affinity of biomolecules. In the present study several prediction methods for a published set of estrogen receptor ligands are investigated and compared. The binding modes of 30 ligands were determined using the docking program AutoDock and were compared with available X-ray structures of estrogen receptor-ligand complexes. On the basis of the docking results an interaction energy-based model, which uses the information of the whole ligand-receptor complex, was generated. Several parameters were modified in order to analyze their influence onto the correlation between binding affinities and calculated ligand-receptor interaction energies. The highest correlation coefficient (r2 = 0.617, q2Loo = 0.570) was obtained considering protein flexibility during the interaction energy evaluation. The second prediction method uses a combination of receptor-based and 3D quantitative structure-activity relationships (3D QSAR) methods. The ligand alignment obtained from the docking simulations was taken as basis for a comparative field analysis applying the GRID/GOLPE program. Using the interaction field derived with a water probe and applying the smart region definition (SRD) variable selection, a significant and robust model was obtained (r2 = 0.991, q2LOO = 0.921). The predictive ability of the established model was further evaluated by using a test set of six additional compounds. The comparison with the generated interaction energy-based model and with a traditional CoMFA model obtained using a ligand-based alignment (r2 = 0.951, q2L00 = 0.796) indicates that the combination of receptor-based and 3D QSAR methods is able to improve the quality of the underlying model. PMID:10921772

  2. 3D-QSAR study on phenoxy-alkylamine compounds of a 1-adrenoceptor antagonist

    2001-01-01

    The study of three-dimensional quantitative structure-activityrelationship (3D-QSAR) of DDPH and its derivatives that have been known with their activity parameters has been developed using the comparative molecular field analysis (CoMFA) method. Here, (+)-DDPH crystal structure was selected as the active conformation model and comparisons between the influences of different charge calculation methods and grid setup were conducted. The coefficients of cross-validation (q2 ) and regression (r2) are 0.481 and 0.997, respectively. The standard error (SE) is 0.102. The research result suggests that the steric field makes more contributions to the activity than the electrostatic field. This model can help us not only in improving our understanding of the receptor-ligand interactions, but also in predicting the activity of derivatives and designing new compounds with better potency.

  3. Identification of potential influenza virus endonuclease inhibitors through virtual screening based on the 3D-QSAR model.

    Kim, J; Lee, C; Chong, Y

    2009-01-01

    Influenza endonucleases have appeared as an attractive target of antiviral therapy for influenza infection. With the purpose of designing a novel antiviral agent with enhanced biological activities against influenza endonuclease, a three-dimensional quantitative structure-activity relationships (3D-QSAR) model was generated based on 34 influenza endonuclease inhibitors. The comparative molecular similarity index analysis (CoMSIA) with a steric, electrostatic and hydrophobic (SEH) model showed the best correlative and predictive capability (q(2) = 0.763, r(2) = 0.969 and F = 174.785), which provided a pharmacophore composed of the electronegative moiety as well as the bulky hydrophobic group. The CoMSIA model was used as a pharmacophore query in the UNITY search of the ChemDiv compound library to give virtual active compounds. The 3D-QSAR model was then used to predict the activity of the selected compounds, which identified three compounds as the most likely inhibitor candidates. PMID:19343586

  4. Combined 3D-QSAR modeling and molecular docking study on azacycles CCR5 antagonists

    Ji, Yongjun; Shu, Mao; Lin, Yong; Wang, Yuanqiang; Wang, Rui; Hu, Yong; Lin, Zhihua

    2013-08-01

    The beta chemokine receptor 5 (CCR5) is an attractive target for pharmaceutical industry in the HIV-1, inflammation and cancer therapeutic areas. In this study, we have developed quantitative structure activity relationship (QSAR) models for a series of 41 azacycles CCR5 antagonists using comparative molecular field analysis (CoMFA), comparative molecular similarity indices analysis (CoMSIA), and Topomer CoMFA methods. The cross-validated coefficient q2 values of 3D-QASR (CoMFA, CoMSIA, and Topomer CoMFA) methods were 0.630, 0.758, and 0.852, respectively, the non-cross-validated R2 values were 0.979, 0.978, and 0.990, respectively. Docking studies were also employed to determine the most probable binding mode. 3D contour maps and docking results suggested that bulky groups and electron-withdrawing groups on the core part would decrease antiviral activity. Furthermore, docking results indicated that H-bonds and π bonds were favorable for antiviral activities. Finally, a set of novel derivatives with predicted activities were designed.

  5. Insight into the structural requirement of substituted quinazolinone biphenyl acylsulfonamides derivatives as Angiotensin II AT1 receptor antagonist: 2D and 3D QSAR approach

    Mukesh C. Sharma

    2014-01-01

    Full Text Available A series of 19 molecules substituted quinazolinone biphenyl acylsulfonamides derivatives displaying variable inhibition of Angiotensin II receptor AT1 activity were selected to develop models for establishing 2D and 3D QSAR. The compounds in the selected series were characterized by spatial, molecular and electro topological descriptors using QSAR module of Molecular Design Suite (VLife MDS™ 3.5. The best 2D QSAR model was selected, having correlation coefficient r2 (0.8056 and cross validated squared correlation coefficient q2 (0.6742 with external predictive ability of pred_r2 0.7583 coefficient of correlation of predicted data set (pred_r2se 0.2165. The results obtained from QSAR studies could be used in designing better Ang II activity among the congeners in future. The optimum QSAR model showed that the parameters SsssCHE index, SddCE-index, T_2_Cl_4, and SssNHE-index contributed in the model. 3D QSAR analysis by kNN-molecular field analysis approach developed based on principles of the k-nearest neighbor method combined with Genetic algorithms, stepwise forward variable selection approach; a leave-one-out cross-validated correlation coefficient (q2 of 0.6516 and a non-cross-validated correlation coefficient (r2 of 0.8316 and pred_r2 0.6954 were obtained. Contour maps using this approach showed that steric, electrostatic, and hydrophobic field effects dominantly determine binding affinities. The information rendered by 3D QSAR models may lead to a better understanding of structural requirements of Angiotensin II receptor and can help in the design of novel potent antihypertensive molecules.

  6. BCL::EMAS — Enantioselective Molecular Asymmetry Descriptor for 3D-QSAR

    Mariusz Butkiewicz

    2012-08-01

    Full Text Available Stereochemistry is an important determinant of a molecule’s biological activity. Stereoisomers can have different degrees of efficacy or even opposing effects when interacting with a target protein. Stereochemistry is a molecular property difficult to represent in 2D-QSAR as it is an inherently three-dimensional phenomenon. A major drawback of most proposed descriptors for 3D-QSAR that encode stereochemistry is that they require a heuristic for defining all stereocenters and rank-ordering its substituents. Here we propose a novel 3D-QSAR descriptor termed Enantioselective Molecular ASymmetry (EMAS that is capable of distinguishing between enantiomers in the absence of such heuristics. The descriptor aims to measure the deviation from an overall symmetric shape of the molecule. A radial-distribution function (RDF determines a signed volume of tetrahedrons of all triplets of atoms and the molecule center. The descriptor can be enriched with atom-centric properties such as partial charge. This descriptor showed good predictability when tested with a dataset of thirty-one steroids commonly used to benchmark stereochemistry descriptors (r2 = 0.89, q2 = 0.78. Additionally, EMAS improved enrichment of 4.38 versus 3.94 without EMAS in a simulated virtual high-throughput screening (vHTS for inhibitors and substrates of cytochrome P450 (PUBCHEM AID891.

  7. A Combined Pharmacophore Modeling, 3D QSAR and Virtual Screening Studies on Imidazopyridines as B-Raf Inhibitors

    Huiding Xie

    2015-05-01

    Full Text Available B-Raf kinase is an important target in treatment of cancers. In order to design and find potent B-Raf inhibitors (BRIs, 3D pharmacophore models were created using the Genetic Algorithm with Linear Assignment of Hypermolecular Alignment of Database (GALAHAD. The best pharmacophore model obtained which was used in effective alignment of the data set contains two acceptor atoms, three donor atoms and three hydrophobes. In succession, comparative molecular field analysis (CoMFA and comparative molecular similarity indices analysis (CoMSIA were performed on 39 imidazopyridine BRIs to build three dimensional quantitative structure-activity relationship (3D QSAR models based on both pharmacophore and docking alignments. The CoMSIA model based on the pharmacophore alignment shows the best result (q2 = 0.621, r2pred = 0.885. This 3D QSAR approach provides significant insights that are useful for designing potent BRIs. In addition, the obtained best pharmacophore model was used for virtual screening against the NCI2000 database. The hit compounds were further filtered with molecular docking, and their biological activities were predicted using the CoMSIA model, and three potential BRIs with new skeletons were obtained.

  8. Antiproliferative activity of NCI-DTP glutarimide derivatives. An alignment independent 3D QSAR study

    JELENA B. POPOVIĆ-DJORDJEVIĆ

    2010-09-01

    Full Text Available Alignment-free, three dimensional structure–activity relationships (3D QSAR of the antiproliferative potency of twenty-two glutarimide-containing compounds, taken from National Cancer Institute Developmental therapeutics Program database, toward eight representative human tumour cell lines are reported. The descriptors used in the QSAR study were derived from GRID molecular interaction fields. The obtained models readily detect structural motifs positively or negatively correlated with the potency of the studied compounds toward each cell line. In this way, the pharmacophoric pattern required for high potency of compounds is reported. This pattern can serve as guidance for the design and syntheses of novel congeners, planned to be tested toward human tumour cell lines.

  9. Synthesis, characterization, antifungal evaluation and 3D-QSAR study of phenylhydrazine substituted tetronic acid derivatives.

    Hu, Ying; Wang, Junjun; Lu, Aimin; Yang, Chunlong

    2014-08-15

    A series of 3-(1-(2-(substituted phenyl)hydrazinyl)alkylidene)furan-2,4(3H,5H)-diones were designed and prepared using two synthetic routes. Their structures were confirmed by FT-IR, (1)H NMR, (13)C NMR, MS, elemental analysis and single-crystal X-ray diffraction. Their bioactivity was evaluated against Botrytis cinerea in vitro. Most target compounds exhibited remarkable antifungal activity. Two compounds 7f and 7h were highly effective and their EC50 values were 0.241 μg/mL and 0.167 μg/mL, respectively, close to that of the control drug procymidone. 3D-QSAR studies of CoMFA and CoMSIA were carried out. Models with good predictive ability were generated with the cross validated q(2) values for CoMFA and CoMSIA being 0.565 and 0.823. Conventional r(2) values were 0.983 and 0.945, respectively. The results provided a practical tool for guiding the design and synthesis of novel and more potent tetronic acid derivatives containing substituted phenylhydrazine moiety. PMID:25042337

  10. 2D/3D-QSAR comparative study on mutagenicity of nitroaromatics

    WANG Xiaodong; LIN Zhifen; YIN Daqiang; LIU Shushen; WANG Liansheng

    2005-01-01

    Nitroaromatics are typical toxic organic pollutants and are ubiquitous in environment with diverse structures. They are widely used in many industries and formed during many natural and anthropogenic processes. Most of these pollutants are potentially carcinogenic and the assessment and prediction of the mutagenicity of nitroaromatics are of great interest. In this paper the structure-mutagenicity relationships of 219 nitroaromatics are investigated by molecular orbital theory based classic structure-activity relationships and comparative molecular field analysis (CoMFA). A comparison is undertaken in respect of the interpretation of mechanism and predictive ability for these two categories of QSAR approaches and highly predictive QSAR models have been developed.

  11. Structure based 3D-QSAR studies of Interleukin-2 inhibitors: Comparing the quality and predictivity of 3D-QSAR models obtained from different alignment methods and charge calculations.

    Halim, Sobia Ahsan; Zaheer-ul-Haq

    2015-08-01

    Interleukin-2 is an essential cytokine in an innate immune response, and is a promising drug target for several immunological disorders. In the present study, structure-based 3D-QSAR modeling was carried out via Comparative Molecular Field Analysis (CoMFA) and Comparative Molecular Similarity Index Analysis (CoMSIA) methods. Six different partial charge calculation methods were used in combination with two different alignment methods to scrutinize their effects on the predictive power of 3D-QSAR models. The best CoMFA and CoMSIA models were obtained with the AM1 charges when used with co-conformer based substructure alignment (CCBSA) method. The obtained models posses excellent correlation coefficient value and also exhibited good predictive power (for CoMFA: q(2)=0.619; r(2)=0.890; r(2)Pred=0.765 and for CoMSIA: q(2)=0.607; r(2)=0.884; r(2)Pred=0.655). The developed models were further validated by using a set of another sixteen compounds as external test set 2 and both models showed strong predictive power with r(2)Pred=>0.8. The contour maps obtained from these models better interpret the structure activity relationship; hence the developed models would help to design and optimize more potent IL-2 inhibitors. The results might have implications for rational design of specific anti-inflammatory compounds with improved affinity and selectivity. PMID:26051521

  12. Combined 3D-QSAR, molecular docking and molecular dynamics study on thyroid hormone activity of hydroxylated polybrominated diphenyl ethers to thyroid receptors β

    Several recent reports suggested that hydroxylated polybrominated diphenyl ethers (HO-PBDEs) may disturb thyroid hormone homeostasis. To illuminate the structural features for thyroid hormone activity of HO-PBDEs and the binding mode between HO-PBDEs and thyroid hormone receptor (TR), the hormone activity of a series of HO-PBDEs to thyroid receptors β was studied based on the combination of 3D-QSAR, molecular docking, and molecular dynamics (MD) methods. The ligand- and receptor-based 3D-QSAR models were obtained using Comparative Molecular Similarity Index Analysis (CoMSIA) method. The optimum CoMSIA model with region focusing yielded satisfactory statistical results: leave-one-out cross-validation correlation coefficient (q2) was 0.571 and non-cross-validation correlation coefficient (r2) was 0.951. Furthermore, the results of internal validation such as bootstrapping, leave-many-out cross-validation, and progressive scrambling as well as external validation indicated the rationality and good predictive ability of the best model. In addition, molecular docking elucidated the conformations of compounds and key amino acid residues at the docking pocket, MD simulation further determined the binding process and validated the rationality of docking results. -- Highlights: ► The thyroid hormone activities of HO-PBDEs were studied by 3D-QSAR. ► The binding modes between HO-PBDEs and TRβ were explored. ► 3D-QSAR, molecular docking, and molecular dynamics (MD) methods were performed.

  13. AutoGPA-Based 3D-QSAR Modeling and Molecular Docking Study on Factor Xa Inhibitors as Anticoagulant Agents

    Guo Fang Yuan

    2016-01-01

    Full Text Available The three-dimensional-quantitative structure activity relationship (3D-QSAR studies were performed on a series of direct factor Xa (FXa inhibitors using AutoGPA-based modeling method in this paper. A training set of 38 molecules and a test set containing 10 molecules were used to build the 3D-QSAR model and validate the derived model, respectively. The developed model with correlation coefficients (r2 of 0.8564 and cross-validated correlation coefficients (q2 of 0.6721 were validated by an external test set of 10 molecules with predicted correlation coefficient (rpred2 of 0.6077. Docking study of FXa inhibitors and FXa active site was performed to check the induced pharmacophore query and comparative molecular field analysis (CoMFA contour maps using MOE2012.10. It was proved to be coincidence with the interaction information between ligand and FXa active site and was rendered to provide a useful tool to improve FXa inhibitors.

  14. 3D-QSAR and docking studies of flavonoids as potent Escherichia coli inhibitors

    Yajing Fang; Yulin Lu; Xixi Zang; Ting Wu; XiaoJuan Qi; Siyi Pan; Xiaoyun Xu

    2016-01-01

    Flavonoids are potential antibacterial agents. However, key substituents and mechanism for their antibacterial activity have not been fully investigated. The quantitative structure-activity relationship (QSAR) and molecular docking of flavonoids relating to potent anti-Escherichia coli agents were investigated. Comparative molecular field analysis (CoMFA) and comparative molecular similarity indices analysis (CoMSIA) were developed by using the pIC50 values of flavonoids. The cross-validated ...

  15. QSAR of Estrogen of Bisphenol A with 3D Vector of Atomic Property Correlation

    CHEN Zhi-Tao; ZHOU Peng; HE Liu; LI Zhi-Liang

    2007-01-01

    Considering atomic property vector and atomic correlative function, the 3-dimensional structural vector of atomic property correlation (3D-VAPC), a novel descriptor,is defined to characterize a 3-dimensional molecular structure by introducing self-adaptability regulation mechanism and the idea of orientating to customers. Characterizing the structures of 25 bisphenol A compounds by this vector, the QSAR models of three kinds of estrogen activities (ER affinities, gene induction and cell proliferation) have high multiple correlation coefficient (Rcum2=0.933, 0.813, 0.959) and cross verification coefficient (Qcum2=0.847, 0.953, 0.798) by support vector machine (SVM), which suits for nonlinear circumstances. The above results show that the models successfully express the correlation between structure and three kinds of estrogen activities. Therefore, 3D-VAPC exactly reflects the molecular structural information and SVM method correctly describes the correlation between information and property of the compounds.

  16. The Three Dimensional Quantitative Structure Activity Relationships (3D-QSAR) and Docking Studies of Curcumin Derivatives as Androgen Receptor Antagonists

    Xu, Guanhong; Chu, Yanyan; Jiang, Nan; YANG Jing; Li, Fei

    2012-01-01

    Androgen receptor antagonists have been proved to be effective anti-prostate cancer agents. 3D-QSAR and Molecular docking methods were performed on curcumin derivatives as androgen receptor antagonists. The bioactive conformation was explored by docking the potent compound 29 into the binding site of AR. The constructed Comparative Molecular Field Analysis (CoMFA) and Comparative Similarity Indices Analysis (CoMSIA) models produced statistically significant results with the cross-validated co...

  17. 3D-QSAR Studies of Dihydropyrazole and Dihydropyrrole Derivatives as Inhibitors of Human Mitotic Kinesin Eg5 Based on Molecular Docking

    Wenjuan Yang; Zhihua Lin; Yuanqiang Wang; Jin Liu; Mao Shu; Xingyan Luo

    2012-01-01

    Human mitotic kinesin Eg5 plays an essential role in mitoses and is an interesting drug target against cancer. To find the correlation between Eg5 and its inhibitors, structure-based 3D-quantitative structure–activity relationship (QSAR) studies were performed on a series of dihydropyrazole and dihydropyrrole derivatives using comparative molecular field analysis (CoMFA) and comparative molecular similarity indices analysis (CoMSIA) methods. Based on the LigandFit docking results, predictive ...

  18. Biological Evaluation and 3D-QSAR Studies of Curcumin Analogues as Aldehyde Dehydrogenase 1 Inhibitors

    Hui Wang

    2014-05-01

    Full Text Available Aldehyde dehydrogenase 1 (ALDH1 is reported as a biomarker for identifying some cancer stem cells, and down-regulation or inhibition of the enzyme can be effective in anti-drug resistance and a potent therapeutic for some tumours. In this paper, the inhibitory activity, mechanism mode, molecular docking and 3D-QSAR (three-dimensional quantitative structure activity relationship of curcumin analogues (CAs against ALDH1 were studied. Results demonstrated that curcumin and CAs possessed potent inhibitory activity against ALDH1, and the CAs compound with ortho di-hydroxyl groups showed the most potent inhibitory activity. This study indicates that CAs may represent a new class of ALDH1 inhibitor.

  19. Molecular docking and 3D-QSAR studies of 2-substituted 1-indanone derivatives as acetylcholinesterase inhibitors

    Liang-liang SHEN; Gui-xia LIU; Yun TANG

    2007-01-01

    Aim: To explore the binding mode of 2-substituted 1-indanone derivatives with acetylcholinesterase (ACHE) and provide hints for the future design of new de- rivatives with higher potency and specificity. Methods: The GOLD-docking con- formations of the compounds in the active site of the enzyme were used in subse- quent studies. The highly reliable and predictive three-dimensional quantitative structure-activity relationship (3D-QSAR) models were achieved by comparative molecular field analysis (CoMFA) and comparative molecular similarity analysis (CoMSIA) methods. The predictive capabilities of the models were validated by an external test set. Moreover, the stabilities of the 3D-QSAR models were veri- fied by the leave-4-out cross-validation method. Results: The CoMFA and CoMSIA models were constructed successfully with a good cross-validated coef- ficient (q2) and a non-cross-validated coefficient (r2). The q2 and r2 obtained from the leave-1-out cross validation method were 0.784 and 0.974 in the CoMFA model and 0.736 and 0.947 in the CoMSIA model, respectively. The coefficient isocontour maps obtained from these models were compatible with the geometrical and physi- cochemical properties of AChE. Conclusion: The contour map demonstrated that the binding affinity could be enhanced when the small protonated nitrogen moi- ety was replaced by a more hydrophobic and bulky group with a highly partial positive charge. The present study provides a better understanding of the inter- action between the inhibitors and ACHE, which is helpful for the discovery of new compounds with more potency and selective activity.

  20. Docking based 3d-QSAR studies applied at the BRAF inhibitors to understand the binding mechanism

    BRAF is a great therapeutic target in a wide variety of human cancers. It is the member of Ras Activating Factor (RAF) family of serine/throenine kinase. The mutated form of the BRAF has diverted all the attention towards itself because of increase severity and elevated kinase activity. The RAF signal transduction cascade is a conserved protein pathway that is involved in cell cycle progression and apoptosis. The ERK regulates phosphorylation of different proteins either in cytosol or in nucleus but disorders in ERK signaling pathway cause mutation in BRAF. This cascade in these cells may provide selection of mutated BRAF in which valine is substituted with glutamatic acid at position 600. This mutation occurs in activation loop. A number of inhibitors reported to target different members of RAF, some of them have potential to target the BRAF as well. Major reason for failure of previously reported inhibitors was due to the highly conserved sequence and confirmation of catalytic cleft which is always a center of consideration for binding of inhibitors to suppress the kinase activity. This is the first attempt to study and understand the BARF inhibitors - protein interactions in detail by utilizing 3D-QSAR and molecular docking techniques. Most reliable techniques of 3D QSAR i.e Comparative Molecular Field Analysis (CoMFA) and Comparative Molecular Similarity Indices Analysis (CoMSIA) were applied for three different data sets. The data sets selected for better evaluation of BRAF inhibitors belongs to 2, 6-Disubstituted Pyrazine, Pyridoimidazolones and its derivatives. Our models would offer help to better understand the structure-activity relationships that exist for these classes of compounds and also facilitate the design of novel inhibitors with good chemical diversity. (Author)

  1. Combined Pharmacophore Modeling, 3D-QSAR, Homology Modeling and Docking Studies on CYP11B1 Inhibitors

    Rui Yu

    2015-01-01

    Full Text Available The mitochondrial cytochrome P450 enzymes inhibitor steroid 11β-hydroxylase (CYP11B1 can decrease the production of cortisol. Therefore, these inhibitors have an effect in the treatment of Cushing’s syndrome. A pharmacophore model generated by Genetic Algorithm with Linear Assignment for Hypermolecular Alignment of Datasets (GALAHAD was used to align the compounds and perform comparative molecular field analysis (CoMFA with Q2 = 0.658, R2 = 0.959. The pharmacophore model contained six hydrophobic regions and one acceptor atom, and electropositive and bulky substituents would be tolerated at the A and B sites, respectively. A three-dimensional quantitative structure-activity relationship (3D-QSAR study based on the alignment with the atom root mean square (RMS was applied using comparative molecular field analysis (CoMFA with Q2 = 0.666, R2 = 0.978, and comparative molecular similarity indices analysis (CoMSIA with Q2 = 0.721, R2 = 0.972. These results proved that all the models have good predictability of the bioactivities of inhibitors. Furthermore, the QSAR models indicated that a hydrogen bond acceptor substituent would be disfavored at the A and B groups, while hydrophobic groups would be favored at the B site. The three-dimensional (3D model of the CYP11B1 was generated based on the crystal structure of the CYP11B2 (PDB code 4DVQ. In order to probe the ligand-binding modes, Surflex-dock was employed to dock CYP11B1 inhibitory compounds into the active site of the receptor. The docking result showed that the imidazolidine ring of CYP11B1 inhibitors form H bonds with the amino group of residue Arg155 and Arg519, which suggested that an electronegative substituent at these positions could enhance the activities of compounds. All the models generated by GALAHAD QSAR and Docking methods provide guidance about how to design novel and potential drugs for Cushing’s syndrome treatment.

  2. Comparison of Different 2D and 3D-QSAR Methods on Activity Prediction of Histamine H3 Receptor Antagonists.

    Dastmalchi, Siavoush; Hamzeh-Mivehroud, Maryam; Asadpour-Zeynali, Karim

    2012-01-01

    Histamine H3 receptor subtype has been the target of several recent drug development programs. Quantitative structure-activity relationship (QSAR) methods are used to predict the pharmaceutically relevant properties of drug candidates whenever it is applicable. The aim of this study was to compare the predictive powers of three different QSAR techniques, namely, multiple linear regression (MLR), artificial neural network (ANN), and HASL as a 3D QSAR method, in predicting the receptor binding affinities of arylbenzofuran histamine H3 receptor antagonists. Genetic algorithm coupled partial least square as well as stepwise multiple regression methods were used to select a number of calculated molecular descriptors to be used in MLR and ANN-based QSAR studies. Using the leave-group-out cross-validation technique, the performances of the MLR and ANN methods were evaluated. The calculated values for the mean absolute percentage error (MAPE), ranging from 2.9 to 3.6, and standard deviation of error of prediction (SDEP), ranging from 0.31 to 0.36, for both MLR and ANN methods were statistically comparable, indicating that both methods perform equally well in predicting the binding affinities of the studied compounds toward the H3 receptors. On the other hand, the results from 3D-QSAR studies using HASL method were not as good as those obtained by 2D methods. It can be concluded that simple traditional approaches such as MLR method can be as reliable as those of more advanced and sophisticated methods like ANN and 3D-QSAR analyses. PMID:25317190

  3. Pharmacophore Modeling, Atom based 3D-QSAR and Docking Studies of Chalcone derivatives as Tubulin inhibitors

    Naresh Kandakatla; Geetha Ramakrishnan; J. Karthikeyan; Rajasekhar Chekkara

    2014-01-01

    Tubulin is attractive target for anticancer drug design and their inhibitors are useful in treatment of various cancers. Pharmacophore and Atom based QSAR studies were carried out for series of Chalcone derivatives. Pharmacophore model was developed using 38 compounds, having pIC50 ranging 4.003 to 6.552. The best Pharmacophoric hypothesis AHHRR.10 (one H-acceptor, two hydrophobic groups, two aromatic rings) had survival score of 4.824. Atom based 3D QSAR was built for the best hypothesis w...

  4. A new computer program for QSAR-analysis: ARTE-QSAR.

    Van Damme, Sofie; Bultinck, Patrick

    2007-08-01

    A new computer program has been designed to build and analyze quantitative-structure activity relationship (QSAR) models through regression analysis. The user is provided with a range of regression and validation techniques. The emphasis of the program lies mainly in the validation of QSAR models in chemical applications. ARTE-QSAR produces an easy interpretable output from which the user can conclude if the obtained model is suitable for prediction and analysis. PMID:17394240

  5. Combined 3D-QSAR, molecular docking and molecular dynamics study on thyroid hormone activity of hydroxylated polybrominated diphenyl ethers to thyroid receptors β

    Li, Xiaolin [State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing 210046 (China); Ye, Li [Suzhou NeuPharma Co.,Ltd, Suzhou 215123 (China); Wang, Xiaoxiang [State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing 210046 (China); Wang, Xinzhou [Suzhou NeuPharma Co.,Ltd, Suzhou 215123 (China); Liu, Hongling [State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing 210046 (China); Zhu, Yongliang [Suzhou NeuPharma Co.,Ltd, Suzhou 215123 (China); Yu, Hongxia, E-mail: hongxiayu01@yahoo.com.cn [State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing 210046 (China)

    2012-12-15

    Several recent reports suggested that hydroxylated polybrominated diphenyl ethers (HO-PBDEs) may disturb thyroid hormone homeostasis. To illuminate the structural features for thyroid hormone activity of HO-PBDEs and the binding mode between HO-PBDEs and thyroid hormone receptor (TR), the hormone activity of a series of HO-PBDEs to thyroid receptors β was studied based on the combination of 3D-QSAR, molecular docking, and molecular dynamics (MD) methods. The ligand- and receptor-based 3D-QSAR models were obtained using Comparative Molecular Similarity Index Analysis (CoMSIA) method. The optimum CoMSIA model with region focusing yielded satisfactory statistical results: leave-one-out cross-validation correlation coefficient (q{sup 2}) was 0.571 and non-cross-validation correlation coefficient (r{sup 2}) was 0.951. Furthermore, the results of internal validation such as bootstrapping, leave-many-out cross-validation, and progressive scrambling as well as external validation indicated the rationality and good predictive ability of the best model. In addition, molecular docking elucidated the conformations of compounds and key amino acid residues at the docking pocket, MD simulation further determined the binding process and validated the rationality of docking results. -- Highlights: ► The thyroid hormone activities of HO-PBDEs were studied by 3D-QSAR. ► The binding modes between HO-PBDEs and TRβ were explored. ► 3D-QSAR, molecular docking, and molecular dynamics (MD) methods were performed.

  6. Pharmacophore modeling, 3D-QSAR and docking study of 2-phenylpyrimidine analogues as selective PDE4B inhibitors.

    Tripuraneni, Naga Srinivas; Azam, Mohammed Afzal

    2016-04-01

    Pharmacophore modeling, molecular docking, and molecular dynamics (MD) simulation studies have been performed, to explore the putative binding modes of 2-phenylpyrimidine series as PDE4B selective inhibitors. A five point pharmacophore model was developed using 87 molecules having pIC50 ranging from 8.52 to 5.07. The pharmacophore hypothesis yielded a statistically significant 3D-QSAR model, with a high correlation coefficient (R(2)=0.918), cross validation coefficient (Q(2)=0.852), and F value (175) at 4 component PLS factor. The external validation indicated that our QSAR model possessed high predictive power (R(2)=0.70). The generated model was further validated by enrichment studies using the decoy test. To evaluate the effectiveness of docking protocol in flexible docking, we have selected crystallographic bound compound to validate our docking procedure as evident from root mean square deviation. A 10ns molecular dynamics simulation confirmed the docking results of both stability of the 1XMU-ligand complex and the presumed active conformation. Further, similar orientation was observed between the superposition of the conformations of 85 after MD simulation and best XP-docking pose; MD simulation and 3D-QSAR pose; best XP-docking and 3D-QSAR poses. Outcomes of the present study provide insight in designing novel molecules with better PDE4B selective inhibitory activity. PMID:26804643

  7. Development and validation of hydrophobic molecular fields derived from the quantum mechanical IEF/PCM-MST solvation models in 3D-QSAR.

    Ginex, Tiziana; Muñoz-Muriedas, Jordi; Herrero, Enric; Gibert, Enric; Cozzini, Pietro; Luque, F J

    2016-05-15

    Since the development of structure-activity relationships about 50 years ago, 3D-QSAR methods belong to the most refined ligand-based in silico techniques for prediction of biological data using physicochemical molecular fields. In this scenario, this study reports the development and validation of quantum mechanical (QM)-based hydrophobic descriptors derived from the parametrized MST continuum solvation model to be used in 3D-QSAR studies within the framework of the Hydrophobic Pharmacophore (HyPhar) method. To this end, five sets of compounds reported in the literature (dopamine D2/D4 antagonists, antifungal 2-aryl-4-chromanones, and inhibitors of GSK-3, cruzain and thermolysin) have been revisited. The results derived from the QM/MST-based hydrophobic descriptors have been compared with previous CoMFA and CoMSIA studies, and examined in light of the available X-ray crystallographic structures of the targets. The analysis reveals that the combination of electrostatic and nonelectrostatic components of the octanol/water partition coefficient yields pharmacophoric models fully comparable with the predictive potential of standard 3D-QSAR techniques. Moreover, the graphical representation of the hydrophobic maps provides a direct linkage with the pattern of interactions found in crystallographic structures. Overall, the introduction of the QM/MST-based descriptors, which could be easily adapted to other continuum solvation formalisms, paves the way to novel computational strategies for disclosing structure-activity relationships in drug design. © 2016 Wiley Periodicals, Inc. PMID:26813046

  8. 3D-QSAR study of 20 (S)-camptothecin analogs

    Ai-jun LU; Zhen-shan ZHANG; Ming-yue ZHENG; Han-jun ZOU; Xiao-min LUO; Hua-liang JIANG

    2007-01-01

    Aim: To build up a quantitative structure-activity relationship (QSAR) model of20 (S)-camptothecin (CPT) analogs for the prediction of the activity of new CPT analogs for drug design. Methods: A training set of 43 structurally diverse CPT analogs which were inhibitors of topoisomerase Ⅰ were used to construct a quan-titative structure-activity relationship model with a comparative molecular field analysis (CoMFA). The QSAR model was optimized using partial least squares(PLS) analysis. A test set of 10 compounds was evaluated using the model. Results: The CoMFA model was constructed successfully, and a good cross-validated correlation was obtained in which q2 was 0.495. Then, the analysis of the non-cross-validated PLS model in which r2 was 0.935 was built and permitted demonstrations of high predictability for the activities of the 10 CPT analogs in the test set selected in random. Conclusion: The CoMFA model indicated that bulky negative-charged group at position 9, 10 and 11 of CPT would increase activity, but excessively increasing bulky group at position 10 is adverse to inhibi-tory activity; substituents that occupy position 7 with the bulky positive group will enhance the inhibitive activity. The model can be used to design new CPT analogs and understand the mechanism of action.

  9. 3D-QSAR and docking studies of flavonoids as potent Escherichia coli inhibitors.

    Fang, Yajing; Lu, Yulin; Zang, Xixi; Wu, Ting; Qi, XiaoJuan; Pan, Siyi; Xu, Xiaoyun

    2016-01-01

    Flavonoids are potential antibacterial agents. However, key substituents and mechanism for their antibacterial activity have not been fully investigated. The quantitative structure-activity relationship (QSAR) and molecular docking of flavonoids relating to potent anti-Escherichia coli agents were investigated. Comparative molecular field analysis (CoMFA) and comparative molecular similarity indices analysis (CoMSIA) were developed by using the pIC50 values of flavonoids. The cross-validated coefficient (q(2)) values for CoMFA (0.743) and for CoMSIA (0.708) were achieved, illustrating high predictive capabilities. Selected descriptors for the CoMFA model were ClogP (logarithm of the octanol/water partition coefficient), steric and electrostatic fields, while, ClogP, electrostatic and hydrogen bond donor fields were used for the CoMSIA model. Molecular docking results confirmed that half of the tested flavonoids inhibited DNA gyrase B (GyrB) by interacting with adenosine-triphosphate (ATP) pocket in a same orientation. Polymethoxyl flavones, flavonoid glycosides, isoflavonoids changed their orientation, resulting in a decrease of inhibitory activity. Moreover, docking results showed that 3-hydroxyl, 5-hydroxyl, 7-hydroxyl and 4-carbonyl groups were found to be crucial active substituents of flavonoids by interacting with key residues of GyrB, which were in agreement with the QSAR study results. These results provide valuable information for structure requirements of flavonoids as antibacterial agents. PMID:27049530

  10. Volume learning algorithm artificial neural networks for 3D QSAR studies.

    Tetko, I V; Kovalishyn, V V; Livingstone, D J

    2001-07-19

    The current study introduces a new method, the volume learning algorithm (VLA), for the investigation of three-dimensional quantitative structure-activity relationships (QSAR) of chemical compounds. This method incorporates the advantages of comparative molecular field analysis (CoMFA) and artificial neural network approaches. VLA is a combination of supervised and unsupervised neural networks applied to solve the same problem. The supervised algorithm is a feed-forward neural network trained with a back-propagation algorithm while the unsupervised network is a self-organizing map of Kohonen. The use of both of these algorithms makes it possible to cluster the input CoMFA field variables and to use only a small number of the most relevant parameters to correlate spatial properties of the molecules with their activity. The statistical coefficients calculated by the proposed algorithm for cannabimimetic aminoalkyl indoles were comparable to, or improved, in comparison to the original study using the partial least squares algorithm. The results of the algorithm can be visualized and easily interpreted. Thus, VLA is a new convenient tool for three-dimensional QSAR studies. PMID:11448223

  11. 3D QSAR AND PHARMACOPHORE IDENTIFICATION OF ISOQUINOLINE AND BENZIMIDAZOLE ANALOGS AS POTENT C-RAF INHIBITORS

    Blessy Christina N*, Manoj Kumar Mahto, Uday Kumar Dasari and Matcha Bhaskar

    2013-01-01

    The C-Raf inhibitors obstruct the activity of other signaling pathways which are implicated in many tumors. Hence C-RAF inhibition has emerged as a promising therapeutic target for many cancers. A series of 33 novel Isoquinoline and benzimidazole derivatives has been reported as C-RAF inhibitors. A combined study of pharmacophore prediction, atom based 3d QSAR and molecular docking explored the structural insights of these inhibitors. A Five point pharmacophore hypothesis AADHR.  719 yielded ...

  12. Tyrosinase Inhibitory Activity, 3D QSAR, and Molecular Docking Study of 2,5-Disubstituted-1,3,4-Oxadiazoles

    Ramesh L. Sawant

    2013-01-01

    Full Text Available In continuation with our research program, in search of potent enzyme tyrosinase inhibitor, a series of synthesized 2,5-disubstituted 1,3,4-oxadiazoles have been evaluated for enzyme tyrosinase inhibitory activity. Subsequently, 3D QSAR and docking studies were performed to find optimum structural requirements for potent enzyme tyrosinase inhibitor from this series. The synthesized 20 compounds of 2,5-disubstituted-1,3,4-oxadiazole series were screened for mushroom tyrosinase inhibitory activity at various concentrations by enzyme inhibition assay. The percentage enzyme inhibition was calculated by recording absorbance at 492 nm with microplate reader. 3D QSAR and docking studies were performed using VLife MDS 3.5 software. In the series 2,5-disubstituted-1,3,4-oxadiazoles enzyme tyrosinase inhibitory activity was found to be dose dependent with maximum activity for compounds 4c, 4h, 4m, and 4r. 3D QSAR and docking studies revealed that more electropositive and less bulky substituents if placed on 1,3,4-oxadiazole nucleus may result in better tyrosinase inhibitory activity in the series.

  13. Pharmacophore Modeling, Atom based 3D-QSAR and Docking Studies of Chalcone derivatives as Tubulin inhibitors

    Naresh Kandakatla

    2014-09-01

    Full Text Available Tubulin is attractive target for anticancer drug design and their inhibitors are useful in treatment of various cancers. Pharmacophore and Atom based QSAR studies were carried out for series of Chalcone derivatives. Pharmacophore model was developed using 38 compounds, having pIC50 ranging 4.003 to 6.552. The best Pharmacophoric hypothesis AHHRR.10 (one H-acceptor, two hydrophobic groups, two aromatic rings had survival score of 4.824. Atom based 3D QSAR was built for the best hypothesis with training set of 31 and test set of 7 compounds using PLS factor. The obtained QSAR model has excellent regression coefficient of R2 = 0.954, cross validated correlation coefficient q2 = 0.681, Pearson-R = 0.886 and Fisher ratio F = 136.9. The QSAR results explain electron withdrawing, positive, negative ionic and hydrophobic groups are crucial for tubulin inhibition. The docking studies of these inhibitors on the active site of the beta-tubulin shows crucial hydrogen bond interactions with the Gln11, Asn101, Thr145 amino acids. These findings provide designing of novel compounds with better tubulin inhibitory potential.

  14. Molecular docking and 3D-QSAR studies on the glucocorticoid receptor antagonistic activity of hydroxylated polychlorinated biphenyls.

    Liu, S; Luo, Y; Fu, J; Zhou, J; Kyzas, G Z

    2016-02-01

    The glucocorticoid receptor (GR) antagonistic activities of hydroxylated polychlorinated biphenyls (HO-PCBs) were recently characterised. To further explore the interactions between HO-PCBs and the GR, and to elucidate structural characteristics that influence the GR antagonistic activity of HO-PCBs, molecular docking and three-dimensional quantitative structure-activity relationship (3D-QSAR) studies were performed. Comparative molecular similarity indices analysis (CoMSIA) was performed using both ligand- and receptor-based alignment schemes. Results generated from the receptor-based model were found to be more satisfactory, with q(2) of 0.632 and r(2) of 0.931 compared with those from the ligand-based model. Some internal validation strategies (e.g. cross-validation analysis, bootstrapping analysis and Y-randomisation) and an external validation method were used respectively to further assess the stability and predictive ability of the derived model. Graphical interpretation of the model provided some insights into the structural features that affected the GR antagonistic activity of HO-PCBs. Molecular docking studies revealed that some key residues were critical for ligand-receptor interactions by forming hydrogen bonds (Glu540) and hydrophobic interactions with ligands (Ile539, Val543 and Trp577). Although CoMSIA sometimes depends on the alignment of the molecules, the information provided is beneficial for predicting the GR antagonistic activities of HO-PCB homologues and is helpful for understanding the binding mechanisms of HO-PCBs to GR. PMID:26848875

  15. Modifying tetramethyl–nitrophenyl–imidazoline with amino acids: design, synthesis, and 3D-QSAR for improving inflammatory pain therapy

    Jiang X

    2015-04-01

    Full Text Available Xueyun Jiang,1 Yuji Wang,1 Haimei Zhu,1 Yaonan Wang,1 Ming Zhao,1,2 Shurui Zhao,1 Jianhui Wu,1 Shan Li,1 Shiqi Peng11Beijing Area Major Laboratory of Peptide and Small Molecular Drugs, Engineering Research Center of Endogenous Prophylactic of Ministry of Education of China, Beijing Laboratory of Biomedical Materials, College of Pharmaceutical Sciences, Capital Medical University, Beijing, People’s Republic of China; 2Faculty of Biomedical Science and Environmental Biology, Kaohsiung Medical University, Kaohsiung, TaiwanAbstract: With the help of pharmacophore analysis and docking investigation, 15 novel 1-(4,4,5,5-tetramethyl-2-(3-nitrophenyl-4,5-dihydroimidazol-1-yl-oxyacetyl-L-amino acids (6a–o were designed, synthesized, and assayed. On tail-flick and xylene-induced ear edema models, 10 µmol/kg 6a–o exhibited excellent oral anti-inflammation and analgesic activity. The dose-dependent assay of their representative 6f indicates that the effective dose should be 3.3 µmol/kg. The correlation of the three-dimensional quantitative structure–activity relationship with the docking analysis provides a basis for the rational design of drugs to treat inflammatory pain.Keywords: tetramethylimidazoline, analgesic, anti-inflammatory, 3D-QSAR

  16. 3D-QSAR modelling dataset of bioflavonoids for predicting the potential modulatory effect on P-glycoprotein activity.

    Wongrattanakamon, Pathomwat; Lee, Vannajan Sanghiran; Nimmanpipug, Piyarat; Jiranusornkul, Supat

    2016-12-01

    The data is obtained from exploring the modulatory activities of bioflavonoids on P-glycoprotein function by ligand-based approaches. Multivariate Linear-QSAR models for predicting the induced/inhibitory activities of the flavonoids were created. Molecular descriptors were initially used as independent variables and a dependent variable was expressed as pFAR. The variables were then used in MLR analysis by stepwise regression calculation to build the linear QSAR data. The entire dataset consisted of 23 bioflavonoids was used as a training set. Regarding the obtained MLR QSAR model, R of 0.963, R (2)=0.927, [Formula: see text], SEE=0.197, F=33.849 and q (2)=0.927 were achieved. The true predictabilities of QSAR model were justified by evaluation with the external dataset (Table 4). The pFARs of representative flavonoids were predicted by MLR QSAR modelling. The data showed that internal and external validations may generate the same conclusion. PMID:27626051

  17. Pharmacophore modeling and 3D-QSAR studies on substituted benzothiazole / benzimidazole analogues as DHFR inhibitors with antimycobacterial activity

    R. Priyadarsini

    2012-08-01

    Full Text Available The resurgence of tuberculosis and the emergence of multidrug-resistant strains of Mycobacteria drugs has propelled the development of new structural classes of antitubercular agents. The present study was undertaken to investigate the opportunities which the enzyme dihydrofolate reductase, a promising drug target for treatmentof Mycobacterial infections offers for the development of new TB drugs. Pharmacophore models were established by using the HipHop and HypoGen algorithms implemented in the Catalyst software package. Thebest quantitative pharmacophore model, consisted of two hydrogen bond acceptor, a hydrophobic aliphatic, and a ring aromatic feature which has the highest correlation coefficient (0.93, as well as enrichment factor of 1.75 and Goodness of hit score of 0.73. Based on the pharmacophore model some leads were optimized and some of its derivatives were synthesized and analysed by following QSAR studies. About 25 compounds of substituted benzothiazole/ benzimidazole derivatives were synthesized as potent DHFR inhibitors and screened for antimycobacterial activity. To further explore the structure-activity relationships of all newly synthesized compounds, 3D-QSAR analyses were developed. MFA studies were performed with the QSAR module of Cerius2 using genetic partial least squares (G/PLS algorithm. The predictive ability of the developed model was assessed using a training set of 25 and a test set of 5 compounds (r2pred = 0.924.The analyzed MF

  18. 3D-QSAR study of tetrahydro-3H-imidazo[4,5-c]pyridine derivatives as VEGFR-2 kinase inhibitors using various charge schemes.

    Balupuri, Anand; Balasubramanian, Pavithra K; Cho, Seung Joo

    2015-08-01

    Vascular endothelial growth factor-2 receptor (VEGFR-2) kinase is a promising target for the development of novel anticancer drugs. Three-dimensional quantitative structure-activity relationship (3D-QSAR) study was performed on a series of tetrahydro-3H-imidazo[4,5-c]pyridine derivatives to understand the structural basis for VEGFR-2 inhibitory activity. Several 3D-QSAR models were developed using various partial atomic charge schemes. Comparative molecular field analysis (CoMFA) and Comparative molecular similarity indices analysis (CoMSIA) methods were employed to derive these models. The CoMFA models performed better than the CoMSIA models. The reliable CoMFA model was obtained with the Gasteiger-Marsili charge scheme. The model produced statistically significant results with a cross-validated correlation coefficient (q(2)) of 0.635 and a coefficient of determination (r(2)) of 0.930. The model showed reasonable predictive power with predictive correlation coefficient ([Formula: see text]) of 0.582. Robustness of the model was further checked by leave-five-out cross-validation, bootstrapping and progressive scrambling analysis. The model was found to be statistically robust and expected to assist in the design of novel compounds with enhanced VEGFR-2 inhibitory activity. PMID:25874606

  19. 3D-QSAR Studies of Dihydropyrazole and Dihydropyrrole Derivatives as Inhibitors of Human Mitotic Kinesin Eg5 Based on Molecular Docking

    Wenjuan Yang

    2012-02-01

    Full Text Available Human mitotic kinesin Eg5 plays an essential role in mitoses and is an interesting drug target against cancer. To find the correlation between Eg5 and its inhibitors, structure-based 3D-quantitative structure–activity relationship (QSAR studies were performed on a series of dihydropyrazole and dihydropyrrole derivatives using comparative molecular field analysis (CoMFA and comparative molecular similarity indices analysis (CoMSIA methods. Based on the LigandFit docking results, predictive 3D-QSAR models were established, with cross-validated coefficient values (q2 up to 0.798 for CoMFA and 0.848 for CoMSIA, respectively. Furthermore, the CoMFA and CoMSIA models were mapped back to the binding sites of Eg5, which could provide a better understanding of vital interactions between the inhibitors and the kinase. Ligands binding in hydrophobic part of the inhibitor-binding pocket were found to be crucial for potent ligand binding and kinases selectivity. The analyses may be used to design more potent EG5 inhibitors and predict their activities prior to synthesis.

  20. 3D-QSAR and Docking Studies of a Series of β-Carboline Derivatives as Antitumor Agents of PLK1

    Jahan B. Ghasemi

    2014-01-01

    Full Text Available An alignment-free, three dimensional quantitative structure-activity relationship (3D-QSAR analysis has been performed on a series of β-carboline derivatives as potent antitumor agents toward HepG2 human tumor cell lines. A highly descriptive and predictive 3D-QSAR model was obtained through the calculation of alignment-independent descriptors (GRIND descriptors using ALMOND software. For a training set of 30 compounds, PLS analyses result in a three-component model which displays a squared correlation coefficient (r2 of 0.957 and a standard deviation of the error of calculation (SDEC of 0.116. Validation of this model was performed using leave-one-out, q2loo of 0.85, and leave-multiple-out. This model gives a remarkably high r2pred(0.66 for a test set of 10 compounds. Docking studies were performed to investigate the mode of interaction between β-carboline derivatives and the active site of the most probable anticancer receptor, polo-like kinase protein.

  1. Identification of the Structural Features of Guanine Derivatives as MGMT Inhibitors Using 3D-QSAR Modeling Combined with Molecular Docking.

    Sun, Guohui; Fan, Tengjiao; Zhang, Na; Ren, Ting; Zhao, Lijiao; Zhong, Rugang

    2016-01-01

    DNA repair enzyme O⁶-methylguanine-DNA methyltransferase (MGMT), which plays an important role in inducing drug resistance against alkylating agents that modify the O⁶ position of guanine in DNA, is an attractive target for anti-tumor chemotherapy. A series of MGMT inhibitors have been synthesized over the past decades to improve the chemotherapeutic effects of O⁶-alkylating agents. In the present study, we performed a three-dimensional quantitative structure activity relationship (3D-QSAR) study on 97 guanine derivatives as MGMT inhibitors using comparative molecular field analysis (CoMFA) and comparative molecular similarity indices analysis (CoMSIA) methods. Three different alignment methods (ligand-based, DFT optimization-based and docking-based alignment) were employed to develop reliable 3D-QSAR models. Statistical parameters derived from the models using the above three alignment methods showed that the ligand-based CoMFA (Qcv² = 0.672 and Rncv² = 0.997) and CoMSIA (Qcv² = 0.703 and Rncv² = 0.946) models were better than the other two alignment methods-based CoMFA and CoMSIA models. The two ligand-based models were further confirmed by an external test-set validation and a Y-randomization examination. The ligand-based CoMFA model (Qext² = 0.691, Rpred² = 0.738 and slope k = 0.91) was observed with acceptable external test-set validation values rather than the CoMSIA model (Qext² = 0.307, Rpred² = 0.4 and slope k = 0.719). Docking studies were carried out to predict the binding modes of the inhibitors with MGMT. The results indicated that the obtained binding interactions were consistent with the 3D contour maps. Overall, the combined results of the 3D-QSAR and the docking obtained in this study provide an insight into the understanding of the interactions between guanine derivatives and MGMT protein, which will assist in designing novel MGMT inhibitors with desired activity. PMID:27347909

  2. Identification of the Structural Features of Guanine Derivatives as MGMT Inhibitors Using 3D-QSAR Modeling Combined with Molecular Docking

    Guohui Sun

    2016-06-01

    Full Text Available DNA repair enzyme O6-methylguanine-DNA methyltransferase (MGMT, which plays an important role in inducing drug resistance against alkylating agents that modify the O6 position of guanine in DNA, is an attractive target for anti-tumor chemotherapy. A series of MGMT inhibitors have been synthesized over the past decades to improve the chemotherapeutic effects of O6-alkylating agents. In the present study, we performed a three-dimensional quantitative structure activity relationship (3D-QSAR study on 97 guanine derivatives as MGMT inhibitors using comparative molecular field analysis (CoMFA and comparative molecular similarity indices analysis (CoMSIA methods. Three different alignment methods (ligand-based, DFT optimization-based and docking-based alignment were employed to develop reliable 3D-QSAR models. Statistical parameters derived from the models using the above three alignment methods showed that the ligand-based CoMFA (Qcv2 = 0.672 and Rncv2 = 0.997 and CoMSIA (Qcv2 = 0.703 and Rncv2 = 0.946 models were better than the other two alignment methods-based CoMFA and CoMSIA models. The two ligand-based models were further confirmed by an external test-set validation and a Y-randomization examination. The ligand-based CoMFA model (Qext2 = 0.691, Rpred2 = 0.738 and slope k = 0.91 was observed with acceptable external test-set validation values rather than the CoMSIA model (Qext2 = 0.307, Rpred2 = 0.4 and slope k = 0.719. Docking studies were carried out to predict the binding modes of the inhibitors with MGMT. The results indicated that the obtained binding interactions were consistent with the 3D contour maps. Overall, the combined results of the 3D-QSAR and the docking obtained in this study provide an insight into the understanding of the interactions between guanine derivatives and MGMT protein, which will assist in designing novel MGMT inhibitors with desired activity.

  3. QSAR modeling of toxicity of diverse organic chemicals to Daphnia magna using 2D and 3D descriptors

    Kar, Supratik [Drug Theoretics and Cheminformatics Laboratory, Department of Pharmaceutical Technology, Jadavpur University, Raja S C Mullick Road, Kolkata 700032 (India); Roy, Kunal, E-mail: kunalroy_in@yahoo.com [Drug Theoretics and Cheminformatics Laboratory, Department of Pharmaceutical Technology, Jadavpur University, Raja S C Mullick Road, Kolkata 700032 (India)

    2010-05-15

    One of the major economic alternatives to experimental toxicity testing is the use of quantitative structure-activity relationships (QSARs) which are used in formulating regulatory decisions of environmental protection agencies. In this background, we have modeled a large diverse group of 297 chemicals for their toxicity to Daphnia magna using mechanistically interpretable descriptors. Three-dimensional (3D) (electronic and spatial) and two-dimensional (2D) (topological and information content indices) descriptors along with physicochemical parameter log K{sub o/w} (n-octanol/water partition coefficient) and structural descriptors were used as predictor variables. The QSAR models were developed by stepwise multiple linear regression (MLR), partial least squares (PLS), genetic function approximation (GFA), and genetic PLS (G/PLS). All the models were validated internally and externally. Among several models developed using different chemometric tools, the best model based on both internal and external validation characteristics was a PLS equation with 7 descriptors and three latent variables explaining 67.8% leave-one-out predicted variance and 74.1% external predicted variance. The PLS model suggests that higher lipophilicity and electrophilicity, less negative charge surface area and presence of ether linkage, hydrogen bond donor groups and acetylenic carbons are responsible for greater toxicity of chemicals. The developed model may be used for prediction of toxicity, safety and risk assessment of chemicals to achieve better ecotoxicological management and prevent adverse health consequences.

  4. Binding Model and 3D-QSAR of 3-(2-Chloropyrid-5-ylmethylamino)-2-cyanoacrylates as PSⅡ Electron Transport Inhibitor

    HAN,Xiao-Feng; LIU,Yu-Xiu; LIU,Ying; LAI,Lu-Hua; HUANG,Run-Qiu; WANG,Qing-Min

    2007-01-01

    The binding model of 3-(2-chloropyrid-5-ylmethylamino)-2-cyanoacrylate photosystem Ⅱ (PSⅡ) electron transport inhibitors with the D1 protein of PSⅡ was built. The high herbicidal activity of this kind of inhibitors was explained by docking studies: in addition to usual factors, the N atom on the pyridine ring could form an H-bond with the backbone amide of Phe265 on the D1 protein. 3D-QSAR analysis on sixteen 3-(2-chloropyrid-5-ylmethylamino)-2-cyanoacrylate compounds was performed using CoMFA method to explain the nature of interactions between the compounds and D1 protein. These studies may provide useful insights for designing new PSⅡ electron transport inhibitors.

  5. Study on structure-activity relationship of mutation-dependent herbicide resistance acetohydroxyacid synthase through 3D-QSAR and mutation

    YU ZhiHong; NIU CongWei; BAN ShuRong; WEN Xin; XI Zhen

    2007-01-01

    Seventy-four sulfonylureas were synthesized and tested for their inhibitory activity against the whole enzyme of E. Coli acetohydroxyacid synthase (AHAS, EC 2.2.1.6) isoenzyme Ⅱ, and 3D-QSAR analyses were performed based on these inhibitory activities. The binding conformation of chlorimuron-ethyl, a commercial herbicide of AHAS, in the crystal structure of AHAS complex was extracted and used as template to build the initial three-dimensional structure of other sulfonylureas, and then all structures were fully geometry optimized. After systematic optimization of the alignment rule, molecular orientation, grid space and attenuation factor, two satisfactory models with excellent performances (CoMFA: q2 = 0.735, r2 = 0.954, n = 7, r 2pred = 0.832; CoMSIA: q2 = 0.721, r2 = 0.913, n = 8, r 2pred = 0.844) were established. By mapping the 3D contour maps of CoMFA and CoMSIA models into the possible inhibitory active site in the crystal structure of catalytic subunit of yeast AHAS, a plausible binding model for AHAS, with best fit QSAR in the literature so far, was proposed. Moreover, the results of 3D-QSAR were further utilized to interpret resistance of site-directed mutants. A relative activity index (RAI) for AHAS enzyme mutant was defined for the first time to relate the 3D-QSAR and resistance of mutants. This study, for the first time, demonstrated that combination of 3D-QSAR and enzyme mutation can be used to decipher the molecular basis of ligand-receptor interaction mechanism. This study refined our understanding of the ligand-receptor interaction and resistance mechanism in AHAS-sulfonylurea system, and provided basis for designing new potent herbicides to combat the herbicide resistance.

  6. Three-dimensional QSAR analysis and design of new 1,2,4-oxadiazole antibacterials.

    Leemans, Erika; Mahasenan, Kiran V; Kumarasiri, Malika; Spink, Edward; Ding, Derong; O'Daniel, Peter I; Boudreau, Marc A; Lastochkin, Elena; Testero, Sebastian A; Yamaguchi, Takao; Lee, Mijoon; Hesek, Dusan; Fisher, Jed F; Chang, Mayland; Mobashery, Shahriar

    2016-02-01

    The oxadiazole antibacterials, a class of newly discovered compounds that are active against Gram-positive bacteria, target bacterial cell-wall biosynthesis by inhibition of a family of essential enzymes, the penicillin-binding proteins. Ligand-based 3D-QSAR analyses by comparative molecular field analysis (CoMFA), comparative molecular shape indices analysis (CoMSIA) and Field-Based 3D-QSAR evaluated a series of 102 members of this class. This series included inactive compounds as well as compounds that were moderately to strongly antibacterial against Staphylococcus aureus. Multiple models were constructed using different types of energy minimization and charge calculations. CoMFA derived contour maps successfully defined favored and disfavored regions of the molecules in terms of steric and electrostatic properties for substitution. PMID:26733473

  7. In silico exploration of c-KIT inhibitors by pharmaco-informatics methodology: pharmacophore modeling, 3D QSAR, docking studies, and virtual screening.

    Chaudhari, Prashant; Bari, Sanjay

    2016-02-01

    c-KIT is a component of the platelet-derived growth factor receptor family, classified as type-III receptor tyrosine kinase. c-KIT has been reported to be involved in, small cell lung cancer, other malignant human cancers, and inflammatory and autoimmune diseases associated with mast cells. Available c-KIT inhibitors suffer from tribulations of growing resistance or cardiac toxicity. A combined in silico pharmacophore and structure-based virtual screening was performed to identify novel potential c-KIT inhibitors. In the present study, five molecules from the ZINC database were retrieved as new potential c-KIT inhibitors, using Schrödinger's Maestro 9.0 molecular modeling suite. An atom-featured 3D QSAR model was built using previously reported c-KIT inhibitors containing the indolin-2-one scaffold. The developed 3D QSAR model ADHRR.24 was found to be significant (R2 = 0.9378, Q2 = 0.7832) and instituted to be sufficiently robust with good predictive accuracy, as confirmed through external validation approaches, Y-randomization and GH approach [GH score 0.84 and Enrichment factor (E) 4.964]. The present QSAR model was further validated for the OECD principle 3, in that the applicability domain was calculated using a "standardization approach." Molecular docking of the QSAR dataset molecules and final ZINC hits were performed on the c-KIT receptor (PDB ID: 3G0E). Docking interactions were in agreement with the developed 3D QSAR model. Model ADHRR.24 was explored for ligand-based virtual screening followed by in silico ADME prediction studies. Five molecules from the ZINC database were obtained as potential c-KIT inhibitors with high in -silico predicted activity and strong key binding interactions with the c-KIT receptor. PMID:26416560

  8. Estudos de QSAR-3D em derivados 5-nitro-2-tiofilidênicos com atividade frente a Staphylococcus aureus multi-resistente 3D QSAR studies of 5-nitrothiophene derivatives with antimicrobial activity against multidrug-resistant Staphylococcus aureus

    Andrea Masunari

    2007-06-01

    Full Text Available Campos moleculares extraídos de aplicativos utilizados em estudos de QSAR-3D apresentam, em geral, grande número de informações, muitas vezes irrelevantes na expressão da atividade biológica. O programa Volsurf converte as informações presentes em mapas de energia de interação tridimensionais em número reduzido de descritores bidimensionais que se caracterizam como de fácil entendimento e interpretação. Assim, foram avaliados, neste estudo, dezoito derivados 5-nitro-2-tiofilidênicos com atividade antimicrobiana frente a Staphylococcus aureus multi-resistente, correlacionando as características tridimensionais destes ligantes com a referida atividade. Para o desenho e conversão tridimensional dos ligantes foram utilizados os aplicativos Sybyl (Tripos Inc e CORINA (Molecular Networks GmbH Computerchemie, respectivamente. Os campos de interação molecular foram calculados no programa GRID (Molecular Discovery Ltd. A aplicação do programa Volsurf (Molecular Discovery Ltd resultou em modelo estatisticamente robusto (r² = 0,93, q² = 0,87 com 48 descritores estruturais, mostrando ser a hidrofobicidade propriedade fundamental no condicionamento da atividade antimicrobiana.Studies in three-dimensional molecular fields generally contain a large amount of data, some of which are redundant or not relevant. The program Volsurf, a quite fast method, is able to compress the relevant information present in 3D molecular structures into a few easy bidimensional descriptors. This study correlates the antimicrobial activity of eighteen 5-nitro-2-thiophylidene derivatives against multidrug-resistant Staphylococcus aureus with three-dimensional molecular fields of these ligands. For molecular structures sketching and 3D conversion, Sybyl and CORINA programs were used, respectively. The GRID force field was applied to generate the 3D interaction energies. The Volsurf characterization results on significant statistic model with 48 descriptors (r

  9. A combination of 3D-QSAR, docking, local-binding energy (LBE) and GRID study of the species differences in the carcinogenicity of benzene derivatives chemicals.

    Fratev, Filip; Benfenati, Emilio

    2008-09-01

    A combination of 3D-QSAR, docking, local-binding energy (LBE) and GRID methods was applied as a tool to study and predict the mechanism of action of 100 carcinogenic benzene derivatives. Two 3D-QSAR models were obtained: (i) model of mouse carcinogenicity on the basis of 100 chemicals (model 1) and (ii) model of the differences in mouse and rat carcinogenicity on the basis of 73 compounds (model 2). 3D-QSAR regression maps indicated the important differences in species carcinogenicity, and the molecular positions associated with them. In order to evaluate the role of P450 metabolic process in carcinogenicity, the following approaches were used. The 3D models of CYP2E1 for mouse and rat were built up. A docking study was applied and the important ligand-protein residues interactions and oxidation positions of the molecules were identified. A new approach for quantitative assessment of metabolism pathways was developed, which enabled us to describe the species differences in CYP2E1 metabolism, and how it can be related to differences in the carcinogenic potential for a subset of compounds. The binding energies of the important substituents (local-binding energy-LBE) were calculated, in order to quantitatively demonstrate the contribution of the substituents in metabolic processes. Furthermore, a computational procedure was used for determining energetically favourable binding sites (GRID examination) of the enzymes. The GRID procedure allowed the identification of some important differences, related to species metabolism in CYP2E1. Comparing GRID, 3D-QSAR maps and LBE results, a similarity was identified, indicating a relationship between P450 metabolic processes and the differences in the carcinogenicity. PMID:18495507

  10. Molecular modelling on small molecular CDK2 inhibitors: an integrated approach using a combination of molecular docking, 3D-QSAR and pharmacophore modelling.

    Yuan, H; Liu, H; Tai, W; Wang, F; Zhang, Y; Yao, S; Ran, T; Lu, S; Ke, Z; Xiong, X; Xu, J; Chen, Y; Lu, T

    2013-10-01

    Cyclin-dependent kinase 2 (CDK2) has been identified as an important target for developing novel anticancer agents. Molecular docking, three-dimensional quantitative structure-activity relationship (3D-QSAR) and pharmacophore modelling were combined with the ultimate goal of studying the structure-activity relationship of CDK2 inhibitors. The comparative molecular similarity indices analysis (CoMSIA) model constructed based on a set of 3-aminopyrazole derivatives as CDK2 inhibitors gave statistically significant results (q (2) = 0.700; r (2) = 0.982). A HypoGen pharmacophore model, constructed using diverse CDK2 inhibitors, also showed significant statistics ([Formula: see text]Cost = 61.483; RMSD = 0.53; Correlation coefficient = 0.98). The small residues and error values between the estimated and experimental activities of the training and test set compounds proved their strong capability of activity prediction. The structural insights obtained from these two models were consistent with each other. The pharmacophore model summarized the important pharmacophoric features required for protein-ligand binding. The 3D contour maps in combination with the comprehensive pharmacophoric features helped to better interpret the structure-activity relationship. The results will be beneficial for the discovery and design of novel CDK2 inhibitors. The simplicity of this approach provides expansion to its applicability in optimizing other classes of small molecular CDK2 inhibitors. PMID:23941641

  11. A Combination of 3D-QSAR, Molecular Docking and Molecular Dynamics Simulation Studies of Benzimidazole-Quinolinone Derivatives as iNOS Inhibitors

    Peixun Liu

    2012-09-01

    Full Text Available Inducible Nitric Oxide Synthase (iNOS has been involved in a variety of diseases, and thus it is interesting to discover and optimize new iNOS inhibitors. In previous studies, a series of benzimidazole-quinolinone derivatives with high inhibitory activity against human iNOS were discovered. In this work, three-dimensional quantitative structure-activity relationships (3D-QSAR, molecular docking and molecular dynamics (MD simulation approaches were applied to investigate the functionalities of active molecular interaction between these active ligands and iNOS. A QSAR model with R2 of 0.9356, Q2 of 0.8373 and Pearson-R value of 0.9406 was constructed, which presents a good predictive ability in both internal and external validation. Furthermore, a combined analysis incorporating the obtained model and the MD results indicates: (1 compounds with the proper-size hydrophobic substituents at position 3 in ring-C (R3 substituent, hydrophilic substituents near the X6 of ring-D and hydrophilic or H-bond acceptor groups at position 2 in ring-B show enhanced biological activities; (2 Met368, Trp366, Gly365, Tyr367, Phe363, Pro344, Gln257, Val346, Asn364, Met349, Thr370, Glu371 and Tyr485 are key amino acids in the active pocket, and activities of iNOS inhibitors are consistent with their capability to alter the position of these important residues, especially Glu371 and Thr370. The results provide a set of useful guidelines for the rational design of novel iNOS inhibitors.

  12. Exploration of Novel Inhibitors for Bruton's Tyrosine Kinase by 3D QSAR Modeling and Molecular Dynamics Simulation.

    Rohit Bavi

    Full Text Available Bruton's tyrosine kinase (BTK is a cytoplasmic, non-receptor tyrosine kinase which is expressed in most of the hematopoietic cells and plays an important role in many cellular signaling pathways. B cell malignancies are dependent on BCR signaling, thus making BTK an efficient therapeutic target. Over the last few years, significant efforts have been made in order to develop BTK inhibitors to treat B-cell malignancies, and autoimmunity or allergy/hypersensitivity but limited success has been achieved. Here in this study, 3D QSAR pharmacophore models were generated for Btk based on known IC50 values and experimental energy scores with extensive validations. The five features pharmacophore model, Hypo1, includes one hydrogen bond acceptor lipid, one hydrogen bond donor, and three hydrophobic features, which has the highest correlation coefficient (0.98, cost difference (112.87, and low RMS (1.68. It was further validated by the Fisher's randomization method and test set. The well validated Hypo1 was used as a 3D query to search novel Btk inhibitors with different chemical scaffold using high throughput virtual screening technique. The screened compounds were further sorted by applying ADMET properties, Lipinski's rule of five and molecular docking studies to refine the retrieved hits. Furthermore, molecular dynamic simulation was employed to study the stability of docked conformation and to investigate the binding interactions in detail. Several important hydrogen bonds with Btk were revealed, which includes the gatekeeper residues Glu475 and Met 477 at the hinge region. Overall, this study suggests that the proposed hits may be more effective inhibitors for cancer and autoimmune therapy.

  13. 3D-QSAR and Molecular Docking Studies on Derivatives of MK-0457, GSK1070916 and SNS-314 as Inhibitors against Aurora B Kinase

    Chunzhi Ai

    2010-11-01

    Full Text Available Development of anticancer drugs targeting Aurora B, an important member of the serine/threonine kinases family, has been extensively focused on in recent years. In this work, by applying an integrated computational method, including comparative molecular field analysis (CoMFA, comparative molecular similarity indices analysis (CoMSIA, homology modeling and molecular docking, we investigated the structural determinants of Aurora B inhibitors based on three different series of derivatives of 108 molecules. The resultant optimum 3D-QSAR models exhibited (q2 = 0.605, r2pred = 0.826, (q2 = 0.52, r2pred = 0.798 and (q2 = 0.582, r2pred = 0.971 for MK-0457, GSK1070916 and SNS-314 classes, respectively, and the 3D contour maps generated from these models were analyzed individually. The contour map analysis for the MK-0457 model revealed the relative importance of steric and electrostatic effects for Aurora B inhibition, whereas, the electronegative groups with hydrogen bond donating capacity showed a great impact on the inhibitory activity for the derivatives of GSK1070916. Additionally, the predictive model of the SNS-314 class revealed the great importance of hydrophobic favorable contour, since hydrophobic favorable substituents added to this region bind to a deep and narrow hydrophobic pocket composed of residues that are hydrophobic in nature and thus enhanced the inhibitory activity. Moreover, based on the docking study, a further comparison of the binding modes was accomplished to identify a set of critical residues that play a key role in stabilizing the drug-target interactions. Overall, the high level of consistency between the 3D contour maps and the topographical features of binding sites led to our identification of several key structural requirements for more potency inhibitors. Taken together, the results will serve as a basis for future drug development of inhibitors against Aurora B kinase for various tumors.

  14. 3D-QSAR Studies on Barbituric Acid Derivatives as Urease Inhibitors and the Effect of Charges on the Quality of a Model.

    Ul-Haq, Zaheer; Ashraf, Sajda; Al-Majid, Abdullah Mohammed; Barakat, Assem

    2016-01-01

    Urease enzyme (EC 3.5.1.5) has been determined as a virulence factor in pathogenic microorganisms that are accountable for the development of different diseases in humans and animals. In continuance of our earlier study on the helicobacter pylori urease inhibition by barbituric acid derivatives, 3D-QSAR (three dimensional quantitative structural activity relationship) advance studies were performed by Comparative Molecular Field Analysis (CoMFA) and Comparative Molecular Similarity Indices Analysis (CoMSIA) methods. Different partial charges were calculated to examine their consequences on the predictive ability of the developed models. The finest developed model for CoMFA and CoMSIA were achieved by using MMFF94 charges. The developed CoMFA model gives significant results with cross-validation (q²) value of 0.597 and correlation coefficients (r²) of 0.897. Moreover, five different fields i.e., steric, electrostatic, and hydrophobic, H-bond acceptor and H-bond donors were used to produce a CoMSIA model, with q² and r² of 0.602 and 0.98, respectively. The generated models were further validated by using an external test set. Both models display good predictive power with r²pred ≥ 0.8. The analysis of obtained CoMFA and CoMSIA contour maps provided detailed insight for the promising modification of the barbituric acid derivatives with an enhanced biological activity. PMID:27144563

  15. 3D-QSAR Studies on Barbituric Acid Derivatives as Urease Inhibitors and the Effect of Charges on the Quality of a Model

    Zaheer Ul-Haq

    2016-04-01

    Full Text Available Urease enzyme (EC 3.5.1.5 has been determined as a virulence factor in pathogenic microorganisms that are accountable for the development of different diseases in humans and animals. In continuance of our earlier study on the helicobacter pylori urease inhibition by barbituric acid derivatives, 3D-QSAR (three dimensional quantitative structural activity relationship advance studies were performed by Comparative Molecular Field Analysis (CoMFA and Comparative Molecular Similarity Indices Analysis (CoMSIA methods. Different partial charges were calculated to examine their consequences on the predictive ability of the developed models. The finest developed model for CoMFA and CoMSIA were achieved by using MMFF94 charges. The developed CoMFA model gives significant results with cross-validation (q2 value of 0.597 and correlation coefficients (r2 of 0.897. Moreover, five different fields i.e., steric, electrostatic, and hydrophobic, H-bond acceptor and H-bond donors were used to produce a CoMSIA model, with q2 and r2 of 0.602 and 0.98, respectively. The generated models were further validated by using an external test set. Both models display good predictive power with r2pred ≥ 0.8. The analysis of obtained CoMFA and CoMSIA contour maps provided detailed insight for the promising modification of the barbituric acid derivatives with an enhanced biological activity.

  16. 3D face modeling, analysis and recognition

    Daoudi, Mohamed; Veltkamp, Remco

    2013-01-01

    3D Face Modeling, Analysis and Recognition presents methodologies for analyzing shapes of facial surfaces, develops computational tools for analyzing 3D face data, and illustrates them using state-of-the-art applications. The methodologies chosen are based on efficient representations, metrics, comparisons, and classifications of features that are especially relevant in the context of 3D measurements of human faces. These frameworks have a long-term utility in face analysis, taking into account the anticipated improvements in data collection, data storage, processing speeds, and application s

  17. Alignment independent 3D-QSAR, quantum calculations and molecular docking of Mer specific tyrosine kinase inhibitors as anticancer drugs

    Fereshteh Shiri

    2016-03-01

    Full Text Available Mer receptor tyrosine kinase is a promising novel cancer therapeutic target in many human cancers, because abnormal activation of Mer has been implicated in survival signaling and chemoresistance. 3D-QSAR analyses based on alignment independent descriptors were performed on a series of 81 Mer specific tyrosine kinase inhibitors. The fractional factorial design (FFD and the enhanced replacement method (ERM were applied and tested as variable selection algorithms for the selection of optimal subsets of molecular descriptors from a much greater pool of such regression variables. The data set was split into 65 molecules as the training set and 16 compounds as the test set. All descriptors were generated by using the GRid INdependent descriptors (GRIND approach. After variable selection, GRIND were correlated with activity values (pIC50 by PLS regression. Of the two applied variable selection methods, ERM had a noticeable improvement on the statistical parameters of PLS model, and yielded a q2 value of 0.77, an rpred2 of 0.94, and a low RMSEP value of 0.25. The GRIND information contents influencing the affinity on Mer specific tyrosine kinase were also confirmed by docking studies. In a quantum calculation study, the energy difference between HOMO and LUMO (gap implied the high interaction of the most active molecule in the active site of the protein. In addition, the molecular electrostatic potential energy at DFT level confirmed results obtained from the molecular docking. The identified key features obtained from the molecular modeling, enabled us to design novel kinase inhibitors.

  18. The Three Dimensional Quantitative Structure Activity Relationships (3D-QSAR and Docking Studies of Curcumin Derivatives as Androgen Receptor Antagonists

    Jing Yang

    2012-05-01

    Full Text Available Androgen receptor antagonists have been proved to be effective anti-prostate cancer agents. 3D-QSAR and Molecular docking methods were performed on curcumin derivatives as androgen receptor antagonists. The bioactive conformation was explored by docking the potent compound 29 into the binding site of AR. The constructed Comparative Molecular Field Analysis (CoMFA and Comparative Similarity Indices Analysis (CoMSIA models produced statistically significant results with the cross-validated correlation coefficients q2 of 0.658 and 0.567, non-cross-validated correlation coefficients r2 of 0.988 and 0.978, and predicted correction coefficients r2pred of 0.715 and 0.793, respectively. These results ensure the CoMFA and CoMSIA models as a tool to guide the design of novel potent AR antagonists. A set of 30 new analogs were proposed by utilizing the results revealed in the present study, and were predicted with potential activities in the developed models.

  19. 3D-QSAR and docking studies of estrogen compounds based on estrogen receptor β

    YANG XuShu; WANG XiaoDong; LUO Si; JI Li; QIN Liang; LI Rong; SUN Cheng; WANG LianSheng

    2009-01-01

    Close attention has been paid to estrogen compounds because these chemicals may pose a serious threat to the health of humans and wildlife.Estrogen receptor (ER) exists as two subtypes,ERo and ERβ.The difference in amino acids sequence of the binding sites of ERo and ERβ might lead to a result that some synthetic estrogens and naturally occurring steroidal ligands have different relative affinities and binding modes for ERa and ERβ.In this investigation,comparative molecular similarity indices analysis (CoMSIA) was performed on 50 estrogen compounds binding ERβ to find out the structural relationship with the activities.We also compared two alignment schemes employed in CoMSIA analysis,namely,atom-fit and receptor-based alignment,with respect to the predictive capability of their respective models for structurally diverse data sets.The model with the significant correlation and the best predictive power (R2=0.961,q2LOO=0.671,Rp2red=0.722) was achieved.The CoMSIA and docking results revealed the structural features related to an activity and provided an insight into molecular mechanisms of estrogenic activities for estrogen compounds.

  20. 3D-QSAR and docking studies of estrogen compounds based on estrogen receptor β

    2009-01-01

    Close attention has been paid to estrogen compounds because these chemicals may pose a serious threat to the health of humans and wildlife. Estrogen receptor (ER) exists as two subtypes, ERα and ERβ. The difference in amino acids sequence of the binding sites of ERα and ERβ might lead to a result that some synthetic estrogens and naturally occurring steroidal ligands have different relative affinities and binding modes for ERα and ERβ. In this investigation, comparative molecular similarity indices analysis (CoMSIA) was performed on 50 estrogen compounds binding ERβ to find out the structural relationship with the activities. We also compared two alignment schemes employed in CoMSIA analy-sis, namely, atom-fit and receptor-based alignment, with respect to the predictive capability of their respective models for structurally diverse data sets. The model with the significant correlation and the best predictive power (R2=0.961, qL 2OO=0.671, RP 2red=0.722) was achieved. The CoMSIA and docking results revealed the structural features related to an activity and provided an insight into molecular mechanisms of estrogenic activities for estrogen compounds.

  1. 3D-QSAR and Cell Wall Permeability of Antitubercular Nitroimidazoles against Mycobacterium tuberculosis

    Pyung Keun Myung

    2013-11-01

    Full Text Available Inhibitory activities of monocyclic nitroimidazoles against Mycobacterium tuberculosis (Mtb deazaflavin-dependent nitroreductase (DDN were modeled by using docking, pharmacophore alignment and comparative molecular similarity indices analysis (CoMSIA methods. A statistically significant model obtained from CoMSIA was established based on a training set using pharmacophore-based molecular alignment. The leave-one out cross-validation correlation coefficients q2 (CoMSIA were 0.681. The CoMSIA model had a good correlation (/CoMSIA = 0.611 between the predicted and experimental activities against excluded test sets. The generated model suggests that electrostatic, hydrophobic and hydrogen bonding interactions all play important roles for interaction between ligands and receptors. The predicted cell wall permeability (logPapp for substrates with high inhibitory activity against Mtb were investigated. The distribution coefficient (logD range was 2.41 < logD < 2.89 for the Mtb cell wall membrane permeability. The larger the polar surface area is, the better the permeability is. A larger radius of gyration (rgry and a small fraction of rotatable bonds (frtob of these molecules leads to higher cell wall penetration ability. The information obtained from the in silico tools might be useful in the design of more potent compounds that are active against Mtb.

  2. Automated analysis of 3D echocardiography

    Stralen, Marijn van

    2009-01-01

    In this thesis we aim at automating the analysis of 3D echocardiography, mainly targeting the functional analysis of the left ventricle. Manual analysis of these data is cumbersome, time-consuming and is associated with inter-observer and inter-institutional variability. Methods for reconstruction o

  3. A combined pharmacophore modeling, 3D-QSAR and molecular docking study of substituted bicyclo-[3.3.0]oct-2-enes as liver receptor homolog-1 (LRH-1) agonists

    Lalit, Manisha; Gangwal, Rahul P.; Dhoke, Gaurao V.; Damre, Mangesh V.; Khandelwal, Kanchan; Sangamwar, Abhay T.

    2013-10-01

    A combined pharmacophore modelling, 3D-QSAR and molecular docking approach was employed to reveal structural and chemical features essential for the development of small molecules as LRH-1 agonists. The best HypoGen pharmacophore hypothesis (Hypo1) consists of one hydrogen-bond donor (HBD), two general hydrophobic (H), one hydrophobic aromatic (HYAr) and one hydrophobic aliphatic (HYA) feature. It has exhibited high correlation coefficient of 0.927, cost difference of 85.178 bit and low RMS value of 1.411. This pharmacophore hypothesis was cross-validated using test set, decoy set and Cat-Scramble methodology. Subsequently, validated pharmacophore hypothesis was used in the screening of small chemical databases. Further, 3D-QSAR models were developed based on the alignment obtained using substructure alignment. The best CoMFA and CoMSIA model has exhibited excellent rncv2 values of 0.991 and 0.987, and rcv2 values of 0.767 and 0.703, respectively. CoMFA predicted rpred2 of 0.87 and CoMSIA predicted rpred2 of 0.78 showed that the predicted values were in good agreement with the experimental values. Molecular docking analysis reveals that π-π interaction with His390 and hydrogen bond interaction with His390/Arg393 is essential for LRH-1 agonistic activity. The results from pharmacophore modelling, 3D-QSAR and molecular docking are complementary to each other and could serve as a powerful tool for the discovery of potent small molecules as LRH-1 agonists.

  4. Drug design for CNS diseases: polypharmacological profiling of compounds using cheminformatic, 3D-QSAR and virtual screening methodologies

    Katarina Nikolic

    2016-06-01

    Full Text Available The diverse cerebral mechanisms implicated in CNS (Central Nervous System diseases together with the heterogeneous and overlapping nature of phenotypes indicated that multitarget strategies may be appropriate for the improved treatment of complex brain diseases. Understanding how the neurotransmitter systems interact is also important in optimizing therapeutic strategies. Pharmacological intervention on one target will often influence another one, such as the well-established serotonin-dopamine interaction or the dopamine-glutamate interaction. It is now accepted that drug action can involve plural targets and that polypharmacological interaction with multiple targets, to address disease in more subtle and effective ways, is a key concept for development of novel drug candidates against complex CNS diseases. A Mmulti-target therapeutic strategy for Alzheimer`s disease resulted in the development of very effective Multi-Target Designed Ligands (MTDL that act on both the cholinergic and monoaminergic systems, and also retard the progression of neurodegeneration by inhibiting amyloid aggregation. Many compounds already in databases have been investigated as ligands for multiple targets in drug-discovery programs. A probabilistic method, the Parzen-Rosenblatt Window approach, was used to build a predictor model using data collected from the ChEMBL database. The model can be used to predict both the primary pharmaceutical target and off-targets of a compound based on its structure. TMining this information data could can provide experimental informationbe very useful for building pharmacophores and developing 3D-QSAR models for activity evaluation at the selected targets. Several multi-target ligands were selected for further study, as compounds with possible additional beneficial pharmacological activities. Based on all these findings, it is assumed concluded that multipotent ligands targeting AChE/MAO-A/MAO-B and also D1-R/D2-R/5-HT2aHT2A-R/H3-R

  5. 3D analysis methods - Study and seminar

    The first part of the report results from a study that was performed as a Nordic co-operation activity with active participation from Studsvik Scandpower and Westinghouse Atom in Sweden, and VTT in Finland. The purpose of the study was to identify and investigate the effects rising from using the 3D transient com-puter codes in BWR safety analysis, and their influence on the transient analysis methodology. One of the main questions involves the critical power ratio (CPR) calculation methodology. The present way, where the CPR calculation is per-formed with a separate hot channel calculation, can be artificially conservative. In the investigated cases, no dramatic minimum CPR effect coming from the 3D calculation is apparent. Some cases show some decrease in the transient change of minimum CPR with the 3D calculation, which confirms the general thinking that the 1D calculation is conservative. On the other hand, the observed effect on neutron flux behaviour is quite large. In a slower transient the 3D effect might be stronger. The second part of the report is a summary of a related seminar that was held on the 3D analysis methods. The seminar was sponsored by the Reactor Safety part (NKS-R) of the Nordic Nuclear Safety Research Programme (NKS). (au)

  6. In Silico Exploration of 1,7-Diazacarbazole Analogs as Checkpoint Kinase 1 Inhibitors by Using 3D QSAR, Molecular Docking Study, and Molecular Dynamics Simulations

    Xiaodong Gao; Liping Han; Yujie Ren

    2016-01-01

    Checkpoint kinase 1 (Chk1) is an important serine/threonine kinase with a self-protection function. The combination of Chk1 inhibitors and anti-cancer drugs can enhance the selectivity of tumor therapy. In this work, a set of 1,7-diazacarbazole analogs were identified as potent Chk1 inhibitors through a series of computer-aided drug design processes, including three-dimensional quantitative structure–activity relationship (3D-QSAR) modeling, molecular docking, and molecular dynamics simulatio...

  7. Volume-Rendering-Based Interactive 3D Measurement for Quantitative Analysis of 3D Medical Images

    Yakang Dai; Jian Zheng; Yuetao Yang; Duojie Kuai; Xiaodong Yang

    2013-01-01

    3D medical images are widely used to assist diagnosis and surgical planning in clinical applications, where quantitative measurement of interesting objects in the image is of great importance. Volume rendering is widely used for qualitative visualization of 3D medical images. In this paper, we introduce a volume-rendering-based interactive 3D measurement framework for quantitative analysis of 3D medical images. In the framework, 3D widgets and volume clipping are integrated with volume render...

  8. 3D-QSAR and molecular docking studies on designing inhibitors of the hepatitis C virus NS5B polymerase

    Li, Wenlian; Si, Hongzong; Li, Yang; Ge, Cuizhu; Song, Fucheng; Ma, Xiuting; Duan, Yunbo; Zhai, Honglin

    2016-08-01

    Viral hepatitis C infection is one of the main causes of the hepatitis after blood transfusion and hepatitis C virus (HCV) infection is a global health threat. The HCV NS5B polymerase, an RNA dependent RNA polymerase (RdRp) and an essential role in the replication of the virus, has no functional equivalent in mammalian cells. So the research and development of efficient NS5B polymerase inhibitors provides a great strategy for antiviral therapy against HCV. A combined three-dimensional quantitative structure-activity relationship (QSAR) modeling was accomplished to profoundly understand the structure-activity correlation of a train of indole-based inhibitors of the HCV NS5B polymerase to against HCV. A comparative molecular similarity indices analysis (COMSIA) model as the foundation of the maximum common substructure alignment was developed. The optimum model exhibited statistically significant results: the cross-validated correlation coefficient q2 was 0.627 and non-cross-validated r2 value was 0.943. In addition, the results of internal validations of bootstrapping and Y-randomization confirmed the rationality and good predictive ability of the model, as well as external validation (the external predictive correlation coefficient rext2 = 0.629). The information obtained from the COMSIA contour maps enables the interpretation of their structure-activity relationship. Furthermore, the molecular docking study of the compounds for 3TYV as the protein target revealed important interactions between active compounds and amino acids, and several new potential inhibitors with higher activity predicted were designed basis on our analyses and supported by the simulation of molecular docking. Meanwhile, the OSIRIS Property Explorer was introduced to help select more satisfactory compounds. The satisfactory results from this study may lay a reliable theoretical base for drug development of hepatitis C virus NS5B polymerase inhibitors.

  9. QSAR Studies on Andrographolide Derivatives as α-Glucosidase Inhibitors

    Shaohui Cai; Jiaolin Bao; Guoji Li; Haibin Luo; Sichao Huang; Jun Xu; Yuqiang Wang

    2010-01-01

    Andrographolide derivatives were shown to inhibit α-glucosidase. To investigate the relationship between activities and structures of andrographolide derivatives, a training set was chosen from 25 andrographolide derivatives by the principal component analysis (PCA) method, and a quantitative structure-activity relationship (QSAR) was established by 2D and 3D QSAR methods. The cross-validation r 2 (0.731) and standard error (0.225) illustrated that the 2D-QSAR model was able to identify the i...

  10. 3D object-oriented image analysis in 3D geophysical modelling

    Fadel, I.; van der Meijde, M.; Kerle, N.;

    2015-01-01

    Non-uniqueness of satellite gravity interpretation has traditionally been reduced by using a priori information from seismic tomography models. This reduction in the non-uniqueness has been based on velocity-density conversion formulas or user interpretation of the 3D subsurface structures (objects......) based on the seismic tomography models and then forward modelling these objects. However, this form of object-based approach has been done without a standardized methodology on how to extract the subsurface structures from the 3D models. In this research, a 3D object-oriented image analysis (3D OOA......) approach was implemented to extract the 3D subsurface structures from geophysical data. The approach was applied on a 3D shear wave seismic tomography model of the central part of the East African Rift System. Subsequently, the extracted 3D objects from the tomography model were reconstructed in the 3D...

  11. QSAR Studies on Andrographolide Derivatives as α-Glucosidase Inhibitors

    Shaohui Cai

    2010-03-01

    Full Text Available Andrographolide derivatives were shown to inhibit α-glucosidase. To investigate the relationship between activities and structures of andrographolide derivatives, a training set was chosen from 25 andrographolide derivatives by the principal component analysis (PCA method, and a quantitative structure-activity relationship (QSAR was established by 2D and 3D QSAR methods. The cross-validation r2 (0.731 and standard error (0.225 illustrated that the 2D-QSAR model was able to identify the important molecular fragments and the cross-validation r2 (0.794 and standard error (0.127 demonstrated that the 3D-QSAR model was capable of exploring the spatial distribution of important fragments. The obtained results suggested that proposed combination of 2D and 3D QSAR models could be useful in predicting the α-glucosidase inhibiting activity of andrographolide derivatives.

  12. Pharmacophore model prediction, 3D-QSAR and molecular docking studies on vinyl sulfones targeting Nrf2-mediated gene transcription intended for anti-Parkinson drug design.

    Athar, Mohd; Lone, Mohsin Yousuf; Khedkar, Vijay M; Jha, Prakash Chandra

    2016-06-01

    Despite intense research efforts towards clinical and molecular causes of Parkinson disease (PD), the etiology of disease still remains unclear. However, recent studies have provided ample evidences that the oxidative stress is the key player that contributes a lot to dopaminergic (DAergic) neurodegeneration in brain. It is due to the discrepancy of antioxidant defence system of which nuclear factor erythroid 2-related factor 2 (Nrf2) signalling is of central contour. In the current study, potent heme oxygenase-1 agonists (Nrf2 signalling regulator), vinyl sulfones, were selected and an optimal pharmacophore model was brought forth which was examined using a decoy set by atom-based 3D-QSAR. The best four-feature model consists of two hydrogen bond acceptors and two aromatic rings, which has the highest correlation coefficient, R(2) = .71 and [Formula: see text] = .73 in QSAR. These ligands were further studied for molecular docking with Nrf2-keap protein to gain insight into the major binding motifs followed by analysing pharmacokinetic properties to evaluate their bioavailability dominance. From this study, it is concluded that vinyl sulfones could be ideal compounds for targeting Nrf2 pathway which in turn halt the PD progression. Hence, these can be considered as potential leads for drug development against the same. PMID:26222438

  13. In Silico Exploration of 1,7-Diazacarbazole Analogs as Checkpoint Kinase 1 Inhibitors by Using 3D QSAR, Molecular Docking Study, and Molecular Dynamics Simulations.

    Gao, Xiaodong; Han, Liping; Ren, Yujie

    2016-01-01

    Checkpoint kinase 1 (Chk1) is an important serine/threonine kinase with a self-protection function. The combination of Chk1 inhibitors and anti-cancer drugs can enhance the selectivity of tumor therapy. In this work, a set of 1,7-diazacarbazole analogs were identified as potent Chk1 inhibitors through a series of computer-aided drug design processes, including three-dimensional quantitative structure-activity relationship (3D-QSAR) modeling, molecular docking, and molecular dynamics simulations. The optimal QSAR models showed significant cross-validated correlation q² values (0.531, 0.726), fitted correlation r² coefficients (higher than 0.90), and standard error of prediction (less than 0.250). These results suggested that the developed models possess good predictive ability. Moreover, molecular docking and molecular dynamics simulations were applied to highlight the important interactions between the ligand and the Chk1 receptor protein. This study shows that hydrogen bonding and electrostatic forces are key interactions that confer bioactivity. PMID:27164065

  14. In Silico Exploration of 1,7-Diazacarbazole Analogs as Checkpoint Kinase 1 Inhibitors by Using 3D QSAR, Molecular Docking Study, and Molecular Dynamics Simulations

    Xiaodong Gao

    2016-05-01

    Full Text Available Checkpoint kinase 1 (Chk1 is an important serine/threonine kinase with a self-protection function. The combination of Chk1 inhibitors and anti-cancer drugs can enhance the selectivity of tumor therapy. In this work, a set of 1,7-diazacarbazole analogs were identified as potent Chk1 inhibitors through a series of computer-aided drug design processes, including three-dimensional quantitative structure–activity relationship (3D-QSAR modeling, molecular docking, and molecular dynamics simulations. The optimal QSAR models showed significant cross-validated correlation q2 values (0.531, 0.726, fitted correlation r2 coefficients (higher than 0.90, and standard error of prediction (less than 0.250. These results suggested that the developed models possess good predictive ability. Moreover, molecular docking and molecular dynamics simulations were applied to highlight the important interactions between the ligand and the Chk1 receptor protein. This study shows that hydrogen bonding and electrostatic forces are key interactions that confer bioactivity.

  15. Investigations and design of pyridine-2-carboxylic acid thiazol-2-ylamide analogs as methionine aminopeptidase inhibitors using 3D-QSAR and molecular docking

    Hauser, Alexander Sebastian

    2014-01-01

    developed using 30 training set molecules. The optimum CoMFA and CoMSIA models obtained for the training set were statistically significant with cross-validated correlation coefficients (q 2) of 0.799 and 0.704 and conventional correlation coefficients (r 2) of 0.989 and 0.954, respectively. These...... inhibitors were docked into MetAP active site. The CoMFA and CoMSIA field contour maps correlate well with the structural characteristics of the binding pocket of MetAP active site. Using the knowledge of structure–activity relationship and receptor–ligand interactions from 3D-QSAR model and the docked...

  16. Docking and 3D-QSAR (quantitative structure activity relationship) studies of flavones, the potent inhibitors of p-glycoprotein targeting the nucleotide binding domain.

    Kothandan, Gugan; Gadhe, Changdev G; Madhavan, Thirumurthy; Choi, Cheol Hee; Cho, Seung Joo

    2011-09-01

    In order to explore the interactions between flavones and P-gp, in silico methodologies such as docking and 3D-QSAR were performed. CoMFA and CoMSIA analyses were done using ligand based and receptor guided alignment schemes. Validation statistics include leave-one-out cross-validated R(2) (q(2)), internal prediction parameter by progressive scrambling (Q(*2)), external prediction with test set. They show that models derived from this study are quite robust. Ligand based CoMFA (q(2) = 0.747, Q(*2) = 0.639, r(pred)(2)=0.802) and CoMSIA model (q(2) = 0.810, Q(*2) = 0.676, r(pred)(2)=0.785) were developed using atom by atom matching. Receptor guided CoMFA (q(2) = 0.712, Q(*2) = 0.497, r(pred)(2) = 0.841) and for CoMSIA (q(2) = 0.805, Q(*2) = 0.589, r(pred)(2) = 0.937) models were developed by docking of highly active flavone into the proposed NBD (nucleotide binding domain) of P-gp. The 3D-QSAR models generated here predicted that hydrophobic and steric parameters are important for activity toward P-gp. Our studies indicate the important amino acid in NBD crucial for binding in accordance with the previous results. This site forms a hydrophobic site. Since flavonoids have potential without toxicity, we propose to inspect this hydrophobic site including Asn1043 and Asp1049 should be considered for future inhibitor design. PMID:21723648

  17. Predictive Comparative QSAR analysis of Sulfathiazole Analogues as Mycobacterium Tuberculosis H37RV Inhabitors

    Doreswamy; Vastrad, Chanabasyya M.

    2014-01-01

    Antitubercular activity of Sulfathiazole Derivitives series were subjected to Quantitative Structure Activity Relationship (QSAR) Analysis with an attempt to derive and understand a correlation between the Biologically Activity as dependent variable and various descriptors as independent variables. QSAR models generated using 28 compounds. Several statistical regression expressions were obtained using Partial Least Squares (PLS) Regression, Multiple Linear Regression (MLR) and Principal Compo...

  18. Multifractal modelling and 3D lacunarity analysis

    This study presents a comparative evaluation of lacunarity of 3D grey level models with different types of inhomogeneity. A new method based on the 'Relative Differential Box Counting' was developed to estimate the lacunarity features of grey level volumes. To validate our method, we generated a set of 3D grey level multifractal models with random, anisotropic and hierarchical properties. Our method gives a lacunarity measurement correlated with the theoretical one and allows a better model classification compared with a classical approach.

  19. 3D face analysis for demographic biometrics

    Tokola, Ryan A [ORNL; Mikkilineni, Aravind K [ORNL; Boehnen, Chris Bensing [ORNL

    2015-01-01

    Despite being increasingly easy to acquire, 3D data is rarely used for face-based biometrics applications beyond identification. Recent work in image-based demographic biometrics has enjoyed much success, but these approaches suffer from the well-known limitations of 2D representations, particularly variations in illumination, texture, and pose, as well as a fundamental inability to describe 3D shape. This paper shows that simple 3D shape features in a face-based coordinate system are capable of representing many biometric attributes without problem-specific models or specialized domain knowledge. The same feature vector achieves impressive results for problems as diverse as age estimation, gender classification, and race classification.

  20. Multifractal modelling and 3D lacunarity analysis

    Hanen, Akkari, E-mail: bettaieb.hanen@topnet.t [Laboratoire de biophysique, TIM, Faculte de Medecine (Tunisia); Imen, Bhouri, E-mail: bhouri_imen@yahoo.f [Unite de recherche ondelettes et multifractals, Faculte des sciences (Tunisia); Asma, Ben Abdallah, E-mail: asma.babdallah@cristal.rnu.t [Laboratoire de biophysique, TIM, Faculte de Medecine (Tunisia); Patrick, Dubois, E-mail: pdubois@chru-lille.f [INSERM, U 703, Lille (France); Hedi, Bedoui Mohamed, E-mail: medhedi.bedoui@fmm.rnu.t [Laboratoire de biophysique, TIM, Faculte de Medecine (Tunisia)

    2009-09-28

    This study presents a comparative evaluation of lacunarity of 3D grey level models with different types of inhomogeneity. A new method based on the 'Relative Differential Box Counting' was developed to estimate the lacunarity features of grey level volumes. To validate our method, we generated a set of 3D grey level multifractal models with random, anisotropic and hierarchical properties. Our method gives a lacunarity measurement correlated with the theoretical one and allows a better model classification compared with a classical approach.

  1. 3D motion analysis via energy minimization

    Wedel, Andreas

    2009-10-16

    This work deals with 3D motion analysis from stereo image sequences for driver assistance systems. It consists of two parts: the estimation of motion from the image data and the segmentation of moving objects in the input images. The content can be summarized with the technical term machine visual kinesthesia, the sensation or perception and cognition of motion. In the first three chapters, the importance of motion information is discussed for driver assistance systems, for machine vision in general, and for the estimation of ego motion. The next two chapters delineate on motion perception, analyzing the apparent movement of pixels in image sequences for both a monocular and binocular camera setup. Then, the obtained motion information is used to segment moving objects in the input video. Thus, one can clearly identify the thread from analyzing the input images to describing the input images by means of stationary and moving objects. Finally, I present possibilities for future applications based on the contents of this thesis. Previous work in each case is presented in the respective chapters. Although the overarching issue of motion estimation from image sequences is related to practice, there is nothing as practical as a good theory (Kurt Lewin). Several problems in computer vision are formulated as intricate energy minimization problems. In this thesis, motion analysis in image sequences is thoroughly investigated, showing that splitting an original complex problem into simplified sub-problems yields improved accuracy, increased robustness, and a clear and accessible approach to state-of-the-art motion estimation techniques. In Chapter 4, optical flow is considered. Optical flow is commonly estimated by minimizing the combined energy, consisting of a data term and a smoothness term. These two parts are decoupled, yielding a novel and iterative approach to optical flow. The derived Refinement Optical Flow framework is a clear and straight-forward approach to

  2. Elastoplastic shell analysis in DYNA3D

    Computer simulation of the elastoplastic behavior of thin shell structures under transient dynamic loads play an important role in many programs at Lawrence Livermore National Laboratory (LLNL) in Livermore, Calif. Often the loads are severe and the structure undergoes plastic (or permanent) deformation. These simulations are effectively performed using DYNA3D, an explicit nonlinear finite element code developed at LLNL for simulating and analyzing the large-deformation dynamic response of solids and structures. It is generally applicable to problems where the loading and response are of short duration and contain significant high-frequency components. Typical problems of this type include the contact of two impacting bodies and the resulting elastoplastic structural behavior. The objective of this investigation was to examine and improve upon the elastoplastic shell modeling capability in DYNA3D. This article summarizes the development of a new four-node quadrilateral finite element shell formulation, the YASE shell, and compares two basic methods (the stress-resultant and the thickness-resultant methods) employed in elastoplastic constitutive algorithms for shell structure modeling

  3. Preprint Big City 3D Visual Analysis

    Lv, Zhihan; Li, Xiaoming; Zhang, Baoyun; Wang, Weixi; Feng, Shengzhong; Hu, Jinxing

    2015-01-01

    This is the preprint version of our paper on EUROGRAPHICS 2015. A big city visual analysis platform based on Web Virtual Reality Geographical Information System (WEBVRGIS) is presented. Extensive model editing functions and spatial analysis functions are available, including terrain analysis, spatial analysis, sunlight analysis, traffic analysis, population analysis and community analysis.

  4. Pharmacophore modeling, 3D-QSAR, and docking study of pyrozolo[1,5-a]pyridine/4,4-dimethylpyrazolone analogues as PDE4 selective inhibitors.

    Tripuraneni, Naga Srinivas; Azam, Mohammed Afzal

    2015-11-01

    Phosphodiesterases 4 enzyme is an attractive target for the design of anti-inflammatory and bronchodilator agents. In the present study pharmacophore and atom based 3D-QSAR studies were carried out for pyrozolo[1,5-a]pyridine/4,4-dimethylpyrazolone analogues. A five point pharmacophore model was developed using 52 molecules having pIC50 values ranging from 9.959 to 3.939. The best predictive pharmacophoric hypothesis AHHRR.3 was characterized by survival score (2.944), cross validated (r(2) = 0.8147), regression coefficient (R(2) = 0.9545) and Fisher ratio (F =173) with 4 component PLS factor. Results explained that one hydrogen bond acceptor, two aromatic rings and two hydrophobic groups are crucial for the PDE4 inhibition. The docking studies of all selected inhibitors in the active site of PDE4 showed crucial hydrogen bond interactions with Asp392, Asn395 Tyr233, and Gln443 residues. The pharmacophoric features R15 and R16 exhibited π-π stacking with His234, Phe414, and Phe446 residues. The generated model was further validated by carrying out the decoy test. The binding free energies of these inhibitors in the catalytic domain of 1XMU were calculated by the molecular mechanics/generalized Born surface area VSGB 2.0 method. The results of molecular dynamics simulation confirmed the extra precision docking-predicted priority for binding sites, the accuracy of docking, and the reliability of active conformations. Pyrozolo[1,5-a]pyridine/4,4-dimethylpyrazolone analogues in this study showed lower binding affinity toward PDE3A in comparison to PDE4. Outcomes of the present study provide insight in designing novel molecules with better PDE4 inhibitory activity. Graphical Abstract Pyrozolo[1,5-a]pyridines/4,4-dimethylpyrazolones. PMID:26499496

  5. 3-D QSAR CoMFA study of nitrogen mustards possessing new chemical entities as possible anticancer agents

    Anand R

    2006-01-01

    Full Text Available This present work is an investigation of anticancer activities of the nitrogen mustards possessing quinazolinone, benzimidazole, benzoxazole, and benzothiazole nuclei by the three-dimensional Quantitative Structure Activity paradigm, Comparative Molecular Field Analysis. A total of 39 compounds were modelled in SYBYL 6.7 (Tripos, USA. The molecules were aligned by root-mean-square fit of atoms and field fit of the steric and electrostatic molecular fields and the resulting databases analysed by partial least squares analysis with cross-validation, leave-one-out and no validation to extract the optimum number of components. The analysis was then repeated with bootstrapping to give the final Quantitative Structure Activity Relationship models. Eight compounds, which were kept separately as test set, were used to test the predictive ability of the Comparative Molecular Field Analysis models. Out of the two models generated, one was found to be useful. The predicted activities of the test set were in good agreement with experimentally determined values.

  6. 3D QSAR Pharmacophore Modeling, in Silico Screening, and Density Functional Theory (DFT Approaches for Identification of Human Chymase Inhibitors

    Keun Woo Lee

    2011-12-01

    Full Text Available Human chymase is a very important target for the treatment of cardiovascular diseases. Using a series of theoretical methods like pharmacophore modeling, database screening, molecular docking and Density Functional Theory (DFT calculations, an investigation for identification of novel chymase inhibitors, and to specify the key factors crucial for the binding and interaction between chymase and inhibitors is performed. A highly correlating (r = 0.942 pharmacophore model (Hypo1 with two hydrogen bond acceptors, and three hydrophobic aromatic features is generated. After successfully validating “Hypo1”, it is further applied in database screening. Hit compounds are subjected to various drug-like filtrations and molecular docking studies. Finally, three structurally diverse compounds with high GOLD fitness scores and interactions with key active site amino acids are identified as potent chymase hits. Moreover, DFT study is performed which confirms very clear trends between electronic properties and inhibitory activity (IC50 data thus successfully validating “Hypo1” by DFT method. Therefore, this research exertion can be helpful in the development of new potent hits for chymase. In addition, the combinational use of docking, orbital energies and molecular electrostatic potential analysis is also demonstrated as a good endeavor to gain an insight into the interaction between chymase and inhibitors.

  7. 3 D Numerical Field Analysis at NAC

    The NAC [1] was established in 1977 as a multi-disciplinary research centre to provide particle beams for basic and applied physics research, for advanced particle radiotherapy and for supplying accelerator-produced radioisotopes for nuclear medicine and research. The finite differences computer programs VEPO 2 and POFEL 3 were developed from the early 1970's over more than one decade for electromagnetic field analysis at NAC[2]. They were successfully used in the design of the sector magnets of our 200 MeV separated-sector cyclotron [3]. In the late 80's NAC implemented the more user-friendly software package Poisson/Super Fish [4], for two-dimensional numerical field analysis

  8. Rethinking 3D-QSAR

    Cramer, Richard D.

    2010-01-01

    The average error of pIC50 prediction reported for 140 structures in make-and-test applications of topomer CoMFA by four discovery organizations is 0.5. This remarkable accuracy can be understood to result from a topomer pose’s goal of generating field differences only at lattice intersections adjacent to intended structural change.

  9. Three-dimensional quantitative structure activity relationship (QSAR of cytotoxic active 3,5-diaryl-4,5-dihydropyrazole analogs: a comparative molecular field analysis (CoMFA revisited study

    Hamad Elgazwy Abdel-Sattar S

    2012-05-01

    Full Text Available Abstract In vitro antitumor evaluation of the synthesized 46 compounds of 3,5-diaryl-4,5-dihydropyrazoles against EAC cell lines and 3D QSAR study using pharmacophore and Comparative Molecular Field Analysis (CoMFA methods were described. CoMFA derived QSAR model shows a good conventional squared correlation coefficient r2 and cross validated correlation coefficient r2cv 0.896 and 0.568 respectively. In this analysis steric and electrostatic field contribute to the QSAR equation by 70% and 30% respectively, suggesting that variation in biological activity of the compounds is dominated by differences in steric (van der Waals interactions. To visualize the CoMFA steric and electrostatic field from partial least squares (PLS analysis, contour maps are plotted as percentage contribution to the QSAR equation and are associated with the differences in biological activity. Background Pyrazole derivatives exhibit a wide range of biological properties including promising antitumor activity. Furthermore, Aldol condensation assisted organic synthesis has delivered rapid routes to N-containing heterocycles, including pyrazoles. Combining these features, the use of chalconisation-assisted processes will provide rapid access to a targeted dihydropyrazoles library bearing a hydrazino 3D QSAR study using pharmacophore and Comparative Molecular Field Analysis (CoMFA methods were described for evaluation of antioxidant properties. Results Chalcones promoted 1 of the 2 steps in a rapid, convergent synthesis of a small library of hydrazinyl pyrazole derivatives, all of which exhibited significant antitumor activity against Ehrlich Ascites Carcinoma (EAC human tumor cell line comparable to that of the natural anticancer doxorubicin, as a reference standard during this study. In order to understand the observed pharmacological properties, quantitative structure-activity relationship (3D QSAR study was initiated. Conclusions Chalcones heating provides a rapid and

  10. 3D surface analysis and classification in neuroimaging segmentation.

    Zagar, Martin; Mlinarić, Hrvoje; Knezović, Josip

    2011-06-01

    This work emphasizes new algorithms for 3D edge and corner detection used in surface extraction and new concept of image segmentation in neuroimaging based on multidimensional shape analysis and classification. We propose using of NifTI standard for describing input data which enables interoperability and enhancement of existing computing tools used widely in neuroimaging research. In methods section we present our newly developed algorithm for 3D edge and corner detection, together with the algorithm for estimating local 3D shape. Surface of estimated shape is analyzed and segmented according to kernel shapes. PMID:21755723

  11. 3D Surface Analysis and Classification in Neuroimaging Segmentation

    Žagar, Martin; Mlinarić, Hrvoje; Knezović, Josip

    2011-01-01

    This work emphasizes new algorithms for 3D edge and corner detection used in surface extraction and new concept of image segmentation in neuroimaging based on multidimensional shape analysis and classification. We propose using of NifTI standard for describing input data which enables interoperability and enhancement of existing computing tools used widely in neuroimaging research. In methods section we present our newly developed algorithm for 3D edge and corner detection, togeth...

  12. QSAR analysis and data extrapolation among mammals in a series of aliphatic alcohols.

    Tichý, M.; Trcka, V; Roth, Z; Krivucová, M

    1985-01-01

    Concepts of QSAR analysis and biological similarity models are combined for use in extrapolation of LD50 values after IP application of a series of aliphatic alcohols (C1-C5) to mouse, hamster, rat, and guinea pig and rabbit. It has been found that although close correlation exists between LD50 values after IP and IV applications for mouse and rat, the QSARs obtained with LD50 after IV application are not suitable for a prediction of LD50 values after IP application for rabbit. Different tran...

  13. Development of a credible 3D-QSAR CoMSIA model and docking studies for a series of triazoles and tetrazoles containing 11β-HSD1 inhibitors.

    Murumkar, P R; Shinde, A C; Sharma, M K; Yamaguchi, H; Miniyar, P B; Yadav, M R

    2016-04-01

    Type 2 diabetes mellitus is described by insulin resistance and high fasting blood glucose. Increased levels of 11β-hydroxysteroid dehydrogenase type 1 (11β-HSD1) enzyme result in insulin resistance and metabolic syndrome. Inhibition of 11β-HSD1 decreases glucose production and increases hepatic insulin sensitivity. Use of selective 11β-HSD1 inhibitors could prove to be an effective strategy for the treatment of the disease. It was decided to identify the essential structural features required by any compound to possess 11β-HSD1 inhibitory activity. A dataset of 139 triazoles and tetrazoles having 11β-HSD1 inhibitory activity was used for the development of a 3D-QSAR model. The best comparative molecular field analysis (CoMFA) model was generated with databased alignment, which was further used for comparative molecular similarity indices analysis (CoMSIA). The optimal CoMSIA model showed [Formula: see text] = 0.809 with five components, [Formula: see text] = 0.931, SEE = 0.323 and F-value = 249.126. The CoMSIA model offered better prediction than the CoMFA model with [Formula: see text] = 0.522 and 0.439, respectively, indicating that the CoMSIA model appeared to be a better one for the prediction of activity for the newly designed 11β-HSD1 inhibitors. The selectivity aspect of 11β-HSD1 over 11β-HSD2 was studied with the help of docking studies. PMID:27094303

  14. Analysis of the of bones through 3D computerized tomography

    This work shows the analysis of the internal structure of the bones samples through 3D micro tomography technique (3D-μTC). The comprehension of the bone structure is particularly important when related to osteoporosis diagnosis because this implies in a deterioration of the trabecular bone architecture, which increases the fragility and the possibility to have bone fractures. Two bone samples (human calcaneous and Wistar rat femur) were used, and the method was a radiographic system in real time with an X Ray microfocus tube. The quantifications parameters are based on stereological principles and they are five: a bone volume fraction, trabecular number, the ratio between surface and bone volume, the trabecular thickness and the trabecular separation. The quantifications were done with a program developed especially for this purpose in Nuclear Instrumentation Laboratory - COPPE/UFRJ. This program uses as input the 3D reconstructions images and generates a table with the quantifications. The results of the human calcaneous quantifications are presented in tables 1 and 2, and the 3D reconstructions are illustrated in Figure 5. The Figure 6 illustrate the 2D reconstructed image and the Figure 7 the 3D visualization respectively of the Wistar femur sample. The obtained results show that the 3D-μTC is a powerful technique that can be used to analyze bone microstructures. (author)

  15. Performance Analysis of a 3D Ionosphere Tomographic Model

    Liu Zhi-zhao; Gao Yang

    2003-01-01

    A 3D high precision ionospheric model is developed based on tomography technique. This tomographic model employs GPS data observed by an operational network of dual-frequency GPS receivers. The methodology of developing a 3D ionospheric tomography model is briefly summarized. However emphasis is put on the analysis and evaluation of the accuracy variation of 3D ionosphere modeling with respect to the change of GPS data cutoff angle.Three typical cutoff angle values (15°, 20° and 25°) are tested. For each testing cutoff angle, the performances of the3D ionospheric model constructed using tomography technique are assessed by calibrating the model predicted ionospheric TEC with the GPS measured TEC and by employing the model predicted TEC to a practical GPS positioning application single point positioning (SPP).Test results indicate the 3D model predicted VTEC has about 0.4 TECU improvement in accuracy when cutoff angle rises from 15° to 20°. However, no apparent improvement is found from 20° to 25°. The model's improvement is also validated by the better SPP accuracy of 3D model than its counterpart-dual frequency model in the 20° and 25° cases.

  16. Computerized diagnostic data analysis and 3-D visualization

    Purpose: To survey methods for 3D data visualization and image analysis which can be used for computer based diagnostics. Material and methods: The methods available are explained in short terms and links to the literature are presented. Methods which allow basic manipulation of 3D data are windowing, rotation and clipping. More complex methods for visualization of 3D data are multiplanar reformation, volume projections (MIP, semi-transparent projections) and surface projections. Methods for image analysis comprise local data transformation (e.g. filtering) and definition and application of complex models (e.g. deformable models). Results: Volume projections produce an impression of the 3D data set without reducing the data amount. This supports the interpretation of the 3D data set and saves time in comparison to any investigation which requires examination of all slice images. More advanced techniques for visualization, e.g. surface projections and hybrid rendering visualize anatomical information to a very detailed extent, but both techniques require the segmentation of the structures of interest. Image analysis methods can be used to extract these structures (e.g. an organ) from the image data. Discussion: At the present time volume projections are robust and fast enough to be used routinely. Surface projections can be used to visualize complex and presegmented anatomical features. (orig.)

  17. SAMA: A Method for 3D Morphological Analysis.

    Paulose, Tessie; Montévil, Maël; Speroni, Lucia; Cerruti, Florent; Sonnenschein, Carlos; Soto, Ana M

    2016-01-01

    Three-dimensional (3D) culture models are critical tools for understanding tissue morphogenesis. A key requirement for their analysis is the ability to reconstruct the tissue into computational models that allow quantitative evaluation of the formed structures. Here, we present Software for Automated Morphological Analysis (SAMA), a method by which epithelial structures grown in 3D cultures can be imaged, reconstructed and analyzed with minimum human intervention. SAMA allows quantitative analysis of key features of epithelial morphogenesis such as ductal elongation, branching and lumen formation that distinguish different hormonal treatments. SAMA is a user-friendly set of customized macros operated via FIJI (http://fiji.sc/Fiji), an open-source image analysis platform in combination with a set of functions in R (http://www.r-project.org/), an open-source program for statistical analysis. SAMA enables a rapid, exhaustive and quantitative 3D analysis of the shape of a population of structures in a 3D image. SAMA is cross-platform, licensed under the GPLv3 and available at http://montevil.theobio.org/content/sama. PMID:27035711

  18. MSLB coupled 3D neutronics-thermalhydraulic analysis of a large PWR using RELAP5-3D

    A RELAP5-3D model of the Westinghouse AP1000 NSSS has been set up and it has been used to analyze the MSLB accident. Main results (both spatial distributions and time trends) have been represented with 3D plots and graphical movies. The method applied allows accounting for the coupled 3D neutronics and thermalyhdraulics effects, suggesting to consider its applicability in Safety Analysis.(author)

  19. Software for 3D diagnostic image reconstruction and analysis

    Recent advances in computer technologies have opened new frontiers in medical diagnostics. Interesting possibilities are the use of three-dimensional (3D) imaging and the combination of images from different modalities. Software prepared in our laboratories devoted to 3D image reconstruction and analysis from computed tomography and ultrasonography is presented. In developing our software it was assumed that it should be applicable in standard medical practice, i.e. it should work effectively with a PC. An additional feature is the possibility of combining 3D images from different modalities. The reconstruction and data processing can be conducted using a standard PC, so low investment costs result in the introduction of advanced and useful diagnostic possibilities. The program was tested on a PC using DICOM data from computed tomography and TIFF files obtained from a 3D ultrasound system. The results of the anthropomorphic phantom and patient data were taken into consideration. A new approach was used to achieve spatial correlation of two independently obtained 3D images. The method relies on the use of four pairs of markers within the regions under consideration. The user selects the markers manually and the computer calculates the transformations necessary for coupling the images. The main software feature is the possibility of 3D image reconstruction from a series of two-dimensional (2D) images. The reconstructed 3D image can be: (1) viewed with the most popular methods of 3D image viewing, (2) filtered and processed to improve image quality, (3) analyzed quantitatively (geometrical measurements), and (4) coupled with another, independently acquired 3D image. The reconstructed and processed 3D image can be stored at every stage of image processing. The overall software performance was good considering the relatively low costs of the hardware used and the huge data sets processed. The program can be freely used and tested (source code and program available at

  20. A spherical harmonics intensity model for 3D segmentation and 3D shape analysis of heterochromatin foci.

    Eck, Simon; Wörz, Stefan; Müller-Ott, Katharina; Hahn, Matthias; Biesdorf, Andreas; Schotta, Gunnar; Rippe, Karsten; Rohr, Karl

    2016-08-01

    The genome is partitioned into regions of euchromatin and heterochromatin. The organization of heterochromatin is important for the regulation of cellular processes such as chromosome segregation and gene silencing, and their misregulation is linked to cancer and other diseases. We present a model-based approach for automatic 3D segmentation and 3D shape analysis of heterochromatin foci from 3D confocal light microscopy images. Our approach employs a novel 3D intensity model based on spherical harmonics, which analytically describes the shape and intensities of the foci. The model parameters are determined by fitting the model to the image intensities using least-squares minimization. To characterize the 3D shape of the foci, we exploit the computed spherical harmonics coefficients and determine a shape descriptor. We applied our approach to 3D synthetic image data as well as real 3D static and real 3D time-lapse microscopy images, and compared the performance with that of previous approaches. It turned out that our approach yields accurate 3D segmentation results and performs better than previous approaches. We also show that our approach can be used for quantifying 3D shape differences of heterochromatin foci. PMID:27037463

  1. Validation of OPERA3D PCMI Analysis Code

    This report will describe introduction of validation of OPERA3D code, and validation results that are directly related with PCMI phenomena. OPERA3D was developed for the PCMI analysis and validated using the in-pile measurement data. Fuel centerline temperature and clad strain calculation results shows close expectations with measurement data. Moreover, 3D FEM fuel model of OPERA3D shows slight hour glassing behavior of fuel pellet in contact case. Further optimization will be conducted for future application of OPERA3D code. Nuclear power plant consists of many complicated systems, and one of the important objects of all the systems is maintaining nuclear fuel integrity. However, it is inevitable to experience PCMI (Pellet Cladding Mechanical Interaction) phenomena at current operating reactors and next generation reactors for advanced safety and economics as well. To evaluate PCMI behavior, many studies are on-going to develop 3-dimensional fuel performance evaluation codes. Moreover, these codes are essential to set the safety limits for the best estimated PCMI phenomena aimed for high burnup fuel

  2. Numerical analysis of 3-D potential flow in centrifugal turbomachines

    Daiguji, H.

    1983-09-01

    A numerical method is developed for analysing a three-dimensional steady incompressible potential flow through an impeller in centrifugal turbomachines. The method is the same as the previous method which was developed for the axial flow turbomachines, except for some treatments in the downstream region. In order to clarify the validity and limitation of the method, a comparison with the existing experimental data and numerical results is made for radial flow compressor impellers. The calculated blade surface pressure distributions almost coincide with the quasi-3-D calculation by Krimerman and Adler (1978), but are different partly from the quasi-3-D calculation using one meridional flow analysis. It is suggested from this comparison that the flow through an impeller with high efficiency near the design point can be predicted by this fully 3-D numerical method.

  3. QSAR analysis on Spodoptera litura antifeedant activities for flavone derivatives

    Duchowicz, Pablo R., E-mail: pabloducho@gmail.com [Instituto de Investigaciones Fisicoquimicas Teoricas y Aplicadas INIFTA (UNLP, CCT La Plata-CONICET), Diag. 113 y 64, Sucursal 4, C.C. 16, 1900 La Plata (Argentina); Goodarzi, Mohammad [Instituto de Investigaciones Fisicoquimicas Teoricas y Aplicadas INIFTA (UNLP, CCT La Plata-CONICET), Diag. 113 y 64, Sucursal 4, C.C. 16, 1900 La Plata (Argentina); Ocsachoque, Marco A. [Centro de Investigacion y Desarrollo en Ciencias Aplicadas ' Dr. J. J. Ronco' (CINDECA), Departamento de Quimica, Facultad de Ciencias Exactas, UNLP-CONICET. Calle 47 No 257, B1900AJK La Plata (Argentina); Romanelli, Gustavo P. [Centro de Investigacion y Desarrollo en Ciencias Aplicadas ' Dr. J. J. Ronco' (CINDECA), Departamento de Quimica, Facultad de Ciencias Exactas, UNLP-CONICET. Calle 47 No 257, B1900AJK La Plata (Argentina); Catedra de Quimica Organica, Facultad de Ciencias Agrarias y Forestales, UNLP. Calles 60 y 119, B1904AAN La Plata (Argentina); Ortiz, Erlinda del V. [Facultad de Tecnologia y Ciencias Aplicadas, Universidad Nacional de Catamarca, Av. Maximio Victoria 55, (4700), Catamarca (Argentina); Autino, Juan C.; Bennardi, Daniel O.; Ruiz, Diego M. [Catedra de Quimica Organica, Facultad de Ciencias Agrarias y Forestales, UNLP. Calles 60 y 119, B1904AAN La Plata (Argentina); Castro, Eduardo A. [Instituto de Investigaciones Fisicoquimicas Teoricas y Aplicadas INIFTA (UNLP, CCT La Plata-CONICET), Diag. 113 y 64, Sucursal 4, C.C. 16, 1900 La Plata (Argentina)

    2009-12-20

    We establish useful models that relate experimentally measured biological activities of compounds to their molecular structure. The pED{sub 50} feeding inhibition on Spodoptera litura species exhibited by aurones, chromones, 3-coumarones and flavones is analyzed in this work through the hypothesis encompassed in the Quantitative Structure-Activity Relationships (QSAR) Theory. This constitutes a first necessary computationally based step during the design of more bio-friendly repellents that could lead to insights for improving the insecticidal activities of the investigated compounds. After optimizing the molecular structure of each furane and pyrane benzoderivative with the semiempirical molecular orbitals method PM3, more than a thousand of constitutional, topological, geometrical and electronic descriptors are calculated and multiparametric linear regression models are established on the antifeedant potencies. The feature selection method employed in this study is the Replacement Method, which has proven to be successful in previous analyzes. We establish the QSAR both for the complete molecular set of compounds and also for each chemical class, so that acceptably describing the variation of the inhibitory activities from the knowledge of their structure and thus achieving useful predictive results. The main interest of developing trustful QSAR models is that these enable the prediction of compounds having no experimentally measured activities for any reason. Therefore, the structure-activity relationships are further employed for investigating the antifeedant activity on previously synthesized 2-,7-substituted benzopyranes, which do not pose any measured values on the biological expression. One of them, 2-({alpha}-naphtyl)-4H-1-benzopyran-4-one, results in a promising structure to be experimentally analyzed as it has predicted pED{sub 50} = 1.162.

  4. QSAR analysis on Spodoptera litura antifeedant activities for flavone derivatives

    We establish useful models that relate experimentally measured biological activities of compounds to their molecular structure. The pED50 feeding inhibition on Spodoptera litura species exhibited by aurones, chromones, 3-coumarones and flavones is analyzed in this work through the hypothesis encompassed in the Quantitative Structure-Activity Relationships (QSAR) Theory. This constitutes a first necessary computationally based step during the design of more bio-friendly repellents that could lead to insights for improving the insecticidal activities of the investigated compounds. After optimizing the molecular structure of each furane and pyrane benzoderivative with the semiempirical molecular orbitals method PM3, more than a thousand of constitutional, topological, geometrical and electronic descriptors are calculated and multiparametric linear regression models are established on the antifeedant potencies. The feature selection method employed in this study is the Replacement Method, which has proven to be successful in previous analyzes. We establish the QSAR both for the complete molecular set of compounds and also for each chemical class, so that acceptably describing the variation of the inhibitory activities from the knowledge of their structure and thus achieving useful predictive results. The main interest of developing trustful QSAR models is that these enable the prediction of compounds having no experimentally measured activities for any reason. Therefore, the structure-activity relationships are further employed for investigating the antifeedant activity on previously synthesized 2-,7-substituted benzopyranes, which do not pose any measured values on the biological expression. One of them, 2-(α-naphtyl)-4H-1-benzopyran-4-one, results in a promising structure to be experimentally analyzed as it has predicted pED50 = 1.162.

  5. 3-D Experimental Fracture Analysis at High Temperature

    John H. Jackson; Albert S. Kobayashi

    2001-09-14

    T*e, which is an elastic-plastic fracture parameter based on incremental theory of plasticity, was determined numerically and experimentally. The T*e integral of a tunneling crack in 2024-T3 aluminum, three point bend specimen was obtained through a hybrid analysis of moire interferometry and 3-D elastic-plastic finite element analysis. The results were verified by the good agreement between the experimentally and numerically determined T*e on the specimen surface.

  6. Skeleton-Sectional Structural Analysis for 3D Printing

    Wen-Peng Xu; Wei Li; Li-Gang Liu

    2016-01-01

    3D printing has become popular and has been widely used in various applications in recent years. More and more home users have motivation to design their own models and then fabricate them using 3D printers. However, the printed objects may have some structural or stress defects as the users may be lack of knowledge on stress analysis on 3D models. In this paper, we present an approach to help users analyze a model’s structural strength while designing its shape. We adopt sectional structural analysis instead of conventional FEM (Finite Element Method) analysis which is computationally expensive. Based on sectional structural analysis, our approach imports skeletons to assist in integrating mesh designing, strength computing and mesh correction well. Skeletons can also guide sections building and load calculation for analysis. For weak regions with high stress over a threshold value in the model from analysis result, our system corrects them by scaling the corresponding bones of skeleton so as to make these regions stiff enough. A number of experiments have demonstrated the applicability and practicability of our approach.

  7. 3D-QSAR studies on CCR2B receptor antagonists: Insight into the structural requirements of (R-3-aminopyrrolidine series of molecules based on CoMFA/CoMSIA models

    Swetha Gade

    2012-01-01

    Full Text Available Objective: Monocyte chemo attractant protein-1 (MCP-1 is a member of the CC-chemokine family and it selectively recruits leukocytes from the circulation to the site of inflammation through binding with the chemotactic cytokine receptor 2B (CCR2B. The recruitment and activation of selected populations of leukocytes is a key feature in a variety of inflammatory conditions. Thus MCP-1 receptor antagonist represents an attractive target for drug discovery. To understand the structural requirements that will lead to enhanced inhibitory potencies, we have carried out 3D-QSAR (quantitative structure-activity relationship studies on (R-3-aminopyrrolidine series of molecules as CCR2B receptor antagonists. Materials and Methods: Comparative molecular field analysis (CoMFA and comparative molecular similarity indices analysis (CoMSIA were performed on a series of (R-3-aminopyrrolidine derivatives as antagonists of CCR2B receptor with Sybyl 6.7v. Results: We have derived statistically significant model from 37 molecules and validated it against an external test set of 13 compounds. The CoMFA model yielded a leave one out r 2 (r 2 loo of 0.847, non-cross-validated r 2 (r 2 ncv of 0.977, F value of 267.930, and bootstrapped r 2 (r 2 bs of 0.988. We have derived the standard error of prediction value of 0.367, standard error of estimate 0.141, and a reliable external predictivity, with a predictive r 2 (r 2 pred of 0.673. While the CoMSIA model yielded an r 2 loo of 0.719, r 2 ncv of 0.964,F value of 135.666, r 2 bs of 0.975, standard error of prediction of 0.512, standard error of estimate of 0.180, and an external predictivity with an r 2 pred of 0.611. These validation tests not only revealed the robustness of the models but also demonstrated that for our models r 2 pred, based on the mean activity of test set compounds can accurately estimate external predictivity. Conclusion: The QSAR model gave satisfactory statistical results in terms of q 2 and r 2

  8. A 3D image analysis tool for SPECT imaging

    Kontos, Despina; Wang, Qiang; Megalooikonomou, Vasileios; Maurer, Alan H.; Knight, Linda C.; Kantor, Steve; Fisher, Robert S.; Simonian, Hrair P.; Parkman, Henry P.

    2005-04-01

    We have developed semi-automated and fully-automated tools for the analysis of 3D single-photon emission computed tomography (SPECT) images. The focus is on the efficient boundary delineation of complex 3D structures that enables accurate measurement of their structural and physiologic properties. We employ intensity based thresholding algorithms for interactive and semi-automated analysis. We also explore fuzzy-connectedness concepts for fully automating the segmentation process. We apply the proposed tools to SPECT image data capturing variation of gastric accommodation and emptying. These image analysis tools were developed within the framework of a noninvasive scintigraphic test to measure simultaneously both gastric emptying and gastric volume after ingestion of a solid or a liquid meal. The clinical focus of the particular analysis was to probe associations between gastric accommodation/emptying and functional dyspepsia. Employing the proposed tools, we outline effectively the complex three dimensional gastric boundaries shown in the 3D SPECT images. We also perform accurate volume calculations in order to quantitatively assess the gastric mass variation. This analysis was performed both with the semi-automated and fully-automated tools. The results were validated against manual segmentation performed by a human expert. We believe that the development of an automated segmentation tool for SPECT imaging of the gastric volume variability will allow for other new applications of SPECT imaging where there is a need to evaluate complex organ function or tumor masses.

  9. A software tool for 3D dose verification and analysis

    Sa'd, M. Al; Graham, J.; Liney, G. P.

    2013-06-01

    The main recent developments in radiotherapy have focused on improved treatment techniques in order to generate further significant improvements in patient prognosis. There is now an internationally recognised need to improve 3D verification of highly conformal radiotherapy treatments. This is because of the very high dose gradients used in modern treatment techniques, which can result in a small error in the spatial dose distribution leading to a serious complication. In order to gain the full benefits of using 3D dosimetric technologies (such as gel dosimetry), it is vital to use 3D evaluation methods and algorithms. We present in this paper a software solution that provides a comprehensive 3D dose evaluation and analysis. The software is applied to gel dosimetry, which is based on magnetic resonance imaging (MRI) as a read-out method. The software can also be used to compare any two dose distributions, such as two distributions planned using different methods of treatment planning systems, or different dose calculation algorithms.

  10. A software tool for 3D dose verification and analysis

    The main recent developments in radiotherapy have focused on improved treatment techniques in order to generate further significant improvements in patient prognosis. There is now an internationally recognised need to improve 3D verification of highly conformal radiotherapy treatments. This is because of the very high dose gradients used in modern treatment techniques, which can result in a small error in the spatial dose distribution leading to a serious complication. In order to gain the full benefits of using 3D dosimetric technologies (such as gel dosimetry), it is vital to use 3D evaluation methods and algorithms. We present in this paper a software solution that provides a comprehensive 3D dose evaluation and analysis. The software is applied to gel dosimetry, which is based on magnetic resonance imaging (MRI) as a read-out method. The software can also be used to compare any two dose distributions, such as two distributions planned using different methods of treatment planning systems, or different dose calculation algorithms.

  11. On applicability of the 3D nodal code DYN3D for the analysis of SFR cores

    DYN3D is an advanced multi-group nodal diffusion code originally developed for the 3D steady-state and transient analysis of the Light Water Reactor (LWR) systems with square and hexagonal fuel assembly geometries. The main objective of this work is to demonstrate the feasibility of using DYN3D for the modeling of Sodium cooled Fast Reactors (SFRs). In this study a prototypic European Sodium Fast Reactor (ESFR) core is simulated by DYN3D using homogenized multi-group cross sections produced with Monte Carlo (MC) reactor physics code Serpent. The results of the full core DYN3D calculations are in a very good agreement with the reference full core Serpent MC solution. (author)

  12. 3D Guided Wave Motion Analysis on Laminated Composites

    Tian, Zhenhua; Leckey, Cara; Yu, Lingyu

    2013-01-01

    Ultrasonic guided waves have proved useful for structural health monitoring (SHM) and nondestructive evaluation (NDE) due to their ability to propagate long distances with less energy loss compared to bulk waves and due to their sensitivity to small defects in the structure. Analysis of actively transmitted ultrasonic signals has long been used to detect and assess damage. However, there remain many challenging tasks for guided wave based SHM due to the complexity involved with propagating guided waves, especially in the case of composite materials. The multimodal nature of the ultrasonic guided waves complicates the related damage analysis. This paper presents results from parallel 3D elastodynamic finite integration technique (EFIT) simulations used to acquire 3D wave motion in the subject laminated carbon fiber reinforced polymer composites. The acquired 3D wave motion is then analyzed by frequency-wavenumber analysis to study the wave propagation and interaction in the composite laminate. The frequency-wavenumber analysis enables the study of individual modes and visualization of mode conversion. Delamination damage has been incorporated into the EFIT model to generate "damaged" data. The potential for damage detection in laminated composites is discussed in the end.

  13. Advanced computational tools for 3-D seismic analysis

    Barhen, J.; Glover, C.W.; Protopopescu, V.A. [Oak Ridge National Lab., TN (United States)] [and others

    1996-06-01

    The global objective of this effort is to develop advanced computational tools for 3-D seismic analysis, and test the products using a model dataset developed under the joint aegis of the United States` Society of Exploration Geophysicists (SEG) and the European Association of Exploration Geophysicists (EAEG). The goal is to enhance the value to the oil industry of the SEG/EAEG modeling project, carried out with US Department of Energy (DOE) funding in FY` 93-95. The primary objective of the ORNL Center for Engineering Systems Advanced Research (CESAR) is to spearhead the computational innovations techniques that would enable a revolutionary advance in 3-D seismic analysis. The CESAR effort is carried out in collaboration with world-class domain experts from leading universities, and in close coordination with other national laboratories and oil industry partners.

  14. Quantitative nanoscale analysis in 3D using electron tomography

    State-of-the-art electron tomography has been established as a powerful tool to image complex structures with nanometer resolution in 3D. Especially STEM tomography is used extensively in materials science in such diverse areas as catalysis, semiconductor materials, and polymer composites mainly providing qualitative information on morphology, shape and distribution of materials. However, for an increasing number of studies quantitative information, e.g. surface area, fractal dimensions, particle distribution or porosity are needed. A quantitative analysis is typically performed after segmenting the tomographic data, which is one of the main sources of error for the quantification. In addition to noise, systematic errors due to the missing wedge and due to artifacts from the reconstruction algorithm itself are responsible for these segmentation errors and improved algorithms are needed. This presentation will provide an overview of the possibilities and limitations of quantitative nanoscale analysis by electron tomography. Using catalysts and nano composites as applications examples, intensities and intensity variations observed for the 3D volume reconstructed by WBP and SIRT will be quantitatively compared to alternative reconstruction algorithms; implications for quantification of electron (or X-ray) tomographic data will be discussed and illustrated for quantification of particle size distributions, particle correlations, surface area, and fractal dimensions in 3D.

  15. 3D Landslides Susceptibility Analysis in Romanian Subcarpathians

    Sandric, Ionuc; Ilinca, Viorel; Chitu, Zenaida; Jurchescu, Marta

    2015-04-01

    Most of the present day studies make use the 2.5D raster data formats for the landslide susceptibility analysis at regional scales. This data format has some disadvantages when geological and lithological settings are spatial discretized, hence these disadvantages propagate in the landslides susceptibility analysis and especially where only surface lithology is used. The main disadvantage when using 3D data models for the assessment of landslide susceptibility at regional scales is represented by the quality of the geological and lithological information that is available for a depth of no more than 100m. In order to mitigate this, a sufficient number of boreholes is required and sometimes is not available. In order to overcome the lack of borehole data, our approach was to make use of the present-day geological maps at scales ranging from 1:25,000 to 1:50,000 and to generate a geological 3D model up to a depth of 100m. The geological model was generated based on expert knowledge interpretations and geological cross sections provided on these geological maps. Using the 3D geological model a more complex 3D model was generated for the landslide susceptibility analysis that also contains information from other predictor factors like slope gradient, land-cover and land-use. For the landslide susceptibility analysis instead of using map algebra equations on classic pixel based data sets, the equations were adapted for 3D data models and map algebra equations on voxels. The test sites are located in the areas of Romanian Subcarpathians. The Romanian Subcarpathians are located to the exterior of the Carpathians. They consist of a large variety of rocks, flysch-type deposits in the inner part and molasse deposits in the outer part, ranging from a Cretacic-Paleogene to a Quaternary age. While some parts of the Subcarpathians have a basic geology, with a monoclinal geological structure, other parts like the Curvature Subcarpathians, present acomplex folded and faulted

  16. 3D Analysis of Nanocrystalline FeAl

    Full text: Nanocrystalline materials and nanostructures receive an increasing interest in materials science, since they often show unexpected physical properties. Their properties are closely linked to the size and 3D morphology of the nanostructures. Conventional transmission electron microscopy (TEM) analysis tools provide information on a projection of the nanostructures. Advanced analysis methods based on TEM can be used to determine the 3D morphology. In the present work a method based on TEM diffraction is developed that can be used to determine the size and morphology of the coherently scattering domains in 3D. In order to make bulk nanocrystalline materials several approaches have been used; one of them is based on their production by severe plastic deformation. Nanocrystalline intermetallic FeAl was made by high pressure torsion deformation of B2 ordered Fe-45at.%Al. The obtained bulk samples allow cutting out samples for TEM that can be directly linked to the shear direction and shear plane. Both, planar and cross sections of nanocrystalline FeAl were investigated to study the shape and morphology of the nanocrystals. In addition to the TEM images, electron diffraction patterns were recorded with a large range of different tilting angles. The morphology of the nanograins was analysed from the electron diffraction patterns by applying different tilting angles of the incident beam. A modified Williamson Hall plot was used to determine the coherently scattering domain size for each tilt angle. The analysis of the diffraction patterns was carried out with the software PASAD tools (www.univie.ac.at/pasad). From the results it was possible to determine quantitatively the size and morphology of the nanograins in 3D. The results show that the nanograins have a ellipsoidal shape and are elongated in shear direction, which is in good agreement with TEM images. In addition to the possibility to analyse nanostructures in 3D, TEM provides conveniently the possibility

  17. Error Analysis Of 3d Polygonal Model:A Survey

    Devendra Singh Rajput

    2012-05-01

    Full Text Available Various applications of computer graphics, (like animation, scientific visualization, and virtual reality involve the manipulation of geometric models. They are generally represented by triangular meshes due to its wide acceptance to process on rendering systems. The need of realism and high visual fidelity and the latest advances on scanning devices has increased complexity and size of triangular meshes. The original 3D model gets modified because of activities like approximation, transmission, processing and storage etc. Mostly the modification occurs due to simplification approaches which primarily use geometric distance metric as their simplification criteria. But it is hard to measure a small distance error accurately whereas other geometric or appearance error (like high curvature, thin region, color, texture, normals and volumetric has greater importance. Hence it is essential to understand the applicability of various parameters to evaluate the quality of 3D model. This paper briefly surveys the various errors analysis techniques, error metrics and tools to assess the quality of 3D mesh models.

  18. Analysis of the of bones through 3D computerized tomography; Analise de estrutura ossea atraves de microtomografia computadorizada 3D

    Lima, I.; Lopes, R.T. [Coordenacao dos Programas de Pos-Graduacao de Engenharia (COPPE), Rio de Janeiro, RJ (Brazil). Lab. de Instrumentacao Nuclear; Oliveira, L.F. [Universidade do Estado do Rio de Janeiro (UERJ), RJ (Brazil). Inst. de Fisica. Dept. de Fisica Aplicada e Termodinamica; Alves, J.M. [Universidade de Sao Paulo (USP), Sao Carlos, SP (Brazil). Escola de Engenharia

    2009-03-15

    This work shows the analysis of the internal structure of the bones samples through 3D micro tomography technique (3D-{mu}TC). The comprehension of the bone structure is particularly important when related to osteoporosis diagnosis because this implies in a deterioration of the trabecular bone architecture, which increases the fragility and the possibility to have bone fractures. Two bone samples (human calcaneous and Wistar rat femur) were used, and the method was a radiographic system in real time with an X Ray microfocus tube. The quantifications parameters are based on stereological principles and they are five: a bone volume fraction, trabecular number, the ratio between surface and bone volume, the trabecular thickness and the trabecular separation. The quantifications were done with a program developed especially for this purpose in Nuclear Instrumentation Laboratory - COPPE/UFRJ. This program uses as input the 3D reconstructions images and generates a table with the quantifications. The results of the human calcaneous quantifications are presented in tables 1 and 2, and the 3D reconstructions are illustrated in Figure 5. The Figure 6 illustrate the 2D reconstructed image and the Figure 7 the 3D visualization respectively of the Wistar femur sample. The obtained results show that the 3D-{mu}TC is a powerful technique that can be used to analyze bone microstructures. (author)

  19. 3D-QSAR, molecular dynamics simulations and molecular docking studies of benzoxazepine moiety as mTOR inhibitor for the treatment of lung cancer.

    Chaube, Udit; Chhatbar, Dhara; Bhatt, Hardik

    2016-02-01

    According to WHO statistics, lung cancer is one of the leading causes of death among all other types of cancer. Many genes get mutated in lung cancer but involvement of EGFR and KRAS are more common. Unavailability of drugs or resistance to the available drugs is the major problem in the treatment of lung cancer. In the present research, mTOR was selected as an alternative target for the treatment of lung cancer which involves PI3K/AKT/mTOR pathway. 28 synthetic mTOR inhibitors were selected from the literature. Ligand based approach (CoMFA and CoMSIA) and structure based approach (molecular dynamics simulations assisted molecular docking study) were applied for the identification of important features of benzoxazepine moiety, responsible for mTOR inhibition. Three different alignments were tried to obtain best QSAR model, of which, distil was found to be the best method, as it gave good statistical results. In CoMFA, Leave One Out (LOO) cross validated coefficients (q(2)), conventional coefficient (r(2)) and predicted correlation coefficient (r(2)pred) values were found to be 0.615, 0.990 and 0.930, respectively. Similarly in CoMSIA, q(2), r(2)ncv and r(2)pred values were found to be 0.748, 0.986 and 0.933, respectively. Molecular dynamics and simulations study revealed that B-chain of mTOR protein was stable at and above 500 FS with respect to temperature (at and above 298 K), Potential energy (at and above 7669.72 kJ/mol) and kinetic energy (at and above 4009.77 kJ/mol). Molecular docking study was performed on simulated protein of mTOR which helped to correlate interactions of amino acids surrounded to the ligand with contour maps generated by QSAR method. Important features of benzoxazepine were identified by contour maps and molecular docking study which would be useful to design novel molecules as mTOR inhibitors for the treatment of lung cancer. PMID:26764189

  20. Evaluation on joint toxicity of chlorinated anilines and cadmium to Photobacterium phosphoreum and QSAR analysis

    Jin, Hao, E-mail: realking163@163.com [School of Life and Chemistry, Jiangsu Second Normal University, Nanjing, Jiangsu 210013 (China); Wang, Chao; Shi, Jiaqi [State Key Laboratory of Pollution Control and Resources Reuse, School of Environment, Nanjing University, Nanjing, Jiangsu 210023 (China); Chen, Lei [School of Life and Chemistry, Jiangsu Second Normal University, Nanjing, Jiangsu 210013 (China)

    2014-08-30

    Highlights: • Cd has different effects on joint toxicity when in different concentrations. • The toxicity of most binary mixtures decreases when Cd concentration rises. • Different QSAR models are developed to predict the joint toxicity. • Descriptors in QSARs can help to elucidate the joint toxicity mechanism. • Van der Waals’ force or complexation may reduce the toxicity of mixtures. - Abstract: The individual IC{sub 50} (the concentrations causing a 50% inhibition of bioluminescence after 15 min exposure) of cadmium ion (Cd) and nine chlorinated anilines to Photobacterium phosphoreum (P. phosphoreum) were determined. In order to evaluate the combined effects of the nine chlorinated anilines and Cd, the toxicities of chlorinated anilines combined with different concentrations of Cd were determined, respectively. The results showed that the number of chlorinated anilines manifesting synergy with Cd decreased with the increasing Cd concentration, and the number manifesting antagonism decreased firstly and then increased. The joint toxicity of mixtures at low Cd concentration was weaker than that of most binary mixtures when combined with Cd at medium and high concentrations as indicated by TU{sub Total}. QSAR analysis showed that the single toxicity of chlorinated anilines was related to the energy of the lowest unoccupied molecular orbital (E{sub LUMO}). When combined with different concentrations of Cd, the toxicity was related to the energy difference (E{sub HOMO} − E{sub LUMO}) with different coefficients. Van der Waals’ force or the complexation between chlorinated anilines and Cd had an impact on the toxicity of combined systems, which could account for QSAR models with different physico-chemical descriptors.

  1. 3D Massive MIMO Systems: Modeling and Performance Analysis

    Nadeem, Qurrat-Ul-Ain

    2015-07-30

    Multiple-input-multiple-output (MIMO) systems of current LTE releases are capable of adaptation in the azimuth only. Recently, the trend is to enhance system performance by exploiting the channel’s degrees of freedom in the elevation, which necessitates the characterization of 3D channels. We present an information-theoretic channel model for MIMO systems that supports the elevation dimension. The model is based on the principle of maximum entropy, which enables us to determine the distribution of the channel matrix consistent with the prior information on the angles. Based on this model, we provide analytical expression for the cumulative density function (CDF) of the mutual information (MI) for systems with a single receive and finite number of transmit antennas in the general signalto- interference-plus-noise-ratio (SINR) regime. The result is extended to systems with finite receive antennas in the low SINR regime. A Gaussian approximation to the asymptotic behavior of MI distribution is derived for the large number of transmit antennas and paths regime. We corroborate our analysis with simulations that study the performance gains realizable through meticulous selection of the transmit antenna downtilt angles, confirming the potential of elevation beamforming to enhance system performance. The results are directly applicable to the analysis of 5G 3D-Massive MIMO-systems.

  2. TECHNICAL ANALYSIS OF REMOTE 3D VISUALIZATION ON MOBILE DEVICES

    Ms. U. S. Junghare; Dr. V. M. Thakare; R. V. Dharaskar; S. S. Sherekar

    2012-01-01

    Considering the limitations of mobile devices like low bandwidth, less computation power, minimumstorage capacity etc it is not possible to store whole data for 3D visualization on mobile devices.Therefore to minimize the load of mobile devices there is use of server in case of remote 3D visualizationon mobile devices (clients). For 3D visualization on mobile devices various techniques are used at serverside as well as at mobile side for different purpose. Some techniques directly provides 3D...

  3. Design, biological evaluation and 3D QSAR studies of novel dioxin-containing pyrazoline derivatives with thiourea skeleton as selective HER-2 inhibitors

    Yang, Bing; Yang, Yu-Shun; Yang, Na; Li, Guigen; Zhu, Hai-Liang

    2016-06-01

    A series of novel dioxin-containing pyrazoline derivatives with thiourea skeleton have been designed, synthesized and evaluated for their EGFR/HER-2 inhibitory and anti-proliferation activities. A majority of them displayed selective HER-2 inhibitory activity against EGFR inhibitory activity. Compound C20 displayed the most potent activity against HER-2 and MDA-MB-453 human breast cancer cell line (IC50 = 0.03 μM and GI50 = 0.15 μM), being slightly more potent than the positive control Erlotinib (IC50 = 0.16 μM and GI50 = 1.56 μM) and comparable with Lapatinib (IC50 = 0.01 μM and GI50 = 0.03 μM). It is a more exciting result that C20 was over 900 times more potent against HER-2 than against EGFR while this value was 0.19 for Erlotinib and 1.00 for Lapatinib, indicating high selectivity. The results of docking simulation indicate that the dioxin moiety occupied the exit of the active pocket and pushed the carbothioamide deep into the active site. QSAR models have been built with activity data and binding conformations to begin our work in this paper as well as to provide a reliable tool for reasonable design of EGFR/HER-2 inhibitors in future.

  4. Uncertainty Analysis of RELAP5-3D

    Alexandra E Gertman; Dr. George L Mesina

    2012-07-01

    As world-wide energy consumption continues to increase, so does the demand for the use of alternative energy sources, such as Nuclear Energy. Nuclear Power Plants currently supply over 370 gigawatts of electricity, and more than 60 new nuclear reactors have been commissioned by 15 different countries. The primary concern for Nuclear Power Plant operation and lisencing has been safety. The safety of the operation of Nuclear Power Plants is no simple matter- it involves the training of operators, design of the reactor, as well as equipment and design upgrades throughout the lifetime of the reactor, etc. To safely design, operate, and understand nuclear power plants, industry and government alike have relied upon the use of best-estimate simulation codes, which allow for an accurate model of any given plant to be created with well-defined margins of safety. The most widely used of these best-estimate simulation codes in the Nuclear Power industry is RELAP5-3D. Our project focused on improving the modeling capabilities of RELAP5-3D by developing uncertainty estimates for its calculations. This work involved analyzing high, medium, and low ranked phenomena from an INL PIRT on a small break Loss-Of-Coolant Accident as wall as an analysis of a large break Loss-Of- Coolant Accident. Statistical analyses were performed using correlation coefficients. To perform the studies, computer programs were written that modify a template RELAP5 input deck to produce one deck for each combination of key input parameters. Python scripting enabled the running of the generated input files with RELAP5-3D on INL’s massively parallel cluster system. Data from the studies was collected and analyzed with SAS. A summary of the results of our studies are presented.

  5. DESIGN AND ANALYSIS OF 3D PRINTING PEN

    Mr. Nayan Jyoti Gogoi *, Prof. T. Jeyapoovan

    2016-01-01

    In present time 3d models and prototypes helping lot of engineers and in many technical areas mainly in design field to design a real model as quickly as possible with the help of 3d printing technology. The demand for 3d printing applications are increasing day by day and it is reaching to a height of end no of applications. In this project I am going to discuss how we can make an affordable and user friendly 3d printing device which can be used as a 3d printing pen as well as a device which...

  6. Comparative visual analysis of 3D urban wind simulations

    Röber, Niklas; Salim, Mohamed; Grawe, David; Leitl, Bernd; Böttinger, Michael; Schlünzen, Heinke

    2016-04-01

    Climate simulations are conducted in large quantity for a variety of different applications. Many of these simulations focus on global developments and study the Earth's climate system using a coupled atmosphere ocean model. Other simulations are performed on much smaller regional scales, to study very small fine grained climatic effects. These microscale climate simulations pose similar, yet also different, challenges for the visualization and the analysis of the simulation data. Modern interactive visualization and data analysis techniques are very powerful tools to assist the researcher in answering and communicating complex research questions. This presentation discusses comparative visualization for several different wind simulations, which were created using the microscale climate model MITRAS. The simulations differ in wind direction and speed, but are all centered on the same simulation domain: An area of Hamburg-Wilhelmsburg that hosted the IGA/IBA exhibition in 2013. The experiments contain a scenario case to analyze the effects of single buildings, as well as examine the impact of the Coriolis force within the simulation. The scenario case is additionally compared with real measurements from a wind tunnel experiment to ascertain the accuracy of the simulation and the model itself. We also compare different approaches for tree modeling and evaluate the stability of the model. In this presentation, we describe not only our workflow to efficiently and effectively visualize microscale climate simulation data using common 3D visualization and data analysis techniques, but also discuss how to compare variations of a simulation and how to highlight the subtle differences in between them. For the visualizations we use a range of different 3D tools that feature techniques for statistical data analysis, data selection, as well as linking and brushing.

  7. Performance Analysis of 3-D Monolithic Integrated Circuits

    Bobba, Shashikanth; Chakraborthy, Ashutosh; Olivier THOMAS (LEREPS-GRES); Batude, Perrine; Pavlidis, Vasileios; Micheli, Giovanni De

    2010-01-01

    3-D monolithic integration (3DMI), also termed as sequential integration, is a potential technology for future gigascale circuits. Since the device layers are processed in sequential order, the size of the vertical contacts is similar to traditional contacts unlike in the case of parallel 3-D integration with through silicon vias (TSVs). Given the advantage of such small contacts, 3DMI supports stacking active layers such that fine-grain integration of 3-D circuits can be implemented. This pa...

  8. Binary pattern analysis for 3D facial action unit detection

    Sandbach, Georgia; Zafeiriou, Stefanos; Pantic, Maja

    2012-01-01

    In this paper we propose new binary pattern features for use in the problem of 3D facial action unit (AU) detection. Two representations of 3D facial geometries are employed, the depth map and the Azimuthal Projection Distance Image (APDI). To these the traditional Local Binary Pattern is applied, a

  9. 3D Modeling and Stress Analysis of Flare Piping

    Navath Ravikiran

    2014-10-01

    Full Text Available For transportation of fluid, steam or air piping system is widely used. For installing the piping system pipes, flanges, piping supports, valves, piping fittings etc. are used, which are piping elements. They are manufactured as per Codes and standards. Equipment and piping layout design as per process requirement and available space. Above layout made out by the help of General arrangement drawing, plant layout and P & ID. Then after flexibility providing to piping system, for compensate the different loads by the engineer. Stresses in pipe or piping systems are generated due to loads like expansion & contraction due to thermal load, seismic load, wind load, sustained load, reaction load etc. the stress analysis is done by help of software like CAESAR II. In this paper, a Flare pipe line is designed and 3D modeling is prepared in PDMS software. Attention is focused for stress analysis by Caesar-II software. So that various stress values, forces and deflections are analyzed at each node to make the design at safe operating conditions

  10. 3D-QSAR (CoMFA, CoMFA-RG, CoMSIA) and molecular docking study of thienopyrimidine and thienopyridine derivatives to explore structural requirements for aurora-B kinase inhibition.

    Borisa, Ankit; Bhatt, Hardik

    2015-11-15

    Aurora-B kinase plays a crucial role in cell cycle events and is identified as an important factor in regulation of spindle check point assembly. Thus, it can be proved as an important target in the field of oncology. 3D-QSAR model was generated using 54 molecules reported in literature containing thienopyrimidine and thienopyridine as scaffolds. All molecules were aligned using Distill function in Sybyl X1.2. This generated best model of CoMFA-RG (Region focusing) and CoMSIA were statistically significant with correlation coefficient r(2)ncv of 0.97, for both & Leave one out coefficient (LOO) q(2) of 0.70 and 0.72, respectively. Best CoMSIA model was built up using various combination of descriptors and proved statistical significant among all models. Best CoMFA-RG and CoMSIA models were validated by 12 test set molecules giving satisfactory prediction (r(2)pred) values of 0.86 and 0.88, respectively. External test set validation was performed using 20 molecules and satisfactory prediction of their biological activity was found. Active compounds were docked on protein (PDB ID: 4C2V) by GOLD module and revealed important interactions with amino acids at ATP-binding region. These data explored insight requirements for Aurora-B inhibition which might be fruitful for understanding mechanisms with kinase ligand interactions. PMID:26343315

  11. 3-D Printed Ultem 9085 Testing and Analysis

    Aguilar, Daniel; Christensen, Sean; Fox, Emmet J.

    2015-01-01

    The purpose of this document is to analyze the mechanical properties of 3-D printed Ultem 9085. This document will focus on the capabilities, limitations, and complexities of 3D printing in general, and explain the methods by which this material is tested. Because 3-D printing is a relatively new process that offers an innovative means to produce hardware, it is important that the aerospace community understands its current advantages and limitations, so that future endeavors involving 3-D printing may be completely safe. This document encompasses three main sections: a Slosh damage assessment, a destructive test of 3-D printed Ultem 9085 samples, and a test to verify simulation for the 3-D printed SDP (SPHERES Docking Port). Described below, 'Slosh' and 'SDP' refer to two experiments that are built using Ultem 9085 for use with the SPHERES (Synchronized Position Hold, Engage, Reorient, Experimental Satellites) program onboard the International Space Station (ISS) [16]. The SPHERES Facility is managed out of the National Aeronautics and Space Administration (NASA) Ames Research Center in California.

  12. Analysis of NEACRP 3D BWR core transient benchmark

    NEACRP BWR cold water injection benchmark is analyzed by two codes: TRAC-BF1/SKETCH-N code system by JAERI, Japan and TRAB-3D code by VTT Energy, Finland. Basic features of the codes are described. Neutronics modules of the codes apply nodal methods; separate calculations are performed to compare their accuracy. Thermal-hydraulics modules are significantly different: TRAC-BF1 uses two-phase two-fluid model, while TRAB-3D applies drift-flux model with four separated equations. A representative set of the global and local reactor parameters is given for both the steady-state and transient conditions. TRAB-3D calculations have been performed with two slip correlations: EPRI and the simple Zuber-Findley correlation. A comparison of the two TRAB results shows the importance of the slip model on some computed reactor parameters. The results of the TRAC-BF1/SKETCH-N and TRAB-3D codes are in a close agreement, especially when the advanced EPRI correlation is used in the TRAB-3D code. The presented data can be useful for assessment of other BWR codes. (author)

  13. 3D statistical failure analysis of monolithic dental ceramic crowns.

    Nasrin, Sadia; Katsube, Noriko; Seghi, Robert R; Rokhlin, Stanislav I

    2016-07-01

    For adhesively retained ceramic crown of various types, it has been clinically observed that the most catastrophic failures initiate from the cement interface as a result of radial crack formation as opposed to Hertzian contact stresses originating on the occlusal surface. In this work, a 3D failure prognosis model is developed for interface initiated failures of monolithic ceramic crowns. The surface flaw distribution parameters determined by biaxial flexural tests on ceramic plates and point-to-point variations of multi-axial stress state at the intaglio surface are obtained by finite element stress analysis. They are combined on the basis of fracture mechanics based statistical failure probability model to predict failure probability of a monolithic crown subjected to single-cycle indentation load. The proposed method is verified by prior 2D axisymmetric model and experimental data. Under conditions where the crowns are completely bonded to the tooth substrate, both high flexural stress and high interfacial shear stress are shown to occur in the wall region where the crown thickness is relatively thin while high interfacial normal tensile stress distribution is observed at the margin region. Significant impact of reduced cement modulus on these stress states is shown. While the analyses are limited to single-cycle load-to-failure tests, high interfacial normal tensile stress or high interfacial shear stress may contribute to degradation of the cement bond between ceramic and dentin. In addition, the crown failure probability is shown to be controlled by high flexural stress concentrations over a small area, and the proposed method might be of some value to detect initial crown design errors. PMID:27215334

  14. Digital holography microscopy in 3D biologic samples analysis

    Ricardo, J O; Palacios, F; Palacios, G F; Sanchez, A [Department of Physics, University of Oriente (Cuba); Muramatsu, M [Department of General Physics, University of Sao Paulo - Sao Paulo (Brazil); Gesualdi, M [Engineering center, Models and Applied Social Science, UFABC - Sao Paulo (Brazil); Font, O [Department of Bio-ingeniering, University of Oriente - Santiago de Cuba (Cuba); Valin, J L [Mechanics Department, ISPJAE, Habana (Cuba); Escobedo, M; Herold, S [Department of Computation, University of Oriente (Cuba); Palacios, D F, E-mail: frpalaciosf@gmail.com [Department of Nuclear physics, University of Simon BolIva (Venezuela, Bolivarian Republic of)

    2011-01-01

    In this work it is used a setup for Digital Holography Microscopy (MHD) for 3D biologic samples reconstruction. The phase contrast image reconstruction is done by using the Double propagation Method. The system was calibrated and tested by using a micrometric scale and pure phase object respectively. It was simulated the human red blood cell (erythrocyte) and beginning from the simulated hologram the digital 3D phase image for erythrocytes it was calculated. Also there was obtained experimental holograms of human erythrocytes and its corresponding 3D phase images, being evident the correspondence qualitative and quantitative between these characteristics in the simulated erythrocyte and in the experimentally calculated by DHM in both cases.

  15. Digital holography microscopy in 3D biologic samples analysis

    In this work it is used a setup for Digital Holography Microscopy (MHD) for 3D biologic samples reconstruction. The phase contrast image reconstruction is done by using the Double propagation Method. The system was calibrated and tested by using a micrometric scale and pure phase object respectively. It was simulated the human red blood cell (erythrocyte) and beginning from the simulated hologram the digital 3D phase image for erythrocytes it was calculated. Also there was obtained experimental holograms of human erythrocytes and its corresponding 3D phase images, being evident the correspondence qualitative and quantitative between these characteristics in the simulated erythrocyte and in the experimentally calculated by DHM in both cases.

  16. Analysis of quality of experience in 3D video systems

    Gutiérrez Sánchez, Jesús

    2016-01-01

    Esta tesis presenta un estudio exhaustivo sobre la evaluación de la calidad de experiencia (QoE, del inglés Quality of Experience) percibida por los usuarios de sistemas de vídeo 3D, analizando el impacto de los efectos introducidos por todos los elementos de la cadena de procesamiento de vídeo 3D. Por lo tanto, se presentan varias pruebas de evaluación subjetiva específicamente diseñadas para evaluar los sistemas considerados, teniendo en cuenta todos los factores perceptuales relacionados c...

  17. Yield and Cost Analysis or 3D Stacked ICs

    Taouil, M.

    2014-01-01

    3D stacking is an emerging technology promising many benefits such as low latency between stacked dies, reduced power consumption, high bandwidth communication, improved form factor and package volume density, heterogeneous integration, and low-cost manufacturing. However, it requires modification o

  18. Hybrid segmentation framework for 3D medical image analysis

    Chen, Ting; Metaxas, Dimitri N.

    2003-05-01

    Medical image segmentation is the process that defines the region of interest in the image volume. Classical segmentation methods such as region-based methods and boundary-based methods cannot make full use of the information provided by the image. In this paper we proposed a general hybrid framework for 3D medical image segmentation purposes. In our approach we combine the Gibbs Prior model, and the deformable model. First, Gibbs Prior models are applied onto each slice in a 3D medical image volume and the segmentation results are combined to a 3D binary masks of the object. Then we create a deformable mesh based on this 3D binary mask. The deformable model will be lead to the edge features in the volume with the help of image derived external forces. The deformable model segmentation result can be used to update the parameters for Gibbs Prior models. These methods will then work recursively to reach a global segmentation solution. The hybrid segmentation framework has been applied to images with the objective of lung, heart, colon, jaw, tumor, and brain. The experimental data includes MRI (T1, T2, PD), CT, X-ray, Ultra-Sound images. High quality results are achieved with relatively efficient time cost. We also did validation work using expert manual segmentation as the ground truth. The result shows that the hybrid segmentation may have further clinical use.

  19. A QSAR Toxicity Study of a Series of Alkaloids with the Lycoctonine Skeleton

    Bakhtiyor F. Rasulev

    2004-12-01

    Full Text Available A QSAR toxicity analysis has been performed for a series of 19 alkaloids with the lycoctonine skeleton. GA-MLRA (Genetic Algorithm combined with Multiple Linear Regression Analysis technique was applied for the generation of two types of QSARs: first, models containing exclusively 3D-descriptors and second, models consisting of physicochemical descriptors. As expected, 3D-descriptor QSARs have better statistical fits. Physicochemical-descriptor containing models, that are in a good agreement with the mode of toxic action exerted by the alkaloids studied, have also been identified and discussed. In particular, TPSA (Topological Polar Surface Area and nC=O (number of –C(O– fragments parameters give the best statistically significant mono- and bidescriptor models (when combined with lipophilicity, MlogP confirming the importance of H-bonding capability of the alkaloids for binding at the receptor site.

  20. Study on 3D-QSAR and molecular docking of HIV-1 reverse transcriptase inhibitors%H IV-1逆转录酶抑制剂的3 D-QSA R和分子对接研究

    仝建波; 吴英纪; 白敏

    2016-01-01

    In this study , using molecular docking and three-dimensional quantitative struc-ture-activity relationship as a method to study the interaction betw een a series of diaryl ani-line analogues and HIV-1 non nucleoside reverse transcriptase ,through the establishment of three-dimensional quantitative structure-activity relationship model and multiple linear re-gression (MLR) model study the relationship between structure and biological activity of the drug moleculesl .The correlation coefficient (Rcum ) of MLR is 0 .949 ,the correlation coeffi-cient (QCV ) is 0 .799 ,the results show that the three-dimensional quantitative structure-activ-ity relationship has good prediction ability for the anti HIV activity of the compound .The binding model of small molecule drugs and macromolecular HIV-1 reverse transcriptase ac-tive amino acid residues was studied by molecular docking .It is a good guide for the design and synthesis of new anti AIDS drugs .%采用分子对接和三维定量构效关系研究了二芳基苯胺衍生物与 HIV-1非核苷类逆转录酶的相互作用,并运用经典的三维全息原子场作用矢量的方法(3D-HoVAIF)和多元线性回归方法(M LR)研究了药物分子的化学结构与生物活性之间的关系.M LR建模得出的复相关系数(Rcum )为0.949、留一法交互校验复相关系数(QCV )为0.799,从该结果可以看出,三维定量构效关系对化合物的抗艾滋病活性具有比较好的预测能力.最后,运用分子对接研究了小分子药物和大分子HIV-1逆转录酶的氨基酸活性残基之间的结合模式,对今后设计合成新的抗艾滋病药物具有很好的指导作用.

  1. Benefits of statistical molecular design, covariance analysis, and reference models in QSAR: a case study on acetylcholinesterase.

    Andersson, C David; Hillgren, J Mikael; Lindgren, Cecilia; Qian, Weixing; Akfur, Christine; Berg, Lotta; Ekström, Fredrik; Linusson, Anna

    2015-03-01

    Scientific disciplines such as medicinal- and environmental chemistry, pharmacology, and toxicology deal with the questions related to the effects small organic compounds exhort on biological targets and the compounds' physicochemical properties responsible for these effects. A common strategy in this endeavor is to establish structure-activity relationships (SARs). The aim of this work was to illustrate benefits of performing a statistical molecular design (SMD) and proper statistical analysis of the molecules' properties before SAR and quantitative structure-activity relationship (QSAR) analysis. Our SMD followed by synthesis yielded a set of inhibitors of the enzyme acetylcholinesterase (AChE) that had very few inherent dependencies between the substructures in the molecules. If such dependencies exist, they cause severe errors in SAR interpretation and predictions by QSAR-models, and leave a set of molecules less suitable for future decision-making. In our study, SAR- and QSAR models could show which molecular sub-structures and physicochemical features that were advantageous for the AChE inhibition. Finally, the QSAR model was used for the prediction of the inhibition of AChE by an external prediction set of molecules. The accuracy of these predictions was asserted by statistical significance tests and by comparisons to simple but relevant reference models. PMID:25351962

  2. QSAR Analysis of Some Antagonists for p38 map kinase Using Combination of Principal Component Analysis and Artificial Intelligence.

    Doosti, Elham; Shahlaei, Mohsen

    2015-01-01

    Quantitative relationships between structures of a set of p38 map kinase inhibitors and their activities were investigated by principal component regression (PCR) and principal componentartificial neural network (PC-ANN). Latent variables (called components) generated by principal component analysis procedure were applied as the input of developed Quantitative structure- activity relationships (QSAR) models. An exact study of predictability of PCR and PC-ANN showed that the later model has much higher ability to calculate the biological activity of the investigated molecules. Also, experimental and estimated biological activities of compounds used in model development step have indicated a good correlation. Obtained results show that a non-linear model explaining the relationship between the pIC50s and the calculated principal components (that extract from structural descriptors of the studied molecules) is superior than linear model. Some typical figures of merit for QSAR studies explaining the accuracy and predictability of the suggested models were calculated. Therefore, to design novel inhibitors of p38 map kinase with high potency and low undesired effects the developed QSAR models were used to estimate biological pIC50 of the studied compounds. PMID:26234506

  3. Design, Synthesis, Antifungal Activities and 3D-QSAR of New N,N'-Diacylhydrazines Containing 2,4-Dichlorophenoxy Moiety

    Bao-Ju Li

    2013-11-01

    Full Text Available A series of new N,N'-diacylhydrazine derivatives were designed and synthesized. Their structures were verified by 1H-NMR, mass spectra (MS and elemental analysis. The antifungal activities of these N,N'-diacylhydrazines were evaluated. The bioassay results showed that most of these N,N'-diacylhydrazines showed excellent antifungal activities against Cladosporium cucumerinum, Corynespora cassiicola, Sclerotinia sclerotiorum, Erysiphe cichoracearum, and Colletotrichum orbiculare in vivo. The half maximal effective concentration (EC50 of one of the compounds was also determined, and found to be comparable with a commercial drug. To further investigate the structure–activity relationship, comparative molecular field analysis (CoMFA was performed on the basis of antifungal activity data. Both the steric and electronic field distributions of CoMFA are in good agreement in this study.

  4. Design, synthesis, antifungal activities and 3D-QSAR of new N,N'-diacylhydrazines containing 2,4-dichlorophenoxy moiety.

    Sun, Na-Bo; Shi, Yan-Xia; Liu, Xing-Hai; Ma, Yi; Tan, Cheng-Xia; Weng, Jian-Quan; Jin, Jian-Zhong; Li, Bao-Ju

    2013-01-01

    A series of new N,N'-diacylhydrazine derivatives were designed and synthesized. Their structures were verified by 1H-NMR, mass spectra (MS) and elemental analysis. The antifungal activities of these N,N'-diacylhydrazines were evaluated. The bioassay results showed that most of these N,N'-diacylhydrazines showed excellent antifungal activities against Cladosporium cucumerinum, Corynespora cassiicola, Sclerotinia sclerotiorum, Erysiphe cichoracearum, and Colletotrichum orbiculare in vivo. The half maximal effective concentration (EC50) of one of the compounds was also determined, and found to be comparable with a commercial drug. To further investigate the structure-activity relationship, comparative molecular field analysis (CoMFA) was performed on the basis of antifungal activity data. Both the steric and electronic field distributions of CoMFA are in good agreement in this study. PMID:24189221

  5. Design, Synthesis, Antifungal Activities and 3D-QSAR of New N,N′-Diacylhydrazines Containing 2,4-Dichlorophenoxy Moiety

    Sun, Na-Bo; Shi, Yan-Xia; Liu, Xing-Hai; Ma, Yi; Tan, Cheng-Xia; Weng, Jian-Quan; Jin, Jian-Zhong; Li, Bao-Ju

    2013-01-01

    A series of new N,N′-diacylhydrazine derivatives were designed and synthesized. Their structures were verified by 1H-NMR, mass spectra (MS) and elemental analysis. The antifungal activities of these N,N′-diacylhydrazines were evaluated. The bioassay results showed that most of these N,N′-diacylhydrazines showed excellent antifungal activities against Cladosporium cucumerinum, Corynespora cassiicola, Sclerotinia sclerotiorum, Erysiphe cichoracearum, and Colletotrichum orbiculare in vivo. The half maximal effective concentration (EC50) of one of the compounds was also determined, and found to be comparable with a commercial drug. To further investigate the structure–activity relationship, comparative molecular field analysis (CoMFA) was performed on the basis of antifungal activity data. Both the steric and electronic field distributions of CoMFA are in good agreement in this study. PMID:24189221

  6. 3D Massive MIMO Systems: Channel Modeling and Performance Analysis

    Nadeem, Qurrat-Ul-Ain

    2015-03-01

    Multiple-input-multiple-output (MIMO) systems of current LTE releases are capable of adaptation in the azimuth only. More recently, the trend is to enhance the system performance by exploiting the channel\\'s degrees of freedom in the elevation through the dynamic adaptation of the vertical antenna beam pattern. This necessitates the derivation and characterization of three-dimensional (3D) channels. Over the years, channel models have evolved to address the challenges of wireless communication technologies. In parallel to theoretical studies on channel modeling, many standardized channel models like COST-based models, 3GPP SCM, WINNER, ITU have emerged that act as references for industries and telecommunication companies to assess system-level and link-level performances of advanced signal processing techniques over real-like channels. Given the existing channels are only two dimensional (2D) in nature; a large effort in channel modeling is needed to study the impact of the channel component in the elevation direction. The first part of this work sheds light on the current 3GPP activity around 3D channel modeling and beamforming, an aspect that to our knowledge has not been extensively covered by a research publication. The standardized MIMO channel model is presented, that incorporates both the propagation effects of the environment and the radio effects of the antennas. In order to facilitate future studies on the use of 3D beamforming, the main features of the proposed 3D channel model are discussed. A brief overview of the future 3GPP 3D channel model being outlined for the next generation of wireless networks is also provided. In the subsequent part of this work, we present an information-theoretic channel model for MIMO systems that supports the elevation dimension. The model is based on the principle of maximum entropy, which enables us to determine the distribution of the channel matrix consistent with the prior information on the angles of departure and

  7. Design, Synthesis, Antifungal Activities and 3D-QSAR of New N,N′-Diacylhydrazines Containing 2,4-Dichlorophenoxy Moiety

    Bao-Ju Li; Jian-Zhong Jin; Jian-Quan Weng; Cheng-Xia Tan; Yi Ma; Xing-Hai Liu; Yan-Xia Shi; Na-Bo Sun

    2013-01-01

    A series of new N,N'-diacylhydrazine derivatives were designed and synthesized. Their structures were verified by 1H-NMR, mass spectra (MS) and elemental analysis. The antifungal activities of these N,N'-diacylhydrazines were evaluated. The bioassay results showed that most of these N,N'-diacylhydrazines showed excellent antifungal activities against Cladosporium cucumerinum, Corynespora cassiicola, Sclerotinia sclerotiorum, Erysiphe cichoracearum, and Colletotrichum orbiculare...

  8. QSAR Studies on Influenza Neuraminidase Inhibitors——Acylthiourea Analogue

    JING Ju-Hua; LIANG Gui-Zhao; MEI Hu; ZHANG Qiao-Xia; LI Zhi-Liang; LV Feng-Lin

    2009-01-01

    The quantitative structure-activity relationship (QSAR) of 30 acylthiourea analogues was studied by using a three-dimensional holographic vector of atomic interaction field (3D-HoVAIF) to describe their chemical structures. The descriptors obtained were screened by stepwise multiple regression (SMR) and a partial least-squares (PLS) regression model was built. The correlation coefficient r2 of the established model and Leave-One-Out (LOP) Cross-Validation (CV) correlation coefficient q2 are 0.624 and 0.409, respectively. The model has favorable stability and good prediction capability, and further QSAR analysis showed that hydrophobic interaction has the most important effect on the activity of acylthiourea analogue and 3D-HoVAIF was applicable to the molecular structural characterization and biologicalactivity prediction.

  9. Correlative Microscopy for 3D Structural Analysis of Dynamic Interactions

    Jun, Sangmi; Zhao, Gongpu; Ning, Jiying; Gibson, Gregory A.; Watkins, Simon C.; Zhang, Peijun

    2013-01-01

    Cryo-electron tomography (cryoET) allows 3D visualization of cellular structures at molecular resolution in a close-to-physiological state1. However, direct visualization of individual viral complexes in their host cellular environment with cryoET is challenging2, due to the infrequent and dynamic nature of viral entry, particularly in the case of HIV-1. While time-lapse live-cell imaging has yielded a great deal of information about many aspects of the life cycle of HIV-13-7, the resolution ...

  10. A highly predictive 3D-QSAR model for binding to the voltage-gated sodium channel: design of potent new ligands.

    Zha, Congxiang; Brown, George B; Brouillette, Wayne J

    2014-01-01

    A comprehensive comparative molecular field analysis (CoMFA) model for the binding of ligands to the neuronal voltage-gated sodium channel was generated based on 67 diverse compounds. Earlier published CoMFA models for this target provided μM ligands, but the improved model described here provided structurally novel compounds with low nM IC₅₀. For example, new compounds 94 and 95 had IC₅₀ values of 129 and 119 nM, respectively. PMID:24332655

  11. Design, synthesis, biological activities, and 3D-QSAR of new N,N'-diacylhydrazines containing 2-(2,4-dichlorophenoxy)propane moiety.

    Liu, Xing-Hai; Pan, Li; Ma, Yi; Weng, Jian-Quan; Tan, Cheng-Xia; Li, Yong-Hong; Shi, Yan-Xia; Li, Bao-Ju; Li, Zheng-Ming; Zhang, Yong-Gang

    2011-10-01

    A series of new N,N'-diacylhydrazine derivatives were synthesized efficiently under microwave irradiation. Their structures were characterized by (1) H NMR, MS, and elemental analysis. Various biological activities of these compounds were tested. Most of them exhibited higher herbicidal activities against dicotyledonous weeds than monocotyledonous weeds. In addition, favorable in vivo fungicidal activities were also found of these compounds against Cladosporium cucumerinum, Corynespora cassiicola, Sclerotinia sclerotiorum(Lib.)de Bary, Erysiphe cichoracearum, and Colletotrichum orbiculare (Berk aLMont) Arx. All compounds displayed excellent plant growth regulatory activities: 100% inhibition was achieved against the radicle growth of cucumber. To further investigate the structure-activity relationship, comparative molecular field analysis was performed on the basis of herbicidal activity data, resulting in a statistically reliable model with good predictive power (r(2) = 0.913, q(2) =0.556). Based on the calculation, five additional novel compounds were designed and synthesized. Satisfyingly, compound 4u displayed excellent herbicidal activity (94.7%) at 1500 g/ha, although it is less active than 2,4-D. Meanwhile, this compound also exhibited good fungicidal activity against C. orbiculare (Berk aLMont) Arx (82.16%). PMID:21816005

  12. Customisable 3D printed microfluidics for integrated analysis and optimisation.

    Monaghan, T; Harding, M J; Harris, R A; Friel, R J; Christie, S D R

    2016-08-16

    The formation of smart Lab-on-a-Chip (LOC) devices featuring integrated sensing optics is currently hindered by convoluted and expensive manufacturing procedures. In this work, a series of 3D-printed LOC devices were designed and manufactured via stereolithography (SL) in a matter of hours. The spectroscopic performance of a variety of optical fibre combinations were tested, and the optimum path length for performing Ultraviolet-visible (UV-vis) spectroscopy determined. The information gained in these trials was then used in a reaction optimisation for the formation of carvone semicarbazone. The production of high resolution surface channels (100-500 μm) means that these devices were capable of handling a wide range of concentrations (9 μM-38 mM), and are ideally suited to both analyte detection and process optimisation. This ability to tailor the chip design and its integrated features as a direct result of the reaction being assessed, at such a low time and cost penalty greatly increases the user's ability to optimise both their device and reaction. As a result of the information gained in this investigation, we are able to report the first instance of a 3D-printed LOC device with fully integrated, in-line monitoring capabilities via the use of embedded optical fibres capable of performing UV-vis spectroscopy directly inside micro channels. PMID:27452498

  13. Design, Synthesis, Binding and Docking-Based 3D-QSAR Studies of 2-Pyridylbenzimidazoles—A New Family of High Affinity CB1 Cannabinoid Ligands

    Patricio Iturriaga-Vásquez

    2013-04-01

    Full Text Available A series of novel 2-pyridylbenzimidazole derivatives was rationally designed and synthesized based on our previous studies on benzimidazole 14, a CB1 agonist used as a template for optimization. In the present series, 21 compounds displayed high affinities with Ki values in the nanomolar range. JM-39 (compound 39 was the most active of the series (KiCB1 = 0.53 nM, while compounds 31 and 44 exhibited similar affinities to WIN 55212-2. CoMFA analysis was performed based on the biological data obtained and resulted in a statistically significant CoMFA model with high predictive value (q2 = 0.710, r2 = 0.998, r2pred = 0.823.

  14. Measuring the impact of 3D data geometric modeling on spatial analysis: Illustration with Skyview factor

    Brasebin, M.; Perret, J.; Mustière, S.; Weber, C.

    2012-10-01

    The increased availability of 3D urban data reflects a growing interest in 3D spatial analysis. As 3D spatial analysis often uses complex 3D data, studies of the potential gains of using more detailed 3D urban databases for specific uses is an important issue. First, more complex data implies an increase in time and memory usage for the analysis (and calls for more research on the efficiency of the algorithms used). Second, detailed 3D urban data are complex to produce, expensive and it is important to be well informed in order to decide whether of not to invest in such data. Currently, many studies have been led about the fitness for use of 2D data but they are very scarce concerning 3D data. This article presents a method to determine the influence of 3D modeling on the results of 3D analysis by isolating the potential sources of errors (such as roof modeling and geometric accuracy). This method is applied on two 3D datasets (LOD1 and LOD2) and a 3D indicator (the sky view factor or SVF). The results show that the significant influence of roof modeling is globally compensated by the difference in geometric modeling but that important local variations are noticed. Nevertheless, for 75% of the SVF processed the difference between the results using these two databases is lower than 2%.

  15. A 3D QSAR Study of Betulinic Acid Derivatives as Anti-Tumor Agents Using Topomer CoMFA: Model Building Studies and Experimental Verification

    Yang Wang

    2013-08-01

    Full Text Available Betulinic acid (BA is a natural product that exerts its cytotoxicity against various malignant carcinomas without side effects by triggering the mitochondrial pathway to apoptosis. Betulin (BE, the 28-hydroxyl analog of BA, is present in large amounts (up to 30% dry weight in the outer bark of birch trees, and shares the same pentacyclic triterpenoid core as BA, yet exhibits no significant cytotoxicity. Topomer CoMFA studies were performed on 37 BA and BE derivatives and their in vitro anti-cancer activity results (reported as IC50 values against HT29 human colon cancer cells in the present study. All derivatives share a common pentacyclic triterpenoid core and the molecules were split into three pieces by cutting at the C-3 and C-28 sites with a consideration toward structural diversity. The analysis gave a leave-one-out cross-validation q2 value of 0.722 and a non-cross-validation r2 value of 0.974, which suggested that the model has good predictive ability (q2 > 0.2. The contour maps illustrated that bulky and electron-donating groups would be favorable for activity at the C-28 site, and a moderately bulky and electron-withdrawing group near the C-3 site would improve this activity. BE derivatives were designed and synthesized according to the modeling result, whereby bulky electronegative groups (maleyl, phthalyl, and hexahydrophthalyl groups were directly introduced at the C-28 position of BE. The in vitro cytotoxicity values of the given analogs against HT29 cells were consistent with the predicted values, proving that the present topomer CoMFA model is successful and that it could potentially guide the synthesis of new betulinic acid derivatives with high anti-cancer activity. The IC50 values of these three new compounds were also assayed in five other tumor cell lines. 28-O-hexahydrophthalyl BE exhibited the greatest anti-cancer activities and its IC50 values were lower than those of BA in all cell lines, excluding DU145 cells.

  16. 3D numerical simulation and analysis of railgun gouging mechanism

    Jin-guo Wu

    2016-04-01

    Full Text Available A gouging phenomenon with a hypervelocity sliding electrical contact in railgun not only shortens the rail lifetime but also affects the interior ballistic performance. In this paper, a 3-D numerical model was introduced to simulate and analyze the generation mechanism and evolution of the rail gouging phenomenon. The results show that a rail surface bulge is an important factor to induce gouging. High density and high pressure material flow on the contact surface, obliquely extruded into the rail when accelerating the armature to a high velocity, can produce gouging. Both controlling the bulge size to a certain range and selecting suitable materials for rail surface coating will suppress the formation of gouging. The numerical simulation had a good agreement with experiments, which validated the computing model and methodology are reliable.

  17. Defect analysis by statistical fitting to 3D atomicmaps

    Balogh, Zoltán, E-mail: zbalo_01@uni-muenster.de [Institut für Materialphysik, Westfälische Wilhelms Universität-Münster, Wilhelm Klemm Straße 10, D-48149 Münster (Germany); Oberdorfer, Christian; Chellali, Mohammed Reda; Stender, Patrick; Nowak, Susann; Schmitz, Guido [Institut für Materialphysik, Westfälische Wilhelms Universität-Münster, Wilhelm Klemm Straße 10, D-48149 Münster (Germany)

    2013-09-15

    In this article we present a statistical fitting method for evaluation of atomic reconstructions which does not require a coarse-graining step. The fitting compares different models of chemical structure in their capability to explain the measured data set by a least square type merit function. Only preliminary qualitative assumptions about the possible chemical structure are required, while accurate quantitative parameters of the chosen model are delivered by fitting. The technique is particularly useful for singular defect structures with very high composition gradients, for which iso-concentration surfaces determined by coarse-graining become questionable or impossible. We demonstrate that particularly detailed information can be gained from triple junctions and grain boundaries. - Highlights: ► Direct fitting to 3D atomic distributions is proposed. ► Quantitative data is gained from small object with high composition gradients. ► Fitting is especially suitable for studying transport properties of defects.

  18. Defect analysis by statistical fitting to 3D atomicmaps

    In this article we present a statistical fitting method for evaluation of atomic reconstructions which does not require a coarse-graining step. The fitting compares different models of chemical structure in their capability to explain the measured data set by a least square type merit function. Only preliminary qualitative assumptions about the possible chemical structure are required, while accurate quantitative parameters of the chosen model are delivered by fitting. The technique is particularly useful for singular defect structures with very high composition gradients, for which iso-concentration surfaces determined by coarse-graining become questionable or impossible. We demonstrate that particularly detailed information can be gained from triple junctions and grain boundaries. - Highlights: ► Direct fitting to 3D atomic distributions is proposed. ► Quantitative data is gained from small object with high composition gradients. ► Fitting is especially suitable for studying transport properties of defects

  19. Analysis of 3-D Frictional Contact Mechanics Problems by a Boundary Element Method

    KEUM Bangyong; LIU Yijun

    2005-01-01

    The development of two boundary element algorithms for solving 3-D, frictional, and linear elastostatic contact problems is reported in this paper. The algorithms employ nonconforming discretizations for solving 3-D boundary element models, which provide much needed flexibility in the boundary element modeling for 3-D contact problems. These algorithms are implemented in a new 3-D boundary element code and verified using several examples. For the numerical examples studied, the results using the new boundary element algorithms match very well with the results using a commercial finite element code, and clearly demonstrate the feasibility of the new boundary element approach for 3-D contact analysis.

  20. 3D/1D Analysis of ICRF Antennas

    Maggiora, Riccardo; Lancellotti, Vito; Vecchi, Giuseppe

    2003-10-01

    An innovative tool has been realized for the 3D/1D simulation of Ion Cyclotron Radio Frequency (ICRF), i.e. accounting for antennas in a realistic 3D geometry and with an accurate 1D plasma model. The approach to the problem is based on an integral-equation formulation for the self-consistent evaluation of the current distribution on the conductors. The environment has been subdivided in two coupled region: the plasma region and the vacuum region. The two problems are linked by means of a magnetic current (electric field) distribution on the aperture between the two regions. In the vacuum region all the calculations are executed in the spatial domain while in the plasma region an extraction in the spectral domain of some integrals is employed that permits to significantly reduce the integration support and to obtain a high numerical efficiency leading to the practical possibility of using a large number of sub-domain (rectangular or triangular) basis functions on each solid conductor of the system. The plasma enters the formalism of the plasma region via a surface impedance matrix; for this reason any plasma model can be used; at present the FELICE code has been adopted, that affords density and temperature profiles, and FLR effects. The source term directly models the TEM mode of the coax feeding the antenna and the current in the coax is determined self-consistently, giving the input impedance/admittance of the antenna itself. Calculation of field distributions (both magnetic and electric), useful for sheath considerations, is included. This tool has been implemented in a suite, called TOPICA, that is modular and applicable to ICRF antenna structures of arbitrary shape. This new simulation tool can assist during the detailed design phase and for this reason can be considered a "Virtual Prototyping Laboratory" (VPL). The TOPICA suite has been tested against assessed codes and against measurements and data of mock-ups and existing antennas. The VPL is being used in

  1. Tensorial analysis of Eshelby stresses in 3D supercooled liquids

    Lemaître, Anaël

    2015-10-01

    It was recently proposed that the local rearrangements governing relaxation in supercooled liquids impress on the liquid medium long-ranged (Eshelby) stress fluctuations that accumulate over time. From this viewpoint, events must be characterized by elastic dipoles, which are second order tensors, and Eshelby fields are expected to show up in stress and stress increment correlations, which are fourth order tensor fields. We construct here an analytical framework that permits analyzing such tensorial correlations in isotropic media in view of accessing Eshelby fields. Two spherical bases are introduced, which correspond to Cartesian and spherical coordinates for tensors. We show how they can be used to decompose stress correlations and thus test such properties as isotropy and power-law scalings. Eshelby fields and the predicted stress correlations in an infinite medium are shown to belong to an algebra that can conveniently be described using the spherical tensor bases. Using this formalism, we demonstrate that the inherent stress field of 3D supercooled liquids is power law correlated and carries the signature of Eshelby fields, thus supporting the idea that relaxation events give rise to Eshelby stresses that accumulate over time.

  2. Tensorial analysis of Eshelby stresses in 3D supercooled liquids.

    Lemaître, Anaël

    2015-10-28

    It was recently proposed that the local rearrangements governing relaxation in supercooled liquids impress on the liquid medium long-ranged (Eshelby) stress fluctuations that accumulate over time. From this viewpoint, events must be characterized by elastic dipoles, which are second order tensors, and Eshelby fields are expected to show up in stress and stress increment correlations, which are fourth order tensor fields. We construct here an analytical framework that permits analyzing such tensorial correlations in isotropic media in view of accessing Eshelby fields. Two spherical bases are introduced, which correspond to Cartesian and spherical coordinates for tensors. We show how they can be used to decompose stress correlations and thus test such properties as isotropy and power-law scalings. Eshelby fields and the predicted stress correlations in an infinite medium are shown to belong to an algebra that can conveniently be described using the spherical tensor bases. Using this formalism, we demonstrate that the inherent stress field of 3D supercooled liquids is power law correlated and carries the signature of Eshelby fields, thus supporting the idea that relaxation events give rise to Eshelby stresses that accumulate over time. PMID:26520535

  3. Predictive Comparative QSAR Analysis Of As 5-Nitofuran-2-YL Derivatives Myco bacterium tuberculosis H37RV Inhibitors Bacterium Tuberculosis H37RV Inhibitors

    Doreswamy; Vastrad, Chanabasayya M.

    2013-01-01

    Antitubercular activity of 5-nitrofuran-2-yl Derivatives series were subjected to Quantitative Structure Activity Relationship (QSAR) Analysis with an effort to derive and understand a correlation between the biological activity as response variable and different molecular descriptors as independent variables. QSAR models are built using 40 molecular descriptor dataset. Different statistical regression expressions were got using Partial Least Squares (PLS),Multiple Linear Regression (MLR) and...

  4. 3D product authenticity model for online retail: An invariance analysis

    Algharabat, R; Dennis, C.

    2009-01-01

    This study investigates the effects of different levels of invariance analysis on three dimensional (3D) product authenticity model (3DPAM) constructs in the e- retailing context. A hypothetical retailer Web site presents a variety of laptops using 3D product visualisations. The proposed conceptual model achieves acceptable fit and the hypothesised paths are all valid. We empirically investigate the invariance across the subgroups to validate the results of our 3DPAM. We concluded that the 3D...

  5. Comprehensive Aerodynamic Analysis of a 10 MW Wind Turbine Rotor Using 3D CFD

    Zahle, Frederik; Bak, Christian; Sørensen, Niels N.;

    2014-01-01

    This article describes a comprehensive aerodynamic analysis carried out on the DTU 10 MW Reference Wind Turbine (DTU 10MW RWT), in which 3D CFD simulations were used to analyse the rotor performance and derive airfoil aerodynamic characteristics for use in aero-elastic simulation tools. The 3D CFD...... airfoil data derived using the Azimuthal Averaging Technique (AAT) was compared to airfoil data based on 2D CFD simulations on airfoil sections in combination with an array of 3D-correction engineering models, which indicated that the model by Chaviaropoulos and Hansen was in best agreement with the 3D...... CFD predictions. BEM simulations on the DTU 10MW RWT using the AAT-based airfoil data were carried out and compared to BEM simulations using the original airfoil data and the 3D CFD results, which showed clear improvements, particularly on the inner part of the rotor. Finally, 3D unsteady Detached...

  6. An optical real-time 3D measurement for analysis of facial shape and movement

    Zhang, Qican; Su, Xianyu; Chen, Wenjing; Cao, Yiping; Xiang, Liqun

    2003-12-01

    Optical non-contact 3-D shape measurement provides a novel and useful tool for analysis of facial shape and movement in presurgical and postsurgical regular check. In this article we present a system, which allows a precise 3-D visualization of the patient's facial before and after craniofacial surgery. We discussed, in this paper, the real time 3-D image capture, processing and the 3-D phase unwrapping method to recover complex shape deformation when the movement of the mouth. The result of real-time measurement for facial shape and movement will be helpful for the more ideal effect in plastic surgery.

  7. Automatic extraction of soft tissues from 3D MRI head images using model driven analysis

    This paper presents an automatic extraction system (called TOPS-3D : Top Down Parallel Pattern Recognition System for 3D Images) of soft tissues from 3D MRI head images by using model driven analysis algorithm. As the construction of system TOPS we developed, two concepts have been considered in the design of system TOPS-3D. One is the system having a hierarchical structure of reasoning using model information in higher level, and the other is a parallel image processing structure used to extract plural candidate regions for a destination entity. The new points of system TOPS-3D are as follows. (1) The TOPS-3D is a three-dimensional image analysis system including 3D model construction and 3D image processing techniques. (2) A technique is proposed to increase connectivity between knowledge processing in higher level and image processing in lower level. The technique is realized by applying opening operation of mathematical morphology, in which a structural model function defined in higher level by knowledge representation is immediately used to the filter function of opening operation as image processing in lower level. The system TOPS-3D applied to 3D MRI head images consists of three levels. First and second levels are reasoning part, and third level is image processing part. In experiments, we applied 5 samples of 3D MRI head images with size 128 x 128 x 128 pixels to the system TOPS-3D to extract the regions of soft tissues such as cerebrum, cerebellum and brain stem. From the experimental results, the system is robust for variation of input data by using model information, and the position and shape of soft tissues are extracted corresponding to anatomical structure. (author)

  8. Heat analysis of iron panel in 3-phase cubicles using 3-D finite element method

    This paper describes how to compute the temperature rise of panels in cubicles carrying 3-phase currents. The temperature rise is obtained by using 3-D finite element method combining the analysis of eddy current distribution in the panels with heat analysis of the cubicles. The usefulness of the 3-D heat analysis has already been obtained by another study. It is shown that our 3-D heat analysis is capable of evaluating a new design of 3-phase cubicles instead of the conventional trial and error approach. (Author)

  9. Analysis of 3D confocal images of capillaries

    Janáček, Jiří; Saxl, Ivan; Mao, X. W.; Eržen, I.; Kubínová, Lucie

    Saint-Etienne : International society for stereology, 2007, s. 12-15. [International congress for stereology /12./. Saint-Etienne (FR), 03.09.2007-07.09.2007] R&D Projects: GA AV ČR(CZ) IAA100110502 Institutional research plan: CEZ:AV0Z50110509; CEZ:AV0Z10190503 Keywords : capillaries * confocal microscopy * image analysis Subject RIV: EA - Cell Biology

  10. Limit Analysis of 3D Reinforced Concrete Beam Elements

    Larsen, Kasper P.; Nielsen, Leif Otto; Poulsen, Peter Noe

    2012-01-01

    A new finite-element framework for lower-bound limit analysis of reinforced concrete beams, subjected to loading in three dimensions, is presented. The method circumvents the need for a direct formulation of a complex section-force-based yield criterion by creating a discrete representation of the...... Coulomb criterion is applied to the concrete stresses. The modified Coulomb criterion is approximated using second-order cone programming for improved performance over implementations using semidefinite programming. The element is verified by comparing the numerical results with analytical solutions....

  11. Stereo Scene Flow for 3D Motion Analysis

    Wedel, Andreas

    2011-01-01

    This book presents methods for estimating optical flow and scene flow motion with high accuracy, focusing on the practical application of these methods in camera-based driver assistance systems. Clearly and logically structured, the book builds from basic themes to more advanced concepts, culminating in the development of a novel, accurate and robust optic flow method. Features: reviews the major advances in motion estimation and motion analysis, and the latest progress of dense optical flow algorithms; investigates the use of residual images for optical flow; examines methods for deriving mot

  12. Analysis of the 3d9ns (n = 5, 6), 3d95p, 3d94f and 3d84s4p configurations of five times ionized arsenic (As VI)

    The spectrum of arsenic was photographed in the 100-1250 A region on grazing and normal incidence spectrographs. The spectrum of As VI was extended. Seven out of eight levels of the 3d95s and 6s configurations, 12 out of 12 levels of the 3d95p configuration, 13 out of 20 levels of the 3d94f configuration and 35 levels belonging to the 3d94s4p configuration have been established. Least-Square-Fitted parametric calculations involving configuration interactions both in even and odd parity systems were carried out to adequately interpret the spectrum. One hundred and thirty-two additional lines were classified in the As VI spectrum. A new value of the ionization limit was obtained. Thus, the 3d92D5/2 ground level in As VII lies 977500 cm-1 (121.17 eV) above the As VI ground state. (orig.)

  13. Solar Burst Analysis with 3D Loop Models

    Costa, Joaquim E R; Pinto, Tereza S N; Melnikov, Victor F

    2013-01-01

    A sample of Nobeyama flares was selected and analyzed using loop model for important flare parameters. The model for the flaring region consists of a three dimensional dipolar magnetic field, and spatial distributions of non-thermal electrons. We constructed a database by calculating the flare microwave emission for a wide range of these parameters. Out of this database with more than 5,000 cases we extracted general flare properties by comparing the observed and calculated microwave spectra. The analysis of NoRP data was mostly based in the center-to-limb variation of the flare properties with looptop and footpoint electron distributions and for NoRH maps on the resultant distribution of emission. One important aspect of this work is the comparison of the analysis of a flare using an inhomogeneous source model and a simplistic homogeneous source model. Our results show clearly that the homogeneous source hypothesis is not appropriate to describe the possible flare geometry and its use can easily produce misl...

  14. Time-Domain Analysis for 3-D Moored Systems

    肖越; 王言英

    2004-01-01

    In the paper, a comprehensive numerical study on the moored system is performed in time domain. The moored system, which is composed of the floating body sub-system and the mooring line sub-system, is calculated as a whole system by coupling. A time-domain method is applied to the analysis of the mooring line sub-system, and at the same time, an indirect time-domain method translated from frequency-domain to time-domain is developed to calculate the floating body sub-system. In the end, an FPSO vessel is calculated as a numerical example by the present method. A comparison of the result of the model test and that of the numerical method indicates that the present method is exact and effective.

  15. Galerkin Boundary Integral Analysis for the 3D Helmholtz Equation

    Swager, Melissa [Emporia State University; Gray, Leonard J [ORNL; Nintcheu Fata, Sylvain [ORNL

    2010-01-01

    A linear element Galerkin boundary integral analysis for the three-dimensional Helmholtz equation is presented. The emphasis is on solving acoustic scattering by an open (crack) surface, and to this end both a dual equation formulation and a symmetric hypersingular formulation have been developed. All singular integrals are defined and evaluated via a boundary limit process, facilitating the evaluation of the (finite) hypersingular Galerkin integral. This limit process is also the basis for the algorithm for post-processing of the surface gradient. The analytic integrations required by the limit process are carried out by employing a Taylor series expansion for the exponential factor in the Helmholtz fundamental solutions. For the open surface, the implementations are validated by comparing the numerical results obtained by using the two different methods.

  16. 2D-QSAR ANALYSIS OF PHTHALIMIDE DERIVATIVES AS POTENT HYPOGLYCEMIC AGENTS

    Mahesh Kumar, Sumitra Nain*, Vachaspati Dubey and B.P. Nagori

    2013-11-01

    Full Text Available A quantitative structure activity relationship study on series of total thirty three pthalimide analogues reported compounds was taken. Pthalimide analogues have several advantages over present ant diabetic drugs. The present drugs target insulin resistance and insulin insufficiency. So, it is believed that agents will be available alternative to other second line treatment options including sulfonylurea TZDs, DPP-4 inhibitors. Several statistical regression expressions were obtained using stepwise multiple linear regression analysis (MLR and partial least square analysis (PLS. Pthalimide analogues activity is described by models that are built on simple 2D molecular descriptors and nevertheless are of good quality and predictive power. The results obtained after performing QSAR were; r2 = 0.8986, (MLR method (equation-1, (equation-2 r2 = 0.6898 (PLS method The parameters that are found to have significant correlation with hypoglycemic activity are Hosoya Index which is signifies the topological index or Z index, negatively contributing in the biological activity (~40%. The next descriptor is T_N_N_4 i.e. number of Nitrogen atoms (single double or triple bonded separated from any other Nitrogen atom (single double or triple bonded by 4 bonds in a molecule. is inversely proportional to the activity (~30% which mainly indicates the relationship with reference to distance between two nitrogen atoms. The descriptor XK Average Hydrophilicity i.e. Average hydrophilic value also negatively. The r2 and r (CV 2 values of PCR and PLS models clearly indicate the predictive ability of these models.

  17. 3D nuclear track analysis by digital holographic microscopy

    Palacios, F. [Universidad de Oriente, Santiago de Cuba (Cuba); Palacios Fernandez, D., E-mail: danpalacios@cantv.ne [Universidad Simon Bolivar, P.O. 89000, Caracas 1080 (Venezuela, Bolivarian Republic of); Ricardo, J.; Palacios, G.F. [Universidad de Oriente, Santiago de Cuba (Cuba); Sajo-Bohus, L. [Universidad Simon Bolivar, P.O. 89000, Caracas 1080 (Venezuela, Bolivarian Republic of); Goncalves, E. [Polytechnical School, Sao Paulo University (USP) (Brazil); Valin, J.L. [Instituto Politecnico Superior ' Jose Antonio Echeverria' , Habana (Cuba); Monroy, F.A. [Universidad Nacional de Colombia, Sede Bogota (Colombia)

    2011-01-15

    A new method, based on Digital Holographic Microscopy (DHM), to visualize and to analyze etched tracks in SSNTD has been developed. The proposed method is based on the possibility of the digital holography to perform whole reconstruction of the recorded wave front, so that phase and intensity distribution at a plane located between the object and recording plane and along the reconstructed image of the object can be determined. In a DHM system, the back focal plane of the lens can be reconstructed so that complex amplitudes of the Fraunhofer diffraction of light distribution across the object can be known. With the knowledge and manipulation of the components of this plane is possible to design different methods of image analysis. In this paper, the DHM method was applied to determine the track parameters in CR-39 detectors, showing that most of studies carried out with Confocal Microscopy and Atomic Force Microscopy could be also done, with the sufficient exactitude and precision, but in a simpler and more economic way. The developed microholographic method provides a new alternative procedure that overcomes the current techniques at least in technological simplicity.

  18. 3D nuclear track analysis by digital holographic microscopy

    A new method, based on Digital Holographic Microscopy (DHM), to visualize and to analyze etched tracks in SSNTD has been developed. The proposed method is based on the possibility of the digital holography to perform whole reconstruction of the recorded wave front, so that phase and intensity distribution at a plane located between the object and recording plane and along the reconstructed image of the object can be determined. In a DHM system, the back focal plane of the lens can be reconstructed so that complex amplitudes of the Fraunhofer diffraction of light distribution across the object can be known. With the knowledge and manipulation of the components of this plane is possible to design different methods of image analysis. In this paper, the DHM method was applied to determine the track parameters in CR-39 detectors, showing that most of studies carried out with Confocal Microscopy and Atomic Force Microscopy could be also done, with the sufficient exactitude and precision, but in a simpler and more economic way. The developed microholographic method provides a new alternative procedure that overcomes the current techniques at least in technological simplicity.

  19. Global stability analysis of turbulent 3D wakes

    Rigas, Georgios; Sipp, Denis; Juniper, Matthew

    2015-11-01

    At low Reynolds numbers, corresponding to laminar and transitional regimes, hydrodynamic stability theory has aided the understanding of the dynamics of bluff body wake-flows and the application of effective control strategies. However, flows of fundamental importance to many industries, in particular the transport industry, involve high Reynolds numbers and turbulent wakes. Despite their turbulence, such wake flows exhibit organisation which is manifested as coherent structures. Recent work has shown that the turbulent coherent structures retain the shape of the symmetry-breaking laminar instabilities and only those manifest as large-scale structures in the near wake (Rigas et al., JFM vol. 750:R5 2014, JFM vol. 778:R2 2015). Based on the findings of the persistence of the laminar instabilities at high Reynolds numbers, we investigate the global stability characteristics of a turbulent wake generated behind a bluff three-dimensional axisymmetric body. We perform a linear global stability analysis on the experimentally obtained mean flow and we recover the dynamic characteristics and spatial structure of the coherent structures, which are linked to the transitional instabilities. A detailed comparison of the predictions with the experimental measurements will be provided.

  20. A nonlinear 3D containment analysis for airplane impact

    In the Federal Republic of Germany, it is pertinent safety philosophy to design nuclear facilities against airplane impact, despite its very unlikely probability of occurrence. For safety reasons, the following conditions have to be met: 1) In the close impact area of the projectile, the structure can be stressed up to its ultimate load capacity, so that impact energy is dissipated partly. Hereby, it must be strictly clarified that local structural failure within the impact zone is avoided. 2) Residual impact energy is transferred to the 'non-disturbed' containment structure and to the interior structure. The subject of reinforced concrete structures under impact loads shows still clear gaps between the findings of experimental and analytical analyses. To clarify this highly nonlinear phenomena comprehensive tests have recently been performed in Germany. It is the aim of this paper to carry out a three-dimensional analysis of a nuclear facility. To perform the calculations, the finite element ADINA code is applied. In order to obtain optimum results, a very fine mesh leading to several thousand DOF is used. To model the impact area of the concrete structure realistically, its linear and mostly nonlinear material behaviour as well as its failure criteria must be taken into account. Herewith the structural response is reduced due to increased energy dissipation. This reduction rate is valued by variation of the assumed size of impact zone, the load impact location and the assumed load-time function. (orig./RW)

  1. Using decision analysis to estimate 3-D seismic value-Minas field, Sumatra Indonesia

    Mangold, K.M.; Whitacre, T.P.; Seffibudianti (Caltex Pacific Indonesia, Sumatra (Indonesia))

    1996-01-01

    Decision Analysis has been used to estimate the value added from a 3-D seismic survey recorded over Minas field, Central Sumatra. The method involves comparing the expected values which result from the various decision options, such as acquiring 3-D or not. Probabilities must be assigned to the various branches of the decision tree. These include for example, the expected reliability of the 3-D data as well as the subsequent interpretation. Anticipated drilling results with and without 3-D are assessed after reviewing historical data and interviewing experts to obtain 10th, 50th and 90th percentile results for various scenarios. In this way the expected value, or cumulative distribution of the expected value of the 3-D can be computed and risk can be assessed. The Minas 3-D survey is the largest (450 square kilometers) of over 25 development 3-D surveys recorded by Caltex Pacific Indonesia (CPI) over its fields in Central Sumatra. This survey was conducted after nearly 50 years of production from more than 750 wells. CPI's 3-D experience has shown that increasing the subsurface resolution within complex high angle faulted areas results in new drilling locations in older mature fields such as Minas. Better knowledge of the oil producing reservoirs can also be used to optimize pattern waterflood locations, horizontal drilling and other tertiary recovery studies.

  2. Using decision analysis to estimate 3-D seismic value-Minas field, Sumatra Indonesia

    Mangold, K.M.; Whitacre, T.P.; Seffibudianti [Caltex Pacific Indonesia, Sumatra (Indonesia)

    1996-12-31

    Decision Analysis has been used to estimate the value added from a 3-D seismic survey recorded over Minas field, Central Sumatra. The method involves comparing the expected values which result from the various decision options, such as acquiring 3-D or not. Probabilities must be assigned to the various branches of the decision tree. These include for example, the expected reliability of the 3-D data as well as the subsequent interpretation. Anticipated drilling results with and without 3-D are assessed after reviewing historical data and interviewing experts to obtain 10th, 50th and 90th percentile results for various scenarios. In this way the expected value, or cumulative distribution of the expected value of the 3-D can be computed and risk can be assessed. The Minas 3-D survey is the largest (450 square kilometers) of over 25 development 3-D surveys recorded by Caltex Pacific Indonesia (CPI) over its fields in Central Sumatra. This survey was conducted after nearly 50 years of production from more than 750 wells. CPI`s 3-D experience has shown that increasing the subsurface resolution within complex high angle faulted areas results in new drilling locations in older mature fields such as Minas. Better knowledge of the oil producing reservoirs can also be used to optimize pattern waterflood locations, horizontal drilling and other tertiary recovery studies.

  3. Static and dynamic stability analysis using 3D-DDA with incision body scheme

    Wang Jianquan; Lin Gao; Liu Jun

    2006-01-01

    Discontinuous deformation analysis (DDA) provides a powerful numerical tool for the analysis of discontinuous media. This method has been widely applied to the 2D analysis of discontinuous deformation. However, it is hindered from analyzing 3D rock engineering problems mainly due to the lack of reliable 3D contact detection algorithms for polyhedra.Contact detection is a key in 3-D DDA analysis. The limitations and advantages of existing contact detection schemes are discussed in this paper, and a new approach, called the incision body (IB), is proposed, taking into account the advantages of the existing methods. A computer code 3DIB, which uses the IB scheme as a 3D contact detection algorithm, was programmed with Visual C++. Static and dynamic stability analysis for three realistic engineering problems has been carried out. Furthermore, the focus is on studying the stability of a gravity dam on jointed rock foundation and dynamic stability of a fractured gravity dam subject to earthquake shaking. The simulation results show that the program 3DIB and incision body scheme are capable of detecting 3D block contacts correctly and hence simulating the open-close and slide process of jointed block masses. In addition, the code 3DIB could provide an effective tool for evaluating the safety of 3D dam structures, which is quite important for engineering problems.

  4. QSAR and molecular docking studies on oxindole derivatives as VEGFR-2 tyrosine kinase inhibitors.

    Kang, Cong-Min; Liu, Dong-Qing; Zhao, Xu-Hao; Dai, Ying-Jie; Cheng, Jia-Gao; Lv, Ying-Tao

    2016-01-01

    The three-dimensional quantitative structure-activity relationships (3D-QSAR) were established for 30 oxindole derivatives as vascular endothelial growth factor receptor-2 (VEGFR-2) tyrosine kinase inhibitors by using comparative molecular field analysis (CoMFA) and comparative similarity indices analysis comparative molecular similarity indices analysis (CoMSIA) techniques. With the CoMFA model, the cross-validated value (q(2)) was 0.777, the non-cross-validated value (R(2)) was 0.987, and the external cross-validated value ([Formula: see text]) was 0.72. And with the CoMSIA model, the corresponding q(2), R(2) and [Formula: see text] values were 0.710, 0.988 and 0.78, respectively. Docking studies were employed to bind the inhibitors into the active site to determine the probable binding conformation. The binding mode obtained by molecular docking was in good agreement with the 3D-QSAR results. Based on the QSAR models and the docking binding mode, a set of new VEGFR-2 tyrosine kinase inhibitors were designed, which showed excellent predicting inhibiting potencies. The result revealed that both QSAR models have good predictive capability to guide the design and structural modification of homologic compounds. It is also helpful for further research and development of new VEGFR-2 tyrosine kinase inhibitors. PMID:26416217

  5. Steady state analysis of SFR cores using DYN3D-Serpent codes sequence

    A few-group cross section generation methodology for the deterministic analysis of SFR cores with DYN3D code has been proposed. The full core DYN3D results obtained using the few-group constants produced by Serpent agreed very well with that of the reference full core MC simulations. Such an agreement demonstrates the feasibility of the proposed few-group cross section generation procedure. In summary, this study showed that the Serpent-DYN3D code sequence can be successfully used for modeling fast spectrum reactor systems. (orig.)

  6. QSAR analyses of DDT analogues and their in silico validation using molecular docking study against voltage-gated sodium channel of Anopheles funestus.

    Saini, V; Kumar, A

    2014-01-01

    DDT has enjoyed the reputation of a successful pesticide in disease control programme and agricultural practices along with the serious opposition and ban later on due to its biomagnification and toxic action against non-target organisms. The present work was carried out to develop QSAR models for analysing DDT analogues for their pesticidal activity and in silico validation of these models. A 2D-QSAR model was generated using stepwise with multiple regression, and the model with a value of r(2) = 0.7324; q(2) = 0.6215; pred r(2) = 0.7038, containing five descriptors, was selected for further study. The 3D QSAR with CoMFA analysis showed that steric contribution of 21% and electrostatic contribution of about 79% were required for larvicidal activity of DDT analogues. A set of 3430 molecules was generated using the basic DDT skeleton as template, and these were evaluated for their mosquito larvicidal activity using the generated QSAR models and DDT as standard. Eleven molecules were selected for in silico validation of these models. For this, a docking study of the selected molecules against the homology-modelled voltage-gated sodium channel of Anopheles funestus was conducted. The study showed that the activities of these analogues as predicted by 2D-QSAR, 3D-QSAR with CoMFA and dock score were observed to be well correlated. PMID:25271473

  7. 3-D QSAR ANALYSIS OF INHIBITION OF MURINE SOLUBLE EPOXIDE HYDROLASE (MSEH) BY BENZOYLUREAS, ARYLUREAS, AND THEIR ANALOGUES. (R825433)

    Two hundred and seventy-one compounds including benzoylureas, arylureas and related compounds were assayed using recombinant murine soluble epoxide hydrolase (MsEH) produced from a baculovirus expression system. Among all the insect growth regulators assayed, 18 benzoylphenylu...

  8. Pore3D: A software library for quantitative analysis of porous media

    Brun, Francesco [Sincrotrone Trieste S.C.p.A, S.S. 14 Km 163.5, 34149 Basovizza, Trieste (Italy); Department of Electrical, Electronic and Computer Engineering, University of Trieste, Via A. Valerio, 10, 34127 Trieste (Italy); Mancini, Lucia, E-mail: lucia.mancini@elettra.trieste.i [Sincrotrone Trieste S.C.p.A, S.S. 14 Km 163.5, 34149 Basovizza, Trieste (Italy); Kasae, Parnian [Sincrotrone Trieste S.C.p.A, S.S. 14 Km 163.5, 34149 Basovizza, Trieste (Italy); International Centre for Theoretical Physics, Strada Costiera, 11, 34151 Trieste (Italy); Favretto, Stefano [Department of Materials and Natural Resources, University of Trieste, Via A. Valerio, 2, 34127 Trieste (Italy); Dreossi, Diego; Tromba, Giuliana [Sincrotrone Trieste S.C.p.A, S.S. 14 Km 163.5, 34149 Basovizza, Trieste (Italy)

    2010-04-11

    In recent years great interest has been posed in imaging techniques like X-ray computed microtomography which in a nondestructive way produce three-dimensional (3D) images of the internal structure of, e.g. porous media. A major challenge lies in the quantitative analysis of the resulting images that allows a more comprehensive and objective characterization of the sample under investigation. A software able to handle and process large 3D image datasets with common hardware is therefore necessary in order to extract morphological and textural information directly from the images. In the present paper the Pore3D software library developed by the SYRMEP research group of the Elettra Synchrotron Light Laboratory in Trieste (Italy) is presented. The library consists of several state-of-the-art functions and procedures for performing filtering, segmentation and quantitative analysis of 3D images. The current status of the project and some applications are here reported.

  9. Pore3D: A software library for quantitative analysis of porous media

    In recent years great interest has been posed in imaging techniques like X-ray computed microtomography which in a nondestructive way produce three-dimensional (3D) images of the internal structure of, e.g. porous media. A major challenge lies in the quantitative analysis of the resulting images that allows a more comprehensive and objective characterization of the sample under investigation. A software able to handle and process large 3D image datasets with common hardware is therefore necessary in order to extract morphological and textural information directly from the images. In the present paper the Pore3D software library developed by the SYRMEP research group of the Elettra Synchrotron Light Laboratory in Trieste (Italy) is presented. The library consists of several state-of-the-art functions and procedures for performing filtering, segmentation and quantitative analysis of 3D images. The current status of the project and some applications are here reported.

  10. STEREOLOGY AND 3D MICROSCOPY: USEFUL ALTERNATIVES OR COMPETITORS IN THE QUANTITATIVE ANALYSIS OF MICROSTRUCTURES?

    Hans Eckart Exner

    2011-05-01

    Full Text Available With the rapid development of modern techniques for producing 3D images, the assessment of 3D geometry from 2D sections of projections by stereological methods seems to become more and more redundant. The paper aims to show the limits of the two approaches and to outline their relative advantages in practical applications. It is concluded that, for a large variety of applications, classical stereological methods are the most effective way to characterize 3D geometry of irregular microstructures. The basic equations for useful global (field parameters are summarized and their assessment by manual techniques is indicated. For other types of applications asking for complex parameters like shape, arrangement or size distribution, preference should be given to direct 3D measurements. Parameters obtained by 2D analysis of sections or projections are useful for comparison purposes, for empirical correlation analysis or for fingerprinting-type description. Field and feature parameters and the problems of data reductions are discussed.

  11. 3D finite elements method (FEM) Analysis of basic process parameters in rotary piercing mill

    Z. Pater; J. Bartnicki; Kazanecki, J.

    2012-01-01

    In this paper 3D FEM analysis of process parameters and its infl uence in rotary piercing mill is presented. The FEM analyze of the rotary piercing process was made under the conditions of 3D state of strain with taking into consideration the thermal phenomena. The calculations were made with application of different rolls’ skew angles and different plug designs. In the result, progression of shapes, temperature and distributions of stress and strain were characterized. The numerical results ...

  12. Shape Analysis of 3D Head Scan Data for U.S. Respirator Users

    Stephanie Lynch; Viscusi, Dennis J.; Stacey Benson; Slice, Dennis E.; Ziqing Zhuang

    2010-01-01

    In 2003, the National Institute for Occupational Safety and Health (NIOSH) conducted a head-and-face anthropometric survey of diverse, civilian respirator users. Of the 3,997 subjects measured using traditional anthropometric techniques, surface scans and 26 three-dimensional (3D) landmark locations were collected for 947 subjects. The objective of this study was to report the size and shape variation of the survey participants using the 3D data. Generalized Procrustes Analysis (GPA) was con...

  13. 3D photography in the objective analysis of volume augmentation including fat augmentation and dermal fillers.

    Meier, Jason D; Glasgold, Robert A; Glasgold, Mark J

    2011-11-01

    The authors present quantitative and objective 3D data from their studies showing long-term results with facial volume augmentation. The first study analyzes fat grafting of the midface and the second study presents augmentation of the tear trough with hyaluronic filler. Surgeons using 3D quantitative analysis can learn the duration of results and the optimal amount to inject, as well as showing patients results that are not demonstrable with standard, 2D photography. PMID:22004863

  14. Proposição, validação e análise dos modelos que correlacionam estrutura química e atividade biológica Proposition, validation and analysis of QSAR models

    Anderson Coser Gaudio

    2001-10-01

    Full Text Available The present paper aims to bring under discussion some theoretical and practical aspects about the proposition, validation and analysis of QSAR models based on multiple linear regression. A comprehensive approach for the derivation of extrathermodynamic equations is reviewed. Some examples of QSAR models published in the literature are analyzed and criticized.

  15. Sensitivity Analysis of the Scattering-Based SARBM3D Despeckling Algorithm.

    Di Simone, Alessio

    2016-01-01

    Synthetic Aperture Radar (SAR) imagery greatly suffers from multiplicative speckle noise, typical of coherent image acquisition sensors, such as SAR systems. Therefore, a proper and accurate despeckling preprocessing step is almost mandatory to aid the interpretation and processing of SAR data by human users and computer algorithms, respectively. Very recently, a scattering-oriented version of the popular SAR Block-Matching 3D (SARBM3D) despeckling filter, named Scattering-Based (SB)-SARBM3D, was proposed. The new filter is based on the a priori knowledge of the local topography of the scene. In this paper, an experimental sensitivity analysis of the above-mentioned despeckling algorithm is carried out, and the main results are shown and discussed. In particular, the role of both electromagnetic and geometrical parameters of the surface and the impact of its scattering behavior are investigated. Furthermore, a comprehensive sensitivity analysis of the SB-SARBM3D filter against the Digital Elevation Model (DEM) resolution and the SAR image-DEM coregistration step is also provided. The sensitivity analysis shows a significant robustness of the algorithm against most of the surface parameters, while the DEM resolution plays a key role in the despeckling process. Furthermore, the SB-SARBM3D algorithm outperforms the original SARBM3D in the presence of the most realistic scattering behaviors of the surface. An actual scenario is also presented to assess the DEM role in real-life conditions. PMID:27347971

  16. Quantitative Analysis and Modeling of 3-D TSV-Based Power Delivery Architectures

    He, Huanyu

    As 3-D technology enters the commercial production stage, it is critical to understand different 3-D power delivery architectures on the stacked ICs and packages with through-silicon vias (TSVs). Appropriate design, modeling, analysis, and optimization approaches of the 3-D power delivery system are of foremost significance and great practical interest to the semiconductor industry in general. Based on fundamental physics of 3-D integration components, the objective of this thesis work is to quantitatively analyze the power delivery for 3D-IC systems, develop appropriate physics-based models and simulation approaches, understand the key issues, and provide potential solutions for design of 3D-IC power delivery architectures. In this work, a hybrid simulation approach is adopted as the major approach along with analytical method to examine 3-D power networks. Combining electromagnetic (EM) tools and circuit simulators, the hybrid approach is able to analyze and model micrometer-scale components as well as centimeter-scale power delivery system with high accuracy and efficiency. The parasitic elements of the components on the power delivery can be precisely modeled by full-wave EM solvers. Stack-up circuit models for the 3-D power delivery networks (PDNs) are constructed through a partition and assembly method. With the efficiency advantage of the SPICE circuit simulation, the overall 3-D system power performance can be analyzed and the 3-D power delivery architectures can be evaluated in a short computing time. The major power delivery issues are the voltage drop (IR drop) and voltage noise. With a baseline of 3-D power delivery architecture, the on-chip PDNs of TSV-based chip stacks are modeled and analyzed for the IR drop and AC noise. The basic design factors are evaluated using the hybrid approach, such as the number of stacked chips, the number of TSVs, and the TSV arrangement. Analytical formulas are also developed to evaluate the IR drop in 3-D chip stack in

  17. 3D thermo-chemical-mechanical analysis of the pultrusion process

    Baran, Ismet; Hattel, Jesper Henri; Tutum, Cem C.

    2013-01-01

    In the present study, a 3D Eulerian thermo-chemical analysis is sequentially coupled with a 3D Lagrangian quasi static mechanical analysis of the pultrusion process. The temperature and degree of cure profiles at the steady state are first calculated in the thermo-chemical analysis. In the...... mechanical analysis, the developments of the process induced stresses and distortions during the process are predicted using the already obtained temperature and degree of cure profiles together with the glass transition temperature. The predictions of the transverse transient stresses and distortions are...... found to be similar as compared to the available data in the literature. Using the proposed 3D mechanical analysis, different mechanical behaviour is obtained for the longitudinal stress development as distinct from the stress development in the transverse directions. Even though the matrix material is...

  18. Detection of Connective Tissue Disorders from 3D Aortic MR Images Using Independent Component Analysis

    Hansen, Michael Sass; Zhao, Fei; Zhang, Honghai;

    2006-01-01

    A computer-aided diagnosis (CAD) method is reported that allows the objective identification of subjects with connective tissue disorders from 3D aortic MR images using segmentation and independent component analysis (ICA). The first step to extend the model to 4D (3D + time) has also been taken....... ICA is an effective tool for connective tissue disease detection in the presence of sparse data using prior knowledge to order the components, and the components can be inspected visually. 3D+time MR image data sets acquired from 31 normal and connective tissue disorder subjects at end-diastole (R......-wave peak) and at 45\\$\\backslash\\$% of the R-R interval were used to evaluate the performance of our method. The automated 3D segmentation result produced accurate aortic surfaces covering the aorta. The CAD method distinguished between normal and connective tissue disorder subjects with a classification...

  19. Employing conformational analysis in the molecular modeling of agrochemicals: insights on QSAR parameters of 2,4-D

    Matheus Puggina de Freitas

    2013-12-01

    Full Text Available A common practice to compute ligand conformations of compounds with various degrees of freedom to be used in molecular modeling (QSAR and docking studies is to perform a conformational distribution based on repeated random sampling, such as Monte-Carlo methods. Further calculations are often required. This short review describes some methods used for conformational analysis and the implications of using selected conformations in QSAR. A case study is developed for 2,4-dichlorophenoxyacetic acid (2,4-D, a widely used herbicide which binds to TIR1 ubiquitin ligase enzyme. The use of such an approach and semi-empirical calculations did not achieve all possible minima for 2,4-D. In addition, the conformations and respective energies obtained by the semi-empirical AM1 method do not match the calculated trends obtained by a high level DFT method. Similar findings were obtained for the carboxylate anion, which is the bioactive form. Finally, the crystal bioactive structure of 2,4-D was not found as a minimum when using Monte-Carlo/AM1 and is similarly populated with another conformer in implicit water solution according to optimization at the B3LYP/aug-cc-pVDZ level. Therefore, quantitative structure-activity relationship (QSAR methods based on three dimensional chemical structures are not fundamental to provide predictive models for 2,4-D congeners as TIR1 ubiquitin ligase ligands, since they do not necessarily reflect the bioactive conformation of this molecule. This probably extends to other systems.

  20. Mathematical modeling and reliability analysis of a 3D Li-ion battery

    RICHARD HONG PENG LIANG

    2014-02-01

    Full Text Available The three-dimensional (3D Li-ion battery presents an effective solution to issues affecting its two-dimensional counterparts, as it is able to attain high energy capacities for the same areal footprint without sacrificing power density. A 3D battery has key structural features extending in and fully utilizing 3D space, allowing it to achieve greater reliability and longevity. This study applies an electrochemical-thermal coupled model to a checkerboard array of alternating positive and negative electrodes in a 3D architecture with either square or circular electrodes. The mathematical model comprises the transient conservation of charge, species, and energy together with electroneutrality, constitutive relations and relevant initial and boundary conditions. A reliability analysis carried out to simulate malfunctioning of either a positive or negative electrode reveals that although there are deviations in electrochemical and thermal behavior for electrodes adjacent to the malfunctioning electrode as compared to that in a fully-functioning array, there is little effect on electrodes further away, demonstrating the redundancy that a 3D electrode array provides. The results demonstrate that implementation of 3D batteries allow it to reliably and safely deliver power even if a component malfunctions, a strong advantage over conventional 2D batteries.

  1. 3D finite element analysis of porous Ti-based alloy prostheses.

    Mircheski, Ile; Gradišar, Marko

    2016-11-01

    In this paper, novel designs of porous acetabular cups are created and tested with 3D finite element analysis (FEA). The aim is to develop a porous acetabular cup with low effective radial stiffness of the structure, which will be near to the architectural and mechanical behavior of the natural bone. For the realization of this research, a 3D-scanner technology was used for obtaining a 3D-CAD model of the pelvis bone, a 3D-CAD software for creating a porous acetabular cup, and a 3D-FEA software for virtual testing of a novel design of the porous acetabular cup. The results obtained from this research reveal that a porous acetabular cup from Ti-based alloys with 60 ± 5% porosity has the mechanical behavior and effective radial stiffness (Young's modulus in radial direction) that meet and exceed the required properties of the natural bone. The virtual testing with 3D-FEA of a novel design with porous structure during the very early stage of the design and the development of orthopedic implants, enables obtaining a new or improved biomedical implant for a relatively short time and reduced price. PMID:27015664

  2. Medical image analysis of 3D CT images based on extensions of Haralick texture features

    Tesař, Ludvík; Shimizu, A.; Smutek, D.; Kobatake, H.; Nawano, S.

    2008-01-01

    Roč. 32, č. 6 (2008), s. 513-520. ISSN 0895-6111 R&D Projects: GA AV ČR 1ET101050403; GA MŠk 1M0572 Institutional research plan: CEZ:AV0Z10750506 Keywords : image segmentation * Gaussian mixture model * 3D image analysis Subject RIV: IN - Informatics, Computer Science Impact factor: 1.192, year: 2008 http://library.utia.cas.cz/separaty/2008/AS/tesar-medical image analysis of 3d ct image s based on extensions of haralick texture features.pdf

  3. The integrated code system CASCADE-3D for advanced core design and safety analysis

    The new program system CASCADE-3D (Core Analysis and Safety Codes for Advanced Design Evaluation) links some of Siemens advanced code packages for in-core fuel management and accident analysis: SAV95, PANBOX/COBRA and RELAP5. Consequently by using CASCADE-3D the potential of modern fuel assemblies and in-core fuel management strategies can be much better utilized because safety margins which had been reduced due to conservative methods are now predicted more accurately. By this innovative code system the customers can now take full advantage of the recent progress in fuel assembly design and in-core fuel management.(author)

  4. 3D analysis of eddy current loss in the permanent magnet coupling

    Zhu, Zina; Meng, Zhuo

    2016-07-01

    This paper first presents a 3D analytical model for analyzing the radial air-gap magnetic field between the inner and outer magnetic rotors of the permanent magnet couplings by using the Amperian current model. Based on the air-gap field analysis, the eddy current loss in the isolation cover is predicted according to the Maxwell's equations. A 3D finite element analysis model is constructed to analyze the magnetic field spatial distributions and vector eddy currents, and then the simulation results obtained are analyzed and compared with the analytical method. Finally, the current losses of two types of practical magnet couplings are measured in the experiment to compare with the theoretical results. It is concluded that the 3D analytical method of eddy current loss in the magnet coupling is viable and could be used for the eddy current loss prediction of magnet couplings.

  5. Digital Curvatures Applied to 3D Object Analysis and Recognition: A Case Study

    Chen, Li

    2009-01-01

    In this paper, we propose using curvatures in digital space for 3D object analysis and recognition. Since direct adjacency has only six types of digital surface points in local configurations, it is easy to determine and classify the discrete curvatures for every point on the boundary of a 3D object. Unlike the boundary simplicial decomposition (triangulation), the curvature can take any real value. It sometimes makes difficulties to find a right value for threshold. This paper focuses on the global properties of categorizing curvatures for small regions. We use both digital Gaussian curvatures and digital mean curvatures to 3D shapes. This paper proposes a multi-scale method for 3D object analysis and a vector method for 3D similarity classification. We use these methods for face recognition and shape classification. We have found that the Gaussian curvatures mainly describe the global features and average characteristics such as the five regions of a human face. However, mean curvatures can be used to find ...

  6. Applications of 3-D reconstruction and 3-D image analysis using computer graphics in surgery of the oral and maxillofacial regions

    Using the 2-D data provided by CT-Tomography and MRI-tomography of oral and maxillofacial diseases (cyst, benign tumor, primary tumor and regional lymphnodes of malignant tumor), 3-D images were reconstructed and spatial analysis was attempted. We report the general concepts. The hardware used consisted of the Hewlett-Packard HP-9000/300, which utilizes a 16-bit CPU. A digitizer was used to construct 3-D images from serial CT-tomography and MRI-tomography images. Output was displayed on a color monitor and photographs. The 3 cases on which we used this technique included a 19-year-old male with plunging ranula, a 50-year-old male with maxillary pleomorphic adenoma, and a 58-year-old male with squamous cell carcinoma of the maxillary sinus (T3N3M0). As 3-D reconstruction can be done in any arbitrary direction or cross section, it is possible to spatially determine the position of the disease inside the body, its progression, and its relationship with adjacent organs. Through image analysis, it is possible to better understand the volume and surface area of the disease. 3-D image reconstruction is an effective tool in the determination of diagnosis, therapeutic guidelines, and surgical indications, as well as effectiveness of treatment. (author)

  7. Application of COREMELT-3D code at analysis of severe fast reactor accidents

    The code COREMELT for calculations of initial and transition stages of severe accident is considered. It is used to conduct connected calculations of nonstationary neutronic and thermohydraulic processes in sodium fast reactor core. The code has some versions depending on dimensions of solving problem and consists of thermohydraulic module COREMELT and neutronic module RADAR. Using the code COREMELT-3D connected calculations of core disassembly accidents of ULOF and UTOP type have been conducted for sodium fast reactors safety analysis. The main problem of code COREMELT-3D use is duration of calculation, speeding of the code is possible when calculating algorithms are parallelized

  8. 3D finite elements method (FEM Analysis of basic process parameters in rotary piercing mill

    Z. Pater

    2012-10-01

    Full Text Available In this paper 3D FEM analysis of process parameters and its infl uence in rotary piercing mill is presented. The FEM analyze of the rotary piercing process was made under the conditions of 3D state of strain with taking into consideration the thermal phenomena. The calculations were made with application of different rolls’ skew angles and different plug designs. In the result, progression of shapes, temperature and distributions of stress and strain were characterized. The numerical results of calculations were compared with results of stand test with use of 100Cr6 steel. The comparisons of numerical and experimental tests confirm good agreement between obtained results.

  9. Measurement of Capillary Length from 3D Confocal Images Using Image Analysis and Stereology

    Janáček, Jiří; Saxl, Ivan; Mao, X. W.; Kubínová, Lucie

    Valencia : University of Valencia, 2007. s. 71-71. [Focus on Microscopy FOM 2007. 10.04.2007-13.04.2007, Valencia] Institutional research plan: CEZ:AV0Z50110509; CEZ:AV0Z10190503 Keywords : spo2 * 3D image analysis * capillaries * confocal microscopy Subject RIV: EA - Cell Biology

  10. Open Plot Project: an open-source toolkit for 3-D structural data analysis

    S. Tavani

    2011-05-01

    Full Text Available In this work we present the Open Plot Project, an open-source software for structural data analysis, including a 3-D environment. The software includes many classical functionalities of structural data analysis tools, like stereoplot, contouring, tensorial regression, scatterplots, histograms and transect analysis. In addition, efficient filtering tools are present allowing the selection of data according to their attributes, including spatial distribution and orientation. This first alpha release represents a stand-alone toolkit for structural data analysis.

    The presence of a 3-D environment with digitalising tools allows the integration of structural data with information extracted from georeferenced images to produce structurally validated dip domains. This, coupled with many import/export facilities, allows easy incorporation of structural analyses in workflows for 3-D geological modelling. Accordingly, Open Plot Project also candidates as a structural add-on for 3-D geological modelling software.

    The software (for both Windows and Linux O.S., the User Manual, a set of example movies (complementary to the User Manual, and the source code are provided as Supplement. We intend the publication of the source code to set the foundation for free, public software that, hopefully, the structural geologists' community will use, modify, and implement. The creation of additional public controls/tools is strongly encouraged.

  11. From motion to faces: 3D-assisted automatic analysis of people

    Iacopo Masi

    2014-01-01

    From motion to faces: 3D-assisted automatic analysis of people. This work proposes new computer vision algorithms about recognizing people by exploiting the face and the imaged appearance of the body. Many computer vision algorithms are covered: tracking, face recognition and person re-identification.

  12. Comparative Analysis of Photogrammetric Methods for 3D Models for Museums

    Hafstað Ármannsdottir, Unnur Erla; Antón Castro, Francesc/François; Mioc, Darka

    2014-01-01

    The goal of this paper is to make a comparative analysis and selection of methodologies for making 3D models of historical items, buildings and cultural heritage and how to preserve information such as temporary exhibitions and archaeological findings. Two of the methodologies analyzed correspond...

  13. Exploring 2D/3D input techniques for medical image analysis

    E.V. Zudilova-Seinstra; P.M.A. Sloot; P.J.H. de Koning; A. Suinesiaputra; R.J. van der Geest; J.H.C. Reiber

    2009-01-01

    We describe a series of experiments that compared the 2D and 3D input methods for selection and positioning tasks related to medical image analysis. For this study, we chose a switchable P5 glove controller, which can be used to provide both 2DOF and 6DOF input control. Our results suggest that for

  14. Evaluation of 2D and 3D glove input applied to medical image analysis

    E.V. Zudilova-Seinstra; P.J.H. de Koning; A. Suinesiaputra; B.W. van Schooten; R.J. van der Geest; J.H.C. Reiber; P.M.A. Sloot

    2010-01-01

    We describe a series of experiments that compared 2D/3D input methods for selection and positioning tasks related to medical image analysis. For our study, we chose a switchable P5 Glove Controller, which can be used to provide both 2DOF and 6DOF input control. Our results suggest that for both task

  15. Analysis of scalability of high-performance 3D image processing platform for virtual colonoscopy

    Yoshida, Hiroyuki; Wu, Yin; Cai, Wenli

    2014-03-01

    One of the key challenges in three-dimensional (3D) medical imaging is to enable the fast turn-around time, which is often required for interactive or real-time response. This inevitably requires not only high computational power but also high memory bandwidth due to the massive amount of data that need to be processed. For this purpose, we previously developed a software platform for high-performance 3D medical image processing, called HPC 3D-MIP platform, which employs increasingly available and affordable commodity computing systems such as the multicore, cluster, and cloud computing systems. To achieve scalable high-performance computing, the platform employed size-adaptive, distributable block volumes as a core data structure for efficient parallelization of a wide range of 3D-MIP algorithms, supported task scheduling for efficient load distribution and balancing, and consisted of a layered parallel software libraries that allow image processing applications to share the common functionalities. We evaluated the performance of the HPC 3D-MIP platform by applying it to computationally intensive processes in virtual colonoscopy. Experimental results showed a 12-fold performance improvement on a workstation with 12-core CPUs over the original sequential implementation of the processes, indicating the efficiency of the platform. Analysis of performance scalability based on the Amdahl's law for symmetric multicore chips showed the potential of a high performance scalability of the HPC 3DMIP platform when a larger number of cores is available.

  16. Quantitative data analysis methods for 3D microstructure characterization of Solid Oxide Cells

    Jørgensen, Peter Stanley

    . Alignment of the individual image slices is performed by automatic detection of ducial marks. Uneven illumination is corrected by tting hypersurfaces to the spatial intensity variation in the 3D image data. Routine use of quantitative three dimensional analysis of microstructure is generally restricted by...... for gaining further fundamental understanding of how microstructure affects performance. In this work, methods for automatic 3D characterization of microstructure are studied: from the acquisition of 3D image data by focused ion beam tomography to the extraction of quantitative measures that......The performance of electrochemical ceramic devices such as solid oxide fuel and electrolyser cells depends on the distribution of constituent phases on the micro or nano scale, also known as the microstructure. The microstructure governs key properties such as ion, electron and gas transport...

  17. 3D city models for CAAD-supported analysis and design of urban areas

    Sinning-Meister, M.; Gruen, A.; Dan, H.

    A joint research project was conducted at ETH Zurich to develop a user-friendly software environment for the representation, visual manipulation, analysis and design of urban areas. Three groups were involved in the project: (1) the 'Architecture and Planning' group defined the requirements and expectations for the system; (2) the 'Photogrammetry' group acquired and processed raster and 3D vector data to form a 3D model of the urban area; and (3) the 'CAAD' (Computer Aided Architectural Design) group embedded the data into AutoCAD and implemented database functionality. Results of the photogrammetry group are presented, including the implementation of a 'topology builder' which automatically fits roof planes to manually or semi-automatically measured roof points in order to create AutoCAD-compatible 3D building models. Digital orthoimages and derived products such as perspective views, and the geometric correction of house roofs in digital orthoimages also were generated for test sites in Switzerland.

  18. A Review of Failure Analysis Methods for Advanced 3D Microelectronic Packages

    Li, Yan; Srinath, Purushotham Kaushik Muthur; Goyal, Deepak

    2016-01-01

    Advanced three dimensional (3D) packaging is a key enabler in driving form factor reduction, performance benefits, and package cost reduction, especially in the fast paced mobility and ultraportable consumer electronics segments. The high level of functional integration and the complex package architecture pose a significant challenge for conventional fault isolation (FI) and failure analysis (FA) methods. Innovative FI/FA tools and techniques are required to tackle the technical and throughput challenges. In this paper, the applications of FI and FA techniques such as Electro Optic Terahertz Pulse Reflectometry, 3D x-ray computed tomography, lock-in thermography, and novel physical sample preparation methods to 3D packages with package on package and stacked die with through silicon via configurations are reviewed, along with the key FI and FA challenges.

  19. The DynDom3D Webserver for the Analysis of Domain Movements in Multimeric Proteins.

    Girdlestone, Christopher; Hayward, Steven

    2016-01-01

    DynDom3D is a program for the analysis of domain movements in multimeric proteins. Its inputs are two structure files that indicate a possible domain movement, but the onus has been on the user to process the files so that there is the necessary one-to-one equivalence between atoms in the two atom lists. This is often a prohibitive task to carry out manually, which has limited the application of DynDom3D. Here we report on a webserver with a preprocessor that automatically creates an equivalence between atoms using sequence alignment methods. The processed structure files are passed to DynDom3D and the results are presented on a webpage that includes molecular graphics for easy visualization. PMID:26540459

  20. Application of 3D X-ray CT data sets to finite element analysis

    Finite Element Modeling (FEM) is becoming more important as industry drives toward concurrent engineering. A fundamental hindrance to fully exploiting the power of FEM is the human effort required to acquire complex part geometry, particularly as-built geometry, as a FEM mesh. Many Quantitative Non Destructive Evaluation (QNDE) techniques that produce three-dimensional (3D) data sets provide a substantial reduction in the effort required to apply FEM to as-built parts. This paper describes progress at LLNL on the application of 3D X-ray computed tomography (CT) data sets to more rapidly produce high-quality FEM meshes of complex, as-built geometries. Issues related to the volume segmentation of the 3D CT data as well as the use of this segmented data to tailor generic hexahedral FEM meshes to part specific geometries are discussed. The application of these techniques to FEM analysis in the medical field is reported here

  1. High-resolution 3D micro-CT imaging of breast microcalcifications: a preliminary analysis

    Detection of microcalcifications on mammograms indicates the presence of breast lesion, and the shapes of the microcalcifications as seen by conventional mammography correlates with the probability of malignancy. This preliminary study evaluated the 3D shape of breast microcalcifications using micro-computed tomography (micro-CT) and compared the findings with those obtained using anatomopathological analysis. The study analyzed breast biopsy samples from 11 women with findings of suspicious microcalcifications on routine mammograms. The samples were imaged using a micro-CT (SkyScan 1076) at a resolution of 35 μm. Images were reconstructed using filtered back-projection and analyzed in 3D using surface rendering. The samples were subsequently analyzed by the pathology service. Reconstructed 3D images were compared with the corresponding histological slices. Anatomopathological analysis showed that 5 of 11 patients had ductal breast carcinoma in situ. One patient was diagnosed with invasive ductal carcinoma. Individual object analysis was performed on 597 microcalcifications. Malignant microcalcifications tended to be thinner and to have a smaller volume and surface area, while their surface area-to-volume ratio was greater than that of benign microcalcifications. The structure model index values were the same for malignant and benign microcalcifications. This is the first study to use micro-CT for quantitative 3D analysis of microcalcifications. This high-resolution imaging technique will be valuable for gaining a greater understanding of the morphologic characteristics of malignant and benign microcalcifications. The presence of many small microcalcifications can be an indication of malignancy. For the larger microcalcifications, 3D parameters confirmed the more irregular shape of malignant microcalcifications

  2. Dynamic Characteristic Analysis of Linear DC Motor by 3D EMCN Considering Input Voltage

    Ha, Kyung Ho; Yeom, Sang Bu [Changwon National University, Changwon(Korea); Hong, JUNG Pyo; Hur Jin; Kang Do Hyunc [Hanyang University(Seoul Campus), Seoul(Korea)

    2002-02-01

    In order to design the Linear DC Motor (LDM) With improved characteristics, transient and steady state analysis are required. Furthermore, 3D analysis is also needed to analyze the precise characteristics like thrust, time harmonics. This paper deals with the transient and dynamic characteristic analysis if LDM by coupling of external circuit and motion equation using 3D Equivalent Magnetic Circuit Network Method (EMCN). For the three dimensional analysis of electric machine, EMCN is very effective method that ensures high accuracy similar to FEM and short computation time. Also, The modeling by EMCN easily allows the mover to move with respect to the Sartre at each time Also, and the spatial moving step is determined by the solution of the mechanical motion equation and the computed electromagnetic thrust. The results are compared with experimental ones to clarify the usefulness and verify the accuracy of the proposed method. (author). 11 refs., 20 figs., 2 tabs.

  3. Pumping simulations using 3D FEM analysis on multi-pumping wells

    Shuhei, KOTANI; Takahumi, KITAOKA; Makoto, NAKAMURA; Harushige, KUSUMI; 楠見, 晴重

    2011-01-01

    In this research, we chiefly conducted on-site measurement and analysis to examine how the pumping wells influence groundwater behavior. We established a 3D model for groundwater and make suggestions for the adequate management of the groundwater by a pumping simulation analysis. As a result, it can be seen from our research that the fluctuation of water level caused by group wells has been reproduced accurately by using our model.

  4. Digital Image Analysis of Cells : Applications in 2D, 3D and Time

    Pinidiyaarachchi, Amalka

    2009-01-01

    Light microscopes are essential research tools in biology and medicine. Cell and tissue staining methods have improved immensely over the years and microscopes are now equipped with digital image acquisition capabilities. The image data produced require development of specialized analysis methods. This thesis presents digital image analysis methods for cell image data in 2D, 3D and time sequences. Stem cells have the capability to differentiate into specific cell types. The mechanism behind di...

  5. Parallel Isosurface Extraction for 3D Data Analysis Workflows in Distributed Environments

    D'Agostino, Daniele; Clematis, Andrea; Gianuzzi, Vittoria

    2011-01-01

    Abstract In this paper we discuss the issues related to the development of efficient parallel implementations of the Marching Cubes algorithm, one of the most used methods for isosurface extraction, which is a fundamental operation for 3D data analysis and visualization. We present three possible parallelization strategies and we outline pros and cons of each of them, considering isosurface extraction as stand-alone operation or as part of a dynamic workflow. Our analysis shows tha...

  6. A comprehensive statistical framework for elastic shape analysis of 3D faces

    Kurtek, Sebastian; Drira, Hassen

    2015-01-01

    We develop a comprehensive statistical framework for analyzing shapes of 3D faces. In particular, we adapt a recent elastic shape analysis framework to the case of hemispherical surfaces, and explore its use in a number of processing applications. This framework provides a parameterization-invariant, elastic Riemannian metric, which allows the development of mathematically rigorous tools for statistical analysis. Specifically, this paper describes methods for registration, comparison and defo...

  7. A 3-D aerodynamic method for the analysis of isolated horizontal-axis wind turbines

    Ammara, I.; Masson, C.; Paraschivoiu, I. [Ecole Polytechnique, Montreal (Canada)

    1997-12-31

    In most existing performance-analysis methods, wind turbines are considered isolated so that interference effects caused by other rotors or by the site topography are neglected. The main objective of this paper is to propose a practical 3-D method suitable for the study of these effects, in order to optimize the arrangement and the positioning of Horizontal-Axis Wind Turbines (HAWTs) in a wind farm. In the proposed methodology, the flow field around isolated HAWTs is predicted by solving the 3-D, time-averaged, steady-state, incompressible, Navier-Stokes equations in which the turbines are represented by distributions of momentum sources. The resulting governing equations are solved using a Control-Volume Finite Element Method (CVFEM). The fundamental aspects related to the development of a practical 3-D method are discussed in this paper, with an emphasis on some of the challenges that arose during its implementation. The current implementation is limited to the analysis of isolated HAWTs. Preliminary results have indicated that, the proposed 3-D method reaches the same level of accuracy, in terms of performance predictions, that the previously developed 2-D axisymmetric model and the well-known momentum-strip theory, while still using reasonable computers resources. It can be considered as a useful tool for the design of HAWTs. Its main advantages, however, are its intrinsic capacity to predict the details of the flow in the wake, and its capabilities of modelling arbitrary wind-turbine arrangements and including ground effects.

  8. Geomorphometric analysis of cave ceiling channels mapped with 3-D terrestrial laser scanning

    Gallay, Michal; Hochmuth, Zdenko; Kaňuk, Ján; Hofierka, Jaroslav

    2016-05-01

    The change of hydrological conditions during the evolution of caves in carbonate rocks often results in a complex subterranean geomorphology, which comprises specific landforms such as ceiling channels, anastomosing half tubes, or speleothems organized vertically in different levels. Studying such complex environments traditionally requires tedious mapping; however, this is being replaced with terrestrial laser scanning technology. Laser scanning overcomes the problem of reaching high ceilings, providing new options to map underground landscapes with unprecedented level of detail and accuracy. The acquired point cloud can be handled conveniently with dedicated software, but applying traditional geomorphometry to analyse the cave surface is limited. This is because geomorphometry has been focused on parameterization and analysis of surficial terrain. The theoretical and methodological concept has been based on two-dimensional (2-D) scalar fields, which are sufficient for most cases of the surficial terrain. The terrain surface is modelled with a bivariate function of altitude (elevation) and represented by a raster digital elevation model. However, the cave is a 3-D entity; therefore, a different approach is required for geomorphometric analysis. In this paper, we demonstrate the benefits of high-resolution cave mapping and 3-D modelling to better understand the palaeohydrography of the Domica cave in Slovakia. This methodological approach adopted traditional geomorphometric methods in a unique manner and also new methods used in 3-D computer graphics, which can be applied to study other 3-D geomorphological forms.

  9. Carotid artery stenosis: reproducibility of automated 3D CT angiography analysis method

    The aim of this study was to assess the reproducibility and anatomical accuracy of automated 3D CT angiography analysis software in the evaluation of carotid artery stenosis with reference to rotational DSA (rDSA). Seventy-two vessels in 36 patients with symptomatic carotid stenosis were evaluated by 3D CT angiography and conventional DSA (cDSA). Thirty-one patients also underwent rotational 3D DSA (rDSA). Multislice CT was performed with bolus tracking and slice thickness of 1.5 mm (1-mm collimation, table feed 5 mm/s) and reconstruction interval of 1.0 mm. Two observers independently performed the stenosis measurements on 3D CTA and on MPR rDSA according to the NASCET criteria. The first measurements on CTA utilized an analysis program with automatic stenosis recognition and quantitation. In the subsequent measurements, manual corrections were applied when necessary. Interfering factors for stenosis quantitation, such as calcifications, ulcerations, and adjacent vessels, were registered. Intraobserver and interobserver correlation for CTA were 0.89 and 0.90, respectively. (p<0.001). The interobserver correlation between two observers for MPR rDSA was 0.90 (p<0.001). The intertechnique correlation between CTA and rDSA was 0.69 (p<0.001) using automated measurements but increased to 0.81 (p<0.001) with the manually corrected measurements. Automated stenosis recognition achieved a markedly poorer correlation with MPR rDSA in carotids with interfering factors than those in cases where there were no such factors. Automated 3D CT angiography analysis methods are highly reproducible. Manually corrected measurements facilitated avoidance of the interfering factors, such as ulcerations, calcifications, and adjacent vessels, and thus increased anatomical accuracy of arterial delineation by automated CT angiography with reference to MPR rDSA. (orig.)

  10. Molecular Modeling Studies of 4,5-Dihydro-1H-pyrazolo[4,3-h] quinazoline Derivatives as Potent CDK2/Cyclin A Inhibitors Using 3D-QSAR and Docking

    Fa-Jun Song

    2010-09-01

    Full Text Available CDK2/cyclin A has appeared as an attractive drug targets over the years with diverse therapeutic potentials. A computational strategy based on comparative molecular fields analysis (CoMFA and comparative molecular similarity indices analysis (CoMSIA followed by molecular docking studies were performed on a series of 4,5-dihydro-1H-pyrazolo[4,3-h]quinazoline derivatives as potent CDK2/cyclin A inhibitors. The CoMFA and CoMSIA models, using 38 molecules in the training set, gave r2cv values of 0.747 and 0.518 and r2 values of 0.970 and 0.934, respectively. 3D contour maps generated by the CoMFA and CoMSIA models were used to identify the key structural requirements responsible for the biological activity. Molecular docking was applied to explore the binding mode between the ligands and the receptor. The information obtained from molecular modeling studies may be helpful to design novel inhibitors of CDK2/cyclin A with desired activity.

  11. QSAR modeling and molecular interaction analysis of natural compounds as potent neuraminidase inhibitors.

    Sun, Jiaying; Mei, Hu

    2016-04-26

    Different QSAR models of 40 natural compounds as neuraminidase inhibitors (NIs) are developed to comprehend chemical-biological interactions and predict activities against neuraminidase (NA) from Clostridium perfringens. Based on the constitutional, topological and conformational descriptors, R(2) and Q(2) values of the obtained SRA model are 0.931 and 0.856. The R(2) and Q(2) values of the constructed HQSAR and almond models are 0.903 and 0.767, 0.904 and 0.511, respectively. Based on the pharmacophore alignment, R(2) and Q(2) values of the optimal CoMSIA model are 0.936 and 0.654. Moreover, Rtest(2) and Qext(2) of values of SRA, HQSAR, almond and CoMSIA models are 0.611 and 0.565, 0.753 and 0.750, 0.612 and 0.582, 0.582 and 0.571, respectively. So, QSAR models have good predictive capability. They can be further used to evaluate and screen new compounds. Moreover, hydrogen bonds and electrostatic factors have high contributions to activities. To understand molecular interactions between natural compounds and NA from Clostridium perfringens, molecular docking is investigated. The docking results elucidate that Arg266, Asp291, Asp328, Tyr485, Glu493, Arg555, Arg615 and Tyr655 are especially the key residues in the active site of 2bf6. Hydrogen bonds and electrostatics are key factors, which impact the interactions between NIs and NA. So, the influential factors of interactions between NIs and NA in the docking results are in agreement with the QSAR results. PMID:27008437

  12. Analysis results from the Los Alamos 2D/3D program

    Los Alamos National Laboratory is a participant in the 2D/3D program. Activities conducted at Los Alamos National Laboratory in support of 2D/3D program goals include analysis support of facility design, construction, and operation; provision of boundary and initial conditions for test-facility operations based on analysis of pressurized water reactors; performance of pretest and posttest predictions and analyses; and use of experimental results to validate and assess the single- and multi-dimensional, nonequilibrium features in the Transient Reactor Analysis Code (TRAC). During fiscal year 1987, Los Alamos conducted analytical assessment activities using data from the Slab Core Test Facility, The Cylindrical Core Test Facility, and the Upper Plenum Test Facility. Finally, Los Alamos continued work to provide TRAC improvements. In this paper, Los Alamos activities during fiscal year 1987 will be summarized; several significant accomplishments will be described in more detail to illustrate the work activities at Los Alamos

  13. Analysis results from the Los Alamos 2D/3D program

    Los Alamos National Laboratory is a participant in the 2D/3D program. Activities conducted at Los Alamos National Laboratory in support of 2D/3D program goals include analysis support of facility design, construction, and operation; provision of boundary and initial conditions for test-facility operations based on analysis of pressurized water reactors; performance of pretest and post-test predictions and analyses; and use of experimental results to validate and assess the single- and multi-dimensional, nonequilibrium features in the Transient Reactor Analysis Code (TRAC). During fiscal year 1987, Los Alamos conducted analytical assessment activities using data from the Slab Core Test Facility, the Cylindrical Core Test Facility, and the Upper Plenum Test Facility. Finally, Los Alamos continued work to provide TRAC improvements. In this paper, Los Alamos activities during fiscal year 1987 are summarized; several significant accomplishments are described in more detail to illustrate the work activities at Los Alamos

  14. Comparison: RELAP5-3D systems analysis code and fluent CFD code momentum equation formulations

    Recently the Idaho National Engineering and Environmental Laboratory (INEEL), in conjunction with Fluent Corporation, have developed a new analysis tool by coupling the Fluent computational fluid dynamics (CFD) code to the RELAP5-3D advanced thermal-hydraulic analysis code. This tool enables researchers to perform detailed, two- or three-dimensional analyses using Fluent's CFD capability while the boundary conditions required by the Fluent calculation are provided by the balance-of-system model created using RELAP5-3D. Fluent and RELAP5-3D have strengths that complement one another. CFD codes, such as Fluent, are commonly used to analyze the flow behavior in regions of a system where complex flow patterns are expected or present. On the other hand, RELAP5-3D was developed to analyze the behavior of two-phase systems that could be modeled in one-dimension. Empirical relationships were used where first-principle physics were not well developed. Both Fluent and RELAP5-3D are exemplary in their areas of specialization. The differences between Fluent and RELAP5 fundamentally stem from their field equations. This study focuses on the differences between the momentum equation representations in the two codes (the continuity equation formulations are equivalent for single phase flow). First the differences between the momentum equations are summarized. Next the effect of the differences in the momentum equations are examined by comparing the results obtained using both codes to study the same problem, i.e., fully-developed turbulent pipe flow. Finally, conclusions regarding the significance of the differences are given. (author)

  15. Integrated 3D-printed reactionware for chemical synthesis and analysis.

    Symes, Mark D; Kitson, Philip J; Yan, Jun; Richmond, Craig J; Cooper, Geoffrey J T; Bowman, Richard W; Vilbrandt, Turlif; Cronin, Leroy

    2012-05-01

    Three-dimensional (3D) printing has the potential to transform science and technology by creating bespoke, low-cost appliances that previously required dedicated facilities to make. An attractive, but unexplored, application is to use a 3D printer to initiate chemical reactions by printing the reagents directly into a 3D reactionware matrix, and so put reactionware design, construction and operation under digital control. Here, using a low-cost 3D printer and open-source design software we produced reactionware for organic and inorganic synthesis, which included printed-in catalysts and other architectures with printed-in components for electrochemical and spectroscopic analysis. This enabled reactions to be monitored in situ so that different reactionware architectures could be screened for their efficacy for a given process, with a digital feedback mechanism for device optimization. Furthermore, solely by modifying reactionware architecture, reaction outcomes can be altered. Taken together, this approach constitutes a relatively cheap, automated and reconfigurable chemical discovery platform that makes techniques from chemical engineering accessible to typical synthetic laboratories. PMID:22522253

  16. Multi-dimensional Seismic Response Analysis of Base-Isolated Frame Structure with 3D Isolator

    Xiong Shishu; Huang Liting; Chen Jinfeng; Su Jingsu

    2005-01-01

    The three-dimensional lead-rubber dish-spring bearing (3DB) is proposed in this paper. The 3DB is composed of lead rubber bearing (LRB) and dish-spring bearing (DSB) with damper in series. The 3DB put forward in this paper is effective in the resolution of difficulties in strong vertical capacity and vertical damping of three-dimensional isolation bearings. It effectively suppresses rocking motions as well. The analytical model and motion equations of multi-dimensional seismic responses of 3D base-isolated frame structures are established. Taking a five-storey frame structure as an example, an extensive simulation analysis is carried out. The results show that the 3D base-isolated structure with the proposed 3DB is effective in 3D isolation; it can reduce seismic responses by 50 % compared to a non-isolated structure. Therefore, the 3D isolation problem in building can be solved easily and effectively with the 3DB proposed in this paper.

  17. A finite element analysis of a 3D auxetic textile structure for composite reinforcement

    This paper reports the finite element analysis of an innovative 3D auxetic textile structure consisting of three yarn systems (weft, warp and stitch yarns). Different from conventional 3D textile structures, the proposed structure exhibits an auxetic behaviour under compression and can be used as a reinforcement to manufacture auxetic composites. The geometry of the structure is first described. Then a 3D finite element model is established using ANSYS software and validated by the experimental results. The deformation process of the structure at different compression strains is demonstrated, and the validated finite element model is finally used to simulate the auxetic behaviour of the structure with different structural parameters and yarn properties. The results show that the auxetic behaviour of the proposed structure increases with increasing compression strain, and all the structural parameters and yarn properties have significant effects on the auxetic behaviour of the structure. It is expected that the study could provide a better understanding of 3D auxetic textile structures and could promote their application in auxetic composites. (paper)

  18. Theoretical studies on QSAR and mechanism of 2-indolinone derivatives as tubulin inhibitors

    Liao, Si Yan; Qian, Li; Miao, Ti Fang; Lu, Hai Liang; Zheng, Kang Cheng

    The theoretical studies on three-dimensional quantitative structure activity relationship (3D-QSAR) and action mechanism of a series of 2-indolinone derivatives as tubulin inhibitors against human breast cancer cell line MDA-MB-231 have been carried out. The established 3D-QSAR model from the comparative molecular field analysis (CoMFA) shows not only significant statistical quality but also predictive ability, with high correlation coefficient (R2 = 0.986) and cross-validation coefficient (q2 = 0.683). In particular, the appropriate binding orientations and conformations of these 2-indolinone derivatives interacting with tubulin are located by docking study, and it is very interesting to find that the plot of the energy scores of these compounds in DOCK versus the corresponding experimental pIC50 values exhibits a considerable linear correlation. Therefore, the inhibition mechanism that 2-indolinone derivatives were regarded as tubulin inhibitors can be theoretically confirmed. Based on such an inhibition mechanism along with 3D-QSAR results, some important factors improving the activities of these compounds were discussed in detail. These factors can be summarized as follows: the H atom adopted as substituent R1, the substituent R2 with higher electropositivity and smaller bulk, the substituents R4-R6 (on the phenyl ring) with higher electropositivity and larger bulk, and so on. These results can offer useful theoretical references for understanding the action mechanism, designing more potent inhibitors, and predicting their activities prior to synthesis.

  19. Error Analysis of Terrestrial Laser Scanning Data by Means of Spherical Statistics and 3D Graphs

    Pedro Arias

    2010-11-01

    Full Text Available This paper presents a complete analysis of the positional errors of terrestrial laser scanning (TLS data based on spherical statistics and 3D graphs. Spherical statistics are preferred because of the 3D vectorial nature of the spatial error. Error vectors have three metric elements (one module and two angles that were analyzed by spherical statistics. A study case has been presented and discussed in detail. Errors were calculating using 53 check points (CP and CP coordinates were measured by a digitizer with submillimetre accuracy. The positional accuracy was analyzed by both the conventional method (modular errors analysis and the proposed method (angular errors analysis by 3D graphics and numerical spherical statistics. Two packages in R programming language were performed to obtain graphics automatically. The results indicated that the proposed method is advantageous as it offers a more complete analysis of the positional accuracy, such as angular error component, uniformity of the vector distribution, error isotropy, and error, in addition the modular error component by linear statistics.

  20. Statistical 3D shape analysis of gender differences in lateral ventricles

    He, Qing; Karpman, Dmitriy; Duan, Ye

    2010-03-01

    This paper aims at analyzing gender differences in the 3D shapes of lateral ventricles, which will provide reference for the analysis of brain abnormalities related to neurological disorders. Previous studies mostly focused on volume analysis, and the main challenge in shape analysis is the required step of establishing shape correspondence among individual shapes. We developed a simple and efficient method based on anatomical landmarks. 14 females and 10 males with matching ages participated in this study. 3D ventricle models were segmented from MR images by a semiautomatic method. Six anatomically meaningful landmarks were identified by detecting the maximum curvature point in a small neighborhood of a manually clicked point on the 3D model. Thin-plate spline was used to transform a randomly selected template shape to each of the rest shape instances, and the point correspondence was established according to Euclidean distance and surface normal. All shapes were spatially aligned by Generalized Procrustes Analysis. Hotelling T2 twosample metric was used to compare the ventricle shapes between males and females, and False Discovery Rate estimation was used to correct for the multiple comparison. The results revealed significant differences in the anterior horn of the right ventricle.

  1. A SAS2H/KENO-V Methodology for 3D Full Core depletion analysis

    This paper describes the use of a SAS2H/KENO-V methodology for 3D full core depletion analysis and illustrates its capabilities by applying it to burnup analysis of the IRIS core benchmarks. This new SAS2H/KENO-V sequence combines a 3D Monte Carlo full core calculation of node power distribution and a 1D Wigner-Seitz equivalent cell transport method for independent depletion calculation of each of the nodes. This approach reduces by more than an order of magnitude the time required for getting comparable results using the MOCUP code system. The SAS2H/KENO-V results for the asymmetric IRIS core benchmark are in good agreement with the results of the ALPHA/PHOENIX/ANC code system. (author)

  2. TMI-1 MSLB coupled 3-D neutronics/thermal hydraulics analysis: application of RELAP5-3D and comparison with different codes

    A comprehensive analysis of the double ended Main Steam Line Break (MSLB) accident assumed to occur in the Babcock and Wilcox nuclear power plant of Three Miles Island Unit 1 (TMI-1) has been carried out of the University of Pisa in co-operation with the University of Zagreb and the Texas A and M University. The overall activity has been completed within the framework of the participation in the OECD-CSNI/NSC (Committee on the Safety of Nuclear Installations - Nuclear Science Committee) 'PWR MSLB Benchmark'. Different code versions have been adopted in the analysis. Results from the following codes (or code versions) are described in this paper: RELAP5/MOD3.2.2, beta version, coupled with the 3-D neutron kinetics Parcs code; RELAP5/MOD3.2.2, gamma version, coupled with the 3-D neutron kinetics Quabbox code; RELAP5/3D, coupled with the 3-D neutron kinetics Nestle code. Boundary and initial conditions of the system including those relevant to the fuel status, have been supplied by Pensilvania State University that had a co-operation GPU (the utility, owner of TMI) and NRC (US Nuclear Regulatory Commission). The capability of the control rods to recover the accident has been demonstrated in all the cases as well as the capability of all the codes to predict the time evolution of the assigned transient. However, one stuck control rod caused some 're-criticality' or 'return-to-power' whose magnitude is largely affected by boundary and initial conditions. The comparison among the results obtained by adopting the same thermalhydraulic nodalization and the different 'coupled' code version is discussed in the present document. (author)

  3. Shape analysis of local facial patches for 3D facial expression recognition

    Maalej, Ahmed; Ben Amor, Boulbaba; Daoudi, Mohamed; Srivastava, Anuj; Berretti, Stefano

    2011-01-01

    International audience In this paper we address the problem of 3D facial expression recognition. We propose a local geometric shape analysis of facial surfaces coupled with machine learning techniques for expression classification. A computation of the length of the geodesic path between corresponding patches, using a Riemannian framework, in a shape space provides a quantitative information about their similarities. These measures are then used as inputs to several classification methods....

  4. MRI ANALYSIS OF 3D NORMAL AND POST-GLOSSECTOMY TONGUE MOTION IN SPEECH

    Xing, Fangxu; Murano, Emi Z.; Lee, Junghoon; Woo, Jonghye; Stone, Maureen; Prince, Jerry L.

    2013-01-01

    Measuring the internal muscular motion and deformation of the tongue during natural human speech is of high interest to head and neck surgeons and speech language pathologists. A pipeline for calculating 3D tongue motion from dynamic cine and tagged Magnetic Resonance (MR) images during speech has been developed. This paper presents the result of a complete analysis of eleven subjects’ (seven normal controls and four glossectomy patients) global tongue motion during speech obtained through MR...

  5. 3D STATE SPACE ANALYSIS AND FREE-EDGE EFFECT OF PIEZOELECTRIC LAMINATED THICK PLATES

    Han, Chao

    2014-01-01

    The accurate evaluation of interlaminar stresses is of great significance in the analysis and design of laminated and piezoelectric laminated structures because complex behaviours of these stresses near free edges initiate edge delamination that raises concerns about the structural integrity and reliability. This thesis presented 3D hybrid analyses on the interlaminar stresses to investigate the electromechanical coupling and free edge effects of piezoelectric laminated plates with an emphasi...

  6. ECOLOGICAL AND TECHNOLOGICAL ANALYSIS OF MATERIALS FOR 3D-PRINTING

    Є.О. Бовсуновський; Зінченко, Р. О.

    2016-01-01

    The article analyzes the main materials used for 3D-printing. Particular attention is paid to the study of ecological and technological analysis of the effects of the most widely used material: Polylactic Acid and Acrylonitrile Butadiene Styrene, as well as their professional series and Nylon, Polyethylene Terephthalate, TPE on the environment. The article deals with the characteristic features of the physical properties of materials (material) for their intended purpose, according sharing al...

  7. Importance of a 3D forward modeling tool for surface wave analysis methods

    Pageot, Damien; Le Feuvre, Mathieu; Donatienne, Leparoux; Philippe, Côte; Yann, Capdeville

    2016-04-01

    Since a few years, seismic surface waves analysis methods (SWM) have been widely developed and tested in the context of subsurface characterization and have demonstrated their effectiveness for sounding and monitoring purposes, e.g., high-resolution tomography of the principal geological units of California or real time monitoring of the Piton de la Fournaise volcano. Historically, these methods are mostly developed under the assumption of semi-infinite 1D layered medium without topography. The forward modeling is generally based on Thomson-Haskell matrix based modeling algorithm and the inversion is driven by Monte-Carlo sampling. Given their efficiency, SWM have been transfered to several scale of which civil engineering structures in order to, e.g., determine the so-called V s30 parameter or assess other critical constructional parameters in pavement engineering. However, at this scale, many structures may often exhibit 3D surface variations which drastically limit the efficiency of SWM application. Indeed, even in the case of an homogeneous structure, 3D geometry can bias the dispersion diagram of Rayleigh waves up to obtain discontinuous phase velocity curves which drastically impact the 1D mean velocity model obtained from dispersion inversion. Taking advantages of high-performance computing center accessibility and wave propagation modeling algorithm development, it is now possible to consider the use of a 3D elastic forward modeling algorithm instead of Thomson-Haskell method in the SWM inversion process. We use a parallelized 3D elastic modeling code based on the spectral element method which allows to obtain accurate synthetic data with very low numerical dispersion and a reasonable numerical cost. In this study, we choose dike embankments as an illustrative example. We first show that their longitudinal geometry may have a significant effect on dispersion diagrams of Rayleigh waves. Then, we demonstrate the necessity of 3D elastic modeling as a forward

  8. Performance analysis of high quality parallel preconditioners applied to 3D finite element structural analysis

    Kolotilina, L.; Nikishin, A.; Yeremin, A. [and others

    1994-12-31

    The solution of large systems of linear equations is a crucial bottleneck when performing 3D finite element analysis of structures. Also, in many cases the reliability and robustness of iterative solution strategies, and their efficiency when exploiting hardware resources, fully determine the scope of industrial applications which can be solved on a particular computer platform. This is especially true for modern vector/parallel supercomputers with large vector length and for modern massively parallel supercomputers. Preconditioned iterative methods have been successfully applied to industrial class finite element analysis of structures. The construction and application of high quality preconditioners constitutes a high percentage of the total solution time. Parallel implementation of high quality preconditioners on such architectures is a formidable challenge. Two common types of existing preconditioners are the implicit preconditioners and the explicit preconditioners. The implicit preconditioners (e.g. incomplete factorizations of several types) are generally high quality but require solution of lower and upper triangular systems of equations per iteration which are difficult to parallelize without deteriorating the convergence rate. The explicit type of preconditionings (e.g. polynomial preconditioners or Jacobi-like preconditioners) require sparse matrix-vector multiplications and can be parallelized but their preconditioning qualities are less than desirable. The authors present results of numerical experiments with Factorized Sparse Approximate Inverses (FSAI) for symmetric positive definite linear systems. These are high quality preconditioners that possess a large resource of parallelism by construction without increasing the serial complexity.

  9. Integrating Data Clustering and Visualization for the Analysis of 3D Gene Expression Data

    Data Analysis and Visualization (IDAV) and the Department of Computer Science, University of California, Davis, One Shields Avenue, Davis CA 95616, USA,; nternational Research Training Group ``Visualization of Large and Unstructured Data Sets,' ' University of Kaiserslautern, Germany; Computational Research Division, Lawrence Berkeley National Laboratory, One Cyclotron Road, Berkeley, CA 94720, USA; Genomics Division, Lawrence Berkeley National Laboratory, One Cyclotron Road, Berkeley CA 94720, USA; Life Sciences Division, Lawrence Berkeley National Laboratory, One Cyclotron Road, Berkeley CA 94720, USA,; Computer Science Division,University of California, Berkeley, CA, USA,; Computer Science Department, University of California, Irvine, CA, USA,; All authors are with the Berkeley Drosophila Transcription Network Project, Lawrence Berkeley National Laboratory,; Rubel, Oliver; Weber, Gunther H.; Huang, Min-Yu; Bethel, E. Wes; Biggin, Mark D.; Fowlkes, Charless C.; Hendriks, Cris L. Luengo; Keranen, Soile V. E.; Eisen, Michael B.; Knowles, David W.; Malik, Jitendra; Hagen, Hans; Hamann, Bernd

    2008-05-12

    The recent development of methods for extracting precise measurements of spatial gene expression patterns from three-dimensional (3D) image data opens the way for new analyses of the complex gene regulatory networks controlling animal development. We present an integrated visualization and analysis framework that supports user-guided data clustering to aid exploration of these new complex datasets. The interplay of data visualization and clustering-based data classification leads to improved visualization and enables a more detailed analysis than previously possible. We discuss (i) integration of data clustering and visualization into one framework; (ii) application of data clustering to 3D gene expression data; (iii) evaluation of the number of clusters k in the context of 3D gene expression clustering; and (iv) improvement of overall analysis quality via dedicated post-processing of clustering results based on visualization. We discuss the use of this framework to objectively define spatial pattern boundaries and temporal profiles of genes and to analyze how mRNA patterns are controlled by their regulatory transcription factors.

  10. 3-D slug flow heat transfer analysis of coupled coolant cells in finite LMFBR bundles

    A three-dimensional single region slug flow heat transfer analysis for finite LMFBR rod bundles using a classical analytical solution method has been performed. According to the isolated single cell analysis, the results show that the peripheral clad temperature variation as well as the thermal entrance length are strongly dependent upon the degree of irregularity displayed by various coolant geometries. Since under the present LMFBR conditions, fully-developed temperature fields may hardly be established in such characteristic rod bundle regions, a 3-D heat transfer analysis seems to be mandatory. This implies that the results of fully developed heat transfer analyses are by far too conservative

  11. A combined 1D/3D fuel burnup analysis of generation IV light water reactor IRIS

    A combined 1D/3D methodology for the fuel burnup analysis of generation IV light water reactors with thin boron coating that covers the fuel rods is described in this paper. This methodology is founded on three approximations. The first approximation assumes that the problem of fuel depletion in the entire 3D core can be resolved into two independent problems. One is a 3D Monte Carlo evolution of power distribution in large volumes (nodes) with the KENO-V.a code, and the other is a transport method evolution of burnup dependent fuel composition in 1D Wigner-Seitz cell for each node independently. With the second approximation, the time-dependent fuel composition in the node (e.g., in the fuel assembly) is calculated by using a 1D fuel depletion analysis with the SAS2H control module from the SCALE-4.4a code system. The third approximation involves smearing the boron coating with the clad (by volume homogenization). The proposed SAS2H/KENO-V.a methodology is verified for the case of 2D x-y model of IRIS 15x15 fuel assembly (with a reflective boundary condition) by using two well benchmarked code systems. The first one is MOCUP, a coupled MCNP-4C and ORIGEN2.1 utility code, and the second is KENO-V.a/ORIGEN2.1 code system recently developed by authors of this paper. It has been found that the proposed SAS2H/KENO-V.a methodology gives a satisfactory accuracy for keff and nuclide composition. Finally, this methodology was applied for 3D burnup analysis of IRIS-1000 benchmark≠44 core. Detailed keff and power density evolution with burnup are reported. (author)

  12. Quantitative analysis of spinal curvature in 3D: application to CT images of normal spine

    The purpose of this study is to present a framework for quantitative analysis of spinal curvature in 3D. In order to study the properties of such complex 3D structures, we propose two descriptors that capture the characteristics of spinal curvature in 3D. The descriptors are the geometric curvature (GC) and curvature angle (CA), which are independent of the orientation and size of spine anatomy. We demonstrate the two descriptors that characterize the spinal curvature in 3D on 30 computed tomography (CT) images of normal spine and on a scoliotic spine. The descriptors are determined from 3D vertebral body lines, which are obtained by two different methods. The first method is based on the least-squares technique that approximates the manually identified vertebra centroids, while the second method searches for vertebra centroids in an automated optimization scheme, based on computer-assisted image analysis. Polynomial functions of the fourth and fifth degree were used for the description of normal and scoliotic spinal curvature in 3D, respectively. The mean distance to vertebra centroids was 1.1 mm (±0.6 mm) for the first and 2.1 mm (±1.4 mm) for the second method. The distributions of GC and CA values were obtained along the 30 images of normal spine at each vertebral level and show that maximal thoracic kyphosis (TK), thoracolumbar junction (TJ) and maximal lumbar lordosis (LL) on average occur at T3/T4, T12/L1 and L4/L5, respectively. The main advantage of GC and CA is that the measurements are independent of the orientation and size of the spine, thus allowing objective intra- and inter-subject comparisons. The positions of maximal TK, TJ and maximal LL can be easily identified by observing the GC and CA distributions at different vertebral levels. The obtained courses of the GC and CA for the scoliotic spine were compared to the distributions of GC and CA for the normal spines. The significant difference in values indicates that the descriptors of GC and CA

  13. Quantitative analysis of spinal curvature in 3D: application to CT images of normal spine

    Vrtovec, Tomaz; Likar, Bostjan; Pernus, Franjo [University of Ljubljana, Faculty of Electrical Engineering, Trzaska 25, SI-1000 Ljubljana (Slovenia)], E-mail: tomaz.vrtovec@fe.uni-lj.si, E-mail: bostjan.likar@fe.uni-lj.si, E-mail: franjo.pernus@fe.uni-lj.si

    2008-04-07

    The purpose of this study is to present a framework for quantitative analysis of spinal curvature in 3D. In order to study the properties of such complex 3D structures, we propose two descriptors that capture the characteristics of spinal curvature in 3D. The descriptors are the geometric curvature (GC) and curvature angle (CA), which are independent of the orientation and size of spine anatomy. We demonstrate the two descriptors that characterize the spinal curvature in 3D on 30 computed tomography (CT) images of normal spine and on a scoliotic spine. The descriptors are determined from 3D vertebral body lines, which are obtained by two different methods. The first method is based on the least-squares technique that approximates the manually identified vertebra centroids, while the second method searches for vertebra centroids in an automated optimization scheme, based on computer-assisted image analysis. Polynomial functions of the fourth and fifth degree were used for the description of normal and scoliotic spinal curvature in 3D, respectively. The mean distance to vertebra centroids was 1.1 mm ({+-}0.6 mm) for the first and 2.1 mm ({+-}1.4 mm) for the second method. The distributions of GC and CA values were obtained along the 30 images of normal spine at each vertebral level and show that maximal thoracic kyphosis (TK), thoracolumbar junction (TJ) and maximal lumbar lordosis (LL) on average occur at T3/T4, T12/L1 and L4/L5, respectively. The main advantage of GC and CA is that the measurements are independent of the orientation and size of the spine, thus allowing objective intra- and inter-subject comparisons. The positions of maximal TK, TJ and maximal LL can be easily identified by observing the GC and CA distributions at different vertebral levels. The obtained courses of the GC and CA for the scoliotic spine were compared to the distributions of GC and CA for the normal spines. The significant difference in values indicates that the descriptors of GC and

  14. A stabilized complementarity formulation for nonlinear analysis of 3D bimodular materials

    Zhang, L.; Zhang, H. W.; Wu, J.; Yan, B.

    2015-10-01

    Bi-modulus materials with different mechanical responses in tension and compression are often found in civil, composite, and biological engineering. Numerical analysis of bimodular materials is strongly nonlinear and convergence is usually a problem for traditional iterative schemes. This paper aims to develop a stabilized computational method for nonlinear analysis of 3D bimodular materials. Based on the parametric variational principle, a unified constitutive equation of 3D bimodular materials is proposed, which allows the eight principal stress states to be indicated by three parametric variables introduced in the principal stress directions. The original problem is transformed into a standard linear complementarity problem (LCP) by the parametric virtual work principle and a quadratic programming algorithm is developed by solving the LCP with the classic Lemke's algorithm. Update of elasticity and stiffness matrices is avoided and, thus, the proposed algorithm shows an excellent convergence behavior compared with traditional iterative schemes. Numerical examples show that the proposed method is valid and can accurately analyze mechanical responses of 3D bimodular materials. Also, stability of the algorithm is greatly improved.

  15. SHADOW EFFECT ON PHOTOVOLTAIC POTENTIALITY ANALYSIS USING 3D CITY MODELS

    N. Alam

    2012-07-01

    Full Text Available Due to global warming, green-house effect and various other drawbacks of existing energy sources, renewable energy like Photovoltaic system is being popular for energy production. The result of photovoltaic potentiality analysis depends on data quality and parameters. Shadow rapidly decreases performance of the Photovoltaic system and it always changes due to the movement of the sun. Solar radiation incident on earth's atmosphere is relatively constant but the radiation at earth's surface varies due to absorption, scattering, reflection, change in spectral content, diffuse component, water vapor, clouds and pollution etc. In this research, it is being investigated that how efficiently real-time shadow can be detected for both direct and diffuse radiation considering reflection and other factors in contrast with the existing shadow detection methods using latest technologies and what is the minimum quality of data required for this purpose. Of course, geometric details of the building geometry and surroundings directly affect the calculation of shadows. In principle, 3D city models or point clouds, which contain roof structure, vegetation, thematically differentiated surface and texture, are suitable to simulate exact real-time shadow. This research would develop an automated procedure to measure exact shadow effect from the 3D city models and a long-term simulation model to determine the produced energy from the photovoltaic system. In this paper, a developed method for detecting shadow for direct radiation has been discussed with its result using a 3D city model to perform a solar energy potentiality analysis.

  16. A 3D transport-based core analysis code for research reactors with unstructured geometry

    Highlights: • A core analysis code package based on 3D neutron transport calculation in complex geometry is developed. • The fine considerations on flux mapping, control rod effects and isotope depletion are modeled. • The code is proved to be with high accuracy and capable of handling flexible operational cases for research reactors. - Abstract: As an effort to enhance the accuracy in simulating the operations of research reactors, a 3D transport core analysis code system named REFT was developed. HELIOS is employed due to the flexibility of describing complex geometry. A 3D triangular nodal SN method transport solver, DNTR, endows the package the capability of modeling cores with unstructured geometry assemblies. A series of dedicated methods were introduced to meet the requirements of research reactor simulations. Afterwards, to make it more user friendly, a graphical user interface was also developed for REFT. In order to validate the developed code system, the calculated results were compared with the experimental results. Both the numerical and experimental results are in close agreement with each other, with the relative errors of keff being less than 0.5%. Results for depletion calculations were also verified by comparing them with the experimental data and acceptable consistency was observed in results

  17. A stabilized complementarity formulation for nonlinear analysis of 3D bimodular materials

    Zhang, L.; Zhang, H. W.; Wu, J.; Yan, B.

    2016-06-01

    Bi-modulus materials with different mechanical responses in tension and compression are often found in civil, composite, and biological engineering. Numerical analysis of bimodular materials is strongly nonlinear and convergence is usually a problem for traditional iterative schemes. This paper aims to develop a stabilized computational method for nonlinear analysis of 3D bimodular materials. Based on the parametric variational principle, a unified constitutive equation of 3D bimodular materials is proposed, which allows the eight principal stress states to be indicated by three parametric variables introduced in the principal stress directions. The original problem is transformed into a standard linear complementarity problem (LCP) by the parametric virtual work principle and a quadratic programming algorithm is developed by solving the LCP with the classic Lemke's algorithm. Update of elasticity and stiffness matrices is avoided and, thus, the proposed algorithm shows an excellent convergence behavior compared with traditional iterative schemes. Numerical examples show that the proposed method is valid and can accurately analyze mechanical responses of 3D bimodular materials. Also, stability of the algorithm is greatly improved.

  18. Quantitative analysis of the central-chest lymph nodes based on 3D MDCT image data

    Lu, Kongkuo; Bascom, Rebecca; Mahraj, Rickhesvar P. M.; Higgins, William E.

    2009-02-01

    Lung cancer is the leading cause of cancer death in the United States. In lung-cancer staging, central-chest lymph nodes and associated nodal stations, as observed in three-dimensional (3D) multidetector CT (MDCT) scans, play a vital role. However, little work has been done in relation to lymph nodes, based on MDCT data, due to the complicated phenomena that give rise to them. Using our custom computer-based system for 3D MDCT-based pulmonary lymph-node analysis, we conduct a detailed study of lymph nodes as depicted in 3D MDCT scans. In this work, the Mountain lymph-node stations are automatically defined by the system. These defined stations, in conjunction with our system's image processing and visualization tools, facilitate lymph-node detection, classification, and segmentation. An expert pulmonologist, chest radiologist, and trained technician verified the accuracy of the automatically defined stations and indicated observable lymph nodes. Next, using semi-automatic tools in our system, we defined all indicated nodes. Finally, we performed a global quantitative analysis of the characteristics of the observed nodes and stations. This study drew upon a database of 32 human MDCT chest scans. 320 Mountain-based stations (10 per scan) and 852 pulmonary lymph nodes were defined overall from this database. Based on the numerical results, over 90% of the automatically defined stations were deemed accurate. This paper also presents a detailed summary of central-chest lymph-node characteristics for the first time.

  19. The analysis of structure-anticancer and antiviral activity relationships for macrocyclic pyridinophanes and their analogues on the basis of 4D QSAR models (simplex representation of molecular structure).

    Kuz'min, Victor E; Artemenko, Anatoly G; Lozitsky, Victor P; Muratov, Eugene N; Fedtchouk, Alla S; Dyachenko, Natalia S; Nosach, Lidiya N; Gridina, Tatiyana L; Shitikova, Larisa I; Mudrik, Liubov M; Mescheriakov, Aleksey K; Chelombitko, Vladislav A; Zheltvay, Andrey I; Vanden Eynde, Jean-Jaques

    2002-01-01

    A new 4D-QSAR approach has been considered. For all investigated molecules the 3D structural models have been created and the set of conformers (fourth dimension) have been used. Each conformer is represented as a system of different simplexes (tetratomic fragments of fixed structure, chirality and symmetry). The investigation of influence of molecular structure of macrocyclic pyridinophanes, their analogues and certain other compounds on anticancer and antiviral (anti-influenza, antiherpes and antiadenovirus) activity has been carried out by means of the 4D-QSAR. Statistic characteristics for QSAR of PLS (partial least squares) models are satisfactory (R = 0.92-0.97; CVR = 0.63-0.83). Molecular fragments increasing and decreasing biological activity were defined. This information may be useful for design, and direct synthesis of novel anticancer and antiviral agents. PMID:12136936

  20. ELASTIC BEHAVIOR ANALYSIS OF 3D ANGLE-INTERLOCK WOVEN CERAMIC COMPOSITES

    Chang Yanjun; Jiao Guiqiong; Wang Bo; Liu Wei

    2006-01-01

    A micromechanical model for elastic behavior analysis of angle-interlock woven ceramic composites is proposed in this paper. This model takes into account the actual fabric structure by considering the fiber undulation and continuity in space, the cavities between adjacent yarns and the actual cross-section geometry of the yarn. Based on the laminate theory, the elastic properties of 3D angle-interlock woven ceramic composites are predicted. Different numbers of interlaced wefts have almost the same elastic moduli. The thickness of ceramic matrix has little effect on elastic moduli. When the undulation ratio increases longitudinal modulus decreases and the other Young's moduli increase. Good agreement between theoretical predictions and experimental results demonstrates the feasibility of the proposed model in analyzing the elastic properties of3D angle-interlock woven ceramic composites. The results of this paper verify the fact that the method of analyzing polyester matrix composites is suitable for woven ceramic composites.

  1. Experimental analysis of mechanical response of stabilized occipitocervical junction by 3D mark tracking technique

    Brémand F.

    2010-06-01

    Full Text Available This study is about a biomechanical comparison of some stabilization solutions for the occipitocervical junction. Four kinds of occipito-cervical fixations are analysed in this work: lateral plates fixed by two kinds of screws, lateral plates fixed by hooks and median plate. To study mechanical rigidity of each one, tests have been performed on human skulls by applying loadings and by studying mechanical response of fixations and bone. For this experimental analysis, a specific setup has been developed to impose a load corresponding to the flexion-extension physiological movements. 3D mark tracking technique is employed to measure 3D displacement fields on the bone and on the fixations. Observations of displacement evolution on the bone according to the fixation show different rigidities given by each solution.

  2. Quantitative analysis and feature recognition in 3-D microstructural data sets

    Lewis, A. C.; Suh, C.; Stukowski, M.; Geltmacher, A. B.; Spanos, G.; Rajan, K.

    2006-12-01

    A three-dimensional (3-D) reconstruction of an austenitic stainless-steel microstructure was used as input for an image-based finite-element model to simulate the anisotropic elastic mechanical response of the microstructure. The quantitative data-mining and data-warehousing techniques used to correlate regions of high stress with critical microstructural features are discussed. Initial analysis of elastic stresses near grain boundaries due to mechanical loading revealed low overall correlation with their location in the microstructure. However, the use of data-mining and feature-tracking techniques to identify high-stress outliers revealed that many of these high-stress points are generated near grain boundaries and grain edges (triple junctions). These techniques also allowed for the differentiation between high stresses due to boundary conditions of the finite volume reconstructed, and those due to 3-D microstructural features.

  3. Nonlinear analysis of chaotic flow in a 3D closed-loop pulsating heat pipe

    Pouryoussefi, S M

    2016-01-01

    Numerical simulation has been conducted for the chaotic flow in a 3D closed-loop pulsating heat pipe (PHP). Heat flux and constant temperature boundary conditions were applied for evaporator and condenser sections, respectively. Water and ethanol were used as working fluids. Volume of Fluid (VOF) method has been employed for two-phase flow simulation. Spectral analysis of temperature time series was carried out using Power Spectrum Density (PSD) method. Existence of dominant peak in PSD diagram indicated periodic or quasi-periodic behavior in temperature oscillations at particular frequencies. Correlation dimension values for ethanol as working fluid was found to be higher than that for water under the same operating conditions. Similar range of Lyapunov exponent values for the PHP with water and ethanol as working fluids indicated strong dependency of Lyapunov exponent to the structure and dimensions of the PHP. An O-ring structure pattern was obtained for reconstructed 3D attractor at periodic or quasi-peri...

  4. Uncertainty analysis for 3D geological modeling using the Kriging variance

    Choi, Yosoon; Choi, Younjung; Park, Sebeom; Um, Jeong-Gi

    2014-05-01

    The credible estimation of geological properties is critical in many geosciences fields including the geotechnical engineering, environmental engineering, mining engineering and petroleum engineering. Many interpolation techniques have been developed to estimate the geological properties from limited sampling data such as borehole logs. The Kriging is an interpolation technique that gives the best linear unbiased prediction of the intermediate values. It also provides the Kriging variance which quantifies the uncertainty of the kriging estimates. This study provides a new method to analyze the uncertainty in 3D geological modeling using the Kriging variance. The cut-off values determined by the Kriging variance were used to effectively visualize the 3D geological models with different confidence levels. This presentation describes the method for uncertainty analysis and a case study which evaluates the amount of recoverable resources by considering the uncertainty.

  5. Mechanical performance and parameter sensitivity analysis of 3D braided composites joints.

    Wu, Yue; Nan, Bo; Chen, Liang

    2014-01-01

    3D braided composite joints are the important components in CFRP truss, which have significant influence on the reliability and lightweight of structures. To investigate the mechanical performance of 3D braided composite joints, a numerical method based on the microscopic mechanics is put forward, the modeling technologies, including the material constants selection, element type, grid size, and the boundary conditions, are discussed in detail. Secondly, a method for determination of ultimate bearing capacity is established, which can consider the strength failure. Finally, the effect of load parameters, geometric parameters, and process parameters on the ultimate bearing capacity of joints is analyzed by the global sensitivity analysis method. The results show that the main pipe diameter thickness ratio γ, the main pipe diameter D, and the braided angle α are sensitive to the ultimate bearing capacity N. PMID:25121121

  6. Stereoscopic motion analysis in densely packed clusters: 3D analysis of the shimmering behaviour in Giant honey bees

    Hoetzl Thomas; Ruether Matthias; Weihmann Frank; Maurer Michael; Kastberger Gerald; Kranner Ilse; Bischof Horst

    2011-01-01

    Abstract Background The detailed interpretation of mass phenomena such as human escape panic or swarm behaviour in birds, fish and insects requires detailed analysis of the 3D movements of individual participants. Here, we describe the adaptation of a 3D stereoscopic imaging method to measure the positional coordinates of individual agents in densely packed clusters. The method was applied to study behavioural aspects of shimmering in Giant honeybees, a collective defence behaviour that deter...

  7. 3D kinematic and dynamic analysis of the front crawl tumble turn in elite male swimmers.

    Puel, F; Morlier, J; Avalos, M; Mesnard, M; Cid, M; Hellard, P

    2012-02-01

    The aim of this study was to identify kinematic and dynamic variables related to the best tumble turn times (3mRTT, the turn time from 3-m in to 3-m out, independent variable) in ten elite male swimmers using a three-dimensional (3D) underwater analysis protocol and the Lasso (least absolute shrinkage and selection operator) as statistical method. For each swimmer, the best-time turn was analyzed with five stationary and synchronized underwater cameras. The 3D reconstruction was performed using the Direct Linear Transformation algorithm. An underwater piezoelectric 3D force platform completed the set-up to compute dynamic variables. Data were smoothed by the Savitzky-Golay filtering method. Three variables were considered relevant in the best Lasso model (3mRTT=2.58-0.425 RD+0.204 VPe+0.0046 TD): the head-wall distance where rotation starts (RD), the horizontal speed at the force peak (VPe), and the 3D length of the path covered during the turn (TD). Furthermore, bivariate analysis showed that upper body (CUBei) and lower limb extension indexes at first contact (CLLei) were also linked to the turn time (r=-0.65 and pvariables). Thus the best turn times were associated with a long RD, slower VPe and reduced TD. By an early transverse rotation, male elite swimmers reach the wall with a slightly flexed posture that results in fast extension. These swimmers opt for a movement that is oriented forward and they focus on reducing the distance covered. PMID:22176710

  8. QSAR study on thiazolidine-2,4-dione derivatives for antihyperglycemic activity

    Prashantha Kumar B

    2008-01-01

    Full Text Available A set of seventy four molecules belonging to the class of thioglitazones were subjected to the QSAR analysis for their antihyperglycemic activity. All the molecules were subjected to energy minimization to get 3D structures, followed by conformational analysis to get the conformation of the molecule associated with the least energy and highest stability. Various physico-chemical parameters were then calculated using ALCHEMY 2000 software, namely, thermodynamic parameters, structure-dependant parameters, topological parameters and charge-dependant parameters. Multiple linear regression analysis was carried out on all the molecules. The final equation was developed by choosing optimal combination of descriptors after removing the outliers. Cross validation was performed by leave one out method to arrive at the final QSAR model for the chosen set of molecules to exhibit antihyperglycemic activity.

  9. Multi-scale uncertainty and sensitivity analysis of the TALL-3D experiment

    Highlights: • The ATHLET-CFX model of the TALL-3D facility behaves in a monotonic way regarding the propagation of the modeling uncertainty. • The biggest variations are observed in the temperature behavior. • A screening analysis identifies the most influential parameters. - Abstract: Over the last decades, the increase of the computational power has made feasible the computer modeling of complex thermal-hydraulic phenomena. These complex models use physical models to account for specific thermal-hydraulic phenomena. Each physical model requires a set of model input data. For several reasons (e.g. measurement uncertainties for stationary and time-dependent values, cost of the measurement campaign), the input data for the physical models cannot always be determined with precision. This lack of accuracy can significantly impair the model results. The analysis of the influence of these input uncertainties is therefore a key step to understand the model behavior and possibly improve its accuracy. The TALL-3D facility, built by KTH in the scope of the THINS project, aims at investigating challenging phenomena in a facility filled with lead–bismuth eutectic (LBE) containing a pool. The experimental data will be used for the validation of the models developed by the project partners. Based on the coupling between ANSYS CFX (CFD) and ATHLET (system code) implemented by the GRS, TUM performed an uncertainty and sensitivity analysis on the model of the TALL-3D facility. This analysis investigates the uncertainty in the output which is due to the uncertainty on the input (uncertainty analysis) and assesses the influence of the uncertain parameters (sensitivity analysis)

  10. Multi-scale uncertainty and sensitivity analysis of the TALL-3D experiment

    Geffray, Clotaire, E-mail: clotaire.geffray@ntech.mw.tum.de; Macián-Juan, Rafael

    2015-08-15

    Highlights: • The ATHLET-CFX model of the TALL-3D facility behaves in a monotonic way regarding the propagation of the modeling uncertainty. • The biggest variations are observed in the temperature behavior. • A screening analysis identifies the most influential parameters. - Abstract: Over the last decades, the increase of the computational power has made feasible the computer modeling of complex thermal-hydraulic phenomena. These complex models use physical models to account for specific thermal-hydraulic phenomena. Each physical model requires a set of model input data. For several reasons (e.g. measurement uncertainties for stationary and time-dependent values, cost of the measurement campaign), the input data for the physical models cannot always be determined with precision. This lack of accuracy can significantly impair the model results. The analysis of the influence of these input uncertainties is therefore a key step to understand the model behavior and possibly improve its accuracy. The TALL-3D facility, built by KTH in the scope of the THINS project, aims at investigating challenging phenomena in a facility filled with lead–bismuth eutectic (LBE) containing a pool. The experimental data will be used for the validation of the models developed by the project partners. Based on the coupling between ANSYS CFX (CFD) and ATHLET (system code) implemented by the GRS, TUM performed an uncertainty and sensitivity analysis on the model of the TALL-3D facility. This analysis investigates the uncertainty in the output which is due to the uncertainty on the input (uncertainty analysis) and assesses the influence of the uncertain parameters (sensitivity analysis)

  11. Coupled fully 3D neutron kinetics thermal-hydraulic computations for DNB analysis on PWRs

    Departure from Nucleate Boiling (DNB) is one of the major limiting factors of Pressurized Water Reactors (PWRs). Safety requires that occurrence of DNB should be precluded under normal or incidental operating conditions. To perform Main Steam Line Break (MSLB) accident calculations EDF have developed its own numerical tool OSCARD based on: the thermal-hydraulic THYC code for DNB analysis, the neutron kinetics COCCINELLE code for power distribution computations, the thermal-hydraulic CATHARE code to provide boundary conditions analysis with system scale computation. With OSCARD a fully three-dimensional (3D) representation of the core is proposed in conjunction with a two-phase flow porous-body approach (THYC) and two-group diffusion equations in the axial and lateral directions with Doppler and void reactivity feedback effects (COCCINELLE). OSCARD provides EDF with an alternative and independent way of evaluating fuel performance and safety margins. In the licensed approach, the coupled 3D neutron kinetics and thermal-hydraulic part of OSCARD steady computations is used to produce 3D power distribution in the reactor core at the most penalizing moment of the transient. Then this distribution is used as an input for THYC to perform thermal-hydraulic subchannel analysis. This 3 steps approach is used with simple conservative and bounding analysis assumptions, that can not occur in reality. In a prospective approach, OSCARD enables to combine thermal-hydraulic subchannel analysis with the neutron kinetics radial average channel model using a nodalization of one quarter of fuel assembly in order to perform one step DNB analysis. (author)

  12. Error analysis of 3D laser scanning system for gangue monitoring

    Hu, Shaoxing; Xia, Yuyang; Zhang, Aiwu

    2012-01-01

    The paper put forward the system error evaluation method of 3D scanning system for gangue monitoring; analyzed system errors including integrated error which can be avoided, and measurement error which needed whole analysis; firstly established the system equation after understanding the relationship of each structure. Then, used error independent effect and spread law to set up the entire error analysis system, and simulated the trend of error changing along X, Y, Z directions. At last, it is analytic that the laser rangefinder carries some weight in system error, and the horizontal and vertical scanning angles have some influences on system error in the certain vertical and horizontal scanning parameters.

  13. Human factors flight trial analysis for 2D/3D SVS

    Schiefele, Jens; Howland, Duncan; Maris, John; Wipplinger, Patrick

    2004-08-01

    The paper describes flight trials performed in Reno, NV. Flight trial were conducted with a Cheyenne 1 from Marinvent. Twelve pilots flew the Cheyenne in seventy-two approaches to the Reno airfield. All pilots flew completely andomized settings. Three different settings (standard displays, 2D moving map, and 2D/3D moving map) were evaluated. They included seamless evaluation for STAR, approach, and taxi operations. The flight trial goal was to evaluate the objective performance of pilots compared among the different settings. As dependent variables, positional and time accuracy were measured. Analysis was conducted by an ANOVA test. In parallel, all pilots answered subjective Cooper-Harper, situation awareness rating technique (SART), situational awareness probe (SAP), and questionnaires.This article describes the human factor analysis from flight trials performed in Reno, NV. Flight trials were conducted with a Cheyenne 1 from Marinvent. Thirteen pilots flew the Cheyenne in seventy-two approaches to the Reno airfield. All pilots flew completely randomized settings. Three different display configurations: Elec. Flight Information System (EFIS), EFIS and 2D moving map, and 3D SVS Primary Flight Display (PFD) and 2D moving map were evaluated. They included normal/abnormal procedure evaluation for: Steep turns and reversals, Unusual attitude recovery, Radar vector guidance towards terrain, Non-precision approaches, En-route alternate for non-IFR rated pilots encountering IMC, and Taxiing on complex taxi-routes. The flight trial goal was to evaluate the objective performance of pilots for the different display configurations. As dependent variables, positional and time data were measured. Analysis was performed by an ANOVA test. In parallel, all pilots answered subjective NASA Task Load Index, Cooper-Harper, Situation Awareness Rating Technique (SART), and questionnaires. The result shows that pilots flying 2D/3D SVS perform no worse than pilots with conventional

  14. 3D Product authenticity model for online retail: An invariance analysis

    Algharabat, R.

    2010-01-01

    Full Text Available This study investigates the effects of different levels of invariance analysis on three dimensional (3D product authenticity model (3DPAM constructs in the e- retailing context. A hypothetical retailer website presents a variety of laptops using 3D product visualisations. The proposed conceptual model achieves acceptable fit and the hypothesised paths are all valid. We empirically investigate the invariance across the subgroups to validate the results of our 3DPAM. We concluded that the 3D product authenticity model construct was invariant for our sample across different gender, level of education and study backgrounds. These findings suggested that all our subgroups conceptualised the 3DPAM similarly. Also the results show some non-invariance results for the structural and latent mean models. The gender group posits a non-invariance latent mean model. Study backgrounds group reveals a non-invariance result for the structural model. These findings allowed us to understand the 3DPAMs validity in the e-retail context. Managerial implications are explained.

  15. An Interactive Tool for Analysis and Optimization of Texture Parameters in Photorealistic Virtual 3d Models

    Sima, A. A.; Buckley, S. J.; Viola, I.

    2012-07-01

    Texture mapping is a common method for combining surface geometry with image data, with the resulting photorealistic 3D models being suitable not only for visualization purposes but also for interpretation and spatiameasurement, in many application fields, such as cultural heritage and the earth sciences. When acquiring images for creation of photorealistic models, it is usual to collect more data than is finally necessary for the texturing process. Images may be collected from multiple locations, sometimes with different cameras or lens configurations and large amounts of overlap may exist. Consequently, much redundancy may be present, requiring sorting to choose the most suitable images to texture the model triangles. This paper presents a framework for visualization and analysis of the geometric relations between triangles of the terrain model and covering image sets. The application provides decision support for selection of an image subset optimized for 3D model texturing purposes, for non-specialists. It aims to improve the communication of geometrical dependencies between model triangles and the available digital images, through the use of static and interactive information visualization methods. The tool was used for computer-aided selection of image subsets optimized for texturing of 3D geological outcrop models. The resulting textured models were of high quality and with a minimum of missing texture, and the time spent in time-consuming reprocessing was reduced. Anecdotal evidence indicated that an increased user confidence in the final textured model quality and completeness makes the framework highly beneficial.

  16. Reconstruction Accuracy Assessment of Surface and Underwater 3D Motion Analysis: A New Approach

    Kelly de Jesus

    2015-01-01

    Full Text Available This study assessed accuracy of surface and underwater 3D reconstruction of a calibration volume with and without homography. A calibration volume (6000 × 2000 × 2500 mm with 236 markers (64 above and 88 underwater control points—with 8 common points at water surface—and 92 validation points was positioned on a 25 m swimming pool and recorded with two surface and four underwater cameras. Planar homography estimation for each calibration plane was computed to perform image rectification. Direct linear transformation algorithm for 3D reconstruction was applied, using 1600000 different combinations of 32 and 44 points out of the 64 and 88 control points for surface and underwater markers (resp.. Root Mean Square (RMS error with homography of control and validations points was lower than without it for surface and underwater cameras (P≤0.03. With homography, RMS errors of control and validation points were similar between surface and underwater cameras (P≥0.47. Without homography, RMS error of control points was greater for underwater than surface cameras (P≤0.04 and the opposite was observed for validation points (P≤0.04. It is recommended that future studies using 3D reconstruction should include homography to improve swimming movement analysis accuracy.

  17. Reconstruction Accuracy Assessment of Surface and Underwater 3D Motion Analysis: A New Approach

    de Jesus, Kelly; de Jesus, Karla; Figueiredo, Pedro; Vilas-Boas, João Paulo; Fernandes, Ricardo Jorge; Machado, Leandro José

    2015-01-01

    This study assessed accuracy of surface and underwater 3D reconstruction of a calibration volume with and without homography. A calibration volume (6000 × 2000 × 2500 mm) with 236 markers (64 above and 88 underwater control points—with 8 common points at water surface—and 92 validation points) was positioned on a 25 m swimming pool and recorded with two surface and four underwater cameras. Planar homography estimation for each calibration plane was computed to perform image rectification. Direct linear transformation algorithm for 3D reconstruction was applied, using 1600000 different combinations of 32 and 44 points out of the 64 and 88 control points for surface and underwater markers (resp.). Root Mean Square (RMS) error with homography of control and validations points was lower than without it for surface and underwater cameras (P ≤ 0.03). With homography, RMS errors of control and validation points were similar between surface and underwater cameras (P ≥ 0.47). Without homography, RMS error of control points was greater for underwater than surface cameras (P ≤ 0.04) and the opposite was observed for validation points (P ≤ 0.04). It is recommended that future studies using 3D reconstruction should include homography to improve swimming movement analysis accuracy. PMID:26175796

  18. 3D Axon structure extraction and analysis in confocal fluorescence microscopy images.

    Zhang, Yong; Zhou, Xiaobo; Lu, Ju; Lichtman, Jeff; Adjeroh, Donald; Wong, Stephen T C

    2008-08-01

    The morphological properties of axons, such as their branching patterns and oriented structures, are of great interest for biologists in the study of the synaptic connectivity of neurons. In these studies, researchers use triple immunofluorescent confocal microscopy to record morphological changes of neuronal processes. Three-dimensional (3D) microscopy image analysis is then required to extract morphological features of the neuronal structures. In this article, we propose a highly automated 3D centerline extraction tool to assist in this task. For this project, the most difficult part is that some axons are overlapping such that the boundaries distinguishing them are barely visible. Our approach combines a 3D dynamic programming (DP) technique and marker-controlled watershed algorithm to solve this problem. The approach consists of tracking and updating along the navigation directions of multiple axons simultaneously. The experimental results show that the proposed method can rapidly and accurately extract multiple axon centerlines and can handle complicated axon structures such as cross-over sections and overlapping objects. PMID:18336075

  19. Dynamic analysis of radial force density in brushless DC motor using 3-D equivalent magnetic circuit network method

    Hur, J.; Chun, Y.D.; Lee, J.; Hyun, D.S. [Hanyang Univ., Seoul (Korea, Republic of). Dept. of Electrical Engineering

    1998-09-01

    The distribution of radial force density in brushless permanent magnet DC motor is not uniform in axial direction. The analysis of radial force density has to consider the 3-D shape of teeth and overhand, because the radial force density causes vibration and acts on the surface of teeth inconstantly. For the analysis, a new 3-D equivalent magnetic circuit network method is used to account the rotor movement without remesh. The radial force density is calculated and analyzed by Maxwell stress tensor and discrete Fourier transform (DFT) respectively. The results of 3-D equivalent magnetic circuit method have been compared with the results of 3-D FEM.

  20. LEWICE3D/GlennHT Particle Analysis of the Honeywell Al502 Low Pressure Compressor

    Bidwell, Colin S.; Rigby, David L.

    2015-01-01

    A flow and ice particle trajectory analysis was performed for the booster of the Honeywell AL502 engine. The analysis focused on two closely related conditions one of which produced a rollback and another which did not rollback during testing in the Propulsion Systems Lab at NASA Glenn Research Center. The flow analysis was generated using the NASA Glenn GlennHT flow solver and the particle analysis was generated using the NASA Glenn LEWICE3D v3.56 ice accretion software. The flow and particle analysis used a 3D steady flow, mixing plane approach to model the transport of flow and particles through the engine. The inflow conditions for the rollback case were: airspeed, 145 ms; static pressure, 33,373 Pa; static temperature, 253.3 K. The inflow conditions for the non-roll-back case were: airspeed, 153 ms; static pressure, 34,252 Pa; static temperature, 260.1 K. Both cases were subjected to an ice particle cloud with a median volume diameter of 24 microns, an ice water content of 2.0 gm3 and a relative humidity of 100 percent. The most significant difference between the rollback and non-rollback conditions was the inflow static temperature which was 6.8 K higher for the non-rollback case.

  1. Study on Human Slip and Fall Gaits Based on 3D Gait Analysis System

    Junxia Zhang

    2014-03-01

    Full Text Available Slip and fall is a serious problem which affects the health and safety of people, and it has become a hot topic in the ergonomics and biomedicine fields in recent years. The causes of slip and fall accidents including external causes and internal causes. And it is the body response coordination ability under the condition of instability that is one of the important internal causes and plays a key role in causing slip and fall accidents. On the sports psychology, total time (TT is defined as the sum of reaction time and movement time and it can be used to measure the body response coordination ability. Slip and fall probability (FP is the frequency of occurrence of slip and fall accidents. When external conditions are consistent, to a certain extent, different FP reflects the difference of body response coordination ability. Theoretically, TT and FP should have a certain relationship, but the detail is unknown. With the development of computer technology, the 3D gaits analysis system has appeared and the study of slip and fall accidents was promoted depending on its powerful functions. Based on the 3D gaits analysis system, this paper innovatively listed the topic as study content and got the study result: the relationship between TT and FP is significant correlation under the 0.01 level. By using the datum, images and videos exported from the system, this paper conducted the gait analysis and verified the reliability of the correlation: different TT lead to different foot-ground contact force, thus lead to different body response coordination ability, namely FP. Therefore, it is very effective to use the 3D gait analysis system to study the slip and fall accidents

  2. 3-D fracture analysis using a partial-reduced integration scheme

    This paper presents details of 3-D elastic-plastic analyses of axially orientated external surface flaw in an internally pressurized thin-walled cylinder and discusses the variation of the J-integral values around the crack tip. A partial-reduced-integration-penalty method is introduced to minimize this variation of the J-integral near the crack tip. Utilizing 3-D symmetry, an eighth segment of a tube containing an elliptically shaped external surface flaw is modelled using 20-noded isoparametric elements. The crack-tip elements are collapsed to form a 1/r stress singularity about the curved crack front. The finite element model is subjected to internal pressure and axial pressure-generated loads. The virtual crack extension method is used to determine linear elastic stress intensity factors from the J-integral results at various points around the crack front. Despite the different material constants and the thinner wall thickness in this analysis, the elastic results compare favourably with those obtained by other researchers. The nonlinear stress-strain behaviour of the tube material is modelled using an incremental theory of plasticity. Variations of the J-integral values around the curved crack front of the 3-D flaw were seen. These variations could not be resolved by neglecting the immediate crack-tip elements J-integral results in favour of the more remote contour paths or else smoothed out when all the path results are averaged. Numerical incompatabilities in the 20-noded 3-D finite elements used to model the surface flaw were found. A partial-reduced integration scheme, using a combination of full and reduced integration elements, is proposed to determine J-integral results for 3-D fracture analyses. This procedure is applied to the analysis of an external semicircular surface flaw projecting halfway into the tube wall thickness. Examples of the J-integral values, before and after the partial-reduced integration method is employed, are given around the

  3. ACOPLAMIENTO MOLECULAR, 3DQSAR Y DISEÑO DE NOVO DE BENZIMIDAZOLES E IMIDAZOLINAS DERIVADOS DE (S-ISOTIAZOLIDINONAS COMO INHIBIDORES DE LA PROTEÍNA PTP 1B MOLECULAR DOCKING, 3D-QSAR AND DE NOVO DESIGN OF BENZIMIDAZOLES AND IMIDAZOLINES (S-ISOTHIAZOLIDINONES DERIVATIVES AS PTP 1B INHIBITORS

    Judith C GRANADOS R

    2010-09-01

    Full Text Available Se realizó un estudio tridimensional cuantitativo de relación-estructura (3D-QSAR con 40 moléculas tipo benzimidazol e imidazolina derivadas de (s-isotiazolidinonas y su unión con el sitio activo de la proteína tirosina fosfatasa 1B (PTP 1B, utilizando el programa GOLD 3.0. La superposición molecular de los ligandos en la plantilla fue llevada a cabo por el método Database Alignment. El mejor modelo fue el constituido por la combinación de los campos estéricos y electrostáticos de CoMFA, los cuales arrojaron los siguientes parámetros: q² = 0,659 y r² = 0,997. Usando el módulo LeapFrog de SYBYL fue posible generar más de 10.000 moléculas nuevas, de las cuales 46 mostraron, teóricamente, un mejor valor de la actividad biológica que su precursora. Los datos obtenidos en el presente estudio podrían impulsar el diseño de nuevos y más potentes inhibidores de la PTP 1B, como agentes para el tratamiento de la diabetes.A study of the relationship-dimensional quantitative structure (3D-QSAR with 40 molecules derived from benzimidazole and imidazoline (s-isotiazolidinonas and their union with the active site of Protein Tyrosine Phosphatase 1B using the program GOLD 3.0 was carried out. The molecular supression of the ligands in the grid was performed by the Database Alignment method. The best model formed by combining the esteric field and electrostatic fields of CoMFA, yielded the following parameters: q² = 0.659 and r² = 0.997. Using LeapFrog module of Sybyl was possible to generate more than 10,000 new molecules of which 46 showed theoretically a better value of biological activity than their forerunner. The data generated by this study could promote the design of new and more potent PTP 1B inhibitors as agents for the treatment of diabetes.

  4. Brain SPECT analysis by 3D-SSP and clinical features of Parkinson's disease

    The aim of the present study is to investigate the association of symptoms in Parkinson's disease (PD) with cerebral perfusion on single photon emission computed tomography (SPECT). The clinical features of PD were compared with SPECT images of the brain obtained by three-dimensional stereotactic surface projection (3D-SSP) analysis. Thirty-eight patients who had PD without dementia (17 men and 21 women with a mean age of 68.6±4.7 years) were enrolled in this study. Their symptoms were rated using the unified parkinson's disease rating scale (UPDRS). Within a week, all patients were examined by SPECT with I-123, and reconstructed images were analyzed with 3D-SSP using an image-analysis software, iSSP ver. 3.5. Data on brain surface perfusion extracted by 3D-SSP analysis were compared between the PD patients and the normal control group. The same comparisons were made for subgroups of PD patients with severe symptoms, such as tremor, gait disturbance, bradykinesia, and the UPDRS motor score. Cerebral perfusion was decreased at the anterior cingulate cortex and occipital lobe of the PD patients compared with the normal controls. In the subgroups with severe gait disturbance and severe bradykinesia, additional hypoperfusion was seen at the lateral frontal association and lateral temporal association and the medial frontal gyrus, and by the pixel-by-pixel comparison, perfusion was significantly decreased (p<0.05) at the medial frontal gyrus and anterior cingulate cortex compared with the normal control group. In PD patients, severe gait disturbance and bradykinesia may be correlated with hypoperfusion of the medial aspect of the frontal lobe. This suggests that functional disturbance of the supplementary motor area and other parts of the frontal lobe are involved in the development of gait disturbance and bradykinesia in PD. (author)

  5. 3D Extension of Haralick Texture Features for Medical Image Analysis

    Tesař, Ludvík; Smutek, D.; Shimizu, A.; Kobatake, H.

    Zurich : ACTA Press, 2007, s. 350-355. ISBN 978-0-88986-646-1. [IASTED International Conference on Signal Processing, Pattern Recognition, and Applications 2007 /4./. Innsbruck (AT), 14.02.2007-16.02.2007] R&D Projects: GA AV ČR 1ET101050403; GA MŠk 1M0572 Institutional research plan: CEZ:AV0Z10750506 Keywords : Haralick texture features * 3D image analysis * image segmentation * CT image s * Gaussian mixture * model-based decision-making * EM algorithm Subject RIV: IN - Informatics, Computer Science

  6. Correction of magnetotelluric static shift by analysis of 3D forward modelling and measured test data

    Zhang, Kun; Wei, Wenbo; Lu, Qingtian; Wang, Huafeng; Zhang, Yawei

    2016-06-01

    To solve the problem of correction of magnetotelluric (MT) static shift, we quantise factors that influence geological environments and observation conditions and study MT static shift according to 3D MT numerical forward modelling and field tests with real data collection. We find that static shift distortions affect both the apparent resistivity and the impedance phase. The distortion results are also related to the frequency. On the basis of synthetic and real data analysis, we propose the concept of generalised static shift resistivity (GSSR) and a new method for correcting MT static shift. The approach is verified by studying 2D inversion models using synthetic and real data.

  7. General beam cross-section analysis using a 3D finite element slice

    Couturier, Philippe; Krenk, Steen

    2014-01-01

    analytical solution is available. The paper also shows an application to wind turbine blade cross-sections and discusses the effect of the finite element discretization on the cross-section properties such as stiffness parameters and the location of the elastic and shear centers.......A formulation for analysis of general cross-section properties has been developed. This formulation is based on the stress-strain states in the classic six equilibrium modes of a beam by considering a finite thickness slice modelled by a single layer of 3D finite elements. The displacement...

  8. World's first ABWR start-up test analysis with 3-D transient computational code

    The Kashiwazaki-Kariwa Nuclear Power Station Unit 6, the world's first Advanced BWR (ABWR), began commercial operation from November 1996 following one year of start-up tests. A large number of variables which may be used to validate the advanced design features were obtained from transient tests. These test data are now being used for the qualification of TRACG, a BWR 3-D transient analysis code. Calculated results show that TRACG is fully capable of accurately predicting ABWR transient response and will be useful for application to future plant designs

  9. Object data mining and analysis on 3D images of high precision industrial CT

    There are some areas of interest on 3D images of the high precision industrial CT, such as defects caused during the production process. In order to take a close analysis of these areas, the image processing software Amira was used on the data of a particular work piece sample to do defects segmentation and display, defects measurement. evaluation and documentation. A data set obtained by scanning a vise sample using the lab CT system was analyzed and the results turn out to be fairly good. (authors)

  10. In-chip fabrication of free-form 3D constructs for directed cell migration analysis

    Olsen, Mark Holm; Hjortø, Gertrud Malene; Hansen, Morten;

    2013-01-01

    Free-form constructs with three-dimensional (3D) microporosity were fabricated by two-photon polymerization inside the closed microchannel of an injection-molded, commercially available polymer chip for analysis of directed cell migration. Acrylate constructs were produced as woodpile topologies...... with a range of pore sizes from 5 × 5 μm to 15 × 15 μm and prefilled with fibrillar collagen. Dendritic cells seeded into the polymer chip in a concentration gradient of the chemoattractant CCL21 efficiently negotiated the microporous maze structure for pore sizes of 8 × 8 μm or larger. The cells...

  11. Analysis of the Possibilities of Using Low-Cost Scanning System in 3d Modeling

    Kedzierski, M.; Wierzbickia, D.; Fryskowska, A.; Chlebowska, B.

    2016-06-01

    The laser scanning technique is still a very popular and fast growing method of obtaining information on modeling 3D objects. The use of low-cost miniature scanners creates new opportunities for small objects of 3D modeling based on point clouds acquired from the scan. The same, the development of accuracy and methods of automatic processing of this data type is noticeable. The article presents methods of collecting raw datasets in the form of a point-cloud using a low-cost ground-based laser scanner FabScan. As part of the research work 3D scanner from an open source FabLab project was constructed. In addition, the results for the analysis of the geometry of the point clouds obtained by using a low-cost laser scanner were presented. Also, some analysis of collecting data of different structures (made of various materials such as: glass, wood, paper, gum, plastic, plaster, ceramics, stoneware clay etc. and of different shapes: oval and similar to oval and prism shaped) have been done. The article presents two methods used for analysis: the first one - visual (general comparison between the 3D model and the real object) and the second one - comparative method (comparison between measurements on models and scanned objects using the mean error of a single sample of observations). The analysis showed, that the low-budget ground-based laser scanner FabScan has difficulties with collecting data of non-oval objects. Items built of glass painted black also caused problems for the scanner. In addition, the more details scanned object contains, the lower the accuracy of the collected point-cloud is. Nevertheless, the accuracy of collected data (using oval-straight shaped objects) is satisfactory. The accuracy, in this case, fluctuates between ± 0,4 mm and ± 1,0 mm whereas when using more detailed objects or a rectangular shaped prism the accuracy is much more lower, between 2,9 mm and ± 9,0 mm. Finally, the publication presents the possibility (for the future expansion of

  12. Stiffness Analysis of 3-d.o.f. Overconstrained Translational Parallel Manipulators

    Pashkevich, Anatoly; Wenger, Philippe

    2008-01-01

    The paper presents a new stiffness modelling method for overconstrained parallel manipulators, which is applied to 3-d.o.f. translational mechanisms. It is based on a multidimensional lumped-parameter model that replaces the link flexibility by localized 6-d.o.f. virtual springs. In contrast to other works, the method includes a FEA-based link stiffness evaluation and employs a new solution strategy of the kinetostatic equations, which allows computing the stiffness matrix for the overconstrained architectures and for the singular manipulator postures. The advantages of the developed technique are confirmed by application examples, which deal with comparative stiffness analysis of two translational parallel manipulators.

  13. 3-D in vivo brain tumor geometry study by scaling analysis

    Torres Hoyos, F.; Martín-Landrove, M.

    2012-02-01

    A new method, based on scaling analysis, is used to calculate fractal dimension and local roughness exponents to characterize in vivo 3-D tumor growth in the brain. Image acquisition was made according to the standard protocol used for brain radiotherapy and radiosurgery, i.e., axial, coronal and sagittal magnetic resonance T1-weighted images, and comprising the brain volume for image registration. Image segmentation was performed by the application of the k-means procedure upon contrasted images. We analyzed glioblastomas, astrocytomas, metastases and benign brain tumors. The results show significant variations of the parameters depending on the tumor stage and histological origin.

  14. Developments in the analysis of 3D piping and shells by means of PAULA code

    Non linear analyses of three dimensional piping and shells are becoming more and more common, in the safety analysis of nuclear power plants. The pipe whip accident, the Hypothetic core Distruptive Accident (HCDA) for LMFBR represent, two significative examples, where non linear analyses of the pressure boundary have been used with considerable success. Seismic analysis and other extreme loading of conditions are other cases, where non linear analyses have been used even if not extensively due to cost reasons. The authors have presented a code, named PAULA to deal with the 3D non linear analysis of piping; it is the aim of this paper to briefly describe the basic library of PAULA and to describe the new shell elements in some more detail. (orig./GL)

  15. Linearized FUN3D for Rapid Aeroelastic and Aeroservoelastic Design and Analysis Project

    National Aeronautics and Space Administration — The overall objective of this Phase I project is to develop a hybrid approach in FUN3D, referred herein to as the Linearized FUN3D, for rapid aeroelastic and...

  16. Improvements of 3D finite element method for eddy current analysis and its application to fusion technology

    The 3D finite element method is improved so that both the computer storage and the CPU time can be reduced by examining the boundary conditions. The improved method is applied to the analysis of the Fusion Electromagnetic Induction Experiment (FELIX) facilities, and the characteristics of 3-D eddy current distributions are investigated. (orig.)

  17. 3-D analysis of semiconductor dopant distributions in a patterned structure using LEAP

    Moore, J.S. [Department of Materials Science and Engineering, University of Florida, P.O. Box 116130, 525 Engineering Builing, Gainesville, FL 32611 (United States)], E-mail: jsm200@ufl.edu; Jones, K.S. [Department of Materials Science and Engineering, University of Florida, P.O. Box 116130, 525 Engineering Builing, Gainesville, FL 32611 (United States); Kennel, H.; Corcoran, S. [Intel Corporation, Hillsboro, OR (United States)

    2008-05-15

    This work presents the first 3-D analysis of lateral dopant diffusion in a patterned structure using a pulsed laser-assisted local electrode atom probe (LEAP). A structure similar to a device channel was created for this work by performing a 3 keV, 1x10{sup 15} cm{sup -2} As{sup +} implant on a poly-Si line patterned wafer with 70 nm line width and 200 nm line pitch. The wafer was subsequently annealed at 950 deg. C for 1 s. LEAP samples were made using a site-selective in-situ focused ion beam (FIB) process. The results from LEAP analysis were then compared with high-resolution transmission electron microscopy (HRTEM) and Florida object-oriented process simulator (FLOOPS) results. Good structural agreement was found between the LEAP and HRTEM results. Several 1-D As concentration profiles extracted from the LEAP data were also found to be in good agreement with FLOOPS process simulation results. These profiles also represent for the first time that results from a 3-D process simulator have been able to be confirmed experimentally using a single sample.

  18. Shape Analysis of 3D Head Scan Data for U.S. Respirator Users

    Zhuang, Ziqing; Slice, DennisE; Benson, Stacey; Lynch, Stephanie; Viscusi, DennisJ

    2010-12-01

    In 2003, the National Institute for Occupational Safety and Health (NIOSH) conducted a head-and-face anthropometric survey of diverse, civilian respirator users. Of the 3,997 subjects measured using traditional anthropometric techniques, surface scans and 26 three-dimensional (3D) landmark locations were collected for 947 subjects. The objective of this study was to report the size and shape variation of the survey participants using the 3D data. Generalized Procrustes Analysis (GPA) was conducted to standardize configurations of landmarks associated with individuals into a common coordinate system. The superimposed coordinates for each individual were used as commensurate variables that describe individual shape and were analyzed using Principal Component Analysis (PCA) to identify population variation. The first four principal components (PC) account for 49% of the total sample variation. The first PC indicates that overall size is an important component of facial variability. The second PC accounts for long and narrow or short and wide faces. Longer narrow orbits versus shorter wider orbits can be described by PC3, and PC4 represents variation in the degree of ortho/prognathism. Geometric Morphometrics provides a detailed and interpretable assessment of morphological variation that may be useful in assessing respirators and devising new test and certification standards.

  19. Quantitative analysis of 3D mitral complex geometry using support vector machines

    Quantitative analysis of 3D mitral complex geometry is crucial for a better understanding of its dysfunction. This work aims to characterize the geometry of the mitral complex and utilize a support-vector-machine-based classifier from geometric parameters to support the diagnosis of congenital mitral regurgitation (MR). The method has the following steps: (1) description of the 3D geometry of the mitral complex and establishment of its local reference coordinate system, (2) calculation of geometric parameters and (3) analysis and classification of these parameters. With a control group of 20 normal young children (11 boys, 9 girls, mean age 5.96 ± 3.12 years) and with the normal structure of mitral apparatus, 20 patients (9 boys, 11 girls, mean age 5.59 ± 3.30 years) suffering from severe congenital MR are studied in this study. The average classification accuracy is up to 90.0% of the present population, with the possibility of exploring quantitative association between the mitral complex geometry and the mechanism of congenital MR. (paper)

  20. Finite element analysis of the impact response of reinforced concrete structures using DYNA3D

    Reinforced concrete structures in nuclear installations are potentially subject to accidental impact from external or internally generated hazards. These include: soft impacts such as aircraft crash on containment structures; and hard impacts such as heavy dropped loads on pond floors, or plant-generated fragments on structural and protective walls. The explicit finite element code DYNA3D has been used extensively for analysis of the response of structures to dynamic loadings, and a constitutive material model for reinforced concrete has been developed within DYNA3D to represent local cracking and crushing due to impact loads, as well as treating the elastic and plastic global response modes of the structure. This model has been extensively validated against impact tests for simulated aircraft impact on containment structures, but more recent interest has concentrated on analysis of hard impacts on floors and walls. Whilst a simplified constitutive model is adequate for the response to soft impacts, in which the dominant response mode is flexural, the local damage and high rates experienced in hard impacts have required further development of the material model. This paper describes the main features of the constitutive model, and presents the results of a validation case of a heavy dropped load on a reinforced concrete floor. (author)

  1. Shape Analysis of 3D Head Scan Data for U.S. Respirator Users

    Slice DennisE

    2010-01-01

    Full Text Available In 2003, the National Institute for Occupational Safety and Health (NIOSH conducted a head-and-face anthropometric survey of diverse, civilian respirator users. Of the 3,997 subjects measured using traditional anthropometric techniques, surface scans and 26 three-dimensional (3D landmark locations were collected for 947 subjects. The objective of this study was to report the size and shape variation of the survey participants using the 3D data. Generalized Procrustes Analysis (GPA was conducted to standardize configurations of landmarks associated with individuals into a common coordinate system. The superimposed coordinates for each individual were used as commensurate variables that describe individual shape and were analyzed using Principal Component Analysis (PCA to identify population variation. The first four principal components (PC account for 49% of the total sample variation. The first PC indicates that overall size is an important component of facial variability. The second PC accounts for long and narrow or short and wide faces. Longer narrow orbits versus shorter wider orbits can be described by PC3, and PC4 represents variation in the degree of ortho/prognathism. Geometric Morphometrics provides a detailed and interpretable assessment of morphological variation that may be useful in assessing respirators and devising new test and certification standards.

  2. A 3D endoscopy reconstruction as a saliency map for analysis of polyp shapes

    Ruano, Josue; Martínez, Fabio; Gómez, Martín.; Romero, Eduardo

    2015-01-01

    A first diagnosis of colorectal cancer is performed by examination of polyp shape and appearance during an endoscopy routine procedure. However, the video-endoscopy is highly noisy because exacerbated physiological conditions like increased motility or secretion may limit the visual analysis of lesions. In this work a 3D reconstruction of the digestive tract is proposed, facilitating the polyp shape evaluation by highlighting its surface geometry and allowing an analysis from different perspectives. The method starts by a spatio-temporal map, constructed to group the different regions of the tract by their similar dynamic patterns during the sequence. Then, such map was convolved with a second derivative of a Gaussian kernel that emulates the camera distortion and allows to highlight the polyp surface. The position initialization in each frame of the kernel was computed from expert manual delineation and propagated along the sequence based on. Results show reliable reconstructions, with a salient 3D polyp structure that can then be better observed.

  3. Segmentation, Reconstruction, and Analysis of Blood Thrombus Formation in 3D 2-Photon Microscopy Images

    Xu Zhiliang

    2010-01-01

    Full Text Available We study the problem of segmenting, reconstructing, and analyzing the structure growth of thrombi (clots in blood vessels in vivo based on 2-photon microscopic image data. First, we develop an algorithm for segmenting clots in 3D microscopic images based on density-based clustering and methods for dealing with imaging artifacts. Next, we apply the union-of-balls (or alpha-shape algorithm to reconstruct the boundary of clots in 3D. Finally, we perform experimental studies and analysis on the reconstructed clots and obtain quantitative data of thrombus growth and structures. We conduct experiments on laser-induced injuries in vessels of two types of mice (the wild type and the type with low levels of coagulation factor VII and analyze and compare the developing clot structures based on their reconstructed clots from image data. The results we obtain are of biomedical significance. Our quantitative analysis of the clot composition leads to better understanding of the thrombus development, and is valuable to the modeling and verification of computational simulation of thrombogenesis.

  4. Analysis of Impact of 3D Printing Technology on Traditional Manufacturing Technology

    Wu, Niyan; Chen, Qi; Liao, Linzhi; Wang, Xin

    With quiet rise of 3D printing technology in automobile, aerospace, industry, medical treatment and other fields, many insiders hold different opinions on its development. This paper objectively analyzes impact of 3D printing technology on mold making technology and puts forward the idea of fusion and complementation of 3D printing technology and mold making technology through comparing advantages and disadvantages of 3D printing mold and traditional mold making technology.

  5. Synthesis and crystal structure of new temephos analogues as cholinesterase inhibitor: molecular docking, QSAR study, and hydrogen bonding analysis of solid state.

    Gholivand, Khodayar; Ebrahimi Valmoozi, Ali Asghar; Bonsaii, Mahyar

    2014-06-25

    A series of temephos (Tem) derivatives were synthesized and characterized by 31P, 13C, and 1H NMR and FT-IR spectral techniques. Also, the crystal structure of compound 9 was investigated. The hydrogen bonding energies (E2) were calculated by NBO analysis of the crystal cluster. The activities and the mixed-type mechanism of Tem derivatives were evaluated using the modified Ellman's and Lineweaver-Burk's methods on cholinesterase (ChE) enzymes. The inhibitory activities of Tem derivatives with a P═S moiety were higher than those with a P═O moiety. Docking analysis disclosed that the hydrogen bonds occurred between the OR (R=CH3 and C2H5) oxygen and N-H nitrogen atoms of the selected compounds and the receptor site (GLN and GLU) of ChEs. PCA-QSAR indicated that the correlation coefficients of the electronic variables were dominant compared to the structural descriptors. MLR-QSAR models clarified that the net charges of nitrogen and phosphorus atoms contribute important electronic function in the inhibition of ChEs. The validity of the QSAR model was confirmed by a LOO cross-validation method with q2=0.965 between the training and testing sets. PMID:24893121

  6. Scaling analysis of the optimized effective potentials for the multiplet states of multivalent 3d ions

    We apply the optimized effective potential method (OPM) to the multivalent 3dn (n = 2, ..., 8) ions; Mν+ (ν = 2, ..., 8). The total energy functional is approximated by the single-configuration Hartree-Fock. The exchange potential for the average energy configuration is decomposed into the potentials derived from F2(3d, 3d) and F4(3d, 3d) Slater integrals. To investigate properties of the density-functional potential, we have checked the scaling properties of several physical quantities such as the density, the 3d orbital and these potentials. We find that the potentials of the Slater integrals do not have the scaling property. Instead, the weighted potential Vi(r) of an ion i, which is the potential of the Slater integrals times the 3d-orbital density, satisfies the scaling property q3diVi(r) ∼ q3djλ4Vj(λr) where qi3d is the occupation number of the 3d-orbital R3d(r) for ion i. Furthermore, the weighted potential can be approximated by the ion-independent functional of the 3d-orbital density ckR8/33d(r)/q3d where c2 = 0.366 and c4 0.223. This suggests that the weighted potential can be expressed as a functional of the 3d-orbital density

  7. 3-D seismic facies analysis of a reefal buildup, offshore North Sumatra

    Alexander, W.L.; Nellia, M.R. (Mobil Oil Indonesia, Jakarta (Indonesia))

    1994-07-01

    The [open quotes]A[close quotes] field is located on the Sunda shelf, offshore north Sumatra. The A-1 discovery well, drilled in 1972, found hydrocarbon gas in middle Miocene carbonate rocks of reefal origin. Six appraisal wells were subsequently drilled, the most recent in late 1990. Because of drilling problems, mainly lost circulation in the carbonate reservoir, the well data obtained from the appraisal program was generally disappointing. Prior to development of the offshore area, an extensive 3-D seismic survey was shot, a portion of which covered the [open quotes]A[close quotes] field. Interpretation of the 3-D data over the [open quotes]A[close quotes] field identified different seismic facies within the carbonate reservoir. These seismic facies have been integrated with the geological data in order to construct a depositional model for the field. The seismic facies analysis was critical for developing the model because of the inadequate geological data obtained from the wells. Three distinct facies could be identified on the 3-D seismic data and correlated with the well data: reef, near-reef and inter-reef. The main concerns this facies mapping addressed were reserve determination, areas of severe lost circulation, and the distribution of dolomite. The near-reef and inter-reef areas were found to have better reservoir properties than the reef core, thereby impacting reserve calculations. In addition, the reef facies, with zones of vuggy to near cavernous type porosity, was correlatable to wells that had experienced severe lost circulation. Finally, dolomite was found to occur only within the reef facies, enabling its distribution to be predicted.

  8. Analysis of bite marks in foodstuffs by computer tomography (cone beam CT)--3D reconstruction.

    Marques, Jeidson; Musse, Jamilly; Caetano, Catarina; Corte-Real, Francisco; Corte-Real, Ana Teresa

    2013-12-01

    The use of three-dimensional (3D) analysis of forensic evidence is highlighted in comparison with traditional methods. This three-dimensional analysis is based on the registration of the surface from a bitten object. The authors propose to use Cone Beam Computed Tomography (CBCT), which is used in dental practice, in order to study the surface and interior of bitten objects and dental casts of suspects. In this study, CBCT is applied to the analysis of bite marks in foodstuffs, which may be found in a forensic case scenario. 6 different types of foodstuffs were used: chocolate, cheese, apple, chewing gum, pizza and tart (flaky pastry and custard). The food was bitten into and dental casts of the possible suspects were made. The dental casts and bitten objects were registered using an x-ray source and the CBCT equipment iCAT® (Pennsylvania, EUA). The software InVivo5® (Anatomage Inc, EUA) was used to visualize and analyze the tomographic slices and 3D reconstructions of the objects. For each material an estimate of its density was assessed by two methods: HU values and specific gravity. All the used materials were successfully reconstructed as good quality 3D images. The relative densities of the materials in study were compared. Amongst the foodstuffs, the chocolate had the highest density (median value 100.5 HU and 1,36 g/cm(3)), while the pizza showed to have the lowest (median value -775 HU and 0,39 g/cm(3)), on both scales. Through tomographic slices and three-dimensional reconstructions it was possible to perform the metric analysis of the bite marks in all the foodstuffs, except for the pizza. These measurements could also be obtained from the dental casts. The depth of the bite mark was also successfully determined in all the foodstuffs except for the pizza. Cone Beam Computed Tomography has the potential to become an important tool for forensic sciences, namely for the registration and analysis of bite marks in foodstuffs that may be found in a crime

  9. International training program in support of safety analysis. 3D S.UN.COP-scaling uncertainty and 3D thermal-hydraulics/neutron-kinetics coupled codes seminars

    Thermal-hydraulic system computer codes are extensively used worldwide for analysis of nuclear facilities by utilities, regulatory bodies, nuclear power plant designers and vendors, nuclear fuel companies, research organizations, consulting companies, and technical support organizations. The computer code user represents a source of uncertainty that can influence the results of system code calculations. This influence is commonly known as the user effect' and stems from the limitations embedded in the codes as well as from the limited capability of the analysis to use the codes. Code user training and qualification is an effective means for reducing the variation of results caused by the application of the codes by different users. This paper describes a systematic approach to training code users who, upon completion of the training, should be able to perform calculations making the best possible use of the capabilities of best estimate codes. In other words, the program aims at contributing towards solving the problem of user effect. The 3D S.UN.COP (Scaling, Uncertainty and 3D COuPled code calculations) seminars have been organized as follow-up of the proposal to IAEA for the Permanent Training Course for System Code Users. Six seminars have been held at University of Pisa (2003, 2004), at The Pennsylvania State University (2004), at University of Zagreb (2005), at the School of Industrial Engineering of Barcelona (January-February 2006) and in Buenos Aires, Argentina (October 2006), being this last one requested by ARN (Autoridad Regulatoria Nuclear), NA-SA (Nucleoelectrica Argentina S.A) and CNEA (Comision Nacional de Energia Atomica). It was recognized that such courses represented both a source of continuing education for current code users and a mean for current code users to enter the formal training structure of a proposed 'permanent' stepwise approach to user training. The 3D S.UN.COP 2006 in Barcelona was successfully held with the attendance of 33

  10. Trend Analysis for the Market and Application Development of 3D Printing

    Chin-Ching Yeh

    2014-01-01

    In 2011, the Economist newspaper declared the advent of 3D printing, also known as Additive Manufacturing (AM), to herald the start of the Third Industrial Revolution. Chris Anderson, originator of the “long-tail theory”, not only authored Makers, a book on3D printing, but also co-founded 3D Robotics to realize his vision for the potential of 3D printing by applying his perspectives embedded in his book. Nevertheless, opposing viewpoints suggest that 3D printing may not be the game changer it...

  11. Analysis of the spectrum six times ionized zinc (Zn VII): the 3d6-3d54p transition array

    The spectrum of zinc was photographed in the 100-300 A region on a 10.7 m grazing incidence spectrograph using a triggered spark light source. 335 lines were classified in the Zn VII 3d6-3d54p transition array, resulting in the establishment of 30 of the 34 levels of the 3d6 configuration and 103 of the 214 levels of the 3d54p. The ground configuration 3d6 was described by a generalized least-squares fit (GLSF) involving orthogonal operators to a set of 3dN configurations. This yielded a mean error of 3 cm-1 for its level values. The excited configruation was described by the conventional Slater Condon parameter set, giving a mean error of 105 cm-1. (orig.)

  12. 3-D geometrical analysis tool for meteoroids/debris impact risk assessment

    Borde, J.; Drolshagen, G.

    1991-01-01

    It is widely appreciated that meteoroids and space debris are critical factors in the safety and reliability of future missions, especially long-term mission such as the Space Station Freedom. In this paper, enhanced a 3-D numerical analysis tool for meteoroids/debris risk evaluation is presented. It is based on presently available environment and particle/wall interaction models together with spacecraft shielding design. This provides impact probabilities and resulting damaging effects using realistic geometrical treatments. The shielding by other parts of the spacecraft is considered. It accounts for directional and geometrical effects both in the environment and in the damage evaluation. It includes the latest environment and design models and allows an easy updating of these data as they are improved upon. This tool is a new application of the ESABASE framework, a geometrical system level analysis and engineering tool developed by MATRA ESPACE for ESA/ESTEC.

  13. Analysis of the SL-1 Accident Using RELAPS5-3D

    On January 3, 1961, at the National Reactor Testing Station, in Idaho Falls, Idaho, the Stationary Low Power Reactor No. 1 (SL-1) experienced a major nuclear excursion, killing three people, and destroying the reactor core. The SL-1 reactor, a 3 MWt boiling water reactor, was shut down and undergoing routine maintenance work at the time. This paper presents an analysis of the SL-1 reactor excursion using the RELAP5-3D thermal-hydraulic and nuclear analysis code, with the intent of simulating the accident from the point of reactivity insertion to destruction and vaporization of the fuel. Results are presented, along with a discussion of sensitivity to some reactor and transient parameters (many of the details are only known with a high level of uncertainty)

  14. Analysis of the SL-1 Accident Using RELAPS5-3D

    Francisco, A.D. and Tomlinson, E. T.

    2007-11-08

    On January 3, 1961, at the National Reactor Testing Station, in Idaho Falls, Idaho, the Stationary Low Power Reactor No. 1 (SL-1) experienced a major nuclear excursion, killing three people, and destroying the reactor core. The SL-1 reactor, a 3 MW{sub t} boiling water reactor, was shut down and undergoing routine maintenance work at the time. This paper presents an analysis of the SL-1 reactor excursion using the RELAP5-3D thermal-hydraulic and nuclear analysis code, with the intent of simulating the accident from the point of reactivity insertion to destruction and vaporization of the fuel. Results are presented, along with a discussion of sensitivity to some reactor and transient parameters (many of the details are only known with a high level of uncertainty).

  15. CAD, 3D modeling, engineering analysis, and prototype experimentation industrial and research applications

    Zheng Li, Jeremy

    2015-01-01

    This succinct book focuses on computer aided design (CAD), 3-D modeling, and engineering analysis and the ways they can be applied effectively in research and industrial sectors including aerospace, defense, automotive, and consumer products. These efficient tools, deployed for R&D in the laboratory and the field, perform efficiently three-dimensional modeling of finished products, render complex geometrical product designs, facilitate structural analysis and optimal product design, produce graphic and engineering drawings, and generate production documentation. Written with an eye toward green energy installations and novel manufacturing facilities, this concise volume enables scientific researchers and engineering professionals to learn design techniques, control existing and complex issues, proficiently use CAD tools, visualize technical fundamentals, and gain analytic and technical skills. This book also: ·       Equips practitioners and researchers to handle powerful tools for engineering desi...

  16. Automated extraction and analysis of rock discontinuity characteristics from 3D point clouds

    Bianchetti, Matteo; Villa, Alberto; Agliardi, Federico; Crosta, Giovanni B.

    2016-04-01

    A reliable characterization of fractured rock masses requires an exhaustive geometrical description of discontinuities, including orientation, spacing, and size. These are required to describe discontinuum rock mass structure, perform Discrete Fracture Network and DEM modelling, or provide input for rock mass classification or equivalent continuum estimate of rock mass properties. Although several advanced methodologies have been developed in the last decades, a complete characterization of discontinuity geometry in practice is still challenging, due to scale-dependent variability of fracture patterns and difficult accessibility to large outcrops. Recent advances in remote survey techniques, such as terrestrial laser scanning and digital photogrammetry, allow a fast and accurate acquisition of dense 3D point clouds, which promoted the development of several semi-automatic approaches to extract discontinuity features. Nevertheless, these often need user supervision on algorithm parameters which can be difficult to assess. To overcome this problem, we developed an original Matlab tool, allowing fast, fully automatic extraction and analysis of discontinuity features with no requirements on point cloud accuracy, density and homogeneity. The tool consists of a set of algorithms which: (i) process raw 3D point clouds, (ii) automatically characterize discontinuity sets, (iii) identify individual discontinuity surfaces, and (iv) analyse their spacing and persistence. The tool operates in either a supervised or unsupervised mode, starting from an automatic preliminary exploration data analysis. The identification and geometrical characterization of discontinuity features is divided in steps. First, coplanar surfaces are identified in the whole point cloud using K-Nearest Neighbor and Principal Component Analysis algorithms optimized on point cloud accuracy and specified typical facet size. Then, discontinuity set orientation is calculated using Kernel Density Estimation and

  17. In vivo analysis of physiological 3D blood flow of cerebral veins

    Schuchardt, Florian; Schroeder, Laure; Baeuerle, Jochen; Harloff, Andreas [University Medical Centre, Department of Neurology, Freiburg (Germany); Anastasopoulos, Constantin [University Medical Center, Department of Neuropaediatrics and Muscle Disorders, Freiburg (Germany); University Medical Centre, Department of Neuroradiology, Freiburg (Germany); Markl, Michael [Northwestern University, Department of Radiology, Feinberg School of Medicine and McCormick School of Engineering, Chicago, IL (United States); Hennemuth, Anja; Drexl, Johann [Fraunhofer MEVIS, Bremen (Germany); Valdueza, Jose M. [Neurological Center, Segeberger Kliniken, Bad Segeberg (Germany); Mader, Irina [University Medical Centre, Department of Neuroradiology, Freiburg (Germany)

    2015-08-15

    To visualize and quantify physiological blood flow of intracranial veins in vivo using time-resolved, 3D phase-contrast MRI (4D flow MRI), and to test measurement accuracy. Fifteen healthy volunteers underwent repeated ECG-triggered 4D flow MRI (3 Tesla, 32-channel head coil). Intracranial venous blood flow was analysed using dedicated software allowing for blood flow visualization and quantification in analysis planes at the superior sagittal, straight, and transverse sinuses. MRI was evaluated for intra- and inter-observer agreement and scan-rescan reproducibility. Measurements of the transverse sinuses were compared with transcranial two-dimensional duplex ultrasound. Visualization of 3D blood flow within cerebral sinuses was feasible in 100 % and within at least one deep cerebral vein in 87 % of the volunteers. Blood flow velocity/volume increased along the superior sagittal sinus and was lower in the left compared to the right transverse sinus. Intra- and inter-observer reliability and reproducibility of blood flow velocity (mean difference 0.01/0.02/0.02 m/s) and volume (mean difference 0.0002/-0.0003/0.00003 l/s) were good to excellent. High/low velocities were more pronounced (8 % overestimation/9 % underestimation) in MRI compared to ultrasound. Four-dimensional flow MRI reliably visualizes and quantifies three-dimensional cerebral venous blood flow in vivo and is promising for studies in patients with sinus thrombosis and related diseases. (orig.)

  18. Advanced 2D and 3D Electron Microscopy Analysis of Clay/PP Nanocomposites

    Mosca, Alessandra; Roberts, Ashley; Daviðsdóttir, Svava;

    2011-01-01

    the improved macroscopic properties of nanocomposites. In this work, a clay/PP nanocomposite is studied by 2D bright field transmission electron microscopy (TEM) and 3D focussed ion beam – field emission gun scanning electron microscopy (FIB/FEG SEM). Materials and Methods A clay/polymer nanocomposite...... consisting of 3 wt% modified clay in a PP matrix was studied. Prior to microscopy analyses, SEM or TEM samples were cryo-microtomed to a flat surface or thin sections (70 nm), respectively. An FEI Titan T20 TEM microscope operating at 200 kV was used for 2D imaging. An FEI Helios focussed ion beam (FIB......) equipped with field emission gun (FEG) and through lens detector (TLD) was used for high resolution 3D imaging of the material via slice-and-view technique [2]. Image analysis was performed using Matlab. Results and Discussion Figure 1 (a) shows a TEM micrograph of a clay/PP nanocomposite, where the clay...

  19. Welding distortion analysis of multipass joint combination with different sequences using 3D FEM and experiment

    This paper presents an investigation of the welding sequence effect on induced angular distortion using FEM and experiments. The specimen of a combined joint geometry was modeled and simulated using Multipass Welding Advisor (MWA) in SYSWELD 2010 based on the thermal-elastic-plastic approach with low manganese carbon steel S3355J2G3 as specimen material and Goldak's double ellipsoid as heat source model. To validate the simulation results, a series of experiments was conducted with two different welding sequences using automated welding process, low carbon steel as parent metal, digital GMAW power source with premixed shielding gas and both-sided clamping technique. Based on the results, it was established that the thermo-elastic-plastic 3D FEM analysis shows good agreement with experimental results and the welding sequence “from outside to inside” induced less angular distortion compared to “from inside to outside”. -- Highlights: • 3D FEM was used to analyze the welding distortion on two different sequences. • Simulation results were validated with experiments using automated welding system. • Simulation results and experiments showed acceptable accuracy. • Welding sequence “outside–inside” showed less distortion than “inside–outside”

  20. VAP3D: a software for dosimetric analysis and visualization of phantons

    The anthropomorphic models used in computational dosimetry of the ionizing radiation, usually called voxel phantom, are produced from image stacks CT (Computed Tomography) or MRI (Magnetic Resonance Imaging) obtained from patient or volunteer scanning. These phantoms are the geometry to be radiated in the computing arrangements of exposure, using a Monte Carlo code, allowing the estimation of the energy deposited in each voxel of the virtual body. From these data collected in the simulation, it is possible to evaluate the average absorbed dose in various organs and tissues radiosensitive cataloged by the International Commission on Radiological Protection (ICRP). Therefore, a computational model of the exhibition is constituted primarily by the Monte Carlo code to simulate the transport, deposition and interaction of radiation and the phantom being irradiated. The construction of voxel phantoms requires computer skills like a transformation format of images, compression of 2D images for 3D image construction, quantization, resampling and image segmentation, among others. Hardly the computational dosimetry researcher finds all these skills into a single software and often this results in a decrease in the pace of their research or the use, sometimes inadequate, the alternative tools. This paper presents the VAP3D (Visualization and Analysis of Phantoms), a software developed with Qt/VTK with C++, in order to operationalize some of the tasks mentioned above. The current version has been based on DIP software (Digital Imaging Processing), containing the File menu, Conversions and tools, where the user interacts with the software. (author)

  1. Shape, size, and atomic composition analysis of nanostructures in 3D by Rutherford backscattering spectrometry

    Zolnai, Zsolt, E-mail: zolnai.zsolt@ttk.mta.hu

    2013-09-15

    The emergence of novel micro- and nanofabrication tools lead to the targeted research of highly ordered three-dimensional nanosystems, constructed from regular building blocks like spheres, cylinders, bricks, pyramids, which can be used in a wide range of applications. As a consequence, the exploration of the potential and limits of efficient analytical techniques to characterize structured nanosystems became a significant task. In this work the scope of conventional Rutherford backscattering spectrometry (RBS) analysis is extended to investigate highly ordered periodic nanostructures in three dimensions. Hexagonally arranged spherical and ellipsoidal silica particles, rectangular gold nano-arrays, and embedded structures in Si substrates and silica particles are analyzed. It is shown that the shape of the measured spectra can be correlated with the shape of individual nano-objects through geometrical considerations. The evaluation of the recorded data for different sample tilt angles can be carried out with the Monte-Carlo type 3D simulation model cell concept considering the details of the applied measurement geometry. It is demonstrated that macrobeam 3D-RBS can provide valuable information on the shape, size, spacing, and atomic composition of nanostructured samples as well as on nanoscale atomic transport processes and consequently, it can be utilized as a highly precise, non-destructive characterization tool for nanotechnology.

  2. SAFE-3D analysis of a piezoelectric transducer to excite guided waves in a rail web

    Ramatlo, Dineo A.; Long, Craig S.; Loveday, Philip W.; Wilke, Daniel N.

    2016-02-01

    Our existing Ultrasonic Broken Rail Detection system detects complete breaks and primarily uses a propagating mode with energy concentrated in the head of the rail. Previous experimental studies have demonstrated that a mode with energy concentrated in the head of the rail, is capable of detecting weld reflections at long distances. Exploiting a mode with energy concentrated in the web of the rail would allow us to effectively detect defects in the web of the rail and could also help to distinguish between reflections from welds and cracks. In this paper, we will demonstrate the analysis of a piezoelectric transducer attached to the rail web. The forced response at different frequencies is computed by the Semi-Analytical Finite Element (SAFE) method and compared to a full three-dimensional finite element method using ABAQUS. The SAFE method only requires the rail track cross-section to be meshed using two-dimensional elements. The ABAQUS model in turn requires a full three-dimensional discretisation of the rail track. The SAFE approach can yield poor predictions at cut-on frequencies associated with other modes in the rail. Problematic frequencies are identified and a suitable frequency range identified for transducer design. The forced response results of the two methods were found to be in good agreement with each other. We then use a previously developed SAFE-3D method to analyse a practical transducer over the selected frequency range. The results obtained from the SAFE-3D method are in good agreement with experimental measurements.

  3. The advanced 3D method for activation analysis of fusion reactor materials

    The method allows analyzing the complex objects activated by neutrons (e.g. fusion reactors) combining advantages of the 3D radiation transport by MCNP program with calculations of multiple activation and radioactive decay chains by FISPACT program. The problem of preparing the gamma-ray sources in cells of 3D geometry was solved by creation of an interface between the MCNP and FISPACT programs. The interface allows optimizing the process of activation analysis by revealing dominant sources of radiation. The developed interface essentially reduces the time needed for calculations. The main advantage of the method is realization of so-called 'multibox' procedure for decay gamma source sampling during decay gamma transport in very large and complex fusion reactor models. Shutdown dose rate calculations are faster (up to 600 times in ITER cryostat) in comparison with applied MCNP standard source definition by using an external user-supplied source subroutine of the 'multibox' procedure. The offered method is intended for solution of the activation tasks with deep penetration of radiation. The method was used in the engineering design of ITER-FEAT and RF DEMO-S

  4. 3D FE Analysis of RC Beams Externally Strengthened with SRG/SRP Systems

    Francesco Bencardino

    2016-05-01

    Full Text Available The purpose of this study is to evaluate, through a nonlinear Finite Element (FE analysis, the structural behavior of Reinforced Concrete (RC beams externally strengthened by using Steel Reinforced Grout (SRG and Steel Reinforced Polymer (SRP systems. The parameters taken into account were the external strengthening configuration, with or without U-wrap end anchorages, as well as the strengthening materials. The numerical simulations were carried out by using a three-dimensional (3D FE model. The linear and nonlinear behavior of all materials was modeled by appropriate constitutive laws and the connection between concrete substrate and external reinforcing layer was simulated by means of cohesive surfaces with appropriate bond-slip laws. In order to overcome convergence difficulties, to simulate the quasi-static response of the strengthened RC beams, a dynamic approach was adopted. The numerical results in terms of load-displacement curves, failure modes, and load and strain values at critical stages were validated against some experimental data. As a result, the proposed 3D FE model can be used to predict the structural behavior up to ultimate stage of similar strengthened beams without carrying out experimental tests.

  5. A 3D finite element model for the vibration analysis of asymmetric rotating machines

    This paper suggests a 3D finite element method based on the modal theory in order to analyse linear periodically time-varying systems. Presentation of the method is given through the particular case of asymmetric rotating machines. First, Hill governing equations of asymmetric rotating oscillators with two degrees of freedom are investigated. These differential equations with periodic coefficients are solved with classic Floquet theory leading to parametric quasi-modes. These mathematical entities are found to have the same fundamental properties as classic Eigenmodes, but contain several harmonics possibly responsible for parametric instabilities. Extension to the vibration analysis (stability, frequency spectrum) of asymmetric rotating machines with multiple degrees of freedom is achieved with a fully 3D finite element model including stator and rotor coupling. Due to Hill expansion, the usual degrees of freedom are duplicated and associated with the relevant harmonic of the Floquet solutions in the frequency domain. Parametric quasi-modes as well as steady-state response of the whole system are ingeniously computed with a component-mode synthesis method. Finally, experimental investigations are performed on a test rig composed of an asymmetric rotor running on non-isotropic supports. Numerical and experimental results are compared to highlight the potential of the numerical method. (authors)

  6. 3D Finite Element Analysis of PWA-Oil Sand Terrain System Interaction

    Y. Li

    2012-01-01

    Full Text Available A simulator for analyzing the interaction between the oil sand terrain and a pipe wagon articulating (PWA system has been developed in this paper. An elastic-plastic oil sand model was built based on the finite element analysis (FEA method and von Mises yield criterion using the Algor mechanical event simulation (MES software. The three-dimensional (3D distribution of the stress, strain, nodal displacement, and deformed shape of the oil sands was animated at an environmental temperature of 25°C. The 3D behavior of the oil sand terrain was investigated with different loading conditions. The effect of the load and contact area on the stress and nodal displacement was analyzed, respectively. The results indicate that both the max stress and max nodal displacement increase with the load varying from 0 to 3.6+7 N and decrease with the contact area varying from 2 to 10 m2. The method presented in this paper forms the basis for evaluating the bearing capacity of oil sand ground.

  7. Web-based visualisation and analysis of 3D electron-microscopy data from EMDB and PDB ☆

    Lagerstedt, Ingvar; Moore, William J.; Patwardhan, Ardan; Sanz-García, Eduardo; Best, Christoph; Swedlow, Jason R.; Kleywegt, Gerard J

    2013-01-01

    The Protein Data Bank in Europe (PDBe) has developed web-based tools for the visualisation and analysis of 3D electron microscopy (3DEM) structures in the Electron Microscopy Data Bank (EMDB) and Protein Data Bank (PDB). The tools include: (1) a volume viewer for 3D visualisation of maps, tomograms and models, (2) a slice viewer for inspecting 2D slices of tomographic reconstructions, and (3) visual analysis pages to facilitate analysis and validation of maps, tomograms and models. These tool...

  8. Trend Analysis for the Market and Application Development of 3D Printing

    Chin-Ching Yeh

    2014-02-01

    Full Text Available In 2011, the Economist newspaper declared the advent of 3D printing, also known as Additive Manufacturing (AM, to herald the start of the Third Industrial Revolution. Chris Anderson, originator of the “long-tail theory”, not only authored Makers, a book on3D printing, but also co-founded 3D Robotics to realize his vision for the potential of 3D printing by applying his perspectives embedded in his book. Nevertheless, opposing viewpoints suggest that 3D printing may not be the game changer its proponents claim. The article explores the technical classification and market growth potential of 3D printing, and analyzes the main markets and countries as well as the application scope of 3D printing.

  9. TORT-TD/ATTICA3D: a coupled neutron transport and thermal hydraulics code system for 3-D transient analysis of gas cooled high temperature reactors

    Comprehensive safety studies of high temperature gas cooled reactors (HTR) require full three dimensional coupled treatments of both neutron kinetics and thermal-hydraulics. In a common effort, GRS and IKE developed the coupled code system TORT-TD/ATTICA3D for pebble bed type HTR that connects the 3-D transient discrete-ordinates transport code TORT-TD with the 3-D porous medium thermal-hydraulics code ATTICA3D. In this paper, the physical models and calculation capabilities of TORT-TD and ATTICA3D are presented, focusing on model improvements in ATTICA3D and extensions made in TORT-TD related to HTR application. For first applications, the OECD/NEA/NSC PBMR-400 benchmark has been chosen. Results obtained with TORT-TD/ATTICA3D will be shown for transient exercises, e.g. control rod withdrawal and a control rod ejection. Results are compared to other benchmark participants' solutions with special focus on fuel temperature modelling features of ATTICA3D. The provided “grey-curtain” nuclear cross section libraries have been used. First results on 3-D effects during a control rod withdrawal transient will be presented. (author)

  10. International Training Program in Support of Safety Analysis: 3D S.UN.COP-Scaling, Uncertainty and 3D Thermal-Hydraulics/Neutron-Kinetics Coupled Codes Seminars

    Thermal-hydraulic system computer codes are extensively used worldwide for analysis of nuclear facilities by utilities, regulatory bodies, nuclear power plant designers and vendors, nuclear fuel companies, research organizations, consulting companies, and technical support organizations. The computer code user represents a source of uncertainty that can influence the results of system code calculations. This influence is commonly known as the 'user effect' and stems from the limitations embedded in the codes as well as from the limited capability of the analysts to use the codes. Code user training and qualification is an effective means for reducing the variation of results caused by the application of the codes by different users. This paper describes a systematic approach to training code users who, upon completion of the training, should be able to perform calculations making the best possible use of the capabilities of best estimate codes. In other words, the program aims at contributing towards solving the problem of user effect. The 3D S.UN.COP (Scaling, Uncertainty and 3D COuPled code calculations) seminars have been organized as follow-up of the proposal to IAEA for the Permanent Training Course for System Code Users [1]. Five seminars have been held at University of Pisa (2003, 2004), at The Pennsylvania State University (2004), at University of Zagreb (2005) and at the School of Industrial Engineering of Barcelona (2006). It was recognized that such courses represented both a source of continuing education for current code users and a mean for current code users to enter the formal training structure of a proposed 'permanent' stepwise approach to user training. The 3D S.UN.COP 2006 was successfully held with the attendance of 33 participants coming from 18 countries and 28 different institutions (universities, vendors, national laboratories and regulatory bodies). More than 30 scientists (coming from 13 countries and 23 different institutions) were

  11. 3D texture analysis of solitary pulmonary nodules using co-occurrence matrix from volumetric lung CT images

    Dhara, Ashis Kumar; Mukhopadhyay, Sudipta; Khandelwal, Niranjan

    2013-02-01

    In this paper we have investigated a new approach for texture features extraction using co-occurrence matrix from volumetric lung CT image. Traditionally texture analysis is performed in 2D and is suitable for images collected from 2D imaging modality. The use of 3D imaging modalities provide the scope of texture analysis from 3D object and 3D texture feature are more realistic to represent 3D object. In this work, Haralick's texture features are extended in 3D and computed from volumetric data considering 26 neighbors. The optimal texture features to characterize the internal structure of Solitary Pulmonary Nodules (SPN) are selected based on area under curve (AUC) values of ROC curve and p values from 2-tailed Student's t-test. The selected texture feature in 3D to represent SPN can be used in efficient Computer Aided Diagnostic (CAD) design plays an important role in fast and accurate lung cancer screening. The reduced number of input features to the CAD system will decrease the computational time and classification errors caused by irrelevant features. In the present work, SPN are classified from Ground Glass Nodule (GGN) using Artificial Neural Network (ANN) classifier considering top five 3D texture features and top five 2D texture features separately. The classification is performed on 92 SPN and 25 GGN from Imaging Database Resources Initiative (IDRI) public database and classification accuracy using 3D texture features and 2D texture features provide 97.17% and 89.1% respectively.

  12. 3D GeoWall Analysis System for Shuttle External Tank Foreign Object Debris Events

    Brown, Richard; Navard, Andrew; Spruce, Joseph

    2010-01-01

    An analytical, advanced imaging method has been developed for the initial monitoring and identification of foam debris and similar anomalies that occur post-launch in reference to the space shuttle s external tank (ET). Remote sensing technologies have been used to perform image enhancement and analysis on high-resolution, true-color images collected with the DCS 760 Kodak digital camera located in the right umbilical well of the space shuttle. Improvements to the camera, using filters, have added sharpness/definition to the image sets; however, image review/analysis of the ET has been limited by the fact that the images acquired by umbilical cameras during launch are two-dimensional, and are usually nonreferenceable between frames due to rotation translation of the ET as it falls away from the space shuttle. Use of stereo pairs of these images can enable strong visual indicators that can immediately portray depth perception of damaged areas or movement of fragments between frames is not perceivable in two-dimensional images. A stereoscopic image visualization system has been developed to allow 3D depth perception of stereo-aligned image pairs taken from in-flight umbilical and handheld digital shuttle cameras. This new system has been developed to augment and optimize existing 2D monitoring capabilities. Using this system, candidate sequential image pairs are identified for transformation into stereo viewing pairs. Image orientation is corrected using control points (similar points) between frames to place the two images in proper X-Y viewing perspective. The images are then imported into the WallView stereo viewing software package. The collected control points are used to generate a transformation equation that is used to re-project one image and effectively co-register it to the other image. The co-registered, oriented image pairs are imported into a WallView image set and are used as a 3D stereo analysis slide show. Multiple sequential image pairs can be used

  13. Feasibility analysis of high resolution tissue image registration using 3-D synthetic data

    Yachna Sharma

    2011-01-01

    Full Text Available Background: Registration of high-resolution tissue images is a critical step in the 3D analysis of protein expression. Because the distance between images (~4-5μm thickness of a tissue section is nearly the size of the objects of interest (~10-20μm cancer cell nucleus, a given object is often not present in both of two adjacent images. Without consistent correspondence of objects between images, registration becomes a difficult task. This work assesses the feasibility of current registration techniques for such images. Methods: We generated high resolution synthetic 3-D image data sets emulating the constraints in real data. We applied multiple registration methods to the synthetic image data sets and assessed the registration performance of three techniques (i.e., mutual information (MI, kernel density estimate (KDE method [1], and principal component analysis (PCA at various slice thicknesses (with increments of 1μm in order to quantify the limitations of each method. Results: Our analysis shows that PCA, when combined with the KDE method based on nuclei centers, aligns images corresponding to 5μm thick sections with acceptable accuracy. We also note that registration error increases rapidly with increasing distance between images, and that the choice of feature points which are conserved between slices improves performance. Conclusions: We used simulation to help select appropriate features and methods for image registration by estimating best-case-scenario errors for given data constraints in histological images. The results of this study suggest that much of the difficulty of stained tissue registration can be reduced to the problem of accurately identifying feature points, such as the center of nuclei.

  14. A customized model for 3D human segmental kinematic coupling analysis by optoelectronic stereophotogrammetry

    2010-01-01

    The study of three-dimensional human kinematics has significant impacts on medical and healthcare technology innovations. As a non-invasive technology, optoelectronic stereophotogrammetry is widely used for in-vivo locomotor evaluations. However, relatively high testing difficulties, poor testing accuracies, and high analysis complexities prohibit its further employment. The objective of this study is to explore an improved modeling technique for quantitative measurement and analysis of human locomotion. Firstly, a 3D whole body model of 17 rigid segments was developed to describe human locomotion. Subsequently, a novel infrared reflective marker cluster for 17 body segments was constructed to calibrate and record the 3D segmental position and orientation of each functional body region simultaneously with high spatial accuracy. In addition, the novel calibration procedure and the conception of kinematic coupling of human locomotion were proposed to investigate the segmental functional characteristics of human motion. Eight healthy male subjects were evaluated with walking and running experiments using the Qualisys motion capture system. The experimental results demonstrated the followings: (i) The kinematic coupling of the upper limbs and the lower limbs both showed the significant characteristics of joint motion, while the torso motion of human possessed remarkable features of segmental motion; (ii) flexion/extension was the main motion feature in sagittal plane, while the lateral bending in coronal plane and the axial rotation in transverse plane were subsidiary motions during an entire walking cycle regarding to all the segments of the human body; (iii) compared with conventional methods, the improved techniques have a competitive advantage in the convenient measurement and accurate analysis of the segmental dynamic functional characteristics during human locomotion. The modeling technique proposed in this paper has great potentials in rehabilitation engineering

  15. 3D pore-network analysis and permeability estimation of deformation bands hosted in carbonate grainstones.

    Zambrano, Miller; Tondi, Emanuele; Mancini, Lucia; Trias, F. Xavier; Arzilli, Fabio; Lanzafame, Gabriele; Aibibula, Nijiati

    2016-04-01

    In porous rocks strain is commonly localized in narrow Deformation Bands (DBs), where the petrophysical properties are significantly modified with respect the pristine rock. As a consequence, DBs could have an important effect on production and development of porous reservoirs representing baffles zones or, in some cases, contribute to reservoir compartmentalization. Taking in consideration that the decrease of permeability within DBs is related to changes in the porous network properties (porosity, connectivity) and the pores morphology (size distribution, specific surface area), an accurate porous network characterization is useful for understanding both the effect of deformation banding on the porous network and their influence upon fluid flow through the deformed rocks. In this work, a 3D characterization of the microstructure and texture of DBs hosted in porous carbonate grainstones was obtained at the Elettra laboratory (Trieste, Italy) by using two different techniques: phase-contrast synchrotron radiation computed microtomography (micro-CT) and microfocus X-ray micro-CT. These techniques are suitable for addressing quantitative analysis of the porous network and implementing Computer Fluid Dynamics (CFD)experiments in porous rocks. Evaluated samples correspond to grainstones highly affected by DBs exposed in San Vito Lo Capo peninsula (Sicily, Italy), Favignana Island (Sicily, Italy) and Majella Mountain (Abruzzo, Italy). For the analysis, the data were segmented in two main components porous and solid phases. The properties of interest are porosity, connectivity, a grain and/or porous textural properties, in order to differentiate host rock and DBs in different zones. Permeability of DB and surrounding host rock were estimated by the implementation of CFD experiments, permeability results are validated by comparing with in situ measurements. In agreement with previous studies, the 3D image analysis and flow simulation indicate that DBs could be constitute

  16. Inlining 3d Reconstruction, Multi-Source Texture Mapping and Semantic Analysis Using Oblique Aerial Imagery

    Frommholz, D.; Linkiewicz, M.; Poznanska, A. M.

    2016-06-01

    This paper proposes an in-line method for the simplified reconstruction of city buildings from nadir and oblique aerial images that at the same time are being used for multi-source texture mapping with minimal resampling. Further, the resulting unrectified texture atlases are analyzed for façade elements like windows to be reintegrated into the original 3D models. Tests on real-world data of Heligoland/ Germany comprising more than 800 buildings exposed a median positional deviation of 0.31 m at the façades compared to the cadastral map, a correctness of 67% for the detected windows and good visual quality when being rendered with GPU-based perspective correction. As part of the process building reconstruction takes the oriented input images and transforms them into dense point clouds by semi-global matching (SGM). The point sets undergo local RANSAC-based regression and topology analysis to detect adjacent planar surfaces and determine their semantics. Based on this information the roof, wall and ground surfaces found get intersected and limited in their extension to form a closed 3D building hull. For texture mapping the hull polygons are projected into each possible input bitmap to find suitable color sources regarding the coverage and resolution. Occlusions are detected by ray-casting a full-scale digital surface model (DSM) of the scene and stored in pixel-precise visibility maps. These maps are used to derive overlap statistics and radiometric adjustment coefficients to be applied when the visible image parts for each building polygon are being copied into a compact texture atlas without resampling whenever possible. The atlas bitmap is passed to a commercial object-based image analysis (OBIA) tool running a custom rule set to identify windows on the contained façade patches. Following multi-resolution segmentation and classification based on brightness and contrast differences potential window objects are evaluated against geometric constraints and

  17. 3D assessments for design and performance analysis of UO2 pellets

    The geometry of a fuel pellet is a compromise among the intention to maximize UO2 content and minimize the temperature profile taking into account the thermo-mechanical behavior, the economy and the safety of the fuel management during and after irradiation. 'Dishings', 'shoulders', 'chamfers' and/or 'a central hole' on a cylinder with an improved l/d relation (length of the pellet / diameter) are introduced in order to optimize the shape of the pellet. The coupling of the BACO code and the MECOM tools constitutes a complete system for the 3D analysis of the stress-strain state of the pellet under irradiation. CANDU and PHWR MOX fuel will be used to illustrate the qualitative agreement between experimental data and calculations. (author)

  18. 3D Finite Elements Modelling for Design and Performance Analysis of UO Pellets

    Gustavo L. Demarco

    2011-01-01

    Full Text Available The geometry of a fuel pellet is a compromise among the intention to maximize UO2 content and minimize the temperature gradient taking into account the thermomechanical behaviour, the economy, and the safety of the fuel management during and after irradiation. “Dishings”, “shoulders”, “chamfers”, and/or “a central hole” on a cylinder with an improved l/d relation (length of the pellet/diameter are introduced in order to optimize the shape of the pellet. The MeCom tools coupled with the BaCo code constitutes a complete system for the 3D analysis of the stress strain state of the pellet under irradiation. CANDU and PHWR MOX fuel will be used to illustrate the excellent qualitative agreement between experimental data and calculations by using these computational tools.

  19. Thermal hydraulic analysis for the Oregon State TRIGA reactor using RELAP5-3D

    Thermal hydraulic analyses have being conducted at Oregon State University (OSU) in support of the conversion of the OSU TRIGA reactor (OSTR) core from high-enriched uranium (HEU) to low-enriched uranium (LEU) fuel as part of the Reduced Enrichment for Research and Test Reactors program. The goals of the thermal hydraulic analyses were to calculate natural circulation flow rates, coolant temperatures and fuel temperatures as a function of core power for both the HEU and LEU cores; calculate peak values of fuel temperature, cladding temperature, surface heat flux as well as departure from nuclear boiling ratio (DNBR) for steady state and pulse operation; and perform accident analyses for the accident scenarios identified in the OSTR safety analysis report. RELAP5-3D Version 2.4.2 was implemented to develop a model for the thermal hydraulic study. The OSTR core conversion is planned to take place in late 2008. (author)

  20. A 3-D Magnetic Analysis of a Linear Alternator For a Stirling Power System

    Geng, Steven M.; Schwarze, Gene E.; Niedra, Janis M.

    2000-01-01

    The NASA Glenn Research Center and the Department of Energy (DOE) are developing advanced radioisotope Stirling convertors, under contract with Stirling Technology Company (STC), for space applications. Of critical importance to the successful development of the Stirling convertor for space power applications is the development of a lightweight and highly efficient linear alternator. This paper presents a 3-D finite element method (FEM) approach for evaluating Stirling convertor linear alternators. Preliminary correlations with open-circuit voltage measurements provide an encouraging level of confidence in the model. Spatial plots of magnetic field strength (H) are presented in the region of the exciting permanent magnets. These plots identify regions of high H, where at elevated temperature and under electrical load, the potential to alter the magnetic moment of the magnets exists. This implies the need for further testing and analysis.

  1. Noise analysis for near field 3-D FM-CW radar imaging systems

    Sheen, David M.

    2015-06-19

    Near field radar imaging systems are used for several applications including concealed weapon detection in airports and other high-security venues. Despite the near-field operation, phase noise and thermal noise can limit the performance in several ways including reduction in system sensitivity and reduction of image dynamic range. In this paper, the effects of thermal noise, phase noise, and processing gain are analyzed in the context of a near field 3-D FM-CW imaging radar as might be used for concealed weapon detection. In addition to traditional frequency domain analysis, a time-domain simulation is employed to graphically demonstrate the effect of these noise sources on a fast-chirping FM-CW system.

  2. The 3D EdgeRunner Pipeline: a novel shape-based analysis for neoplasms characterization

    Yepes-C, Fernando; Johnson, Rebecca; Lao, Yi; Hwang, Darryl; Coloigner, Julie; Yap, Felix; Bushan, Desai; Cheng, Phillip; Gill, Inderbir; Duddalwar, Vinay; Lepore, Natasha

    2016-03-01

    The characterization of tumors after being imaged is currently a qualitative process performed by skilled professionals. If we can aid their diagnosis by identifying quantifiable features associated with tumor classification, we may avoid invasive procedures such as biopsies and enhance efficiency. The aim of this paper is to describe the 3D EdgeRunner Pipeline which characterizes the shape of a tumor. Shape analysis is relevant as malignant tumors tend to be more lobular and benign ones tare generally more symmetrical. The method described considers the distance from each point on the edge of the tumor to the centre of a synthetically created field of view. The method then determines coordinates where the measured distances are rapidly changing (peaks) using a second derivative found by five point differentiation. The list of coordinates considered to be peaks can then be used as statistical data to compare tumors quantitatively. We have found this process effectively captures the peaks on a selection of kidney tumors.

  3. Analysis and modeling of coupled thermo-hydro-mechanical phenomena in 3D fractured media

    This doctoral research was conducted as part of a joint France-Spain co-tutelage PhD thesis in the framework of a bilateral agreement between two universities, the Institut National Polytechnique de Toulouse (INPT) and the Universidad Politecnica de Madrid (UPM). It concerns a problem of common interest at the national and international levels, namely, the disposal of radioactive waste in deep geological repositories. The present work is devoted, more precisely, to near-field hydrogeological aspects involving mass and heat transport phenomena. The first part of the work is devoted to a specific data interpretation problem (pressures, relative humidities, temperatures) in a multi-barrier experimental system at the scale of a few meters - the 'Mock-Up Test' of the FEBEX project, conducted in Spain. Over 500 time series are characterized in terms of spatial, temporal, and/or frequency/scale-based statistical analysis techniques. The time evolution and coupling of physical phenomena during the experiment are analyzed, and conclusions are drawn concerning the behavior and reliability of the sensors. The second part of the thesis develops in more detail the 3-Dimensional (3D) modeling of coupled Thermo-Hydro-Mechanical phenomena in a fractured porous rock, this time at the scale of a hundred meters, based on the data of the 'In-Situ Test' of the FEBEX project conducted at the Grimsel Test Site in the Swiss Alps. As a first step, a reconstruction of the 3D fracture network is obtained by Monte Carlo simulation, taking into account through optimization the geomorphological data collected around the FEBEX gallery. The heterogeneous distribution of traces observed on the cylindrical wall of the tunnel is fairly well reproduced in the simulated network. In a second step, we develop a method to estimate the equivalent permeability of a many-fractured block by extending the superposition method of Ababou et al. [1994] to the case where the permeability of the rock matrix is not

  4. ROC analysis for assessment of lesion detection performance in 3D PET: Influence of reconstruction algorithms

    Image quality in positron emission tomography (PET) can be assessed with physical parameters, as spatial resolution and signal-to-noise ratio, or using psychophysical approaches, which include the observer performance and the considered task (ROC analysis). For PET in oncology, such a task is the detection of hot lesions. The aim of the present study was to assess the lesion detection performance due to adequate modeling of the scanner and the measurement process in the image reconstruction process. We compared the standard OSEM software of the manufacturer with a sophisticated fully 3D iterative reconstruction technique (USC MAP). A rectangular phantom with 6 oblique line sources in a homogeneous background (2.6 kBq/ml 18F) was imaged dynamically with an ECAT EXACT HR+ scanner in 3D mode. Reconstructed activity contrasts varied between 15 and 0, as the line sources were filled with 11C (3.2 MBq/ml). Measured attenuation and standard randoms, dead time, and scatter corrections of the manufacturer were employed. For the ROC analysis, a software tool presented a cut-out of the phantom (15x15 pixels) to two observers. These cut-outs were rated (5 classes) and the area Az under the ROC curve was determined as a measure of detection performance. The improvement for Az with USC MAP compared to the OSEM reconstructions ranged between 0.02 and 0.23 for signal-to-noise ratios of the background between 2.8 and 3.1 and lesion contrast between 2.1 and 4.2. This study demonstrates that adequate modeling of the measurement process in the reconstruction algorithm improves the detection of small hot lesions markedly

  5. ADVANCED 3D LASER MICROSCOPY FOR MEASUREMENTS AND ANALYSIS OF VITRIFIED BONDED ABRASIVE TOOLS

    WOJCIECH KAPLONEK

    2012-12-01

    Full Text Available In many applications, when a precise non-contact assessment of an abrasive tools’ surface is required, alternative measurement methods are often used. Their use offers numerous advantages (referential method as they introduce new qualities into routinely realized measurements. Over the past few years there has been a dynamic increase in the interest for using new types of classical confocal microscopy. These new types are often defined as 3D laser microscopy. This paper presents select aspects of one such method’s application – confocal laser scanning microscopy – for diagnostic analysis of abrasive tools. In addition this paper also looks at the basis for operation, the origins and the development of this measurement technique.The experimental part of this paper presents the select results of tests carried out on grinding wheel active surfaces with sintered microcrystalline corundum grains SG™ bound with glass-crystalline bond. The 3D laser measuring microscopes LEXT OLS3100 and LEXT OLS4000 by Olympus were used in the experiments. Analysis of the obtained measurement data was carried out in dedicated OLS 5.0.9 and OLS4100 2.1 programs, supported by specialist TalyMap Platinum 5.0 software. The realized experiments confirmed the possibility of using the offered measurement method. This concerns both the assessment of grinding wheel active surfaces and their defects, as well as the internal structures of the tools (grain-bond connections. The method presented is an interesting alternative to the typical methods used in the diagnostics of abrasive tools.

  6. Algorithms for the Analysis of 3D Magnetic Resonance Angiography Images

    Atherosclerosis is a disease of the arterial wall, progressively impairing blood flow as it spreads throughout the body. The heart attacks and strokes that result of this condition cause more deaths than cancer in industrial countries. Angiography refers to the group of imaging techniques used through the diagnosis, treatment planning and follow-up of atherosclerosis. In recent years, Magnetic Resonance Angiography (MRA) has shown promising abilities to supplant conventional, invasive, X-ray-based angiography. In order to fully benefit from this modality, there is a need for more objective and reproducible methods. This thesis shows, in two applications, how computerized image analysis can help define and implement these methods. First, by using segmentation to improve visualization of blood-pool contrast enhanced (CE)-MRA, with an additional application in coronary Computerized Tomographic Angiography. We show that, using a limited amount of user interaction and an algorithmic framework borrowed from graph theory and fuzzy logic theory, we can simplify the display of complex 3D structures like vessels. Second, by proposing a methodology to analyze the geometry of arteries in whole-body CE-MRA. The vessel centreline is extracted, and geometrical properties of this 3D curve are measured, to improve interpretation of the angiograms. It represents a more global approach than the conventional evaluation of atherosclerosis, as a first step towards screening for vascular diseases. We have developed the methods presented in this thesis with clinical practice in mind. However, they have the potential to be useful to other applications of computerized image analysis

  7. 3D-CT imaging processing for qualitative and quantitative analysis of maxillofacial cysts and tumors

    The objective of this study was to evaluate spiral-computed tomography (3D-CT) images of 20 patients presenting with cysts and tumors in the maxillofacial complex, in order to compare the surface and volume techniques of image rendering. The qualitative and quantitative appraisal indicated that the volume technique allowed a more precise and accurate observation than the surface method. On the average, the measurements obtained by means of the 3D volume-rendering technique were 6.28% higher than those obtained by means of the surface method. The sensitivity of the 3D surface technique was lower than that of the 3D volume technique for all conditions stipulated in the diagnosis and evaluation of lesions. We concluded that the 3D-CT volume rendering technique was more reproducible and sensitive than the 3D-CT surface method, in the diagnosis, treatment planning and evaluation of maxillofacial lesions, especially those with intra-osseous involvement. (author)

  8. UNIQUIMER 3D, a software system for structural DNA nanotechnology design, analysis and evaluation

    Zhu, Jinhao; Wei, Bryan; Yuan, Yuan; Mi, Yongli

    2009-01-01

    A user-friendly software system, UNIQUIMER 3D, was developed to design DNA structures for nanotechnology applications. It consists of 3D visualization, internal energy minimization, sequence generation and construction of motif array simulations (2D tiles and 3D lattices) functionalities. The system can be used to check structural deformation and design errors under scaled-up conditions. UNIQUIMER 3D has been tested on the design of both existing motifs (holiday junction, 4 × 4 tile, double crossover, DNA tetrahedron, DNA cube, etc.) and nonexisting motifs (soccer ball). The results demonstrated UNIQUIMER 3D's capability in designing large complex structures. We also designed a de novo sequence generation algorithm. UNIQUIMER 3D was developed for the Windows environment and is provided free of charge to the nonprofit research institutions. PMID:19228709

  9. An Integrated System for 3D Gaze Recovery and Semantic Analysis of Human Attention

    Paletta, Lucas; Santner, Katrin; Fritz, Gerald

    2013-01-01

    This work describes a computer vision system that enables pervasive mapping and monitoring of human attention. The key contribution is that our methodology enables full 3D recovery of the gaze pointer, human view frustum and associated human centered measurements directly into an automatically computed 3D model in real-time. We apply RGB-D SLAM and descriptor matching methodologies for the 3D modeling, localization and fully automated annotation of ROIs (regions of interest) within the acquir...

  10. 3D analysis of the reactivity insertion accident in VVER-1000

    Abdullayev, A. M.; Zhukov, A. I.; Slyeptsov, S. M. [NSC Kharkov Inst. for Physics and Technology, 1, Akademicheskaya Str., Kharkov 61108 (Ukraine)

    2012-07-01

    Fuel parameters such as peak enthalpy and temperature during rod ejection accident are calculated. The calculations are performed by 3D neutron kinetics code NESTLE and 3D thermal-hydraulic code VIPRE-W. Both hot zero power and hot full power cases were studied for an equilibrium cycle with Westinghouse hex fuel in VVER-1000. It is shown that the use of 3D methodology can significantly increase safety margins for current criteria and met future criteria. (authors)

  11. Comprehensive Aerodynamic Analysis of a 10 MW Wind Turbine Rotor Using 3D CFD

    Zahle, Frederik; Bak, Christian; Sørensen, Niels N.; Guntur, Srinivas; Troldborg, Niels

    2014-01-01

    airfoil data derived using the Azimuthal Averaging Technique (AAT) was compared to airfoil data based on 2D CFD simulations on airfoil sections in combination with an array of 3D-correction engineering models, which indicated that the model by Chaviaropoulos and Hansen was in best agreement with the 3D...... CFD predictions. BEM simulations on the DTU 10MW RWT using the AAT-based airfoil data were carried out and compared to BEM simulations using the original airfoil data and the 3D CFD results, which showed clear improvements, particularly on the inner part of the rotor. Finally, 3D unsteady Detached...

  12. 3D combinational curves for accuracy and performance analysis of positive biometrics identification

    Du, Yingzi; Chang, Chein-I.

    2008-06-01

    The receiver operating characteristic (ROC) curve has been widely used as an evaluation criterion to measure the accuracy of biometrics system. Unfortunately, such an ROC curve provides no indication of the optimum threshold and cost function. In this paper, two kinds of 3D combinational curves are proposed: the 3D combinational accuracy curve and the 3D combinational performance curve. The 3D combinational accuracy curve gives a balanced view of the relationships among FAR (false alarm rate), FRR (false rejection rate), threshold t, and Cost. Six 2D curves can be derived from the 3D combinational accuracy curve: the conventional 2D ROC curve, 2D curve of (FRR, t), 2D curve of (FAR, t), 2D curve of (FRR, Cost), 2D curve of (FAR, Cost), and 2D curve of ( t, Cost). The 3D combinational performance curve can be derived from the 3D combinational accuracy curve which can give a balanced view among Security, Convenience, threshold t, and Cost. The advantages of using the proposed 3D combinational curves are demonstrated by iris recognition systems where the experimental results show that the proposed 3D combinational curves can provide more comprehensive information of the system accuracy and performance.

  13. 3-D MT modelling and HMT analysis for the north-west part of Poland

    Ślęzak, Katarzyna; Brasse, Heinrich; Jóźwiak, Waldemar; Nowożyński, Krzysztof

    2014-05-01

    The area covered by magnetotelluric survey is a part of the Trans-European Suture Zone (TESZ). The TESZ is the largest tectonic boundary in Europe, extending from the British Isles through Poland to the Black Sea. Several two-dimensional (2-D) models of the electrical resistivity distribution have already been constructed for this area but it turned out that the region had a complicated, three-dimensional structure. Thus a three-dimensional (3-D) inversion model appears to be relevant and interesting to investigate. In cooperation with the Berlin Magnetotelluric Work Group several additional long-period magnetotelluric (LMT) sites were assembled in 2012 and 2013. The mesh was located in the north-west part of Poland (Pomerania region). As a result we obtained 17 new sites over the surface area of approximately of 100 km × 50 km, in addition to 9 stations set up earlier. The collected data were converted to a uniform format and the initial processing was executed. By using the latest software the transfer functions (impedances) and the ellipses of the phase tensor for the sites of our mesh have been calculated. The apparent resistivities and phase responses as functions of period are calculated from the impedance components. The computer program ModEM (Egbert G.D., Kelbert A., 2012), which is used for this work, is a parallel 3-D inversion program for magnetotelluric data. The inversion code employs MPI and, besides impedances, includes tippers and magnetic tensor. The main result of this work is a 3-D model with a good RMS fit of ~2.2 which we could compare with previous outcomes. In this model two prominent, NW-SE striking conductive lineaments located in the mid-crustal levels are noticed. These structures we relate tentatively to the Variscan and Caledonian deformation fronts. Also the analysis of the invariants of the Horizontal Magnetic Tensor (HMT) obtained from previous results (Jozwiak, 2012) allowed us to examine the TESZ in more detail.

  14. 3D models as a platform for urban analysis and studies on human perception of space

    Fisher-Gewirtzman, D.

    2012-10-01

    The objective of this work is to develop an integrated visual analysis and modelling for environmental and urban systems in respect to interior space layout and functionality. This work involves interdisciplinary research efforts that focus primarily on architecture design discipline, yet incorporates experts from other and different disciplines, such as Geoinformatics, computer sciences and environment-behavior studies. This work integrates an advanced Spatial Openness Index (SOI) model within realistic geovisualized Geographical Information System (GIS) environment and assessment using subjective residents' evaluation. The advanced SOI model measures the volume of visible space at any required view point practically, for every room or function. This model enables accurate 3D simulation of the built environment regarding built structure and surrounding vegetation. This paper demonstrates the work on a case study. A 3D model of Neve-Shaanan neighbourhood in Haifa was developed. Students that live in this neighbourhood had participated in this research. Their apartments were modelled in details and inserted into a general model, representing topography and the volumes of buildings. The visual space for each room in every apartment was documented and measured and at the same time the students were asked to answer questions regarding their perception of space and view from their residence. The results of this research work had shown potential contribution to professional users, such as researchers, designers and city planners. This model can be easily used by professionals and by non-professionals such as city dwellers, contractors and developers. This work continues with additional case studies having different building typologies and functions variety, using virtual reality tools.

  15. 3D tomography analysis of the inner structure of pebbles and pebble beds

    An analytical tool to monitor the arrangement of pebbles in a pebble bed as well as the morphology of gas bubbles in as fabricated and neutron irradiated beryllium pebbles is presented. The context of this study is the Helium Cooled Pebble Bed (HPCB) blanket design for the forthcoming generation of fusion reactors. The thermal-mechanical behavior of pebble beds is a basic issue for the HPCB. It depends strongly on the configuration of the pebbles in the bed, and in particular on the number of contacts between pebbles, and between pebbles and the blanket walls. The related contact surfaces play also a major role. The knowledge on the inner structure of the pebbles is required since during the life cycle of a power reactor helium and tritium bubbles are produced inside the beryllium pebbles and the tritium build-up can be in excess of several kilograms, being thereby a key safety issue. All the non-destructive analyses are based on 3D computer aided microtomography using a very powerful synchrotron radiation x-ray source with high spatial resolution. The data analysis relies on a topological operator called filtered medial line applied to the entire data volumes and the related graph representation. By this technique the number of contacts between the pebbles in pebble packs and their angular distribution are obtained, as well as the corresponding contact surfaces. The evaluation of bubble sizes and densities in single pebbles, the assessment of the pore channel network topology, the 3D reconstruction of the fraction of interconnected bubble porosity, and the open-to-closed-porosity ratio are among the most interesting findings. (Copyright copyright 2011 WILEY-VCH Verlag GmbH and Co. KGaA, Weinheim)

  16. 3D linearized stability analysis of various forms of Burnett equations

    Zhao, Wenwen; Chen, Weifang; Liu, Hualin; Agarwal, Ramesh K.

    2014-12-01

    Burnett equations were originally derived in 1935 by Burnett by employing the Chapman-Enskog expansion to Classical Boltzmann equation to second order in Knudsen number Kn. Since then several variants of these equations have been proposed in the literature; these variants have differing physical and numerical properties. In this paper, we consider three such variants which are known in the literature as `the Original Burnett (OB) equations', the Conventional Burnett (CB) equations' and the recently formulated by the authors `the Simplified Conventional (SCB) equations.' One of the most important issues in obtaining numerical solutions of the Burnett equations is their stability under small perturbations. In this paper, we perform the linearized stability (known as the Bobylev Stability) analysis of three-dimensional Burnett equations for all the three variants (OB, CB, and SCB) for the first time in the literature on this subject. By introducing small perturbations in the steady state flow field, the trajectory curve and the variation in attenuation coefficient with wave frequency of the characteristic equation are obtained for all the three variants of Burnett equations to determine their stability. The results show that the Simplified Conventional Burnett (SCB) equations are unconditionally stable under small wavelength perturbations. However, the Original Burnett (OB) and the Conventional Burnett (CB) equations are unstable when the Knudsen number becomes greater than a critical value and the stability condition worsens in 3D when compared to the stability condition for 1-D and 2-D equations. The critical Knudsen number for 3-D OB and CB equations is 0.061 and 0.287 respectively.

  17. Prospective in (Primate) dental analysis through tooth 3D topographical quantification.

    Guy, Franck; Gouvard, Florent; Boistel, Renaud; Euriat, Adelaïde; Lazzari, Vincent

    2013-01-01

    The occlusal morphology of the teeth is mostly determined by the enamel-dentine junction morphology; the enamel-dentine junction plays the role of a primer and conditions the formation of the occlusal enamel reliefs. However, the accretion of the enamel cap yields thickness variations that alter the morphology and the topography of the enamel-dentine junction (i.e., the differential deposition of enamel by the ameloblasts create an external surface that does not necessarily perfectly parallel the enamel-dentine junction). This self-reliant influence of the enamel on tooth morphology is poorly understood and still under-investigated. Studies considering the relationship between enamel and dentine morphologies are rare, and none of them tackled this relationship in a quantitative way. Major limitations arose from: (1) the difficulties to characterize the tooth morphology in its comprehensive tridimensional aspect and (2) practical issues in relating enamel and enamel-dentine junction quantitative traits. We present new aspects of form representation based exclusively on 3D analytical tools and procedures. Our method is applied to a set of 21 unworn upper second molars belonging to eight extant anthropoid genera. Using geometrical analysis of polygonal meshes representatives of the tooth form, we propose a 3D dataset that constitutes a detailed characterization of the enamel and of the enamel-dentine junction morphologies. Also, for the first time, to our knowledge, we intend to establish a quantitative method for comparing enamel and enamel-dentine junction surfaces descriptors (elevation, inclination, orientation, etc.). New indices that allow characterizing the occlusal morphology are proposed and discussed. In this note, we present technical aspects of our method with the example of anthropoid molars. First results show notable individual variations and taxonomic heterogeneities for the selected topographic parameters and for the pattern and strength of

  18. A novel asymptotic expansion homogenization analysis for 3-D composite with relieved periodicity in the thickness direction

    Nasution, Muhammad Ridlo Erdata

    2014-06-01

    A new asymptotic expansion homogenization analysis is proposed to analyze 3-D composite in which thermomechanical and finite thickness effects are considered. Finite thickness effect is captured by relieving periodic boundary condition at the top and bottom of unit-cell surfaces. The mathematical treatment yields that only 2-D periodicity (i.e. in in-plane directions) is taken into account. A unit-cell representing the whole thickness of 3-D composite is built to facilitate the present method. The equivalent in-plane thermomechanical properties of 3-D orthogonal interlock composites are calculated by present method, and the results are compared with those obtained by standard homogenization method (with 3-D periodicity). Young\\'s modulus and Poisson\\'s ratio obtained by present method are also compared with experiments whereby a good agreement is particularly found for the Young\\'s modulus. Localization analysis is carried out to evaluate the stress responses within the unit-cell of 3-D composites for two cases: thermal and biaxial tensile loading. Standard finite element (FE) analysis is also performed to validate the stress responses obtained by localization analysis. It is found that present method results are in a good agreement with standard FE analysis. This fact emphasizes that relieving periodicity in the thickness direction is necessary to accurately simulate the real free-traction condition in 3-D composite. © 2014 Elsevier Ltd.

  19. RAVE code system for 3-D core non-LOCA accident analysis

    Full text of publication follows: This paper provides an overview of the application of the Westinghouse updated RAVE three dimensional (3-D) core transient analysis code system for PWR non-LOCA accident analysis. The RAVE code system consists of a linkage of the following USNRC-approved codes: the EPRI RETRAN-02 (RETRAN) system transient analysis code, the Westinghouse SPNOVA (also referred to as ANC-K) reactor core neutron kinetic nodal code, and the EPRI VIPRE-01 (VIPRE) reactor core thermal-hydraulic (T/H) code. The RETRAN code is used for calculating transient conditions in the reactor coolant system (RCS), including reactor vessel, RCS loops, pressurizer and steam generators. RETRAN also models reactor trips, engineering safety feature (ESF) functions, and the control systems. The SPNOVA code is used to perform 3-D core neutronic calculations for core average power and power distributions in the core. Its reactivity feedback calculation is based on transient fluid conditions and fuel temperatures obtained from the VIPRE code. Based on core inlet temperature, inlet flow and core exit pressure from RETRAN, and the nodal nuclear power from SPNOVA, VIPRE provides back to RETRAN transient nodal heat flux in the reactor core region. An effective 3-D analysis requires RETRAN, SPNOVA and VIPRE calculations to be closely linked for the entire reactor core. The linking architecture uses a standard external communication interface protocol for communication among the running programs on the same or different computers. The RAVE code system currently uses the Parallel Virtual Machine (PVM) software for the data transfer. Besides the necessary changes for data transfer, no other changes were made to RETRAN, SPNOVA or VIPRE fundamental code algorithms or solution methods. The RETRAN model in the RAVE system uses the same detailed reactor vessel, RCS loops, pressurizer, and steam generator, and control and protection models as has been licensed for current plant Safety

  20. Comparison of a quasi-3D analysis and experimental performance for three compact radial turbines

    Simonyi, P. S.; Boyle, R. J.

    1991-01-01

    An experimental aerodynamic evaluation of three compact radial turbine builds was performed. Two rotors which were 40-50 percent shorter in axial length than conventional state-of-the-art radial rotors were tested. A single nozzle design was used. One rotor was tested with the nozzle at two stagger angle settings. A second rotor was tested with the nozzle in only the closed down setting. Experimental results were compared to predicted results from a quasi-3D inviscid and boundary layer analysis, called MTSB (Meridl/Tsonic/Blayer). This analysis was used to predict turbine performance. It has previously been calibrated only for axial, not radial, turbomachinery. The predicted and measured efficiencies were compared at the design point for the three turbines. At the design points the analysis overpredicted the efficiency by less than 1.7 points. Comparisons were also made at off-design operating points. The results of these comparisons showed the importance of an accurate clearance model for efficiency predictions and also that there are deficiencies in the incidence loss model used.

  1. Estimation of Hydraulic Fracturing in the Earth Fill Dam by 3-D Analysis

    Nishimura, Shin-Ichi

    It is necessary to calculate strength and strain for estimation of hydraulic fracturing in the earth fill dam, and to which the FEM is effective. 2-D analysis can produce good results to some extent if an embankment is linear and the plain strain condition can be set to the cross section. However, there may be some conditions not possible to express in the 2-D plain because the actual embankment of agricultural reservoirs is formed by straight and curved lines. Moreover, it may not be possible to precisely calculate strain in the direction of dam axis because the 2-D analysis in the cross section cannot take the shape in the vertical section into consideration. Therefore, we performed 3-D built up analysis targeting the actually-leaked agricultural reservoir to examine hazards of hydraulic fracturing based on the shape of an embankment and by rapid impoundment of water. It resulted in the occurrence of hydraulic fracturing to develop by water pressure due to the vertical cracks caused by tensile strain in the valley and refractive section of the foundation.

  2. Earthscape, a Multi-Purpose Interactive 3d Globe Viewer for Hybrid Data Visualization and Analysis

    Sarthou, A.; Mas, S.; Jacquin, M.; Moreno, N.; Salamon, A.

    2015-08-01

    The hybrid visualization and interaction tool EarthScape is presented here. The software is able to display simultaneously LiDAR point clouds, draped videos with moving footprint, volume scientific data (using volume rendering, isosurface and slice plane), raster data such as still satellite images, vector data and 3D models such as buildings or vehicles. The application runs on touch screen devices such as tablets. The software is based on open source libraries, such as OpenSceneGraph, osgEarth and OpenCV, and shader programming is used to implement volume rendering of scientific data. The next goal of EarthScape is to perform data analysis using ENVI Services Engine, a cloud data analysis solution. EarthScape is also designed to be a client of Jagwire which provides multisource geo-referenced video fluxes. When all these components will be included, EarthScape will be a multi-purpose platform that will provide at the same time data analysis, hybrid visualization and complex interactions. The software is available on demand for free at france@exelisvis.com.

  3. EARTHSCAPE, A MULTI-PURPOSE INTERACTIVE 3D GLOBE VIEWER FOR HYBRID DATA VISUALIZATION AND ANALYSIS

    A. Sarthou

    2015-08-01

    Full Text Available The hybrid visualization and interaction tool EarthScape is presented here. The software is able to display simultaneously LiDAR point clouds, draped videos with moving footprint, volume scientific data (using volume rendering, isosurface and slice plane, raster data such as still satellite images, vector data and 3D models such as buildings or vehicles. The application runs on touch screen devices such as tablets. The software is based on open source libraries, such as OpenSceneGraph, osgEarth and OpenCV, and shader programming is used to implement volume rendering of scientific data. The next goal of EarthScape is to perform data analysis using ENVI Services Engine, a cloud data analysis solution. EarthScape is also designed to be a client of Jagwire which provides multisource geo-referenced video fluxes. When all these components will be included, EarthScape will be a multi-purpose platform that will provide at the same time data analysis, hybrid visualization and complex interactions. The software is available on demand for free at france@exelisvis.com.

  4. Reservoir lithofacies analysis using 3D seismic data in dissimilarity space

    Seismic data interpretation is one of the most important steps in exploration seismology. Seismic facies analysis (SFA) with emphasis on lithofacies can be used to extract more information about structures and geology, which results in seismic interpretation enhancement. Facies analysis is based on unsupervised and supervised classification using seismic attributes. In this paper, supervised classification by a support vector machine using well logs and seismic attributes is applied. Dissimilarity as a new measuring space is employed, after which classification is carried out. Often, SFA is carried out in a feature space in which each dimension stands as a seismic attribute. Different facies show lots of class overlap in the feature space; hence, high classification error values are reported. Therefore, decreasing class overlap before classification is a necessary step to be targeted. To achieve this goal, a dissimilarity space is initially created. As a result of the definition of the new space, the class overlap between objects (seismic samples) is reduced and hence the classification can be done reliably. This strategy causes an increase in the accuracy of classification, and a more trustworthy lithofacies analysis is attained. For applying this method, 3D seismic data from an oil field in Iran were selected and the results obtained by a support vector classifier (SVC) in dissimilarity space are presented, discussed and compared with the SVC applied in conventional feature space. (paper)

  5. Analysis of writing characteristics of CF-SPT head using 3-D read/write simulation system

    Ohtake, Masaya; Takahashi, Norio; Shinagawa, Kiminari

    2004-01-01

    Recently, the increase of areal recording density is remarkable. In order to develop a high density recording device, a read/write (R/W) simulation using three dimensional (3-D) magnetic field analysis is indispensable. In this paper, the magnetic field in a cusp-field single-pole-type (CF-SPT) head with discrete track media is analyzed using a 3-D R/W simulation system, in which edge-based finite element method and 3-D medium hysteresis model based on the ensemble of the Stoner-Wohlfarth (SW...

  6. Pipe3D, a pipeline to analyse integral field spectroscopy data: II. Analysis sequence and CALIFA dataproducts

    Sánchez, S. F.; Pérez, E; Sánchez-Blázquez, P.; García-Benito, R.; Ibarra-Mede, H. J.; González, J. J.; Rosales-Ortega, F. F.; Sánchez-Menguiano, L.; Ascasibar, Y.; Bitsakis, T.; Law, D; Cano-Díaz, M.; López-Cobá, C.; Marino, R.A.; de Paz, A. Gil

    2016-01-01

    We present Pipe3D, an analysis pipeline based on the FIT3D fitting tool, devel- oped to explore the properties of the stellar populations and ionized gas of Integral Field Spectroscopy data. Pipe3D was created to provide with coherent, simple to distribute, and comparable dataproducts, independently of the origin of the data, focused on the data of the most recent IFU surveys (e.g., CALIFA, MaNGA, and SAMI), and the last generation IFS instruments (e.g., MUSE). Along this article we describe ...

  7. Analysis of the KROTOS KFC test by coupling X-Ray image analysis and MC3D calculations

    During a hypothetical severe accident sequence in a Pressurized Water Reactor (PWR), the hot molten materials (corium) issuing from the degraded reactor core may generate a steam explosion if they come in contact with water and may damage the structures and threaten the reactor integrity. The SERENA program is an international OECD project that aims at helping the understanding of this phenomenon also called Fuel Coolant Interaction (FCI) by providing data. CEA takes part in this program by performing tests in its KROTOS facility where steam explosions using prototypic corium can be triggered. Data about the different phases in the premixing are extracted from the KROTOS X-Ray radioscopy images by using KIWI software (KROTOS Image analysis of Water-corium Interaction) currently developed by CEA. The MC3D code, developed by IRSN, is a thermal-hydraulic multiphase code mainly dedicated to FCI studies. It is composed of two applications: premixing and explosion. An overall FCI calculation with MC3D requires a premixing calculation followed by an explosion calculation. The present paper proposes an alternative approach in which all the features of the premixing are extracted from the X-Ray pictures using the KIWI software and transferred to an MC3D dataset for a direct simulation of the explosion. The main hypothesis are discussed as well as the first explosion results obtained with MC3D for the KROTOS KFC test. These results are rather encouraging and are analyzed on the basis of comparisons with the experimental data. (authors)

  8. Analysis of the KROTOS KFC test by coupling X-Ray image analysis and MC3D calculations

    Brayer, C.; Charton, A.; Grishchenko, D.; Fouquart, P.; Bullado, Y.; Compagnon, F.; Correggio, P.; Cassiaut-Louis, N.; Piluso, P. [Commissariat a l' Energie Atomique et Aux Energies Alternatives, CEA Cadarache, DEN, F-13108 Saint-Paul-Les-Durance (France)

    2012-07-01

    During a hypothetical severe accident sequence in a Pressurized Water Reactor (PWR), the hot molten materials (corium) issuing from the degraded reactor core may generate a steam explosion if they come in contact with water and may damage the structures and threaten the reactor integrity. The SERENA program is an international OECD project that aims at helping the understanding of this phenomenon also called Fuel Coolant Interaction (FCI) by providing data. CEA takes part in this program by performing tests in its KROTOS facility where steam explosions using prototypic corium can be triggered. Data about the different phases in the premixing are extracted from the KROTOS X-Ray radioscopy images by using KIWI software (KROTOS Image analysis of Water-corium Interaction) currently developed by CEA. The MC3D code, developed by IRSN, is a thermal-hydraulic multiphase code mainly dedicated to FCI studies. It is composed of two applications: premixing and explosion. An overall FCI calculation with MC3D requires a premixing calculation followed by an explosion calculation. The present paper proposes an alternative approach in which all the features of the premixing are extracted from the X-Ray pictures using the KIWI software and transferred to an MC3D dataset for a direct simulation of the explosion. The main hypothesis are discussed as well as the first explosion results obtained with MC3D for the KROTOS KFC test. These results are rather encouraging and are analyzed on the basis of comparisons with the experimental data. (authors)

  9. Analysis of the Boiling Water Reactor Turbine Trip Benchmark with the Codes DYN3D and ATHLET/DYN3D

    The OECD/NRC Boiling Water Reactor (BWR) Turbine Trip Benchmark was analyzed by the code DYN3D and the coupled code system ATHLET/DYN3D. For the exercise 2 benchmark calculations with given thermal-hydraulic boundary conditions of the core, the analyses were performed with the core model DYN3D. Concerning the modeling of the BWR core in the DYN3D code, several simplifications and their influence on the results were investigated. The standard calculations with DYN3D were performed with 764 coolant channels (one channel per fuel assembly), the assembly discontinuity factors (ADF), and the phase slip model of Molochnikov. Comparisons were performed with the results obtained by calculations with 33 thermal-hydraulic channels, without the ADF and with the slip model of Zuber and Findlay. It is shown that the influence on core-averaged values of the steady state and the transient is small. Considering local parameters, the influence of the ADF or the reduced number of coolant channels is not negligible. For the calculations of exercise 3, the DYN3D model validated during the exercise 2 calculations in combination with the ATHLET system model, developed at Gesellschaft fuer Anlagen- und Reaktorsicherheit for exercise 1, has been used. Calculations were performed for the basic scenario as well as for all specified extreme versions. They were carried out using a modified version of the external coupling of the codes, the 'parallel' coupling. This coupling shows a stable performance at the low time step sizes necessary for an appropriate description of the feedback during the transient. The influence of assumed failures of different relevant safety systems on the plant and the core behavior was investigated in the calculations of the extreme scenarios. The calculations of exercises 2 and 3 contribute to the validation of DYN3D and ATHLET/DYN3D for BWR systems

  10. Latest developments and opportunities for 3D analysis of biological samples by confocal mu-XRF

    Perez, Roberto D., E-mail: danperez@famaf.unc.edu.a [FaMAF, Universidad Nacional de Cordoba, Ciudad Universitaria, 5000 Cordoba (Argentina); CONICET, Rivadavia 1917, 1033 Buenos Aires (Argentina); Sanchez, Hector J. [FaMAF, Universidad Nacional de Cordoba, Ciudad Universitaria, 5000 Cordoba (Argentina); CONICET, Rivadavia 1917, 1033 Buenos Aires (Argentina); Perez, Carlos A. [Laboratorio Nacional de Luz Sincrotron-LNLS, POB 6192, 13084-971 Campinas, SP (Brazil); Rubio, Marcelo [FaMAF, Universidad Nacional de Cordoba, Ciudad Universitaria, 5000 Cordoba (Argentina); CONICET, Rivadavia 1917, 1033 Buenos Aires (Argentina); CEPROCOR, Ministerio de Ciencia y Tecnologia de Cordoba, 5164 Santa Maria de Punilla, Cordoba (Argentina)

    2010-02-15

    X-ray fluorescence analysis performed with a primary radiation focused in the micrometer range is known as micro-X-ray fluorescence (mu-XRF). It is characterized by a penetration depth higher than other micro-analytical methods, reaching hundreds of micrometers in biological samples. This characteristic of the X-ray beam can be employed in 3D analysis. An innovative method to perform 3D analysis by mu-XRF is the so-called confocal setup. The confocal setup consists of X-ray lenses in the excitation as well as in the detection channel. In this configuration, a micro-volume defined by the overlap of the foci of both X-ray lenses is analyzed. Scanning this micro-volume through the sample can be used to perform a study in three dimensions. At present, X-ray lenses used in confocal mu-XRF experiments are mainly glass capillaries and polycapillaries. Glass capillaries are used in the excitation channel with sources of high photon flux like synchrotron radiation. Half polycapillaries or conical polycapillary concentrators are used almost exclusively in the detection channel. Spatial resolution of the confocal mu-XRF depends on the dimensions of the foci of both X-ray lenses. The overlap of these foci forms an ellipsoid which is the probing volume of the confocal setup. The axis length of the probing volume reported in confocal mu-XRF experiments are of order of few tens of micrometer. In our confocal setup, we used a commercial glass monocapillary in the excitation channel and a monolithic half polycapillary in the detection channel. The polycapillary was home-made by means of drawing of multibundles of glass capillaries in a heating furnace. The experiment was carried out at the beamline D09B-XRF of the Synchrotron Light National Laboratory (Laboratorio Nacional de Luz Sincrotron, LNLS) using white beam. A model for the theoretical description of X-ray fluorescence intensity registered by confocal mu-XRF was introduced by Malzer and Kanngiebetaer [2005. A model for the

  11. Design of 3-D Nacelle near Flat-Plate Wing Using Multiblock Sensitivity Analysis (ADOS)

    Eleshaky, Mohamed E.; Baysal, Oktay

    1994-01-01

    One of the major design tasks involved in reducing aircraft drag is the integration of the engine nacelles and airframe. With this impetus, nacelle shapes with and without the presence of a flat-plate wing nearby were optimized. This also served as a demonstration of the 3-D version of the recently developed aerodynamic design optimization methodology using sensitivity analysis, ADOS. The required flow analyses were obtained by solving the three-dimensional, compressible, thin-layer Navier-Stokes equations using an implicit, upwind-biased, finite volume scheme. The sensitivity analyses were performed using the preconditioned version of the SADD scheme (sensitivity analysis on domain decomposition). In addition to demonstrating the present method's capability for automatic optimization, the results offered some insight into two important issues related to optimizing the shapes of multicomponent configurations in close proximity. First, inclusion of the mutual interference between the components resulted in a different shape as opposed to shaping an isolated component. Secondly, exclusion of the viscous effects compromised not only the flow physics but also the optimized shapes even for isolated components.

  12. Computer-assisted 3D kinematic analysis of all leg joints in walking insects.

    John A Bender

    Full Text Available High-speed video can provide fine-scaled analysis of animal behavior. However, extracting behavioral data from video sequences is a time-consuming, tedious, subjective task. These issues are exacerbated where accurate behavioral descriptions require analysis of multiple points in three dimensions. We describe a new computer program written to assist a user in simultaneously extracting three-dimensional kinematics of multiple points on each of an insect's six legs. Digital video of a walking cockroach was collected in grayscale at 500 fps from two synchronized, calibrated cameras. We improved the legs' visibility by painting white dots on the joints, similar to techniques used for digitizing human motion. Compared to manual digitization of 26 points on the legs over a single, 8-second bout of walking (or 106,496 individual 3D points, our software achieved approximately 90% of the accuracy with 10% of the labor. Our experimental design reduced the complexity of the tracking problem by tethering the insect and allowing it to walk in place on a lightly oiled glass surface, but in principle, the algorithms implemented are extensible to free walking. Our software is free and open-source, written in the free language Python and including a graphical user interface for configuration and control. We encourage collaborative enhancements to make this tool both better and widely utilized.

  13. In vivo analysis of the human superficial cerebral venous anatomy by using 3D-MRI

    The purpose of this study is to show the reliability of three dimensional magnetic resonance imaging (3D-MRI), and to classify the drainage patterns of the superficial cerebral veins. At first, toothpicks were stuck into fixed brain surface of a dog. To examine the best methods for making 3D-MRI, the 3D-MRI, including the diameter of the holes, of the dog's brain were analyzed in four threshold values. The holes on the 3D-MRI appeared smaller than their actual size due to the partial volume effect. The low threshold showed more errors than the higher. This result showed it was necessary to display the good 3D-MRI to refer the original MR images. Next, the 3D-MRI of clinical patients who had brain tumors were correlated with operative findings especially in relation to the lesions and brain surface, vessels, ventricles. The relation between the lesions and brain surface, vessels were displayed well, but there were some problems with inadequate ventricular display. Finally, anatomical study using 3D-MRI was performed, because 3D-MRI could display the relation between the brain surface and the superficial cerebral veins in the basic studies. The third study demonstrated that the transverse frontal vein was found in 15%, vein of Trolard ran in front of the central sulcus in 91.5% and several anastomosing veins were frequently observed. These studies showed the progress of technology in bringing about a lot of new information by using 3D-MRI. (author)

  14. Tensile Behavior Analysis on Different Structures of 3D Glass Woven Perform for Fibre Reinforced Composites

    Mazhar Hussain Peerzada

    2013-01-01

    Full Text Available Three common 3D (Three Dimensional Glass woven structures were studied to analyze the tensile behavior. Each type of strand (Warp, weft and binder of 3D woven structure was studied in detail. Crimp percentage of those strands was measured by crimp meter. Standard size samples of each 3D woven structure were cut in warp and weft direction and were stretched by Instron Tensile testing computerized machine. Results reveal that hybrid possesses lowest crimp in core strands and higher strength in warp as well as weft direction. Layer to layer woven structure appeared with lower strength and higher strain value due to highest crimp percentage in core strands.

  15. Analysis of 3D-printed metal for rapid-prototyped reflective terahertz optics

    Headland, Daniel; Withayachumnankul, Withawat; Webb, Michael; Ebendorff-Heidepriem, Heike; Luiten, Andre; Abbott, Derek

    2016-07-01

    We explore the potential of 3D metal printing to realize complex conductive terahertz devices. Factors impacting performance such as printing resolution, surface roughness, oxidation, and material loss are investigated via analytical, numerical, and experimental approaches. The high degree of control offered by a 3D-printed topology is exploited to realize a zone plate operating at 530 GHz. Reflection efficiency at this frequency is found to be over 90%. The high-performance of this preliminary device suggest that 3D metal printing can play a strong role in guided-wave and general beam control devices in the terahertz range.

  16. Analysis of 3D-printed metal for rapid-prototyped reflective terahertz optics

    Headland, Daniel; Webb, Michael; Ebendorff-Heidepriem, Heike; Luiten, Andre; Abbott, Derek

    2016-01-01

    We explore the potential of 3D metal printing to realize complex conductive terahertz devices. Factors impacting performance such as printing resolution, surface roughness, oxidation, and material loss are investigated via analytical, numerical, and experimental approaches. The high degree of control offered by a 3D-printed topology is exploited to realize a zone plate operating at 530 GHz. Reflection efficiency at this frequency is found to be over 90%. The high-performance of this preliminary device suggest that 3D metal printing can play a strong role in guided-wave and general beam control devices in the terahertz range.

  17. A analysis of differences between common types of 3D stereoscopic movie & TV technology

    Chen Shuangyin

    2013-06-01

    Full Text Available 3D stereoscopic movie & TV technology develops rapidly.It is spreading into common people's life day by day.In this thesis,the author analyzes 3D stereoscopic movie & TV technology thoroughly.By comparing and studying the different technical solutions of the stereoscopic photography and video recording,production process and playing back,the author generalizes the characteristics of various programs and analyzes their strength and weakness.Eventually,the thesis gives the specific application of existing technical solutions and the future development.At last,it puts improvement goals of 3D stereoscopic movie & TV technology and gives large future development.

  18. RESTRUCTURING RELAP5-3D FOR NEXT GENERATION NUCLEAR PLANT ANALYSIS

    Donna Post Guillen; George L. Mesina; Joshua M. Hykes

    2006-06-01

    RELAP5-3D is used worldwide for analyzing nuclear reactors under both operational transients and postulated accident conditions. Development of the RELAP code series began in 1975 and since that time the code has been continuously improved, enhanced, verified and validated [1]. Since RELAP5-3D will continue to be the premier thermal hydraulics tool well into the future, it is necessary to modernize the code to accommodate the incorporation of additional capabilities to support the development of the next generation of nuclear reactors [2]. This paper discusses the reengineering of RELAP5-3D into structured code.

  19. Analysis of 3D-printed metal for rapid-prototyped reflective terahertz optics.

    Headland, Daniel; Withayachumnankul, Withawat; Webb, Michael; Ebendorff-Heidepriem, Heike; Luiten, Andre; Abbott, Derek

    2016-07-25

    We explore the potential of 3D metal printing to realize complex conductive terahertz devices. Factors impacting performance such as printing resolution, surface roughness, oxidation, and material loss are investigated via analytical, numerical, and experimental approaches. The high degree of control offered by a 3D-printed topology is exploited to realize a zone plate operating at 530 GHz. Reflection efficiency at this frequency is found to be over 90%. The high-performance of this preliminary device suggest that 3D metal printing can play a strong role in guided-wave and general beam control devices in the terahertz range. PMID:27464185

  20. Super Cooled Large Droplet Analysis of Several Geometries Using LEWICE3D Version 3

    Bidwell, Colin S.

    2011-01-01

    Super Cooled Large Droplet (SLD) collection efficiency calculations were performed for several geometries using the LEWICE3D Version 3 software. The computations were performed using the NASA Glenn Research Center SLD splashing model which has been incorporated into the LEWICE3D Version 3 software. Comparisons to experiment were made where available. The geometries included two straight wings, a swept 64A008 wing tip, two high lift geometries, and the generic commercial transport DLR-F4 wing body configuration. In general the LEWICE3D Version 3 computations compared well with the 2D LEWICE 3.2.2 results and with experimental data where available.

  1. Analysis of linear motion systems for a large scale FDM 3D printer

    Eiður Örn Þórsson 1979

    2013-01-01

    3D printers have been around for quite some time in one way or another. Only in resent years with programs such as Reprap, an open source 3D printer that can self replicate a lot of it's own parts, has helped greatly in bringing 3D printing into the price range and homes of hobbyists. When constructing one, the current models are small and not sturdy looking, which is not good for scaling up so that it would be able to do a large quality print. This of course does not matter if detail in the ...

  2. Wide area 2D/3D imaging development, analysis and applications

    Langmann, Benjamin

    2014-01-01

    Imaging technology is an important research area and it is widely utilized in a growing number of disciplines ranging from gaming, robotics and automation to medicine. In the last decade 3D imaging became popular mainly driven by the introduction of novel 3D cameras and measuring devices. These cameras are usually limited to indoor scenes with relatively low distances. Benjamin Langmann introduces medium and long-range 2D/3D cameras to overcome these limitations. He reports measurement results for these devices and studies their characteristic behavior. In order to facilitate the application o

  3. 2D and 3D finite element analysis of buffer-backfill interaction

    Methods for backfilling and sealing of disposal tunnels in an underground repository for spent nuclear fuel are studied in cooperation between Finland (Posiva Oy) and Sweden (Svensk Kaernbraenslehantering AB, SKB) in 'BAckfilling and CLOsure of the deep repository' (Baclo) programme. Baclo phase III included modelling task force SP1: Finite element modelling of deformation of the backfill due to swelling of the buffer. The objective of the finite element modelling of the backfill was to study the interaction between the buffer and backfilling. The calculations aimed to find out how large deformations can happen in the buffer-backfill interface causing loosening of the buffer bentonite above the canister. The criterion used was that the saturated density of the buffer right above the canister should be higher than 1990 kg/m3. This report presents the results of finite element numerical analyses carried out by Wesi Geotecnica Srl. The modelling calculations were conducted with the so-called OL1-2 deposition tunnel geometry (Juvankoski 2009). Several parameters have been considered, varying from geometry variations to different mechanical constitutive models for different components of the model. In all analyses it has been assumed that the buffer material is fully saturated, thus exerting the isotropic swelling pressure estimated in the range 7 MPa .. 15 MPa, against a fully-dry backfill, which is no doubt the 'worst case scenario' with the highest risk to lead in decrease in dry density of the buffer. Friedland clay has been considered for backfill blocks and 30/70 mixture for foundation bed on which backfill blocks are installed. Preliminarily, finite element analyses have been performed with newly released PLAXIS 2D 2010 within the assumption of axial symmetry, the purpose of this first set of calculations being the evaluation of most relevant parameters influencing the deformations of buffer material. Hence, full 3D calculations have been performed with PLAXIS 3D

  4. 3D TOCSY-HSQC NMR for Metabolic Flux Analysis using Non-Uniform Sampling

    Reardon, Patrick N.; Marean-Reardon, Carrie; Bukovec, Melanie A.; Coggins, B. E.; Isern, Nancy G.

    2016-02-05

    13C-Metabolic Flux Analysis (13C-MFA) is rapidly being recognized as the authoritative method for determining fluxes through metabolic networks. Site-specific 13C enrichment information obtained using NMR spectroscopy is a valuable input for 13C-MFA experiments. Chemical shift overlaps in the 1D or 2D NMR experiments typically used for 13C-MFA frequently hinder assignment and quantitation of site-specific 13C enrichment. Here we propose the use of a 3D TOCSY-HSQC experiment for 13C-MFA. We employ Non-Uniform Sampling (NUS) to reduce the acquisition time of the experiment to a few hours, making it practical for use in 13C-MFA experiments. Our data show that the NUS experiment is linear and quantitative. Identification of metabolites in complex mixtures, such as a biomass hydrolysate, is simplified by virtue of the 13C chemical shift obtained in the experiment. In addition, the experiment reports 13C-labeling information that reveals the position specific labeling of subsets of isotopomers. The information provided by this technique will enable more accurate estimation of metabolic fluxes in larger metabolic networks.

  5. CCTV Coverage Index Based on Surveillance Resolution and Its Evaluation Using 3D Spatial Analysis

    Kyoungah Choi

    2015-09-01

    Full Text Available We propose a novel approach to evaluating how effectively a closed circuit television (CCTV system can monitor a targeted area. With 3D models of the target area and the camera parameters of the CCTV system, the approach produces surveillance coverage index, which is newly defined in this study as a quantitative measure for surveillance performance. This index indicates the proportion of the space being monitored with a sufficient resolution to the entire space of the target area. It is determined by computing surveillance resolution at every position and orientation, which indicates how closely a specific object can be monitored with a CCTV system. We present full mathematical derivation for the resolution, which depends on the location and orientation of the object as well as the geometric model of a camera. With the proposed approach, we quantitatively evaluated the surveillance coverage of a CCTV system in an underground parking area. Our evaluation process provided various quantitative-analysis results, compelling us to examine the design of the CCTV system prior to its installation and understand the surveillance capability of an existing CCTV system.

  6. Analysis of ex-vessel steam explosion with MC3D

    An ex-vessel steam explosion may occur when, during a severe reactor accident, the reactor vessel fails and the molten core pours into the water in the reactor cavity. A steam explosion is a fuel coolant interaction process where the heat transfer from the melt to water is so intense and rapid that the timescale for heat transfer is shorter than the timescale for pressure relief. This can lead to the formation of shock waves and production of missiles that may endanger surrounding structures. A strong enough steam explosion in a nuclear power plant could jeopardize the containment integrity and so lead to a direct release of radioactive material to the environment. In the paper, different scenarios of ex-vessel steam explosions in a typical pressurized water reactor cavity are analyzed with the code MC3D, which was developed for the simulation of fuel-coolant interactions. A comprehensive parametric study was performed varying the location of the melt release (central, left and right side melt pour), the cavity water subcooling, the primary system overpressure at vessel failure and the triggering time for explosion calculations. The main purpose of the study was to determine the most challenging ex-vessel steam explosion cases in a typical pressurized water reactor and to estimate the expected pressure loadings on the cavity walls. The performed analysis shows that for some ex-vessel steam explosion scenarios significantly higher pressure loads are predicted than obtained in the OECD programme SERENA Phase 1. (author)

  7. Analysis and modeling of 3D complex modulus tests on hot and warm bituminous mixtures

    Pham, Nguyen Hoang; Sauzéat, Cédric; Di Benedetto, Hervé; González-León, Juan A.; Barreto, Gilles; Nicolaï, Aurélia; Jakubowski, Marc

    2015-05-01

    This paper presents the results of laboratory testing of hot and warm bituminous mixtures containing Reclaimed Asphalt Pavement (RAP). Complex modulus measurements, using the tension-compression test on cylindrical specimens, were conducted to determine linear viscoelastic (LVE) behavior. Sinusoidal cyclic loadings, with strain amplitude of approximately 50ṡ10-6, were applied at several temperatures (from -25 to +45 °C) and frequencies (from 0.03 Hz to 10 Hz). In addition to axial stresses and strains, radial strains were also measured. The complex modulus E ∗ and complex Poisson's ratios ν ∗ were then obtained in two perpendicular directions. Measured values in these two directions do not indicate anisotropy on Poisson's ratio. The time-temperature superposition principle (TTSP) was verified with good approximation in one-dimensional (1D) and three-dimensional (3D) conditions for the same values of shift factor. Experimental results were modeled using the 2S2P1D model previously developed at the University of Lyon/ENTPE. In addition, specific analysis showed that eventual damage created during complex modulus test is very small and is equivalent to the effect of an increase of temperature of about 0.25 °C.

  8. Electrical performance analysis of HTS synchronous motor based on 3D FEM

    A 1-MW class superconducting motor with High-Temperature Superconducting (HTS) field coil is analyzed and tested. This machine is a prototype to make sure applicability aimed at generator and industrial motor applications such as blowers, pumps and compressors installed in large plants. This machine has the HTS field coil made of Bi-2223 HTS wire and the conventional copper armature (stator) coils cooled by water. The 1-MW class HTS motor is analyzed by 3D electromagnetic Finite Element Method (FEM) to get magnetic field distribution, self and mutual inductance, and so forth. Especially excitation voltage (Back EMF) is estimated by using the mutual inductance between armature and field coils and compared with experimental result. Open and short circuit tests were conducted in generator mode while a 1.1-MW rated induction machine was rotating the HTS machine. Electrical parameters such as mutual inductance and synchronous inductance are deduced from these tests and also compared with the analysis results from FEM.

  9. Electrical performance analysis of HTS synchronous motor based on 3D FEM

    Baik, S. K.; Kwon, Y. K.; Kim, H. M.; Lee, J. D.; Kim, Y. C.; Park, G. S.

    2010-11-01

    A 1-MW class superconducting motor with High-Temperature Superconducting (HTS) field coil is analyzed and tested. This machine is a prototype to make sure applicability aimed at generator and industrial motor applications such as blowers, pumps and compressors installed in large plants. This machine has the HTS field coil made of Bi-2223 HTS wire and the conventional copper armature (stator) coils cooled by water. The 1-MW class HTS motor is analyzed by 3D electromagnetic Finite Element Method (FEM) to get magnetic field distribution, self and mutual inductance, and so forth. Especially excitation voltage (Back EMF) is estimated by using the mutual inductance between armature and field coils and compared with experimental result. Open and short circuit tests were conducted in generator mode while a 1.1-MW rated induction machine was rotating the HTS machine. Electrical parameters such as mutual inductance and synchronous inductance are deduced from these tests and also compared with the analysis results from FEM.

  10. 3D Finite Element Analysis of a Man Hip Joint Femur under Impact Loads

    YU Xue-zhong; GUO Yi-mu; LI Jun; ZHANG Yun-qiu; HE Rong-xin

    2007-01-01

    The biomechanical characters of the bone fracture of the man femoral hip joint under impact loads are explored. Methods: A biosystem model of the man femoral hip joint by using the GE ( General Electric) lightspeed multi-lay spiral CT is conducted. A 3D finite element model is established by employing the finite element software ANSYS. The FE analysis mainly concentrates on the effects of the impact directions arising from intense movements and the parenchyma on the femoral hip joint on the stress distributions of the proximal femur. Results:The parenchyma on the hip joint has relatively large relaxation effect on the impact loads. Conclusion:Effects of the angle δ of the impact load to the anterior direction and the angle γ of the impact load to the femur shaft on the bone fracture are given;δ has larger effect on the stress and strain distributions than the angle γ, which mainly represents the fracture of the upper femur including the femoral neck fracture when the posterolateral femur is impacted, consistent with the clinical results.

  11. Analysis of heterogeneous boron dilution transients during outages with APROS 3D nodal core model

    A diluted water plug can form inside the primary coolant circuit if the coolant flow has stopped at least temporarily. The source of the clean water can be external or the fresh water can build up internally during boiling/condensing heat transfer mode, which can occur if the primary coolant inventory has decreased enough during an accident. If the flow restarts in the stagnant primary loop, the diluted water plug can enter the reactor core. During outages after the fresh fuel has been loaded and the temperature of the coolant is low, the dilution potential is the highest because the critical boron concentration is at the maximum. This paper examines the behaviour of the core as clean or diluted water plugs of different sizes enter the core during outages. The analysis were performed with the APROS 3D nodal core model of Loviisa VVER-440, which contains an own flow channel and 10 axial nodes for each fuel assembly. The widerange cross section data was calculated with CASMO-4E. According to the results, the core can withstand even large pure water plugs without fuel failures on natural circulation. The analyses emphasize the importance of the simulation of the backflows inside the core when the reactor is on natural circulation.

  12. 3D thermal-hydraulic analysis of an ITER vacuum vessel regular Field Joint

    The ITER vacuum vessel (VV), located inside the cryostat and housing the in-vessel components, is made of 9 40° sectors, connected through splice plates to form the full torus. The regions at the interface between adjacent sectors are the so-called Field Joints (FJs). While each sector has its own cooling loop to remove the heat deposition due to nuclear heating, each FJ is separately cooled. Individual inlet/outlet pipes for the water flow are thus provided for each FJ, located in the outboard bottom segment and on the upper port frame, respectively. The coolant flow splits in two streams, inboard and outboard, passing through the borated In-Wall Shielding (IWS). In this paper we present the 3D steady state thermal-hydraulic analysis of one so-called regular FJ (RFJ), at the interface between two VV regular sectors, using the commercial CFD software ANSYS-FLUENT®. The water flow field, the pressure drop, the temperature maps and the heat transfer coefficients are computed, and the effects of considering different levels of simplification of the IWS model, as well as the influence of buoyancy (natural convection), are discussed

  13. STATICS ANALYSIS AND OPENGL BASED 3D SIMULATION OF COLLABORATIVE RECONFIGURABLE PLANETARY ROBOTS

    Zhang Zheng; Ma Shugen; Li Bin; Zhang Liping; Cao Binggang

    2006-01-01

    Objective To study mechanics characteristics of two cooperative reconfigurable planetary robots when they get across an obstacle, and to find out the relationship between the maximum height of a stair with the configuration of the two-robot, and to find some restrictions of kinematics for the cooperation. Methods Multirobot cooperation theory is used in the whole study process. Inverse kinematics of the robot is used to form a desired configuration in the cooperation process. Static equations are established to analyze the relations between the friction factor, the configuration of robots and the maximum height of a stair. Kinematics analysis is used to find the restrictions of the two collaborative robots in position, velocity and acceleration. Results 3D simulation shows that the two cooperative robots can climb up a stair under the condition of a certain height and a certain friction factor between robot wheel and the surface of the stair. Following the restrictions of kinematics, the climbing mission is fulfilled successfully and smoothly. Conclusion The maximum height of a stair, which the two cooperative robots can climb up, is involved in the configuration of robots, friction factor between the stair and the robots. The most strict restriction of the friction factor does not appear in the horizontal position. In any case, the maximum height is smaller than half of the distance between the centroid of robot1 with the centroid of robot2. However, the height can be higher than the radius of one robot wheel, which profit from the collaboration.

  14. 3-D seakeeping analysis with water on deck and slamming. Part 2: Experiments and physical investigation

    Greco, M.; Bouscasse, B.; Lugni, C.

    2012-08-01

    A synergic 3-D experimental and numerical investigation is conducted for wave-ship interactions involving the water-on-deck and slamming phenomena. The adopted solver has been developed in Greco and Lugni (in press) and combines (A) a weakly nonlinear external solution for the wave-vessel interactions with (B) a 2-D in-deck shallow-water approximation, which describes water shipping events, and (C) a local analytical analysis of the bottom-slamming phenomenon. This solver can handle regular and irregular sea states and vessels at rest or with limited speed. The experiments examine a patrol ship at rest or with forward speed that is free to oscillate in heave and pitch in regular and irregular waves. In this study, the head-sea regular-wave conditions are examined in terms of (1) response amplitude operators (RAOs) and relative motions, (2) occurrence, features and loads of water-on-deck, bottom-slamming and flare-slamming events and (3) added resistance in waves. A systematic and comprehensive analysis of the phenomena is made available in terms of the Froude number, incoming wavelength-to-ship length ratio and wave steepness for the examined ship geometry. The main parameters that affect the global and local quantities are identified and possible danger in terms of water-on-deck severity and structural consequences are determined. Different slamming behaviors were identified, depending on the spatial location of the impact on the vessel: single-peak, church-roof and double-peak behaviors. A bottom-slamming criterion, using the Ochi's (1964) velocity condition and the Greco and Lugni's (2012) pressure condition, is assessed. A statistical analysis of more than 100 events is needed for the bottom-slamming pressure peaks. The numerical solver is promising. The major discrepancies with the experiments are discussed, and the importance of viscous hull damping and flare impact for the most violent conditions is emphasized. Inclusion of these effects improved the

  15. A analysis of differences between common types of 3D stereoscopic movie & TV technology

    Chen Shuangyin

    2013-01-01

    3D stereoscopic movie & TV technology develops rapidly.It is spreading into common people's life day by day.In this thesis,the author analyzes 3D stereoscopic movie & TV technology thoroughly.By comparing and studying the different technical solutions of the stereoscopic photography and video recording,production process and playing back,the author generalizes the characteristics of various programs and analyzes their strength and weakness.Eventually,the thesis gives the specific application ...

  16. Savage Modeling and Analysis Language (SMAL) metadata for tactical simulations and X3D visualizations

    Rauch, Travis M.

    2006-01-01

    Visualizing operations environments in three dimensions (3D) supports the warfighters' ability to make rapid, well-informed decisions by presenting complex systems in a naturalistic, integrated display format. Unfortunately, constructing these environments is a time-consuming task requiring specific expertise not typically available in the command center. The future use of 3D visualization in military operations depends on the ability of personnel with minimal graphics experience to create vi...

  17. Meshless deformable models for 3D cardiac motion and strain analysis from tagged MRI.

    Wang, Xiaoxu; Chen, Ting; Zhang, Shaoting; Schaerer, Joël; Qian, Zhen; Huh, Suejung; Metaxas, Dimitris; Axel, Leon

    2015-01-01

    Tagged magnetic resonance imaging (TMRI) provides a direct and noninvasive way to visualize the in-wall deformation of the myocardium. Due to the through-plane motion, the tracking of 3D trajectories of the material points and the computation of 3D strain field call for the necessity of building 3D cardiac deformable models. The intersections of three stacks of orthogonal tagging planes are material points in the myocardium. With these intersections as control points, 3D motion can be reconstructed with a novel meshless deformable model (MDM). Volumetric MDMs describe an object as point cloud inside the object boundary and the coordinate of each point can be written in parametric functions. A generic heart mesh is registered on the TMRI with polar decomposition. A 3D MDM is generated and deformed with MR image tagging lines. Volumetric MDMs are deformed by calculating the dynamics function and minimizing the local Laplacian coordinates. The similarity transformation of each point is computed by assuming its neighboring points are making the same transformation. The deformation is computed iteratively until the control points match the target positions in the consecutive image frame. The 3D strain field is computed from the 3D displacement field with moving least squares. We demonstrate that MDMs outperformed the finite element method and the spline method with a numerical phantom. Meshless deformable models can track the trajectory of any material point in the myocardium and compute the 3D strain field of any particular area. The experimental results on in vivo healthy and patient heart MRI show that the MDM can fully recover the myocardium motion in three dimensions. PMID:25157446

  18. International training program in support of safety analysis: 3D S.UN.COP - Scaling, uncertainty and 3D thermal-hydraulics/neutron-kinetics coupled codes seminars

    The best estimate thermal-hydraulic codes used in the area of nuclear reactor safety have reached a marked level of sophistication and they require to be used by competent analysts. The need for user qualification and training is clearly recognized. An effort is being made to develop a proposal for a systematic approach to user training. The estimated duration of training at the course venue, including a set of training seminars, workshops, and practical exercises, is approximately two years. In addition, the specification and assignment of tasks to be performed by the participants at their home institutions, with continuous supervision from the training center, has been foreseen. The 3D S.UN.COP seminars constitute the follow-up of the presented proposal. The seminar is subdivided into three main parts, each of one with a program to be developed in one week: the first week is dedicated to fundamental theoretical aspects, the second week deals with industrial application, coupling methodologies and hands-on training, and the third week focuses on training for transient analysis in the interaction between thermal-hydraulics and fuel behaviour. The responses of the participants during the training have demonstrated an increase in the capabilities to develop and/or modify nodalization and to perform a qualitative and quantitative accuracy evaluation. It is expected that the participants will be able to set up more accurate, reliable and efficient simulation models, applying the procedures for qualifying the thermal-hydraulic system code calculations, and for the evaluation of the uncertainty

  19. Intelligent Autonomous Primary 3D Feature Extraction in Vehicle System Dynamics' Analysis: Theory and Application

    Annamária R. Várkonyi-Kóczy

    2008-01-01

    Full Text Available 3D model reconstruction plays a very important role in computer vision as wellas in different engineering applications. The determination of the 3D model from multipleimages is of key importance. One of the most important difficulties in autonomous 3Dreconstruction is the (automatic selection of the ‘significant’ points which carryinformation about the shape of the 3D bodies i.e. are characteristic from the model point ofview. Another problem to be solved is the point correspondence matching in differentimages.In this paper a 3D reconstruction technique is introduced, which is capable to determinethe 3D model of a scene without any external (human intervention. The method is based onrecent results of image processing, epipolar geometry, and intelligent and soft techniques.Possible applications of the presented algorithm in vehicle system dynamics are alsopresented. The results can be applied advantageously at other engineering fields, like carcrashanalysis, robot guiding, object recognition, supervision of 3D scenes, etc,. as well.

  20. A Shell/3D Modeling Technique for the Analysis of Delaminated Composite Laminates

    Krueger, Ronald; OBrien, T. Kevin

    2000-01-01

    A shell/3D modeling technique was developed for which a local solid finite element model is used only in the immediate vicinity of the delamination front. The goal was to combine the accuracy of the full three-dimensional solution with the computational efficiency of a shell finite element model. Multi-point constraints provided a kinematically compatible interface between the local 3D model and the global structural model which has been meshed with shell finite elements. Double Cantilever Beam, End Notched Flexure, and Single Leg Bending specimens were analyzed first using full 3D finite element models to obtain reference solutions. Mixed mode strain energy release rate distributions were computed using the virtual crack closure technique. The analyses were repeated using the shell/3D technique to study the feasibility for pure mode I, mode II and mixed mode I/II cases. Specimens with a unidirectional layup and with a multidirectional layup were simulated. For a local 3D model, extending to a minimum of about three specimen thicknesses on either side of the delamination front, the results were in good agreement with mixed mode strain energy release rates obtained from computations where the entire specimen had been modeled with solid elements. For large built-up composite structures the shell/3D modeling technique offers a great potential for reducing the model size, since only a relatively small section in the vicinity of the delamination front needs to be modeled with solid elements.

  1. Performance Analysis of a Low-Cost Triangulation-Based 3d Camera: Microsoft Kinect System

    . K. Chow, J. C.; Ang, K. D.; Lichti, D. D.; Teskey, W. F.

    2012-07-01

    Recent technological advancements have made active imaging sensors popular for 3D modelling and motion tracking. The 3D coordinates of signalised targets are traditionally estimated by matching conjugate points in overlapping images. Current 3D cameras can acquire point clouds at video frame rates from a single exposure station. In the area of 3D cameras, Microsoft and PrimeSense have collaborated and developed an active 3D camera based on the triangulation principle, known as the Kinect system. This off-the-shelf system costs less than 150 USD and has drawn a lot of attention from the robotics, computer vision, and photogrammetry disciplines. In this paper, the prospect of using the Kinect system for precise engineering applications was evaluated. The geometric quality of the Kinect system as a function of the scene (i.e. variation of depth, ambient light conditions, incidence angle, and object reflectivity) and the sensor (i.e. warm-up time and distance averaging) were analysed quantitatively. This system's potential in human body measurements was tested against a laser scanner and 3D range camera. A new calibration model for simultaneously determining the exterior orientation parameters, interior orientation parameters, boresight angles, leverarm, and object space features parameters was developed and the effectiveness of this calibration approach was explored.

  2. State-of-the-art 3-D neutronics analysis methods for fusion energy systems

    Wilson, P.P.H. [Wisconsin-Madison Univ., Madison, WI (United States); Feder, R. [Princeton Plasma Physics Lab. (United States); Fischer, U. [Forschungszentrum Karlsruhe (Germany); Loughlin, M. [United Kingdom Atomic Energy Authority (United Kingdom); Petrizzi, L. [ENEA-Frascati (Italy); Wu, Y. [Academy of Sciences (China). Inst. of Plasma Physics; Youssef, M. [California Univ., Los Angeles, CA (United States)

    2007-07-01

    Recent advances in radiation transport simulation tools enable an increased fidelity and accuracy in modeling complex geometries in fusion systems. Future neutronics calculations for design and analysis will increasingly be based directly on 3-D CAD-based geometries, allowing enhanced model complexity, reduced human effort and improved quality assurance. Improvements have been made in both stochastic and deterministic radiation transport methodologies. To adapt the MCNP stochastic transport software, the translator approach allows CAD geometries to be converted from their native formats into standard input files, while the direct geometry approach uses computer graphics algorithms to perform the radiation transport on the CAD geometry itself. The former takes advantage of the efficiency of the native MCNP software without modifications while the latter permits the modeling of more complex surfaces. The ATTILA radiation transport package uses a finite-element formulation of the discrete-ordinate methodology to provide a deterministic solution on a tetrahedral mesh derived automatically from a CAD-based geometry. All of these tools are being applied to a dedicated benchmark problem consisting of a 40 degree sector of the ITER machine defined only in a CAD-based solid model. The specific benchmark problems exercise the ability to use a CAD-based geometry to solve a range of fusion neutronics problems including neutron wall loading, deep penetration and narrow duct streaming. The results of this exercise will be used to validate/qualify these tools for use on ITER. At the same time, many of these tools are being used to support the design of ITER components and other related fusion systems. UW has provided high-fidelity nuclear analysis of ITER first wall and shield modules identifying local effects of geometric features. ASIPP has used the MCAM tool to update and extend the existing ITER basic model and used it for neutronics analysis of the proposed Chinese ITER

  3. State-of-the-art 3-D neutronics analysis methods for fusion energy systems

    Recent advances in radiation transport simulation tools enable an increased fidelity and accuracy in modeling complex geometries in fusion systems. Future neutronics calculations for design and analysis will increasingly be based directly on 3-D CAD-based geometries, allowing enhanced model complexity, reduced human effort and improved quality assurance. Improvements have been made in both stochastic and deterministic radiation transport methodologies. To adapt the MCNP stochastic transport software, the translator approach allows CAD geometries to be converted from their native formats into standard input files, while the direct geometry approach uses computer graphics algorithms to perform the radiation transport on the CAD geometry itself. The former takes advantage of the efficiency of the native MCNP software without modifications while the latter permits the modeling of more complex surfaces. The ATTILA radiation transport package uses a finite-element formulation of the discrete-ordinate methodology to provide a deterministic solution on a tetrahedral mesh derived automatically from a CAD-based geometry. All of these tools are being applied to a dedicated benchmark problem consisting of a 40 degree sector of the ITER machine defined only in a CAD-based solid model. The specific benchmark problems exercise the ability to use a CAD-based geometry to solve a range of fusion neutronics problems including neutron wall loading, deep penetration and narrow duct streaming. The results of this exercise will be used to validate/qualify these tools for use on ITER. At the same time, many of these tools are being used to support the design of ITER components and other related fusion systems. UW has provided high-fidelity nuclear analysis of ITER first wall and shield modules identifying local effects of geometric features. ASIPP has used the MCAM tool to update and extend the existing ITER basic model and used it for neutronics analysis of the proposed Chinese ITER

  4. Structural analysis of San Leo (RN, Italy) east and north cliffs using 3D point clouds

    Spreafico, Margherita Cecilia; Bacenetti, Marco; Borgatti, Lisa; Cignetti, Martina; Giardino, Marco; Perotti, Luigi

    2013-04-01

    The town of San Leo, like many others in the historical region of Montefeltro (Northern Apennines, Italy), was built in medieval period on a calcarenite and sandstone slab, bordered by subvertical and overhanging cliffs up to 100 m high, for defense purposes. The slab and the underlying clayey substratum show widespread landslide phenomena: the first is tectonized and crossed by joints and faults, and it is affected by lateral spreading with associated rock falls, topples and tilting. Moreover, the underlying clayey substratum is involved in plastic movements, like earth flows and slides. The main cause of instability in the area, which brings about these movements, is the high deformability contrast between the plate and the underlying clays. The aim of our research is to set up a numerical model that can well describe the processes and take into account the different factors that influence the evolution of the movements. One of these factors is certainly the structural setting of the slab, characterized by several joints and faults; in order to better identify and detect the main joint sets affecting the study area a structural analysis was performed. Up to date, a series of scans of San Leo cliff taken in 2008 and 2011, with a Riegl Z420i were analyzed. Initially, we chose a test area, located in the east side of the cliff, in which analyses were performed using two different softwares: COLTOP 3D and Polyworks. We repeated the analysis using COLTOP for all the east wall and for a part of the north wall, including an area affected by a rock fall in 2006. In the test area we identified five sets with different dips and dip directions. The analysis of the east and north walls permitted to identify eight sets (seven plus the bedding) of discontinuities. We compared these results with previous ones from surveys taken by others authors in some areas and with some preliminary data from a traditional geological survey of the whole area. With traditional methods only a

  5. A Scheme of 3-D Breakdown-whip Analysis Methodology for High Energy Piping

    excessive conservatism. It is thought that more accurate and effective system design is possible by making a combination of fluid transient analysis and 3-D structural analysis. The main purpose of this study is to introduce the procedure and method for analyzing 3-dimensional breakdown-whip of high energy piping. This study also shows some results of analyzing the fluid transient loads at the main steam line of APR1400

  6. Analysis of Intensity-Modulated Radiation Therapy (IMRT, Proton and 3D Conformal Radiotherapy (3D-CRT for Reducing Perioperative Cardiopulmonary Complications in Esophageal Cancer Patients

    Ted C. Ling

    2014-12-01

    Full Text Available Background. While neoadjuvant concurrent chemoradiotherapy has improved outcomes for esophageal cancer patients, surgical complication rates remain high. The most frequent perioperative complications after trimodality therapy were cardiopulmonary in nature. The radiation modality utilized can be a strong mitigating factor of perioperative complications given the location of the esophagus and its proximity to the heart and lungs. The purpose of this study is to make a dosimetric comparison of Intensity-Modulated Radiation Therapy (IMRT, proton and 3D conformal radiotherapy (3D-CRT with regard to reducing perioperative cardiopulmonary complications in esophageal cancer patients. Materials. Ten patients with esophageal cancer treated between 2010 and 2013 were evaluated in this study. All patients were simulated with contrast-enhanced CT imaging. Separate treatment plans using proton radiotherapy, IMRT, and 3D-CRT modalities were created for each patient. Dose-volume histograms were calculated and analyzed to compare plans between the three modalities. The organs at risk (OAR being evaluated in this study are the heart, lungs, and spinal cord. To determine statistical significance, ANOVA and two-tailed paired t-tests were performed for all data parameters. Results. The proton plans showed decreased dose to various volumes of the heart and lungs in comparison to both the IMRT and 3D-CRT plans. There was no difference between the IMRT and 3D-CRT plans in dose delivered to the lung or heart. This finding was seen consistently across the parameters analyzed in this study. Conclusions. In patients receiving radiation therapy for esophageal cancer, proton plans are technically feasible while achieving adequate coverage with lower doses delivered to the lungs and cardiac structures. This may result in decreased cardiopulmonary toxicity and less morbidity to esophageal cancer patients.

  7. Analysis of Intensity-Modulated Radiation Therapy (IMRT), Proton and 3D Conformal Radiotherapy (3D-CRT) for Reducing Perioperative Cardiopulmonary Complications in Esophageal Cancer Patients

    Ling, Ted C.; Slater, Jerry M.; Nookala, Prashanth; Mifflin, Rachel; Grove, Roger; Ly, Anh M.; Patyal, Baldev; Slater, Jerry D.; Yang, Gary Y., E-mail: gyang@llu.edu [Department of Radiation Medicine, Loma Linda University Medical Center, 11234 Anderson Street, A875, Loma Linda, CA 92354 (United States)

    2014-12-05

    Background. While neoadjuvant concurrent chemoradiotherapy has improved outcomes for esophageal cancer patients, surgical complication rates remain high. The most frequent perioperative complications after trimodality therapy were cardiopulmonary in nature. The radiation modality utilized can be a strong mitigating factor of perioperative complications given the location of the esophagus and its proximity to the heart and lungs. The purpose of this study is to make a dosimetric comparison of Intensity-Modulated Radiation Therapy (IMRT), proton and 3D conformal radiotherapy (3D-CRT) with regard to reducing perioperative cardiopulmonary complications in esophageal cancer patients. Materials. Ten patients with esophageal cancer treated between 2010 and 2013 were evaluated in this study. All patients were simulated with contrast-enhanced CT imaging. Separate treatment plans using proton radiotherapy, IMRT, and 3D-CRT modalities were created for each patient. Dose-volume histograms were calculated and analyzed to compare plans between the three modalities. The organs at risk (OAR) being evaluated in this study are the heart, lungs, and spinal cord. To determine statistical significance, ANOVA and two-tailed paired t-tests were performed for all data parameters. Results. The proton plans showed decreased dose to various volumes of the heart and lungs in comparison to both the IMRT and 3D-CRT plans. There was no difference between the IMRT and 3D-CRT plans in dose delivered to the lung or heart. This finding was seen consistently across the parameters analyzed in this study. Conclusions. In patients receiving radiation therapy for esophageal cancer, proton plans are technically feasible while achieving adequate coverage with lower doses delivered to the lungs and cardiac structures. This may result in decreased cardiopulmonary toxicity and less morbidity to esophageal cancer patients.

  8. Mixed-Mode Fracture and Fatigue Analysis of Cracked 3D Complex Structures using a 3D SGBEM-FEM Alternating Method

    Bhavanam, Sharada

    The aim of this thesis is to numerically evaluate the mixed-mode Stress Intensity Factors (SIFs) of complex 3D structural geometries with arbitrary 3D cracks using the Symmetric Galerkin Boundary Element Method-Finite Element Method (SGBEM-FEM) Alternating Method. Various structural geometries with different loading scenarios and crack configurations were examined in this thesis to understand the behavior and trends of the mixed-mode SIFs as well as the fatigue life for these complex structural geometries. Although some 3D structures have empirical and numerical solutions that are readily available in the open literature, some do not; therefore this thesis presents the results of fracture and fatigue analyses of these 3D complex structures using the SGBEM-FEM Alternating Method to serve as reference for future studies. Furthermore, there are advantages of using the SGBEM-FEM Alternating Method compared to traditional FEM methods. For example, the fatigue-crack-growth and fatigue life can be better estimated for a structure because different fatigue models (i.e. Walker, Paris, and NASGRO) can be used within the same framework of the SGBEM-FEM Alternating Method. The FEM (un-cracked structure)/BEM(crack model) meshes are modeled independently, which speeds up the computation process and reduces the cost of human labor. A simple coarse mesh can be used for all fracture and fatigue analyses of complex structures. In this thesis, simple coarse meshes were used for 3D complex structures, which were below 5000 elements as compared to traditional FEM, which require meshes where the elements range on the order of ˜250,000 to ˜106 and sometimes even more than that.

  9. Stereoscopic motion analysis in densely packed clusters: 3D analysis of the shimmering behaviour in Giant honey bees

    Hoetzl Thomas

    2011-02-01

    Full Text Available Abstract Background The detailed interpretation of mass phenomena such as human escape panic or swarm behaviour in birds, fish and insects requires detailed analysis of the 3D movements of individual participants. Here, we describe the adaptation of a 3D stereoscopic imaging method to measure the positional coordinates of individual agents in densely packed clusters. The method was applied to study behavioural aspects of shimmering in Giant honeybees, a collective defence behaviour that deters predatory wasps by visual cues, whereby individual bees flip their abdomen upwards in a split second, producing Mexican wave-like patterns. Results Stereoscopic imaging provided non-invasive, automated, simultaneous, in-situ 3D measurements of hundreds of bees on the nest surface regarding their thoracic position and orientation of the body length axis. Segmentation was the basis for the stereo matching, which defined correspondences of individual bees in pairs of stereo images. Stereo-matched "agent bees" were re-identified in subsequent frames by the tracking procedure and triangulated into real-world coordinates. These algorithms were required to calculate the three spatial motion components (dx: horizontal, dy: vertical and dz: towards and from the comb of individual bees over time. Conclusions The method enables the assessment of the 3D positions of individual Giant honeybees, which is not possible with single-view cameras. The method can be applied to distinguish at the individual bee level active movements of the thoraces produced by abdominal flipping from passive motions generated by the moving bee curtain. The data provide evidence that the z-deflections of thoraces are potential cues for colony-intrinsic communication. The method helps to understand the phenomenon of collective decision-making through mechanoceptive synchronization and to associate shimmering with the principles of wave propagation. With further, minor modifications, the method

  10. Uncovering the true nature of deformation microstructures using 3D analysis methods

    Ferry, M.; Quadir, M. Z.; Afrin, N.; Xu, W.; Loeb, A.; Soe, B.; McMahon, C.; George, C.; Bassman, L.

    2015-08-01

    Three-dimensional electron backscatter diffraction (3D EBSD) has emerged as a powerful technique for generating 3D crystallographic information in reasonably large volumes of a microstructure. The technique uses a focused ion beam (FIB) as a high precision serial sectioning device for generating consecutive ion milled surfaces of a material, with each milled surface subsequently mapped by EBSD. The successive EBSD maps are combined using a suitable post-processing method to generate a crystallographic volume of the microstructure. The first part of this paper shows the usefulness of 3D EBSD for understanding the origin of various structural features associated with the plastic deformation of metals. The second part describes a new method for automatically identifying the various types of low and high angle boundaries found in deformed and annealed metals, particularly those associated with grains exhibiting subtle and gradual variations in orientation. We have adapted a 2D image segmentation technique, fast multiscale clustering, to 3D EBSD data using a novel variance function to accommodate quaternion data. This adaptation is capable of segmenting based on subtle and gradual variation as well as on sharp boundaries within the data. We demonstrate the excellent capabilities of this technique with application to 3D EBSD data sets generated from a range of cold rolled and annealed metals described in the paper.

  11. 3D FACE RECOGNITION FROM RANGE IMAGES BASED ON CURVATURE ANALYSIS

    Suranjan Ganguly

    2014-02-01

    Full Text Available In this paper, we present a novel approach for three-dimensional face recognition by extracting the curvature maps from range images. There are four types of curvature maps: Gaussian, Mean, Maximum and Minimum curvature maps. These curvature maps are used as a feature for 3D face recognition purpose. The dimension of these feature vectors is reduced using Singular Value Decomposition (SVD technique. Now from calculated three components of SVD, the non-negative values of ‘S’ part of SVD is ranked and used as feature vector. In this proposed method, two pair-wise curvature computations are done. One is Mean, and Maximum curvature pair and another is Gaussian and Mean curvature pair. These are used to compare the result for better recognition rate. This automated 3D face recognition system is focused in different directions like, frontal pose with expression and illumination variation, frontal face along with registered face, only registered face and registered face from different pose orientation across X, Y and Z axes. 3D face images used for this research work are taken from FRAV3D database. The pose variation of 3D facial image is being registered to frontal pose by applying one to all registration technique then curvature mapping is applied on registered face images along with remaining frontal face images. For the classification and recognition purpose five layer feed-forward back propagation neural network classifiers is used, and the corresponding result is discussed in section 4.

  12. Uncertainty propagation methodology and nuclear data sensitivity analysis in 3D heterogeneous problems

    This paper presents a 3D uncertainty propagation methodology and its application to the case of a small heterogeneous reactor system ('slab' reactor benchmark). Key neutron parameters (keff, reactivity worth, local power, ...) and their corresponding cross-section sensitivities are derived by using the French calculation route APOLLO2 (2D transport lattice code), CRONOS2 (3D diffusion code) and TRIPOLI4 (3D Monte-Carlo reference calculations) with consistent JEF2.2 cross-section libraries (punctual or CEA93 multigroup cross-sections) and adapted perturbation methods (the Heuristically-based Generalized Perturbation Theory implemented in the framework of the CRONOS2 diffusion method or the correlation techniques used in Monte-Carlo simulations). The investigation of the slab system underlined notable differences between the 2D/3D computed sensitivity coefficients and consequently a priori uncertainties (when sensitivity coefficients are combined with covariance matrices the discrepancies rise up to 20% due to thermal and fast flux variations). In addition, the induced local power effect of nuclear data perturbations (JEF-2.2 vs. Leal-Derrien-Wright-Larson 235U evaluation) had been be correctly estimated with the standard 3D CRONOS2 depletion calculations. For industrial applications (PWR neutron parameters optimization problems, R and D studies dealing with the design of future fission reactors, ...), the same calculation route could be advantageously applied to infer the target accuracies (knowing the required safety criteria) of future nuclear data evaluation (JEFF-3 data library for instance). (author)

  13. 3D numerical analysis of crack propagation of heterogeneous notched rock under uniaxial tension

    Wang, S. Y.; Sloan, S. W.; Sheng, D. C.; Tang, C. A.

    2016-05-01

    Macroscopic notches play an important role in evaluating the fracture process zone (FPZ) and the strengths of a heterogeneous rock mass. Crack initiation, propagation and coalescence for unnotched, single-notched and double-notched rock specimens are numerically simulated in a 3-D numerical model (RFPA3D). A feature of the code RFPA3D is that it can numerically simulate the evolution of cracks in three-dimensional space, as well as the heterogeneity of the rock mass. For the unnotched case, special attention is given to the complete stress-strain curve and the corresponding AE events for the failure process of rock specimen. By comparing with published experimental results, the simulation results from RFPA3D are found to be satisfactory. For the single-notched case, the effect of the length and the depth of the single notch and the thickness of the specimen on the failure mode and peak stress are evaluated. The 3D FPZ is very different from that in two dimensions. For the double-notched case, the effects of the separation distance and overlap distance of the double notches, as well as influence of the homogeneity index (m) are also investigated. As the overlap distance increases, the direction of the principal tensile stress at each notch-end changes from a perpendicular direction (tensile stress field) to a nearly parallel direction (compressive stress field), which affects the evolution of the cracks from the two notches.

  14. Seepage Analysis of Upper Gotvand Dam Concerning Gypsum Karstification (2D and 3D Approaches)

    Sadrekarimi, Jamshid; Kiyani, Majid; Fakhri, Behnam;

    2011-01-01

    model locates the phreatic surface somewhat higher than the 2D model. This means that the 2D model estimates lower pore water pressure pattern in comparison with the 3D model. These may be attributed to the fact that with 2D model the lateral components of vectors of seepage velocity are ignored. In the......Upper Gotvand Dam is constructed on the Karun River at the south west of Iran. In this paper, 2D and 3D models of the dam together with the foundation and abutments were established, and several seepage analyses were carried out. Then, the gypsum veins that are scattered throughout the foundation...... ground were included in the models, and the seepage pattern, considering the dissolution law of gypsum, was analyzed. It was disclosed that the discharge fluxes obtained from 2D and 3D analyses are not similar, and the discharge flux in 3D model is about four times that of the 2D model. Also, the 3D...

  15. A procedure for the evaluation of 2D radiographic texture analysis to assess 3D bone micro-architecture

    Although the diagnosis of osteoporosis is mainly based on Dual X-ray Absorptiometry, it has been shown that trabecular bone micro-architecture is also an important factor in regards of fracture risk, which can be efficiently assessed in vitro using three-dimensional x-ray microtomography (μCT). In vivo, techniques based on high-resolution x-ray radiography associated to texture analysis have been proposed to investigate bone micro-architecture, but their relevance for giving pertinent 3D information is unclear. The purpose of this work was to develop a method for evaluating the relationships between 3D micro-architecture and 2D texture parameters, and optimizing the conditions for radiographic imaging. Bone sample images taken from cortical to cortical were acquired using 3D-synchrotron x-ray μCT at the ESRF. The 3D digital images were further used for two purposes: 1) quantification of three-dimensional bone micro-architecture, 2) simulation of realistic x-ray radiographs under different acquisition conditions. Texture analysis was then applied to these 2D radiographs using a large variety of methods (co-occurrence, spectrum, fractal...). First results of the statistical analysis between 2D and 3D parameters allowed identifying the most relevant 2D texture parameters. (authors)

  16. Development of QSAR models using artificial neural network analysis for risk assessment of repeated-dose, reproductive, and developmental toxicities of cosmetic ingredients.

    Hisaki, Tomoka; Aiba Née Kaneko, Maki; Yamaguchi, Masahiko; Sasa, Hitoshi; Kouzuki, Hirokazu

    2015-04-01

    Use of laboratory animals for systemic toxicity testing is subject to strong ethical and regulatory constraints, but few alternatives are yet available. One possible approach to predict systemic toxicity of chemicals in the absence of experimental data is quantitative structure-activity relationship (QSAR) analysis. Here, we present QSAR models for prediction of maximum "no observed effect level" (NOEL) for repeated-dose, developmental and reproductive toxicities. NOEL values of 421 chemicals for repeated-dose toxicity, 315 for reproductive toxicity, and 156 for developmental toxicity were collected from Japan Existing Chemical Data Base (JECDB). Descriptors to predict toxicity were selected based on molecular orbital (MO) calculations, and QSAR models employing multiple independent descriptors as the input layer of an artificial neural network (ANN) were constructed to predict NOEL values. Robustness of the models was indicated by the root-mean-square (RMS) errors after 10-fold cross-validation (0.529 for repeated-dose, 0.508 for reproductive, and 0.558 for developmental toxicity). Evaluation of the models in terms of the percentages of predicted NOELs falling within factors of 2, 5 and 10 of the in-vivo-determined NOELs suggested that the model is applicable to both general chemicals and the subset of chemicals listed in International Nomenclature of Cosmetic Ingredients (INCI). Our results indicate that ANN models using in silico parameters have useful predictive performance, and should contribute to integrated risk assessment of systemic toxicity using a weight-of-evidence approach. Availability of predicted NOELs will allow calculation of the margin of safety, as recommended by the Scientific Committee on Consumer Safety (SCCS). PMID:25786522

  17. Analysis of a 3D imaging device by reconstruction from cone beam X ray radiographs

    The aim of our study is to analyse the principle of a 3D imaging device which attempts to restore the local density on a cuberill from a set of digital radiographs taken around the object. We have to use a ponctual radiation source to localize the acquisition lines. Therefore the attenuation measurements are modelled by the cone beam X ray transform. In the analysis of the inverse problem, we work out two inversion diagrams which compute the original function, the image of the object, by a sequence of transforms. The theoretical and algorithmical difficulty comes from the fact that, even in the simple case of a circular acquisition trajectory, the cone-shaped geometry prohibits splitting the problem into a superposition of reconstructions in two dimensions. We describe a novel theoretical framework based on the Radon transform. In this new representation space, it becomes possible by a rebinning operation to redistribute the integral values associated to planes from the coordinates system linked to source positions to the spherical coordinates system of the domain. To ensure this shift of space, we have established two formulas, the first approximate but leading to faster processing, related to the Radon transform, the second exact, related to the first derivative of the Radon transform. The inversion of these transforms completes the reconstruction. We state a theorem where we present the hypothesis under which the exact diagram does restore the original function. These are not verified for a circular trajectory, owing to a shadow zone in the Radon domain associated to the planes which intersect the object but not the trajectory. We propose either to restore the missing information or to use an oscillating trajectory

  18. 3-D nuclear analysis of the final optics of a laser driven fusion power plant

    In the High Average Power Laser (HAPL) program, power plant designs are assessed with 350 MJ yield targets driven by 40 KrF laser beams. The final optics system that focuses the laser onto the target includes a grazing incidence metallic mirror (GIMM) located at 24 m from the target with 85 angle of incidence. The GIMM is in direct line of sight of the target and has a 50 microns thick aluminum coating. Several options were considered for the substrate material. We performed three-dimensional (3-D) neutronics calculations to assess the impact of the GIMM design options on the nuclear environment at the dielectric focusing and turning mirrors. We used the recently developed MCNPX-CGM Monte Carlo code that allows performing the neutronics calculations directly in the exact CAD model. The most recent continuous energy fusion evaluated nuclear data library (FENDL-2.1) was used. One of the 40 beamlines was modeled with surrounding reflective boundaries. We considered beam duct configuration modifications such as utilizing neutron traps behind the mirrors to reduce radiation streaming. Several variance reduction techniques were utilized to reduce the statistical uncertainties. The results indicate that material choice and thickness for the GIMM impact the nuclear environment at all mirrors. The neutron flux and nuclear heating at the dielectric mirrors are a factor of ∝1.6 higher when AlBeMet is used instead of SiC as substrate in the GIMM. The fast neutron flux decreases by about two orders of magnitude as one moves from the GIMM to the focusing mirror with an additional two orders of magnitude attenuation at the turning mirror accompanied with significant spectrum softening. In this paper, the details of the analysis and results will be presented and the expected optics lifetime will be assessed. (orig.)

  19. 3D surface analysis of hippocampal microvasculature in the irradiated brain.

    Craver, Brianna M; Acharya, Munjal M; Allen, Barrett D; Benke, Sarah N; Hultgren, Nan W; Baulch, Janet E; Limoli, Charles L

    2016-06-01

    Cranial irradiation used to control CNS malignancies can also disrupt the vasculature and impair neurotransmission and cognition. Here we describe two distinct methodologies for quantifying early and late radiation injury in CNS microvasculature. Intravascular fluorescently labeled lectin was used to visualize microvessels in the brain of the irradiated mouse 2 days post exposure and RECA-1 immunostaining was similarly used to visualize microvessels in the brain of the irradiated rat 1-month post exposure. Confocal microscopy, image deconvolution and 3-dimensional rendering methods were used to define vascular structure in a ∼4 × 10(7) μm(3) defined region of the brain. Quantitative analysis of these 3D images revealed that irradiation caused significant short- and long-term reductions in capillary density, diameter and volume. In mice, irradiation reduced mean vessel volume from 2,250 to 1,470 μm(3) and mean vessel diameter from 5.0 to 4.5 μm, resulting in significant reductions of 34% and 10%, in the hippocampus respectively. The number of vessel branch points and area was also found to also drop significantly in mice 2 days after irradiation. For rats, immunostaining revealed a significant, three-fold drop in capillary density 1 month after exposure compared to controls. Such radiation-induced disruption of the CNS microvasculature may be contributory if not causal to any number of neurocognitive side effects that manifest in cancer patients following cranial radiotherapy. This study demonstrates the utility of two distinct methodologies for quantifying these important adverse effects of radiotherapy. Environ. Mol. Mutagen. 57:341-349, 2016. © 2016 Wiley Periodicals, Inc. PMID:27175611

  20. Noise analysis for near-field 3D FM-CW radar imaging systems

    Sheen, David M.

    2015-05-01

    Near field radar imaging systems are used for demanding security applications including concealed weapon detection in airports and other high-security venues. Despite the near-field operation, phase noise and thermal noise can limit performance in several ways. Practical imaging systems can employ arrays with low gain antennas and relatively large signal distribution networks that have substantial losses which limit transmit power and increase the effective noise figure of the receiver chain, resulting in substantial thermal noise. Phase noise can also limit system performance. The signal coupled from transmitter to receiver is much larger than expected target signals. Phase noise from this coupled signal can set the system noise floor if the oscillator is too noisy. Frequency modulated continuous wave (FM-CW) radar transceivers used in short range systems are relatively immune to the effects of the coupled phase noise due to range correlation effects. This effect can reduce the phase-noise floor such that it is below the thermal noise floor for moderate performance oscillators. Phase noise is also manifested in the range response around bright targets, and can cause smaller targets to be obscured. Noise in synthetic aperture imaging systems is mitigated by the processing gain of the system. In this paper, the effects of thermal noise, phase noise, and processing gain are analyzed in the context of a near field 3-D FM-CW imaging radar as might be used for concealed weapon detection. In addition to traditional frequency domain analysis, a time-domain simulation is employed to graphically demonstrate the effect of these noise sources on a fast-chirping FM-CW system.

  1. 3-D Finite Element Analysis of Induction Logging in a Dipping Formation

    EVERETT,MARK E.; BADEA,EUGENE A.; SHEN,LIANG C.; MERCHANT,GULAMABBAS A.; WEISS,CHESTER J.

    2000-07-20

    Electromagnetic induction by a magnetic dipole located above a dipping interface is of relevance to the petroleum well-logging industry. The problem is fully three-dimensional (3-D) when formulated as above, but reduces to an analytically tractable one-dimensional (1-D) problem when cast as a small tilted coil above a horizontal interface. The two problems are related by a simple coordinate rotation. An examination of the induced eddy currents and the electric charge accumulation at the interface help to explain the inductive and polarization effects commonly observed in induction logs from dipping geological formations. The equivalence between the 1-D and 3-D formulations of the problem enables the validation of a previously published finite element solver for 3-D controlled-source electromagnetic induction.

  2. Laser Welding Analysis for 3D Printed Thermoplastic and Poly-acetate Polymers

    Choi, Hae Woon; Yun, Sung Chul [Keimyung University, Daegu (Korea, Republic of)

    2015-07-15

    In this study, experimental and computer simulation results are compared and analyzed. Three-dimensional (3D) fabricated matrices from an MJM 3D printer were joined with poly-acetate thermoplastic polymers using a diode laser. A power range of 5-7 W was used to irradiate the boundary of two polymers. The heated polymers flowed into the matrices of the 3D fabricated structure, and reliable mechanical joining was achieved. Computer simulation showed the temperature distribution in the polymers, and flow direction was estimated based on the flux and temperature information. It was found that the more than the minimum energy threshold was required to effectively join the polymers and that two scans at low-speed were more effective than four scans at high speed.

  3. 3D numerical simulation analysis of passive drag near free surface in swimming

    Zhan, Jie-min; Li, Tian-zeng; Chen, Xue-bin; Li, Yok-sheung; Wai, Wing-hong Onyx

    2015-04-01

    The aim of this work is to build a 3D numerical model to study the characteristics of passive drag on competitive swimmers taking into account the impact of the free surface. This model solves the 3D incompressible Navier-Stokes equations using RNG k- ɛ turbulence closure. The volume of fluid (VOF) method is used to locate the free surface. The 3D virtual model is created by Computer Aided Industrial Design (CAID) software, Rhinoceros. Firstly, a specific posture of swimming is studied. The simulation results are in good agreement with the data from mannequin towing experiments. The effects of a swimmer's arms and legs positions on swimming performance are then studied. Finally, it is demonstrated that the present method is capable of simulating gliding near the free surface.

  4. Laser Welding Analysis for 3D Printed Thermoplastic and Poly-acetate Polymers

    In this study, experimental and computer simulation results are compared and analyzed. Three-dimensional (3D) fabricated matrices from an MJM 3D printer were joined with poly-acetate thermoplastic polymers using a diode laser. A power range of 5-7 W was used to irradiate the boundary of two polymers. The heated polymers flowed into the matrices of the 3D fabricated structure, and reliable mechanical joining was achieved. Computer simulation showed the temperature distribution in the polymers, and flow direction was estimated based on the flux and temperature information. It was found that the more than the minimum energy threshold was required to effectively join the polymers and that two scans at low-speed were more effective than four scans at high speed

  5. Design, Analysis, and Initial Testing of a Fiber-Optic Shear Gage for 3D, High-Temperature Flows

    Orr, Matthew William

    2004-01-01

    Design, Analysis, and Initial Testing of a Fiber-Optic Shear Gage for 3D, High-Temperature Flows Matthew W. Orr Dr. Joseph A. Schetz, Chairman Aerospace Engineering Abstract This investigation concerns the design, analysis, and initial testing of a new, two-component wall shear gage for 3D, high-temperature flows. This gage is a direct-measuring, non-nulling design with a round head surrounded by a small gap. Two flexure wheels are used to allow small motions of the flo...

  6. Neutron-induced complex reaction analysis with 3D nuclear track simulation

    Complex (multiple) etched tracks are analysed through digitised images and 3D simulation by a purpose-built algorithm. From a binary track image an unfolding procedure is followed to generate a 3D track model, from which several track parameters are estimated. The method presented here allows the deposited energy, that originated from particle fragmentation or carbon spallation by means of induced tracks in commercially available PADC detectors, to be estimated. Results of evaluated nuclear tracks related to 12C (n,3αn') reaction are presented here. The detectors were exposed on the ISS in 2001

  7. 3D DVH-based metric analysis versus per-beam planar analysis in IMRT pretreatment verification

    Purpose: To evaluate methods of pretreatment IMRT analysis, using real measurements performed with a commercial 2D detector array, for clinical relevance and accuracy by comparing clinical DVH parameters. Methods: We divided the work into two parts. The first part consisted of six in-phantom tests aimed to study the sensitivity of the different analysis methods. Beam fluences, 3D dose distribution, and DVH of an unaltered original plan were compared to those of the delivered plan, in which an error had been intentionally introduced. The second part consisted of comparing gamma analysis with DVH metrics for 17 patient plans from various sites. Beam fluences were measured with the MapCHECK 2 detector, per-beam planar analysis was performed with the MapCHECK software, and 3D gamma analysis and the DVH evaluation were performed using 3DVH software. Results: In a per-beam gamma analysis some of the tests yielded false positives or false negatives. However, the 3DVH software correctly described the DVH of the plan which included the error. The measured DVH from the plan with controlled error agreed with the planned DVH within 2% dose or 2% volume. We also found that a gamma criterion of 3%/3 mm was too lax to detect some of the forced errors. Global analysis masked some problems, while local analysis magnified irrelevant errors at low doses. Small hotspots were missed for all metrics due to the spatial resolution of the detector panel. DVH analysis for patient plans revealed small differences between treatment plan calculations and 3DVH results, with the exception of very small volume structures such as the eyes and the lenses. Target coverage (D98 and D95) of the measured plan was systematically lower than that predicted by the treatment planning system, while other DVH characteristics varied depending on the parameter and organ. Conclusions: We found no correlation between the gamma index and the clinical impact of a discrepancy for any of the gamma index evaluation

  8. A comparative analysis between active and passive techniques for underwater 3D reconstruction of close-range objects.

    Bianco, Gianfranco; Gallo, Alessandro; Bruno, Fabio; Muzzupappa, Maurizio

    2013-01-01

    In some application fields, such as underwater archaeology or marine biology, there is the need to collect three-dimensional, close-range data from objects that cannot be removed from their site. In particular, 3D imaging techniques are widely employed for close-range acquisitions in underwater environment. In this work we have compared in water two 3D imaging techniques based on active and passive approaches, respectively, and whole-field acquisition. The comparison is performed under poor visibility conditions, produced in the laboratory by suspending different quantities of clay in a water tank. For a fair comparison, a stereo configuration has been adopted for both the techniques, using the same setup, working distance, calibration, and objects. At the moment, the proposed setup is not suitable for real world applications, but it allowed us to conduct a preliminary analysis on the performances of the two techniques and to understand their capability to acquire 3D points in presence of turbidity. The performances have been evaluated in terms of accuracy and density of the acquired 3D points. Our results can be used as a reference for further comparisons in the analysis of other 3D techniques and algorithms. PMID:23966193

  9. A Comparative Analysis between Active and Passive Techniques for Underwater 3D Reconstruction of Close-Range Objects

    Maurizio Muzzupappa

    2013-08-01

    Full Text Available In some application fields, such as underwater archaeology or marine biology, there is the need to collect three-dimensional, close-range data from objects that cannot be removed from their site. In particular, 3D imaging techniques are widely employed for close-range acquisitions in underwater environment. In this work we have compared in water two 3D imaging techniques based on active and passive approaches, respectively, and whole-field acquisition. The comparison is performed under poor visibility conditions, produced in the laboratory by suspending different quantities of clay in a water tank. For a fair comparison, a stereo configuration has been adopted for both the techniques, using the same setup, working distance, calibration, and objects. At the moment, the proposed setup is not suitable for real world applications, but it allowed us to conduct a preliminary analysis on the performances of the two techniques and to understand their capability to acquire 3D points in presence of turbidity. The performances have been evaluated in terms of accuracy and density of the acquired 3D points. Our results can be used as a reference for further comparisons in the analysis of other 3D techniques and algorithms.

  10. Feasibility study on 3-D shape analysis of high-aspect-ratio features using through-focus scanning optical microscopy.

    Attota, Ravi Kiran; Weck, Peter; Kramar, John A; Bunday, Benjamin; Vartanian, Victor

    2016-07-25

    In-line metrologies currently used in the semiconductor industry are being challenged by the aggressive pace of device scaling and the adoption of novel device architectures. Metrology and process control of three-dimensional (3-D) high-aspect-ratio (HAR) features are becoming increasingly important and also challenging. In this paper we present a feasibility study of through-focus scanning optical microscopy (TSOM) for 3-D shape analysis of HAR features. TSOM makes use of 3-D optical data collected using a conventional optical microscope for 3-D shape analysis. Simulation results of trenches and holes down to the 11 nm node are presented. The ability of TSOM to analyze an array of HAR features or a single isolated HAR feature is also presented. This allows for the use of targets with area over 100 times smaller than that of conventional gratings, saving valuable real estate on the wafers. Indications are that the sensitivity of TSOM may match or exceed the International Technology Roadmap for Semiconductors (ITRS) measurement requirements for the next several years. Both simulations and preliminary experimental results are presented. The simplicity, lowcost, high throughput, and nanometer scale 3-D shape sensitivity of TSOM make it an attractive inspection and process monitoring solution for nanomanufacturing. PMID:27464112

  11. Quantitative analysis of two-phase 3D+time aortic MR images

    Zhao, Fei; Zhang, Honghai; Walker, Nicholas E.; Yang, Fuxing; Olszewski, Mark E.; Wahle, Andreas; Scholz, Thomas; Sonka, Milan

    2006-03-01

    Automated and accurate segmentation of the aorta in 3D+time MR image data is important for early detection of connective tissue disorders leading to aortic aneurysms and dissections. A computer-aided diagnosis method is reported that allows the objective identification of subjects with connective tissue disorders from two-phase 3D+time aortic MR images. Our automated segmentation method combines level-set and optimal border detection. The resulting aortic lumen surface was registered with an aortic model followed by calculation of modal indices of aortic shape and motion. The modal indices reflect the differences of any individual aortic shape and motion from an average aortic behavior. The indices were input to a Support Vector Machine (SVM) classifier and a discrimination model was constructed. 3D+time MR image data sets acquired from 22 normal and connective tissue disorder subjects at end-diastole (R-wave peak) and at 45% of the R-R interval were used to evaluate the performance of our method. The automated 3D segmentation result produced accurate aortic surfaces covering the aorta from the left-ventricular outflow tract to the diaphragm and yielded subvoxel accuracy with signed surface positioning errors of -0.09+/-1.21 voxel (-0.15+/-2.11 mm). The computer aided diagnosis method distinguished between normal and connective tissue disorder subjects with a classification correctness of 90.1 %.

  12. Some Methods of Applied Numerical Analysis to 3d Facial Reconstruction Software

    Roşu, Şerban; Ianeş, Emilia; Roşu, Doina

    2010-09-01

    This paper deals with the collective work performed by medical doctors from the University Of Medicine and Pharmacy Timisoara and engineers from the Politechnical Institute Timisoara in the effort to create the first Romanian 3d reconstruction software based on CT or MRI scans and to test the created software in clinical practice.

  13. A Critical Analysis of a Hand Orthosis Reverse Engineering and 3D Printing Process.

    Baronio, Gabriele; Harran, Sami; Signoroni, Alberto

    2016-01-01

    The possibility to realize highly customized orthoses is receiving boost thanks to the widespread diffusion of low-cost 3D printing technologies. However, rapid prototyping (RP) with 3D printers is only the final stage of patient personalized orthotics processes. A reverse engineering (RE) process is in fact essential before RP, to digitize the 3D anatomy of interest and to process the obtained surface with suitable modeling software, in order to produce the virtual solid model of the orthosis to be printed. In this paper, we focus on the specific and demanding case of the customized production of hand orthosis. We design and test the essential steps of the entire production process with particular emphasis on the accurate acquisition of the forearm geometry and on the subsequent production of a printable model of the orthosis. The choice of the various hardware and software tools (3D scanner, modeling software, and FDM printer) is aimed at the mitigation of the design and production costs while guaranteeing suitable levels of data accuracy, process efficiency, and design versatility. Eventually, the proposed method is critically analyzed so that the residual issues and critical aspects are highlighted in order to discuss possible alternative approaches and to derive insightful observations that could guide future research activities. PMID:27594781

  14. A Critical Analysis of a Hand Orthosis Reverse Engineering and 3D Printing Process

    Gabriele Baronio

    2016-01-01

    Full Text Available The possibility to realize highly customized orthoses is receiving boost thanks to the widespread diffusion of low-cost 3D printing technologies. However, rapid prototyping (RP with 3D printers is only the final stage of patient personalized orthotics processes. A reverse engineering (RE process is in fact essential before RP, to digitize the 3D anatomy of interest and to process the obtained surface with suitable modeling software, in order to produce the virtual solid model of the orthosis to be printed. In this paper, we focus on the specific and demanding case of the customized production of hand orthosis. We design and test the essential steps of the entire production process with particular emphasis on the accurate acquisition of the forearm geometry and on the subsequent production of a printable model of the orthosis. The choice of the various hardware and software tools (3D scanner, modeling software, and FDM printer is aimed at the mitigation of the design and production costs while guaranteeing suitable levels of data accuracy, process efficiency, and design versatility. Eventually, the proposed method is critically analyzed so that the residual issues and critical aspects are highlighted in order to discuss possible alternative approaches and to derive insightful observations that could guide future research activities.

  15. 3-D finite element analysis of claw-poled stepping motor

    Stepping motors are widely used for various electric instruments. It is necessary for the optimum design to analyze the magnetic field accurately. The 3-D finite element method with edge elements taking into account the rotation of the rotor has been applied to analyze the magnetic field of a claw-poled stepping motor. (Author)

  16. PRONTO3D users` instructions: A transient dynamic code for nonlinear structural analysis

    Attaway, S.W.; Mello, F.J.; Heinstein, M.W.; Swegle, J.W.; Ratner, J.A. [Sandia National Labs., Albuquerque, NM (United States); Zadoks, R.I. [Univ. of Texas, El Paso, TX (United States)

    1998-06-01

    This report provides an updated set of users` instructions for PRONTO3D. PRONTO3D is a three-dimensional, transient, solid dynamics code for analyzing large deformations of highly nonlinear materials subjected to extremely high strain rates. This Lagrangian finite element program uses an explicit time integration operator to integrate the equations of motion. Eight-node, uniform strain, hexahedral elements and four-node, quadrilateral, uniform strain shells are used in the finite element formulation. An adaptive time step control algorithm is used to improve stability and performance in plasticity problems. Hourglass distortions can be eliminated without disturbing the finite element solution using either the Flanagan-Belytschko hourglass control scheme or an assumed strain hourglass control scheme. All constitutive models in PRONTO3D are cast in an unrotated configuration defined using the rotation determined from the polar decomposition of the deformation gradient. A robust contact algorithm allows for the impact and interaction of deforming contact surfaces of quite general geometry. The Smooth Particle Hydrodynamics method has been embedded into PRONTO3D using the contact algorithm to couple it with the finite element method.

  17. Full Waveform Analysis for Long-Range 3D Imaging Laser Radar

    Wallace AndrewM

    2010-01-01

    Full Text Available The new generation of 3D imaging systems based on laser radar (ladar offers significant advantages in defense and security applications. In particular, it is possible to retrieve 3D shape information directly from the scene and separate a target from background or foreground clutter by extracting a narrow depth range from the field of view by range gating, either in the sensor or by postprocessing. We discuss and demonstrate the applicability of full-waveform ladar to produce multilayer 3D imagery, in which each pixel produces a complex temporal response that describes the scene structure. Such complexity caused by multiple and distributed reflection arises in many relevant scenarios, for example in viewing partially occluded targets, through semitransparent materials (e.g., windows and through distributed reflective media such as foliage. We demonstrate our methodology on 3D image data acquired by a scanning time-of-flight system, developed in our own laboratories, which uses the time-correlated single-photon counting technique.

  18. BER Analysis Using Beat Probability Method of 3D Optical CDMA Networks with Double Balanced Detection

    Chih-Ta Yen

    2015-01-01

    Full Text Available This study proposes novel three-dimensional (3D matrices of wavelength/time/spatial code for code-division multiple-access (OCDMA networks, with a double balanced detection mechanism. We construct 3D carrier-hopping prime/modified prime (CHP/MP codes by extending a two-dimensional (2D CHP code integrated with a one-dimensional (1D MP code. The corresponding coder/decoder pairs were based on fiber Bragg gratings (FBGs and tunable optical delay lines integrated with splitters/combiners. System performance was enhanced by the low cross correlation properties of the 3D code designed to avoid the beat noise phenomenon. The CHP/MP code cardinality increased significantly compared to the CHP code under the same bit error rate (BER. The results indicate that the 3D code method can enhance system performance because both the beating terms and multiple-access interference (MAI were reduced by the double balanced detection mechanism. Additionally, the optical component can also be relaxed for high transmission scenery.

  19. Evaluation and Performance Analysis of 3D Printing Technique for Ka-Band Antenna Production

    Armendariz, Unai; Rommel, Simon; Rodríguez Páez, Juan Sebastián;

    2016-01-01

    This paper presents the design and fabrication of 3D printed WR-28 waveguide horn antennas operating in the Ka-band frequency range between 26.5GHz and 40GHz. Three antennas are fabricated from polylactide acid filaments in conductive and non-conductive variants; the latter is covered with...

  20. 3-D seismic mapping and amplitude analysis: a Gulf of Mexico case history

    Kidney, R.L.; Silver, R.S.; Hussein, H.A. (Oryx Energy Co. (United States))

    1992-01-01

    Utilization of 3-D seismic data and Direct Hydrocarbon Indicators led to the successful drilling of appraisal and development wells in the Gulf of Mexico block South Timbalier 198 (ST 198), significantly reducing time and cost. Based on 2-D seismic mapping, a Pliocene Lower Buliminella (L BUL) prospect was drilled in ST 198. An Upper Buliminella (U BUL) gas sandstone was encountered instead. An appraisal well of the U BUL interval confirmed this discovery. It became apparent that the structural complexities and the seismic amplitude anomalies of the area could not be adequately resolved using the 2-D seismic grid. A 3-D seismic survey was shot to investigate the remaining potential of ST 198. Direct Hydrocarbon Indicators (DHIs), which are seismic anomalies resulting from the hydrocarbon effect on rock properties, are generally expected from these age sands. While the 3-D survey shows a seismic amplitude anomaly associated with the U BUL reservoir, the areal extent of the anomaly did not match the findings of the two wells. A DHI study was performed to determine if this inconsistency could be explained and if the anomaly could be used in the well planning. The two key steps which confirmed that this amplitude anomaly is a DHI were properly calibrating the seismic data to the well control and determining the theoretical seismic response of the gas sandstones. The DHI study along with the 3-D mapping led to the successful development of the ST 198 U BUL reservoir and to setting up a successful adjacent fault block play. Finally, 3-D mapping also identified a L BUL trap updip from the original L BUL prospect which resulted in a successful drilling effort. (author).

  1. A new method to create depth information based on lighting analysis for 2D/3D conversion

    Hyunho; Han; Gangseong; Lee; Jongyong; Lee; Jinsoo; Kim; Sanghun; Lee

    2013-01-01

    A new method creating depth information for 2D/3D conversion was proposed. The distance between objects is determined by the distances between objects and light source position which is estimated by the analysis of the image. The estimated lighting value is used to normalize the image. A threshold value is determined by some weighted operation between the original image and the normalized image. By applying the threshold value to the original image, background area is removed. Depth information of interested area is calculated from the lighting changes. The final 3D images converted with the proposed method are used to verify its effectiveness.

  2. Analysis of surface cracks at hole by a 3-D weight function method with stresses from finite element method

    Zhao, W.; Newman, J. C., Jr.; Sutton, M. A.; Shivakumar, K. N.; Wu, X. R.

    1995-01-01

    Parallel with the work in Part-1, stress intensity factors for semi-elliptical surface cracks emanating from a circular hole are determined. The 3-D weight function method with the 3D finite element solutions for the uncracked stress distribution as in Part-1 is used for the analysis. Two different loading conditions, i.e. remote tension and wedge loading, are considered for a wide range in geometrical parameters. Both single and double surface cracks are studied and compared with other solutions available in the literature. Typical crack opening displacements are also provided.

  3. Segment-interaction in sprint start: Analysis of 3D angular velocity and kinetic energy in elite sprinters

    Slawinski, Jean; BONNEFOY, Alice; ONTANON, Guy; LEVEQUE, Jean-Michel; Miller, Christian; RIQUET, Annie; CHEZE, Laurence; Dumas, Raphaël

    2010-01-01

    The aim of the present study was to measure during a sprint start the joint angularv elocity and the kinetic energy of the different segments in elite sprinters.This was performed using a 3D kinematic analysis of the wholebody.

  4. A unified and efficient framework for court-net sports video analysis using 3D camera modeling

    Han, Jungong; de With, Peter H. N.

    2007-01-01

    The extensive amount of video data stored on available media (hard and optical disks) necessitates video content analysis, which is a cornerstone for different user-friendly applications, such as, smart video retrieval and intelligent video summarization. This paper aims at finding a unified and efficient framework for court-net sports video analysis. We concentrate on techniques that are generally applicable for more than one sports type to come to a unified approach. To this end, our framework employs the concept of multi-level analysis, where a novel 3-D camera modeling is utilized to bridge the gap between the object-level and the scene-level analysis. The new 3-D camera modeling is based on collecting features points from two planes, which are perpendicular to each other, so that a true 3-D reference is obtained. Another important contribution is a new tracking algorithm for the objects (i.e. players). The algorithm can track up to four players simultaneously. The complete system contributes to summarization by various forms of information, of which the most important are the moving trajectory and real-speed of each player, as well as 3-D height information of objects and the semantic event segments in a game. We illustrate the performance of the proposed system by evaluating it for a variety of court-net sports videos containing badminton, tennis and volleyball, and we show that the feature detection performance is above 92% and events detection about 90%.

  5. Combining measurements and 3D neutron transport calculations. A powerful tool in detailed neutron dosimetry and damage analysis

    It is shown that the combination of 3D neutron transport calculations and the results from activation foil measurements at a limited number of locations in a materials testing irradiation experiment can provide information at any position in the experiment for detailed neutron dosimetry and damage analysis. 4 refs

  6. Variation and diversity in Homo erectus: a 3D geometric morphometric analysis of the temporal bone.

    Terhune, Claire E; Kimbel, William H; Lockwood, Charles A

    2007-07-01

    Although the level of taxonomic diversity within the fossil hominin species Homo erectus (sensu lato) is continually debated, there have been relatively few studies aiming to quantify the morphology of this species. Instead, most researchers have relied on qualitative descriptions or the evaluation of nonmetric characters, which in many cases display continuous variation. Also, only a few studies have used quantitative data to formally test hypotheses regarding the taxonomic composition of the "erectus" hypodigm. Despite these previous analyses, however, and perhaps in part due to these varied approaches for assessing variation within specimens typically referred to H. erectus (sensu lato) and the general lack of rigorous statistical testing of how variation within this taxon is partitioned, there is currently little consensus regarding whether this group is a single species, or whether it should instead be split into separate temporal or geographically delimited taxa. In order to evaluate possible explanations for variation within H. erectus, we tested the general hypothesis that variation within the temporal bone morphology of H. erectus is consistent with that of a single species, using great apes and humans as comparative taxa. Eighteen three-dimensional (3D) landmarks of the temporal bone were digitized on a total of 520 extant and fossil hominid crania. Landmarks were registered by Generalized Procrustes Analysis, and Procrustes distances were calculated for comparisons of individuals within and between the extant taxa. Distances between fossil specimens and between a priori groupings of fossils were then compared to the distances calculated within the extant taxa to assess the variation within the H. erectus sample relative to that of known species, subspecies, and populations. Results of these analyses indicate that shape variation within the entire H. erectus sample is generally higher than extant hominid intraspecific variation, and putative H. ergaster

  7. An experimental analysis for the impact of 3D variation assi- milation of satellite data on typhoon track simulation

    XIE Hongqin; WU Zengmao; GAO Shanhong

    2004-01-01

    A series of test simulations are performed to evaluate the impact of satellite-derived meteorological data on numerical typhoon track prediction. Geostationary meteorological satellite (GMS-5) and NOAA's TIROS operational vertical sounder (TOVS) observations are used in the experiments. A three-dimensional variational (3D-Var) assimilation scheme is developed to assimilate the satellite data directly into the Penn State-NCAR nonhydrostatic meteorological model (MM5). Three-dimensional objective analysis fields based on the T213 results and conventional observations are employed as the background fields of the initialization. The comparisons of the simulated typhoon tracks are carried out, which correspond respectively to assimilate different kinds of satellite data. It is found that, compared with the experiment without satellite data assimilation, the 3D-Var assimilation schemes lead to significant improvements on typhoon track prediction. Track errors reduce from approximately 25% at 24 h to approximately 30% at 48 h for 3D-Var assimilation experiments.

  8. High-throughput analysis of horse sperms' 3D swimming patterns using computational on-chip imaging.

    Su, Ting-Wei; Choi, Inkyum; Feng, Jiawen; Huang, Kalvin; Ozcan, Aydogan

    2016-06-01

    Using a high-throughput optical tracking technique that is based on partially-coherent digital in-line holography, here we report a detailed analysis of the statistical behavior of horse sperms' three-dimensional (3D) swimming dynamics. This dual-color and dual-angle lensfree imaging platform enables us to track individual 3D trajectories of ∼1000 horse sperms at sub-micron level within a sample volume of ∼9μL at a frame rate of 143 frames per second (FPS) and collect thousands of sperm trajectories within a few hours for statistical analysis of their 3D dynamics. Using this high-throughput imaging platform, we recorded >17,000 horse sperm trajectories that can be grouped into six major categories: irregular, linear, planar, helical, ribbon, and hyperactivated, where the hyperactivated swimming patterns can be further divided into four sub-categories, namely hyper-progressive, hyper-planar, hyper-ribbon, and star-spin. The large spatio-temporal statistics that we collected with this 3D tracking platform revealed that irregular, planar, and ribbon trajectories are the dominant 3D swimming patterns observed in horse sperms, which altogether account for >97% of the trajectories that we imaged in plasma-free semen extender medium. Through our experiments we also found out that horse seminal plasma in general increases sperms' straightness in their 3D trajectories, enhancing the relative percentage of linear swimming patterns and suppressing planar swimming patterns, while barely affecting the overall percentage of ribbon patterns. PMID:26826909

  9. Automated Rock Detection and Shape Analysis from Mars Rover Imagery and 3D Point Cloud Data

    Kaichang Di; Zongyu Yue; Zhaoqin Liu; Shuliang Wang

    2013-01-01

    A new object-oriented method has been developed for the extraction of Mars rocks from Mars rover data.It is based on a combination of Mars rover imagery and 3D point cloud data.First,Navcam or Pancam images taken by the Mars rovers are segmented into homogeneous objects with a mean-shift algorithm.Then,the objects in the segmented images are classified into small rock candidates,rock shadows,and large objects.Rock shadows and large objects are considered as the regions within which large rocks may exist.In these regions,large rock candidates are extracted through ground-plane fitting with the 3D point cloud data.Small and large rock candidates are combined and postprocessed to obtain the final rock extraction results.The shape properties of the rocks (angularity,circularity,width,height,and width-height ratio) have been calculated for subsequent geological studies.

  10. A 3D multilevel model of damage and strength of wood: Analysis of microstructural effects

    Qing, Hai; Mishnaevsky, Leon

    2011-01-01

    A 3D hierarchical computational model of damage and strength of wood is developed. The model takes into account the four scale microstructures of wood, including the microfibril reinforced structure at nanoscale, multilayered cell walls at microscale, hexagon-shape-tube cellular structure at meso...... arrangements and cellulose strength distributions on the tensile strength of wood is studied numerically. Good agreement of the theoretical results with experimental data has been obtained.......A 3D hierarchical computational model of damage and strength of wood is developed. The model takes into account the four scale microstructures of wood, including the microfibril reinforced structure at nanoscale, multilayered cell walls at microscale, hexagon-shape-tube cellular structure at...... mesoscale and annual rings at the macroscale. With the use of the developed hierarchical model, the influence of the microstructure, including microfibril angle (MFA), the cell shape and the wood density (annual ring structure), differences between earlywood and latewood as well as microstructural...

  11. Measurement error analysis of the 3D four-wheel aligner

    Zhao, Qiancheng; Yang, Tianlong; Huang, Dongzhao; Ding, Xun

    2013-10-01

    Positioning parameters of four-wheel have significant effects on maneuverabilities, securities and energy saving abilities of automobiles. Aiming at this issue, the error factors of 3D four-wheel aligner, which exist in extracting image feature points, calibrating internal and exeternal parameters of cameras, calculating positional parameters and measuring target pose, are analyzed respectively based on the elaborations of structure and measurement principle of 3D four-wheel aligner, as well as toe-in and camber of four-wheel, kingpin inclination and caster, and other major positional parameters. After that, some technical solutions are proposed for reducing the above error factors, and on this basis, a new type of aligner is developed and marketed, it's highly estimated among customers because the technical indicators meet requirements well.

  12. 3D RECONSTRUCTION AND ANALYSIS OF THE FRAGMENTED GRAINS IN A COMPOSITE MATERIAL

    Luc Gillibert

    2013-06-01

    Full Text Available X-ray microtomography from solid propellant allows studying the microstructure of fragmented grains in damaged samples. A new reconstruction algorithm of fragmented grains for 3D images is introduced. Based on a watershed transform of a morphological closing of the input image, the algorithm can be used  with different sets of markers. Two of them are compared. After the grain reconstruction, a multiscale segmentation  algorithm is used to extract each fragment of the damaged grains. This allows an original quantitative study of the  fragmentation of each grain in 3D. Experimental results on X-ray microtomographic images of a solid propellant fragmented under compression are presented and validated.

  13. Code portability and data management considerations in the SAS3D LMFBR accident-analysis code

    The SAS3D code was produced from a predecessor in order to reduce or eliminate interrelated problems in the areas of code portability, the large size of the code, inflexibility in the use of memory and the size of cases that can be run, code maintenance, and running speed. Many conventional solutions, such as variable dimensioning, disk storage, virtual memory, and existing code-maintenance utilities were not feasible or did not help in this case. A new data management scheme was developed, coding standards and procedures were adopted, special machine-dependent routines were written, and a portable source code processing code was written. The resulting code is quite portable, quite flexible in the use of memory and the size of cases that can be run, much easier to maintain, and faster running. SAS3D is still a large, long running code that only runs well if sufficient main memory is available

  14. 3D structural analysis of proteins using electrostatic surfaces based on image segmentation

    Vlachakis, Dimitrios; Champeris Tsaniras, Spyridon; Tsiliki, Georgia; Megalooikonomou, Vasileios; Kossida, Sophia

    2016-01-01

    Herein, we present a novel strategy to analyse and characterize proteins using protein molecular electro-static surfaces. Our approach starts by calculating a series of distinct molecular surfaces for each protein that are subsequently flattened out, thus reducing 3D information noise. RGB images are appropriately scaled by means of standard image processing techniques whilst retaining the weight information of each protein’s molecular electrostatic surface. Then homogeneous areas in the protein surface are estimated based on unsupervised clustering of the 3D images, while performing similarity searches. This is a computationally fast approach, which efficiently highlights interesting structural areas among a group of proteins. Multiple protein electrostatic surfaces can be combined together and in conjunction with their processed images, they can provide the starting material for protein structural similarity and molecular docking experiments.

  15. Initial Work on the Characterization of Additive Manufacturing (3D Printing) Using Software Image Analysis

    Jeremy Straub

    2015-01-01

    A current challenge in additive manufacturing (commonly known as 3D printing) is the detection of defects. Detection of defects (or the lack thereof) in bespoke industrial manufacturing may be safety critical and reduce or eliminate the need for testing of printed objects. In consumer and prototype printing, early defect detection may facilitate the printer taking corrective measures (or pausing printing and alerting a user), preventing the need to re-print objects after the compounding of a ...

  16. A Prototype System for Acquisition and Analysis of 3D Mandibular Movement

    Santos, Isa C. T.; João Manuel R. S. Tavares; Joaquim G. Mendes; Manuel P. F. Paulo

    2006-01-01

    This paper presents the development of a new prototype system for the acquisition of the 3D mandibular movement.In Dental Medicine, the study of the mandibular movement is very important in oral rehabilitation treatments because it allows to determine if exists, or not, pathologies in the temporomandibular joints and helps medical doctors to elaborate an adequate treatment plan.In this work a facial arc, commonly used in Dental Medicine, was adapted to use electromagnetic sensors to acquire t...

  17. A System for Analysis of the 3D Mandibular Movement using Magnetic Sensors and Neuronal Networks

    Santos, Isa C. T.; João Manuel R. S. Tavares; Joaquim G. Mendes; Manuel P. F. Paulo

    2006-01-01

    In Dental Medicine, the study of the mandibular movement has an important role in the development of oral rehabilitation treatments, because it allows to determine if exists or not pathologies in the temporomandibular joints and helps the definition of adequate treatment plans. In this paper, is presented the development of a new system for the acquisition of the 3D mandibular movement. A common facial arc used in Dental Medicine was adapted as main support structure, and electromagnetic sens...

  18. 3D Finite Element Analysis of HMA Overlay Mix Design to Control Reflective Cracking

    Ghauch, Ziad G.

    2011-01-01

    This study examines the effectiveness of HMA overlay design strategies for the purpose of controlling the development of reflective cracking. A parametric study was conducted using a 3D Finite Element (FE) model of a rigid pavement section including Linear Viscoelastic (LVE) material properties for the Hot Mix Asphalt (HMA) overlay and non-uniform tire-pavement contact stresses. Several asphalt mixtures were tested in the surface, intermediate, and leveling course of the HMA overlay. Results ...

  19. 3D segmentation of lung CT data with graph-cuts: analysis of parameter sensitivities

    Cha, Jung won; Dunlap, Neal; Wang, Brian; Amini, Amir

    2016-03-01

    Lung boundary image segmentation is important for many tasks including for example in development of radiation treatment plans for subjects with thoracic malignancies. In this paper, we describe a method and parameter settings for accurate 3D lung boundary segmentation based on graph-cuts from X-ray CT data1. Even though previously several researchers have used graph-cuts for image segmentation, to date, no systematic studies have been performed regarding the range of parameter that give accurate results. The energy function in the graph-cuts algorithm requires 3 suitable parameter settings: K, a large constant for assigning seed points, c, the similarity coefficient for n-links, and λ, the terminal coefficient for t-links. We analyzed the parameter sensitivity with four lung data sets from subjects with lung cancer using error metrics. Large values of K created artifacts on segmented images, and relatively much larger value of c than the value of λ influenced the balance between the boundary term and the data term in the energy function, leading to unacceptable segmentation results. For a range of parameter settings, we performed 3D image segmentation, and in each case compared the results with the expert-delineated lung boundaries. We used simple 6-neighborhood systems for n-link in 3D. The 3D image segmentation took 10 minutes for a 512x512x118 ~ 512x512x190 lung CT image volume. Our results indicate that the graph-cuts algorithm was more sensitive to the K and λ parameter settings than to the C parameter and furthermore that amongst the range of parameters tested, K=5 and λ=0.5 yielded good results.

  20. A Multimodal Discourse Analysis of the First Movie Poster of Titanic (3D)

    鞠彤

    2013-01-01

    Movie posters are designed to publicize the movies and boost the bill-office receipts. To read a movie poster is to decode a multimodal discourse which contains a variety of semiotic factors such as image, word, and color. The first movie poster of Titanic (3D) aims to find out how images as social semi-otic work together with words and to improve readers’multiliteracy.

  1. A 3D tomographic EBSD analysis of a CVD diamond thin film

    Tao Liu, Dierk Raabe and Stefan Zaefferer

    2008-01-01

    Full Text Available We have studied the nucleation and growth processes in a chemical vapor deposition (CVD diamond film using a tomographic electron backscattering diffraction method (3D EBSD. The approach is based on the combination of a focused ion beam (FIB unit for serial sectioning in conjunction with high-resolution EBSD. Individual diamond grains were investigated in 3-dimensions particularly with regard to the role of twinning.

  2. 3D modeling design and engineering analysis of automotive suspension beam

    Ju Zhi Lan

    2016-01-01

    Full Text Available Automotive suspension is an important device for transmission and torque. The main parameters and dimensions of 40 tons of heavy duty truck spring suspension system are designed in the paper. According to the data, the 3D modeling and virtual assembly of the leaf spring suspension are carried out by using parametric design. Structural stress of spring suspension is analyzed which can provide a guide and basis for the design of the leaf spring suspension.

  3. GIANT: pattern analysis of molecular interactions in 3D structures of protein–small ligand complexes

    Kasahara, Kota; Kinoshita, Kengo

    2014-01-01

    Background Interpretation of binding modes of protein–small ligand complexes from 3D structure data is essential for understanding selective ligand recognition by proteins. It is often performed by visual inspection and sometimes largely depends on a priori knowledge about typical interactions such as hydrogen bonds and π-π stacking. Because it can introduce some biases due to scientists’ subjective perspectives, more objective viewpoints considering a wide range of interactions are required....

  4. Statistical 2D and 3D shape analysis using Non-Euclidean Metrics

    Larsen, Rasmus; Hilger, Klaus Baggesen; Wrobel, Mark Christoph

    2002-01-01

    . Furthermore, we study metrics based on repated annotations of a training set. We define a way of assessing the correlation between landmarks contrary to landmark coordinates. Finally, we apply the proposed methods to a 2D data set consisting of outlines of lungs and a 3D/(4D) data set consisting of sets of...... mandible surfaces. In the latter case the end goal is to construct a model for growth prediction and simulation....

  5. A fully automatic 3-D analysis tool for expansion chamber mufflers

    Srinivasan, R.; Munjal, ML

    1998-01-01

    The matrix condensation technique in conjunction with the substructuring principle has been previously used to model complex commercial automotive mufflers. Though complete 3-D finite element modelling is partially eliminated, it still requires the nodal-coordinate data and connectivity data of the elements forming the segment of each substructure. It also demands the connectivity of the degrees of freedom left after matrix condensation. Thus, the data preparation phase is tedious and cannot ...

  6. 3-D analysis of eddy current in permanent magnet of interior permanent magnet motors

    Interior permanent magnet motors are widely used in various fields. However, in high-speed operations, it is important to decrease the eddy current loss in the permanent magnet. In order to decrease the eddy current loss, we propose to divide the permanent magnet. In this paper, we clarified the effect of division of permanent magnet on the eddy current loss using the 3-D finite element method. (Author)

  7. Extending a teleradiology system by tools for 3D-visualization and volumetric analysis through a plug-in mechanism.

    Evers, H; Mayer, A; Engelmann, U; Schröter, A; Baur, U; Wolsiffer, K; Meinzer, H P

    1998-01-01

    This paper describes ongoing research concerning interactive volume visualization coupled with tools for volumetric analysis. To establish an easy to use application, the 3D-visualization has been embedded in a state of the art teleradiology system, where additional functionality is often desired beyond basic image transfer and management. Major clinical requirements for deriving spatial measures are covered by the tools, in order to realize extended diagnosis support and therapy planning. Introducing the general plug-in mechanism this work exemplarily describes the useful extension of an approved application. Interactive visualization was achieved by a hybrid approach taking advantage of both the precise volume visualization based on the Heidelberg Raytracing Model and the graphics acceleration of modern workstations. Several tools for volumetric analysis extend the 3D-viewing. They offer 3D-pointing devices to select locations in the data volume, measure anatomical structures or control segmentation processes. A haptic interface provides a realistic perception while navigating within the 3D-reconstruction. The work is closely related to research work in the field of heart, liver and head surgery. In cooperation with our medical partners the development of tools as presented proceed the integration of image analysis into clinical routine. PMID:10384617

  8. 3D stereoscopic analysis of a Coronal Mass Ejection and comparison with UV spectroscopic data

    Susino, Roberto; Dolei, Sergio

    2014-01-01

    A three-dimensional (3D) reconstruction of the 2007, May 20 partial-halo Coronal Mass Ejection (CME) has been made using STEREO/EUVI and STEREO/COR1 coronagraphic images. The trajectory and kinematics of the erupting filament have been derived from EUVI image pairs with the "tie-pointing" triangulation technique, while the polarization ratio technique has been applied to COR1 data to determine the average position and depth of the CME front along the line of sight. These 3D geometrical information have been combined for the first time with spectroscopic measurements of the OVI $\\lambda\\lambda$1031.91, 1037.61 \\AA\\ line profiles made with the Ultraviolet Coronagraph Spectrometer (UVCS) on board SOHO. Comparison between the prominence trajectory extrapolated at the altitude of UVCS observations and the core transit time measured from UVCS data made possible a firm identification of the CME core observed in white light and UV with the prominence plasma expelled during the CME. Results on the 3D structure of the ...

  9. 3D Analysis of Crack Growth in Metal Using Tension Tests and XFEM

    To prevent the occurrence of fractures in metal structures, it is very important to evaluate the 3D crack growth process in those structures and any related parts. In this study, tension tests and two simulations, namely, Simulation-I and Simulation-II, were performed using XFEM to evaluate crack growth in three dimensions. In the tension test, Mode I crack growth was observed for a notched metal specimen. In Simulation-I, a 3D reconstructed model of the specimen was created using CT images of the specimen. Using this model, an FE model was constructed, and crack growth was simulated using XFEM. In Simulation-II, an ideal notch FE model of the same geometric size as the actual specimen was created and then used for simulation. Obtained crack growth simulation results were then compared. Crack growth in the metal specimen was evaluated in three dimensions. It was shown that modeling the real shape of a structure with a crack may be essential for accurately evaluating 3D crack growth

  10. 3-D Human Action Recognition by Shape Analysis of Motion Trajectories on Riemannian Manifold.

    Devanne, Maxime; Wannous, Hazem; Berretti, Stefano; Pala, Pietro; Daoudi, Mohamed; Del Bimbo, Alberto

    2015-07-01

    Recognizing human actions in 3-D video sequences is an important open problem that is currently at the heart of many research domains including surveillance, natural interfaces and rehabilitation. However, the design and development of models for action recognition that are both accurate and efficient is a challenging task due to the variability of the human pose, clothing and appearance. In this paper, we propose a new framework to extract a compact representation of a human action captured through a depth sensor, and enable accurate action recognition. The proposed solution develops on fitting a human skeleton model to acquired data so as to represent the 3-D coordinates of the joints and their change over time as a trajectory in a suitable action space. Thanks to such a 3-D joint-based framework, the proposed solution is capable to capture both the shape and the dynamics of the human body, simultaneously. The action recognition problem is then formulated as the problem of computing the similarity between the shape of trajectories in a Riemannian manifold. Classification using k-nearest neighbors is finally performed on this manifold taking advantage of Riemannian geometry in the open curve shape space. Experiments are carried out on four representative benchmarks to demonstrate the potential of the proposed solution in terms of accuracy/latency for a low-latency action recognition. Comparative results with state-of-the-art methods are reported. PMID:25216492

  11. Quality Analysis on 3d Buidling Models Reconstructed from Uav Imagery

    Jarzabek-Rychard, M.; Karpina, M.

    2016-06-01

    Recent developments in UAV technology and structure from motion techniques have effected that UAVs are becoming standard platforms for 3D data collection. Because of their flexibility and ability to reach inaccessible urban parts, drones appear as optimal solution for urban applications. Building reconstruction from the data collected with UAV has the important potential to reduce labour cost for fast update of already reconstructed 3D cities. However, especially for updating of existing scenes derived from different sensors (e.g. airborne laser scanning), a proper quality assessment is necessary. The objective of this paper is thus to evaluate the potential of UAV imagery as an information source for automatic 3D building modeling at LOD2. The investigation process is conducted threefold: (1) comparing generated SfM point cloud to ALS data; (2) computing internal consistency measures of the reconstruction process; (3) analysing the deviation of Check Points identified on building roofs and measured with a tacheometer. In order to gain deep insight in the modeling performance, various quality indicators are computed and analysed. The assessment performed according to the ground truth shows that the building models acquired with UAV-photogrammetry have the accuracy of less than 18 cm for the plannimetric position and about 15 cm for the height component.

  12. Interactive visualization and analysis of 3D medical images for neurosurgery

    We propose a method that makes it possible to interactively rotate and zoom a volume-rendered object and to interactively manipulate a function for transferring data values to color and opacity. The method ray-traces a Value-Intensity-Strength volume (VIS volume) instead of a color-opacity volume, and uses an adaptive refinement technique in generating images. The VIS volume tracing method can reduce by 20-90 percent the computational time of re-calculation necessitated by changing the function for transferring data values to color and opacity, and can reduce the computational time of pre-processing by 20 percent. It can also reduce the required memory space by 40 percent. The combination of VIS volume tracing and adaptive refinement method makes it possible to interactively visualize and analyze 3D medical image data. Once we can see detailed image of 3D objects to determine their orientation, we can easily manipulate the viewing and rendering parameters even while viewing rough, blurred images. The increase in the computation time for generating full-resolution images by using the adaptive refinement technique is approximately five to ten percent. Its effectiveness is evaluated by using the results of visualization for some 3D medical image data. (author)

  13. Segment-interaction in sprint start: Analysis of 3D angular velocity and kinetic energy in elite sprinters.

    Slawinski, J; Bonnefoy, A; Ontanon, G; Leveque, J M; Miller, C; Riquet, A; Chèze, L; Dumas, R

    2010-05-28

    The aim of the present study was to measure during a sprint start the joint angular velocity and the kinetic energy of the different segments in elite sprinters. This was performed using a 3D kinematic analysis of the whole body. Eight elite sprinters (10.30+/-0.14s 100 m time), equipped with 63 passive reflective markers, realised four maximal 10 m sprints start on an indoor track. An opto-electronic Motion Analysis system consisting of 12 digital cameras (250 Hz) was used to collect the 3D marker trajectories. During the pushing phase on the blocks, the 3D angular velocity vector and its norm were calculated for each joint. The kinetic energy of 16 segments of the lower and upper limbs and of the total body was calculated. The 3D kinematic analysis of the whole body demonstrated that joints such as shoulders, thoracic or hips did not reach their maximal angular velocity with a movement of flexion-extension, but with a combination of flexion-extension, abduction-adduction and internal-external rotation. The maximal kinetic energy of the total body was reached before clearing block (respectively, 537+/-59.3 J vs. 514.9+/-66.0 J; p< or =0.01). These results suggested that a better synchronization between the upper and lower limbs could increase the efficiency of pushing phase on the blocks. Besides, to understand low interindividual variances in the sprint start performance in elite athletes, a 3D complete body kinematic analysis shall be used. PMID:20226465

  14. Aging effect on successful reactive-recovery from unexpected slips: a 3D lower extremity joint moment analysis

    Liu, Jian

    2004-01-01

    The objective of the proposed study was to perform three-dimensional (3D) inverse dynamics analysis to determine lower extremity (ankle, knee and hip) joint moments on previously collected slip perturbation experimental data. In addition, the aging effect on the joint moment generation in both normal walking and reactive-recovery conditions was examined. Dataset collected during previous slip and fall experiments, which were conducted in a typical gait analysis setting, were analyzed in cu...

  15. Pipe3D, a pipeline to analyse integral field spectroscopy data: II. Analysis sequence and CALIFA dataproducts

    Sánchez, S F; Sánchez-Blázquez, P; García-Benito, R; Ibarra-Mede, H J; González, J J; Rosales-Ortega, F F; Sánchez-Menguiano, L; Ascasibar, Y; Bitsakis, T; Law, D; Cano-Díaz, M; López-Cobá, C; Marino, R A; de Paz, A Gil; López-Sánchez, A R; Barrera-Ballesteros, J; Galbany, L; Mast, D; Abril-Melgarejo, V; Roman-Lopes, A

    2016-01-01

    We present Pipe3D, an analysis pipeline based on the FIT3D fitting tool, devel- oped to explore the properties of the stellar populations and ionized gas of Integral Field Spectroscopy data. Pipe3D was created to provide with coherent, simple to distribute, and comparable dataproducts, independently of the origin of the data, focused on the data of the most recent IFU surveys (e.g., CALIFA, MaNGA, and SAMI), and the last generation IFS instruments (e.g., MUSE). Along this article we describe the different steps involved in the analysis of the data, illustrating them by showing the dataproducts derived for NGC 2916, observed by CALIFA and P-MaNGA. As a practical use of the pipeline we present the complete set of dataproducts derived for the 200 datacubes that comprises the V500 setup of the CALIFA Data Release 2 (DR2), making them freely available through the network (ftp://ftp.caha.es/CALIFA/dataproducts/DR2/Pipe3D). Finally, we explore the hypothesis that the properties of the stellar populations and ionized...

  16. Using the RELAP5-3D advanced systems analysis code with commercial and advanced CFD software

    The Idaho National Engineering and Environmental Laboratory (INEEL), in conjunction with Fluent Corporation, has developed a new analysis tool by coupling the Fluent computational fluid dynamics (CFD) code to the RELAP5-3D/ATHENA advanced thermal-hydraulic analysis code. This tool enables researchers to perform detailed, three-dimensional analyses using Fluent's CFD capability while the boundary conditions required by the Fluent calculation are provided by the balance-of-system model created using RELAP5-3D/ATHENA. Both steady-state and transient calculations can be performed using many working fluids and also point to three-dimensional neutronics. The Fluent/RELAP5-3D coupled code is intended as a state-of-the-art tool to study the behavior of systems with single-phase working fluids, such as advanced gas-cooled reactors. For systems with two-phase working fluids, particularly during loss-of-coolant accident (LOCA) scenarios where a multitude of flow regimes, heat transfer regimes, and phenomena are present, the Fluent-RELAP5-3D coupling will have less general applicability since Fluent's capabilities to analyze global two-phase problems are limited. Consequently, for two-phase advanced reactor analysis, INEEL plans to employ not only the Fluent-RELAP5-3D coupling, but also to make use of state-of-the-art experimental CFD tools such as CFDLib (available from the Los Alamos National Laboratory). A general description of the techniques used to couple the codes is given. A summary of the process used to checkout the coupled configuration is given. A demonstration calculation is presented. Finally, future tasks and plans are outlined. (author)

  17. Coupling the RELAP5-3d advanced systems analysis code with commercial and advanced CFD software

    The Idaho National Engineering and Environmental Laboratory (INEEL), in conjunction with Fluent Corporation, has developed a new analysis tool by coupling the Fluent computational fluid dynamics (CFD) code to the RELAP5-3D/ATHENA advanced thermal-hydraulic analysis code. This tool enables researchers to perform detailed, three-dimensional analyses using Fluent's CFD capability while the boundary conditions required by the Fluent calculation are provided by the balance-of-system model created using RELAP5-3D/ATHENA. Both steady-state and transient calculations can be performed using many working fluids and also point to three-dimensional neutronics. The Fluent/RELAP5-3D coupled code is intended as a state-of-the-art tool to study the behavior of systems with single-phase working fluids, such as advanced gas-cooled reactors. For systems with two-phase working fluids, particularly during loss-of-coolant accident (LOCA) scenarios where a multitude of flow regimes, heat transfer regimes, and phenomena are present, the Fluent-RELAP5-3D coupling will have less general applicability since Fluent's capabilities to analyze global two-phase problems are limited. Consequently, for two-phase advanced reactor analysis, INEEL plans to employ not only the Fluent-RELAP5-3D coupling, but also to make use of state-of-the-art experimental CFD tools such as CFDLib (available from the Los Alamos National Laboratory). A general description of the techniques used to couple the codes is given. A summary of the process used to checkout the coupled configuration is given. Finally, future tasks and plans are outlined. (author)

  18. Effect of Frictions on the Ballistic Performance of a 3D Warp Interlock Fabric: Numerical Analysis

    Ha-Minh, Cuong; Boussu, François; Kanit, Toufik; Crépin, David; Imad, Abdellatif

    2012-06-01

    3D interlock woven fabrics are promising materials to replace the 2D structures in the field of ballistic protection. The structural complexity of this material caused many difficulties in numerical modeling. This paper presents a new tool that permits to generate a geometry model of any woven fabric, then, mesh this model in shell or solid elements, and apply the mechanical properties of yarns to them. The tool shows many advantages over existing software. It is very handy in use with an organization of the functions in menu and using a graphic interface. It can describe correctly the geometry of all textile woven fabrics. With this tool, the orientation of the local axes of finite elements following the yarn direction facilitates defining the yarn mechanical properties in a numerical model. This tool can be largely applied because it is compatible with popular finite element codes such as Abaqus, Ansys, Radioss etc. Thanks to this tool, a finite element model was carried out to describe a ballistic impact on a 3D warp interlock Kevlar KM2® fabric. This work focuses on studying the effect of friction onto the ballistic impact behavior of this textile interlock structure. Results showed that the friction among yarns affects considerably on the impact behavior of this fabric. The effect of the friction between projectile and yarn is less important. The friction plays an important role in keeping the fabric structural stability during the impact event. This phenomenon explained why the projectile is easier to penetrate this 3D warp interlock fabric in the no-friction case. This result also indicates that the ballistic performance of the interlock woven fabrics can be improved by using fibers with great friction coefficients.

  19. Transcriptomic analysis and 3D bioengineering of astrocytes indicate ROCK inhibition produces cytotrophic astrogliosis

    Ross D O'Shea

    2015-02-01

    Full Text Available Astrocytes provide trophic, structural and metabolic support to neurons, and are considered genuine targets in regenerative neurobiology, as their phenotype arbitrates brain integrity during injury. Inhibitors of Rho kinase (ROCK cause stellation of cultured 2D astrocytes, increased L-glutamate transport, augmented G-actin, and elevated expression of BDNF and anti-oxidant genes. Here we further explored the signposts of a cytotrophic, healthy phenotype by data-mining of our astrocytic transcriptome in the presence of Fasudil. Gene expression profiles of motor and autophagic cellular cascades and inflammatory / angiogenic responses were all inhibited, favouring adoption of an anti-migratory phenotype. Like ROCK inhibition, tissue engineered bioscaffolds can influence the extracellular matrix. We built upon our evidence that astrocytes maintained on 3D poly-Ɛ-caprolactone (PCL electrospun scaffolds adopt a cytotrophic phenotype similar to that produced by Fasudil. Using these procedures, employing mature 3D cultured astrocytes, Fasudil (100 µM or Y27632 (30 µM added for the last 72 h of culture altered arborization, which featured numerous additional minor processes as shown by GFAP and AHNAK immunolabelling. Both ROCK inhibitors decreased F-actin, but increased G-actin labelling, indicative of disassembly of actin stress fibres. ROCK inhibitors provide additional beneficial effects for bioengineered 3D astrocytes, including enlargement of the overall arbour. Potentially, the combined strategy of bio-compatible scaffolds with ROCK inhibition offers unique advantages for the management of glial scarring. Overall these data emphasize that manipulation of the astrocyte phenotype to achieve a healthy biology offers new hope for the management of inflammation in neuropathologies.

  20. Analysis of edge and surface TCTs for irradiated 3D silicon strip detectors

    We performed edge and surface Transient Current Technique (TCT) measurements of short, double sided 3D silicon strip detectors. Double sided 3D devices are a useful counterpart to traditional planar devices for use in the highest radiation environments. The TCT technique allows the electric field in the 3D devices to be probed in a way not possible before. The TCT technique uses the current waveform produced by the detector in response to a near delta function point laser pulse (illumination). The waveforms are recorded as a function of illumination position over the surface of the device under test as a function of detector bias. This data gives information on the portion of the induced signal from electron or hole motion. From the rise times of the signals the velocity profile of the carriers in the devices and therefore electric fields can be determined. The collected charge was calculated from the integral of the waveforms. The detectors were tested prior to irradiation, after irradiating to a dose of 5 × 1015 1 MeV equivalent neutrons/cm2, and after periods of annealing at elevated temperatures. Annealing was achieved in situ by warming to 60°C for 20 to 600 minutes corresponding to room temperature annealing of between 8 and 200 days. While before irradiation, full lateral depletion between the columns occurs at low bias voltages, at approximately 3 V, a uniform carrier velocity between the columns is not achieved until 40 V. Both the drift of electrons and holes provide equal contributions to the measured signals. After irradiation there is clear charge multiplication enhancement along the line between columns with a very non-uniform velocity profile in the unit cell of the device. In addition, charge trapping greatly suppresses the contribution of the holes on the signal produced.