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Sample records for 3d qsar analysis

  1. 3D-QSAR studies on glycogen phosphorylase inhibitors by flexible comparative molecular field analysis

    Institute of Scientific and Technical Information of China (English)

    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.

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

    Institute of Scientific and Technical Information of China (English)

    ZHOU Peng; LI ZhiLiang

    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 attempts 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 analysis of a new type of acetylcholinesterase inhibitors

    Institute of Scientific and Technical Information of China (English)

    LIU; AiLin; GUANG; HongMei; ZHU; LiYa; DU; GuanHua; LEE; Simon; M.; Y.; WANG; YiTao

    2007-01-01

    Acetylcholinesterase (AChE) inhibitors are an important class of medicinal agents used for the treatment of Alzheimer's disease. A screening model of AChE inhibitor was used to evaluate the inhibition of a series of phenyl pentenone derivatives. The assay result showed that some compounds displayed higher inhibitory effects. In order to study the relationship between the bioactivities and the structures, 26 compounds with phenyl pentenone scaffold were analyzed. A 3D-QSAR model was constructed using the method of comparative molecular field analysis (CoMFA). The results of cross-validated R2cv=0.629, non-cross-validated R2=0.972, SE=0.331, and F=72.41 indicate that the 3D-model possesses an ability to predict the activities of new inhibitors, and the CoMFA model would be useful for the future design of new AChE inhibitors.

  4. 3D-QSAR Investigation of Synthetic Antioxidant Chromone Derivatives by Molecular Field Analysis

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    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.

  5. CoMFA 3D-QSAR Analysis of Epothilones Based on Docking Conformation and Alignment

    Institute of Scientific and Technical Information of China (English)

    YUAN,Wei; LUAN,Lin-Bo; LI,Yan-Ni

    2007-01-01

    Epothilones belong to a class of novel microtubule stabilizing and anti-mitotic agents.which have a paclitaxel-like mechanism of action.A three-dimensional quantitative structure-activity relationship(3D-QSAR)model was built for epothilones by the method of comparative molecular field analysis (CoMFA)combined with the flexible docking technology.The docking CoMFA model gave a good cross-validated value of q2=0.784 with an optimized component of 6 and the conventional correlation coefficient of r2=0.985.The statistical results show that the model has good ability to predict the activity of the studied compounds.At last.the docking CoMFA model was analyzed through contour maps complemented with MOLCAD-generated active site potential surface in the α,β-tubulin receptor,which can provide important information for the structure-based drug design.

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

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    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.

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

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    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.

  8. 3D-QSAR Study on Diindolylmethane and Its Analogues with Comparative Molecular Field Analysis (CoMFA)

    Institute of Scientific and Technical Information of China (English)

    BENABADJI,Sakina Hayat; CHEN,Hai-Feng; YUAN,Shen-Gang; WEN,Ren

    2003-01-01

    Comparative molecular field analysis (CoMFA), a three dimensional quantitative structure-activity relationship (3D-QSAR)method was applied to a series of diindolylmethane(DIM) analogs to study the relationship between their structure and theirinnduction of CYP 1A1-associated ethoxyresorufin-O-deethylase (EROD) activity. A DISCO model of pharmacophore was derived to guide the superposition of the compounds. The coefficient of cross-validation (p2) and non cross-validation (r2) for the model established by the study are 0.827 and 0.988 respectively, the value of variance ratio(F) is 103.53 and standard error estimate (SEE) is 0.044. These values indicate that the CoMFA model derived is significant and might have a good prediction for the catalytic activity of DIM compound. As a consequence, the predicted activity values of new designed compounds were all higher than that of the reported value.

  9. Molecular field analysis and 3D-quantitative structure-activity relationship study (MFA 3D-QSAR) unveil novel features of bile acid recognition at TGR5.

    Science.gov (United States)

    Macchiarulo, Antonio; Gioiello, Antimo; Thomas, Charles; Massarotti, Alberto; Nuti, Roberto; Rosatelli, Emiliano; Sabbatini, Paola; Schoonjans, Kristina; Auwerx, Johan; Pellicciari, Roberto

    2008-09-01

    Bile acids regulate nongenomic actions through the activation of TGR5, a membrane receptor that is G protein-coupled to the induction of adenylate cyclase. In this work, a training set of 43 bile acid derivatives is used to develop a molecular interaction field analysis (MFA) and a 3D-quantitative structure-activity relationship study (3D-QSAR) of TGR5 agonists. The predictive ability of the resulting model is evaluated using an external set of compounds with known TGR5 activity, and six bile acid derivatives whose unknown TGR5 activity is herein assessed with in vitro luciferase assay of cAMP formation. The results show a good predictive model and indicate a statistically relevant degree of correlation between the TGR5 activity and the molecular interaction fields produced by discrete positions of the bile acid scaffold. This information is instrumental to extend on a quantitative basis the current structure-activity relationships of bile acids as TGR5 modulators and will be fruitful to design new potent and selective agonists of the receptor.

  10. 3D-QSAR and molecular docking analysis of (4-piperidinyl-piperazines as acetyl-CoA carboxylases inhibitors

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    Udghosh Singh

    2017-02-01

    Full Text Available Acetyl-CoA carboxylase (ACC is a crucial metabolic enzyme, which plays a vital role in fatty acid metabolism and obesity induced type 2 diabetes. Herein, we have performed 3D-QSAR and molecular docking analysis on a novel series of (4-piperidinyl-piperazines to design potent ACC inhibitors. This study correlates the ACC inhibitory activities of 68 (4-piperidinyl-piperazine derivatives with several stereo-chemical parameters representing steric, electrostatic, hydrophobic, hydrogen bond donor and acceptor fields. The CoMFA and CoMSIA models exhibited excellent rncv2 values of 0.974 and 0.985, and rcv2 values of 0.671 and 0.693, respectively. CoMFA predicted rpred2 of 0.910 and CoMSIA predicted rpred2 of 0.963 showed that the predicted values were in good agreement with experimental values. Glide5.5 program was used to explore the binding mode of inhibitors inside the active site of ACC. We have accordingly designed novel ACC inhibitors by utilising the LeapFrog and predicted with excellent inhibitory activity in the developed models.

  11. Novel substituted benzothiophene and thienothiophene carboxanilides and quinolones: synthesis, photochemical synthesis, DNA-binding properties, antitumor evaluation and 3D-derived QSAR analysis.

    Science.gov (United States)

    Aleksić, Maja; Bertoša, Branimir; Nhili, Raja; Uzelac, Lidija; Jarak, Ivana; Depauw, Sabine; David-Cordonnier, Marie-Hélène; Kralj, Marijeta; Tomić, Sanja; Karminski-Zamola, Grace

    2012-06-14

    A series of new N,N-dimethylaminopropyl- and 2-imidazolinyl-substituted derivatives of benzo[b]thienyl- and thieno[2,3-b]thienylcarboxanilides and benzo[b]thieno[2,3-c]- and thieno[3',2':4,5]thieno[2,3-c]quinolones were prepared. Quinolones were prepared by the reaction of photochemical dehydrohalogenation of corresponding anilides. Carboxanilides and quinolones were tested for the antiproliferative activity. 2-Imidazolinyl-substituted derivatives showed very prominent activity. By use of the experimentally obtained antitumor measurements, 3D-derived QSAR analysis was performed for the set of compounds. Highly predictive 3D-derived QSAR models were obtained, and molecular properties that have the highest impact on antitumor activity were identified. Carboxanilides 6a-c and quinolones 9a-c and 11a were evaluated for DNA binding propensities and topoisomerases I and II inhibition as part of their mechanism of action assessment. The evaluated differences in the mode of action nicely correlate with the results of the 3D-QSAR analysis. Taken together, the results indicate which modifications of the compounds from the series should further improve their anticancer properties.

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

    Science.gov (United States)

    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.

  13. 3D-QSAR analysis of a series of S-DABO derivatives as anti-HIV agents by CoMFA and CoMSIA.

    Science.gov (United States)

    Xu, H R; Fu, L; Zhan, P; Liu, X Y

    2016-12-01

    In this study, we retrieved a series of 59 dihydroalkylthio-benzyloxopyrimidine (S-DABO) derivatives, which is a class of highly potent HIV-1 non-nucleoside reverse transcriptase inhibitors (NNRTIs) reported from published articles, and analysed them with comparative molecular field analysis (CoMFA) and comparative molecular similarity indices analysis (CoMSIA). Statistically significant three-dimensional quantitative structure-activity relationship (3D-QSAR) models by CoMFA and CoMSIA were derived from a training set of 46 compounds on the basis of the rigid body alignment. Further, the predictive ability of the QSAR models was validated by a test set of 13 compounds. Based on the information derived from CoMFA and CoMSIA contour maps, we have identified some steric and electrostatic features for improving the activities of these inhibitors, and we validated the 3D-QSAR results by a molecular docking method. On the basis of the obtained results, we designed a new series of S-DABO derivatives with high activities. Therefore, this study could be utilized to design more potent S-DABO analogues as anti-HIV agents.

  14. Receptor-based 3D-QSAR in Drug Design: Methods and Applications in Kinase Studies.

    Science.gov (United States)

    Fang, Cheng; Xiao, Zhiyan

    2016-01-01

    Receptor-based 3D-QSAR strategy represents a superior integration of structure-based drug design (SBDD) and three-dimensional quantitative structure-activity relationship (3D-QSAR) analysis. It combines the accurate prediction of ligand poses by the SBDD approach with the good predictability and interpretability of statistical models derived from the 3D-QSAR approach. Extensive efforts have been devoted to the development of receptor-based 3D-QSAR methods and two alternative approaches have been exploited. One associates with computing the binding interactions between a receptor and a ligand to generate structure-based descriptors for QSAR analyses. The other concerns the application of various docking protocols to generate optimal ligand poses so as to provide reliable molecular alignments for the conventional 3D-QSAR operations. This review highlights new concepts and methodologies recently developed in the field of receptorbased 3D-QSAR, and in particular, covers its application in kinase studies.

  15. 3D-QSAR analysis on broad-spectrum arenavirus inhibitors%广谱沙粒病毒抑制剂的3D-QSAR分析

    Institute of Scientific and Technical Information of China (English)

    杨银凤; 王斌; 王景辉; 李燕; 杨凌

    2014-01-01

    沙粒病毒(Arenaviruses)遍布全球,其中的拉沙热病毒可引起致命的拉沙热.通过应用比较分子场分析(CoMFA)和比较相似性指数分析法(CoMSIA)对47个广谱沙粒病毒抑制剂进行了三维定量构效关系(3D-QSAR)分析.使用立体场、静电场、疏水场和氢键受体场组合获得最优模型CoMSIA的统计结果为Q2=0.518,Rncv2=0.972,Rpre2=0.911,说明该模型的可靠性和较好预测能力.此外,模型等势线图直观地解释了分子结构与其活性的关系,为进一步设计新型高效的沙粒病毒抑制剂提供了理论依据.

  16. A 3D-QSAR-driven approach to binding mode and affinity prediction

    DEFF Research Database (Denmark)

    Tosco, Paolo; Balle, Thomas

    2012-01-01

    A method for predicting the binding mode of a series of ligands is proposed. The procedure relies on three-dimensional quantitative structure-activity relationships (3D-QSAR) and does not require structural knowledge of the binding site. Candidate alignments are automatically built and ranked...... according to a consensus scoring function. 3D-QSAR analysis based on the selected binding mode enables affinity prediction of new drug candidates having less than 10 rotatable bonds....

  17. 3D-QSAR and docking studies of arylmethylamine-based DPP IV inhibitors

    Directory of Open Access Journals (Sweden)

    Chaoyi Jiang

    2012-08-01

    Full Text Available The present work was focused on the study of the three-dimensional (3D structural requirements for the highly potent bioactivity of dipeptidyl peptidase (DPP IV's inhibitor. At first, molecular dynamic and mechanic (MD/MM simulations were performed to research the conformations of the potent DPP IV's inhibitor 5-(aminomethyl-6-(2,4-dichlorophenyl-2-(3,5-dimethoxy-phenylpyrimidin-4-amine. Using the MD/MM-determined molecular conformers as templates, the 3D quantitative structure activity relationship (QSAR studies were carried out based on a set of arylmethylamine DPP IV inhibitors with the comparative molecular field analysis (CoMFA approach. The best 3D-QSAR model was constructed with good statistic values of rcv2 and R2 using PLS analyses (CoMFA: rcv2=0.660, R2=0.953. The generated 3D-QSAR model was proved to be reliable by internal and external validations. Docking studies were further performed to analyze the interaction mode between the highly potent or low potent arylmethylamine derivatives and DPP IV. Our flexible docking results also confirmed the possible bioactive conformation obtained from the 3D-QSAR model, of arylmethylamine-based DPP IV inhibitors. The 3D-QSAR model may provide information of pharmacophoric features for further design and optimization of new scaffold compounds with high inhibitory activity to DPP IV.

  18. Structural requirements of 3-carboxyl-4(1H)-quinolones as potential antimalarials from 2D and 3D QSAR analysis.

    Science.gov (United States)

    Li, Jiazhong; Li, Shuyan; Bai, Chongliang; Liu, Huanxiang; Gramatica, Paola

    2013-07-01

    Malaria is a fatal tropical and subtropical disease caused by the protozoal species Plasmodium. Many commonly available antimalarial drugs and therapies are becoming ineffective because of the emergence of multidrug resistant Plasmodium falciparum, which drives the need for the development of new antimalarial drugs. Recently, a series of 3-carboxyl-4(1H)-quinolone analogs, derived from the famous compound endochin, were reported as promising candidates for orally efficacious antimalarials. In this study, to analyze the structure-activity relationships (SAR) of these quinolones and investigate the structural requirements for antimalarial activity, the 2D multiple linear regressions (MLR) method and 3D comparative molecular field analysis (CoMFA) and comparative molecular similarity indices analysis (CoMSIA) methods are employed to evolve different QSAR models. All these models give satisfactory results with highly accurate fitting and strong external predictive abilities for chemicals not used in model development. Furthermore, the contour maps from 3D models can provide an intuitive understanding of the key structure features responsible for the antimalarial activities. In conclusion, we summarize the detailed position-specific structural requirements of these derivatives accordingly. All these results are helpful for the rational design of new compounds with higher antimalarial bioactivities.

  19. Structure/response correlations and similarity/diversity analysis by GETAWAY descriptors. 2. Application of the novel 3D molecular descriptors to QSAR/QSPR studies.

    Science.gov (United States)

    Consonni, Viviana; Todeschini, Roberto; Pavan, Manuela; Gramatica, Paola

    2002-01-01

    In a previous paper the theory of the new molecular descriptors called GETAWAY (GEometry, Topology, and Atom-Weights AssemblY) was explained. These descriptors have been proposed with the aim of matching 3D-molecular geometry, atom relatedness, and chemical information. In this paper prediction ability in structure-property correlations of GETAWAY descriptors has been tested extensively by analyzing the regressions of these descriptors for selected properties of some reference compound classes. Moreover, the general performance of the new descriptors in QSAR/QSPR has been evaluated with respect to other well-known sets of molecular descriptors.

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

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    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.

  1. Synthesis, 3D-QSAR analysis and biological evaluation of quinoxaline 1,4-di-N-oxide derivatives as antituberculosis agents.

    Science.gov (United States)

    Pan, Yuanhu; Li, Panpan; Xie, Shuyu; Tao, Yanfei; Chen, Dongmei; Dai, Menghong; Hao, Haihong; Huang, Lingli; Wang, Yulian; Wang, Liye; Liu, Zhenli; Yuan, Zonghui

    2016-08-15

    A series of quinoxaline 1,4-di-N-oxide derivatives variously substituted at C-2 position were synthesized and evaluated for in vitro antimycobacterial activity. Seventeen compounds exhibited potential activity (MIC ⩽6.25μg/mL) against Mycobacterium tuberculosis (H37Rv), in particular the compounds 3d and 3j having an MIC value of 0.39μg/mL. None of the compounds exhibited cytotoxicity when using an MTT assay in VERO cells. To further investigate the structure-activity relationship, CoMFA (q(2)=0.507, r(2)=0.923) and CoMSIA (q(2)=0.665, r(2)=0.977) models were performed on the basis of antimycobacterial activity data. The 3D-QSAR study of these compounds can provide useful information for further rational design of novel quinoxaline 1,4-di-N-oxides for treatment of tuberculosis.

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

    Indian Academy of Sciences (India)

    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.

  3. 3D-QSAR Study on Apicidin Inhibit Histone Deacetylase

    Institute of Scientific and Technical Information of China (English)

    陈海峰; 康九红; 李强; 曾宝珊; 姚小军; 范波涛; 袁身刚; Panay,A.; Doucet,J.P.

    2003-01-01

    For Histone Deacetylase (HDAC) Inhibitor, four 3D-QSAR models for four types of different activities, were constructed.The cross-valldated q2 value of CoMFA Model 1 is 0.624 and the noncross-validated r2 value is 0.939. The cross-validated q2 value of Model 2 for training set is 0.652 and the noncross-validated r2 value is 0.963. The cross-validated q2 value for Model 3 is 0.713, with noncross-validated r2 value 0.947. The crossvalidated q2 value for Model 4 is 0.566 with noncross-validated r2 value 0.959. Their predicted abilities were validated by different test sets which did not include in training set. Then the relationship between substituents and activities was analyzed by using these models and the main influence elements in different positions (positions 8 and 14) were found. The polar donor electron group of position 8 could increase the activity of inhibition of HDAC, because it could form chelation with the catalytic Zn. Suitable bulk and positive groups at position 14 are favorable to anti-HDAC activity. These models could web interpret the relationship between inhibition activity and apicidin structure affording us important information for structurebased drug design.

  4. Identification of novel histone deacetylase 1 inhibitors by combined pharmacophore modeling, 3D-QSAR analysis, in silico screening and Density Functional Theory (DFT) approaches

    Science.gov (United States)

    Choubey, Sanjay K.; Mariadasse, Richard; Rajendran, Santhosh; Jeyaraman, Jeyakanthan

    2016-12-01

    Overexpression of HDAC1, a member of Class I histone deacetylase is reported to be implicated in breast cancer. Epigenetic alteration in carcinogenesis has been the thrust of research for few decades. Increased deacetylation leads to accelerated cell proliferation, cell migration, angiogenesis and invasion. HDAC1 is pronounced as the potential drug target towards the treatment of breast cancer. In this study, the biochemical potential of 6-aminonicotinamide derivatives was rationalized. Five point pharmacophore model with one hydrogen-bond acceptor (A3), two hydrogen-bond donors (D5, D6), one ring (R12) and one hydrophobic group (H8) was developed using 6-aminonicotinamide derivatives. The pharmacophore hypothesis yielded a 3D-QSAR model with correlation-coefficient (r2 = 0.977, q2 = 0.801) and it was externally validated with (r2pred = 0.929, r2cv = 0.850 and r2m = 0.856) which reveals the statistical significance of the model having high predictive power. The model was then employed as 3D search query for virtual screening against compound libraries (Zinc, Maybridge, Enamine, Asinex, Toslab, LifeChem and Specs) in order to identify novel scaffolds which can be experimentally validated to design future drug molecule. Density Functional Theory (DFT) at B3LYP/6-31G* level was employed to explore the electronic features of the ligands involved in charge transfer reaction during receptor ligand interaction. Binding free energy (ΔGbind) calculation was done using MM/GBSA which defines the affinity of ligands towards the receptor.

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

    Directory of Open Access Journals (Sweden)

    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.

  6. 氯代苯胺对斑马鱼的急性毒性及3D-QSAR分析%Acute Toxicity of Chloroanilines to Zebra Fish and 3D-QSAR Analysis

    Institute of Scientific and Technical Information of China (English)

    李伟民; 尹大强; 李时银; 王学江; 王连生

    2002-01-01

    研究了2-氯-4-硝基苯胺、4-氯-3-硝基苯胺、2-氯-5-硝基苯胺、2,4-二氯苯胺、3,4-二氯苯胺、2,5-二氯苯胺、2,3-二氯苯胺对斑马鱼(Brachydanio rerio)的96 h急性毒性,96 h LC50分别为6.99,2.58,8.63,7.79,6.08,5.23,0.49 mg/L.运用三维定量结构活性相关模型(3D-QSAR)对这些化合物的毒性效应和构效关系进行了分析和评价,估算毒性值与实际观测值相关性较好,相关系数R2=0.907.

  7. 3D-QSAR and molecular docking studies on HIV protease inhibitors

    Science.gov (United States)

    Tong, Jianbo; Wu, Yingji; Bai, Min; Zhan, Pei

    2017-02-01

    In order to well understand the chemical-biological interactions governing their activities toward HIV protease activity, QSAR models of 34 cyclic-urea derivatives with inhibitory HIV were developed. The quantitative structure activity relationship (QSAR) model was built by using comparative molecular similarity indices analysis (CoMSIA) technique. And the best CoMSIA model has rcv2, rncv2 values of 0.586 and 0.931 for cross-validated and non-cross-validated. The predictive ability of CoMSIA model was further validated by a test set of 7 compounds, giving rpred2 value of 0.973. Docking studies were used to find the actual conformations of chemicals in active site of HIV protease, as well as the binding mode pattern to the binding site in protease enzyme. The information provided by 3D-QSAR model and molecular docking may lead to a better understanding of the structural requirements of 34 cyclic-urea derivatives and help to design potential anti-HIV protease molecules.

  8. Molecular docking and 3D-QSAR studies on inhibitors of DNA damage signaling enzyme human PARP-1.

    Science.gov (United States)

    Fatima, Sabiha; Bathini, Raju; Sivan, Sree Kanth; Manga, Vijjulatha

    2012-08-01

    Poly (ADP-ribose) polymerase-1 (PARP-1) operates in a DNA damage signaling network. Molecular docking and three dimensional-quantitative structure activity relationship (3D-QSAR) studies were performed on human PARP-1 inhibitors. Docked conformation obtained for each molecule was used as such for 3D-QSAR analysis. Molecules were divided into a training set and a test set randomly in four different ways, partial least square analysis was performed to obtain QSAR models using the comparative molecular field analysis (CoMFA) and comparative molecular similarity indices analysis (CoMSIA). Derived models showed good statistical reliability that is evident from their r², q²(loo) and r²(pred) values. To obtain a consensus for predictive ability from all the models, average regression coefficient r²(avg) was calculated. CoMFA and CoMSIA models showed a value of 0.930 and 0.936, respectively. Information obtained from the best 3D-QSAR model was applied for optimization of lead molecule and design of novel potential inhibitors.

  9. QSAR and 3D-QSAR studies of the diacyl-hydrazine derivatives containing furan rings based on the density functional theory

    Institute of Scientific and Technical Information of China (English)

    2010-01-01

    QSAR studies of 27 diacyl-hydrazine derivatives containing furan rings were conducted and compared with the DFT method and AM1-MOPAC method.q2 values of 0.61 and 0.40 validated the predictability and reliability of eq.(5) from the DFT method were higher than those of eq.(6) from the AM1-MOPAC method.The DFT-optimized conformations and ESP-fitting charges of the target compounds were also used for 3D-QSAR analysis,including CoMFA and CoMSIA.The leave-one-out cross-validation correlation coefficient and the good correlation between the predicted and experimental activities of excluded test compounds revealed that CoMFA and CoMSIA models were robust.The QSAR results were consistent with the 3D-QSAR results,indicating that the electrostatic and hydrophobic properties of the target compounds were significant to the biological activity.These models are useful tools for predicting the larvicidal activities of new compounds and designing new specific insect growth regulators.

  10. A PLS QSAR analysis using 3D generated aromatic descriptors of principal property type: Application to some dopamine D2 benzamide antagonists

    Science.gov (United States)

    Norinder, Ulf

    1993-12-01

    A simple and computationally nonintensive technique based on principal component analysis of 3D fields to derive theoretical descriptors is presented. The descriptors are then applied to a quantitative structure-activity relationship study on some dopamine D2 antagonists of benzamide type.

  11. QSAR-3D/CoMFA em compostos imídicos com atividade antinociceptiva

    Directory of Open Access Journals (Sweden)

    Maria Elena Walter

    2013-01-01

    Full Text Available Imide compounds have shown biological activity. These compounds can be easily synthesized with good yields. The objective of this paper was the rational planning of imides and sulfonamides with antinociceptive activity using the 3D-QSAR/CoMFA approach. The studies were performed using two data sets. The first set consisted of 39 cyclic imides while the second set consisted of 39 imides and 15 sulfonamides. The 3D- QSAR/CoMFA models have shown that the steric effect is important for the antinociceptive activity of imide and sulphonamide compounds. Ten new compounds with improved potential antinociceptive activity have been proposed by de novo design leapfrog simulations.

  12. 3D-QSAR Study of 7,8-Dialkyl-1,3-diaminopyrrolo-[3,2-f]Quinazolines with Anticancer Activity as DHFR Inhibitors

    Institute of Scientific and Technical Information of China (English)

    Jin-can Chen; Lan-mei Chen; Si-yan Liao; Li Qian; Kang-cheng Zheng

    2009-01-01

    A three-dimensional quantitative structure-activity relationship (3D-QSAR) study of a series of 7,8-dialkyl-1,3-diaminopyrrolo-[3,2-f]quinazolines with anticancer activity as dihydrofo-late reductase (DHFR) inhibitors was carried out by using the comparative molecular field analysis (CoMFA), on the basis of our reported 2D-QSAR of these compounds. The es-tablished 3D-QSAR model has good quality of statistics and good prediction ability; the non cross-validation correlation coefficient and the cross-validation value of this model are 0.993 and 0.619, respectively, the F value is 193.4, and the standard deviation SD is 0.208. This model indicates that the steric field factor plays a much more important role than the electrostatic one, in satisfying agreement with the published 2D-QSAR model. However, the 3D-QSAR model offers visual imagcs of the steric field and the electrostatic field. The 3D-QSAR study further suggests the following: to improve the activity, the substituent R' should be selected to be a group with an adaptive bulk like Et or i-Pr, and the substituent R should be sclected to be a larger alkyl. In particular, based on our present 3D-QSAR as well as the published 2D-QSAR, the experimentally-proposed hydrophobic binding mechanism on the receptor-binding site of the DHFR can be further explained in theory. Therefore, the QSAR studies help to further understand the "hydrophobic binding" action mechanism of this kind of compounds, and to direct the molecular design of new drugs with higher activity.

  13. 3D-QSAR study on phenoxy-alkylamine compounds of a 1-adrenoceptor antagonist

    Institute of Scientific and Technical Information of China (English)

    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.

  14. Azolium analogues as CDK4 inhibitors: Pharmacophore modeling, 3D QSAR study and new lead drug discovery

    Science.gov (United States)

    Rondla, Rohini; Padma Rao, Lavanya Souda; Ramatenki, Vishwanath; Vadija, Rajender; Mukkera, Thirupathi; Potlapally, Sarita Rajender; Vuruputuri, Uma

    2017-04-01

    The cyclin-dependent kinase 4 (CDK4) enzyme is a key regulator in cell cycle G1 phase progression. It is often overexpressed in variety of cancer cells, which makes it an attractive therapeutic target for cancer treatment. A number of chemical scaffolds have been reported as CDK4 inhibitors in the literature, and in particular azolium scaffolds as potential inhibitors. Here, a ligand based pharmacophore modeling and an atom based 3D-QSAR analyses for a series of azolium based CDK4 inhibitors are presented. A five point pharmacophore hypothesis, i.e. APRRR with one H-bond acceptor (A), one positive cationic feature (P) and three ring aromatic sites (R) is developed, which yielded an atom based 3D-QSAR model that shows an excellent correlation coefficient value- R2 = 0.93, fisher ratio- F = 207, along with good predictive ability- Q2 = 0.79, and Pearson R value = 0.89. The visual inspection of the 3D-QSAR model, with the most active and the least active ligands, demonstrates the favorable and unfavorable structural regions for the activity towards CDK4. The roles of positively charged nitrogen, the steric effect, ligand flexibility, and the substituents on the activity are in good agreement with the previously reported experimental results. The generated 3D QSAR model is further applied as query for a 3D database screening, which identifies 23 lead drug candidates with good predicted activities and diverse scaffolds. The ADME analysis reveals that, the pharmacokinetic parameters of all the identified new leads are within the acceptable range.

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

    Science.gov (United States)

    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.

  16. 3D-QSAR Study of Indol-2-yl Ethanones Derivatives as Novel Indoleamine 2,3-Dioxygenase (IDO Inhibitors

    Directory of Open Access Journals (Sweden)

    Kamlendra S. Bhadoriya

    2012-01-01

    Full Text Available 3D-QSAR approach using kNN-MFA was applied to a series of Indol-2-yl ethanones derivatives as novel IDO inhibitors. For the purpose, 22 compounds were used to develop models. To elucidate the structural properties required for IDO inhibitory activity, we report here k-nearest neighbor molecular field analysis (kNN-MFA-based 3D-QSAR model for Indol-2-yl ethanones derivatives as novel IDO inhibitors. Overall model classification accuracy was 76.27% (q2 = 0.7627, representing internal validation in training set and 79.35% (pred_r2 = 0.7935, representing external validation in test set using sphere exclusion and forward as a method of data selection and variable selection, respectively. Contour maps using this approach showed that hydrophobic and steric effects dominantly determine binding affinities. The information rendered by 3D-QSAR model may lead to a better understanding of structural requirements of IDO inhibitors and can help in the design of novel potent molecules.

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

    Science.gov (United States)

    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.

  18. Anilides and quinolones with nitrogen-bearing substituents from benzothiophene and thienothiophene series: synthesis, photochemical synthesis, cytostatic evaluation, 3D-derived QSAR analysis and DNA-binding properties.

    Science.gov (United States)

    Aleksić, Maja; Bertoša, Branimir; Nhili, Raja; Depauw, Sabine; Martin-Kleiner, Irena; David-Cordonnier, Marie-Hélène; Tomić, Sanja; Kralj, Marijeta; Karminski-Zamola, Grace

    2014-01-01

    A series of new anilides (2a-c, 4-7, 17a-c, 18) and quinolones (3a-b, 8a-b, 9a-b, 10-15, 19) with nitrogen-bearing substituents from benzo[b]thiophene and thieno[2,3-c]thiophene series are prepared. Benzo[b]thieno[2,3-c]- and thieno[3',2':4,5]thieno[2,3-c]quinolones (3a-b, 8a-b) are synthesized by the reaction of photochemical dehydrohalogenation from corresponding anilides. Anilides and quinolones were tested for the antiproliferative activity. Fused quinolones bearing protonated aminium group, quaternary ammonium group, N-methylated and protonated aminium group, amino and protonated amino group (8a, 9b, 10-12) showed very prominent anticancer activity, whereby the hydrochloride salt of N',N'-dimethylaminopropyl-substituted quinolone (14) was the most active one, having the IC50 concentration at submicromolar range in accordance with previous QSAR predictions. On the other hand, flexible anilides were among the less active. Chemometric analysis of investigated compounds was performed. 3D-derived QSAR analysis identified solubility, metabolitic stability and the possibility of the compound to be ionized at pH 4-8 as molecular properties that are positively correlated with anticancer activity of investigated compounds, while molecular flexibility, polarizability and sum of hydrophobic surface areas were found to be negatively correlated. Anilides 2a-b, 4-7 and quinolones 3a-b, 8a-b, 9b and 10-14 were evaluated for DNA binding propensities and topoisomerases I/II inhibition as part of their mechanism of action. Among the anilides, only compound 7 presented some DNA binding propensity whereas the quinolones 8b, 9b and 10-14 intercalate in the DNA base pairs, compounds 8b, 9b and 14 being the most efficient ones. The strongest DNA intercalators, compounds 8b, 9b and 14, were clearly distinguished from the other compounds according to their molecular descriptors by the PCA and PLS analysis.

  19. 3D-QSAR and Docking Studies of Pyrido[2,3-d]pyrimidine Derivatives as Weel Inhibitors

    Institute of Scientific and Technical Information of China (English)

    Guo-hua Zeng; Wen-juan Wu; Rong Zhang; Jun Sun; Wen-guo Xie; Yong Shen

    2012-01-01

    In order to investigate the inhibiting mechanism and obtain some helpful information for designing functional inhibitors against Weel,three-dimensional quantitative structure-activity relationship (3D-QSAR) and docking studies have been performed on 45 pyrido[2,3-d] pyrimidine derivatives acting as Weel inhibitors.Two optimal 3D-QSAR models with significant statistical quality and satisfactory predictive ability were established,including the CoMFA model (q2=0.707,R2=0.964) and CoMSIA model (q2=0.645,R2=0.972).The external validation indicated that both CoMFA and CoMSIA models were quite robust and had high predictive power with the predictive correlation coefficient values of 0.707 and 0.794,essential parameter r2m values of 0.792 and 0.826,the leave-one-out r2m(LOO) values of 0.781 and 0.809,r2m(overall) values of 0.787 and 0.810,respectively.Moreover,the appropriate binding orientations and conformations of these compounds interacting with Weel were revealed by the docking studies.Based on the CoMFA and CoMSIA contour maps and docking analyses,several key structural requirements of these compounds responsible for inhibitory activity were identified as follows:simultaneously introducing high electropositive groups to the substituents R1 and R5 may increase the activity,the substituent R2 should be smaller bulky and higher electronegative,moderate-size and strong electron-withdrawing groups for the substituent R3 is advantageous to the activity,but the substituent X should be medium-size and hydrophilic.These theoretical results help to understand the action mechanism and design novel potential Weel inhibitors.

  20. 3D-QSAR Studies of Dimethoxyphenoxyphenoxy pyrimidines and Analogues

    Institute of Scientific and Technical Information of China (English)

    李爱秀; 王瑾玲; 苏华庆; 缪方明

    2000-01-01

    Three-dimensional quantitative structure-activity relationships (3DQSAR) of a series of dimethoxyphenoxyphenoxypyrimidines and analogues which are known to be photosystem Ⅱ (PS Ⅱ )inhibitors have been studied using comparative molecular field analysis (CoMFA) method. The results suggest that the steric and electronic properties of substitutes at m-position on the end phenyl ring have important influence on the Hill reaction inhibition.

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

    Directory of Open Access Journals (Sweden)

    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.

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

    Directory of Open Access Journals (Sweden)

    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.

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

    Institute of Scientific and Technical Information of China (English)

    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.

  4. Genotoxicity of quinolones: substituents contribution and transformation products QSAR evaluation using 2D and 3D models.

    Science.gov (United States)

    Li, Min; Wei, Dongbin; Zhao, Huimin; Du, Yuguo

    2014-01-01

    The genotoxicity of 21 quinolones antibiotics was determined using SOS/umu assay. Some quinolones exhibited high genotoxicity, and the chemical substituent on quinolone ring significantly affected genotoxicity. To establish the relationship between genotoxicity and substituent, a 2D-QSAR model based on quantum chemical parameters was developed. Calculation suggested that both steric and electrostatic properties were correlated well with genotoxicity. Furthermore, the specific effect on three key active sites (1-, 7- and 8-positions) of quinolone ring was investigated using a 3D-QSAR (comparative molecular field analysis, CoMFA) method. From our modeling, the genotoxicity increased when substituents had: (1) big volume and/or positive charge at 1-position; (2) negative charge at 7-position; and (3) small volume and/or negative charge at 8-position. The developed QSAR models were applicable to estimate genotoxicity of quinolones antibiotics and their transformation products. It is noted that some of the transformation products exhibited higher genotoxicity comparing to their precursor (e.g., ciprofloxacin). This study provided an alternative way to understand the molecule genotoxicity of quinolones derivatives, as well as to evaluate their potential environmental risks.

  5. Recent Advances in Fragment-Based QSAR and Multi-Dimensional QSAR Methods

    Directory of Open Access Journals (Sweden)

    Kyaw Zeyar Myint

    2010-10-01

    Full Text Available This paper provides an overview of recently developed two dimensional (2D fragment-based QSAR methods as well as other multi-dimensional approaches. In particular, we present recent fragment-based QSAR methods such as fragment-similarity-based QSAR (FS-QSAR, fragment-based QSAR (FB-QSAR, Hologram QSAR (HQSAR, and top priority fragment QSAR in addition to 3D- and nD-QSAR methods such as comparative molecular field analysis (CoMFA, comparative molecular similarity analysis (CoMSIA, Topomer CoMFA, self-organizing molecular field analysis (SOMFA, comparative molecular moment analysis (COMMA, autocorrelation of molecular surfaces properties (AMSP, weighted holistic invariant molecular (WHIM descriptor-based QSAR (WHIM, grid-independent descriptors (GRIND-based QSAR, 4D-QSAR, 5D-QSAR and 6D-QSAR methods.

  6. Entwicklung, Validierung und Anwendung einer neuen translations- und rotationsinvarianten 3D-QSAR-Methodik

    OpenAIRE

    Stiefl, Nikolaus Johannes

    2004-01-01

    Die vorliegende Arbeit beschreibt die Entwicklung und Validierung der neuartigen 3D-QSAR Technik Mapping Property Distributions of Molecular Surfaces (MaP). Die Methode ist gegenüber Translation und Rotation invariant, d. h. eine Überlagerung der Moleküle, wie sie zum Beispiel für CoMFA nötig ist, entfällt. MaP basiert auf der Charakterisierung der Moleküle nach ihrer Fähigkeit Wasserstoffbrücken auszubilden, sowie ihrer Hydrophobie / Hydrophilie. Dabei werden jedoch nicht nur die atombasiert...

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

    Directory of Open Access Journals (Sweden)

    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.

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

    Institute of Scientific and Technical Information of China (English)

    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.

  9. Chemosensitizing acridones: in vitro calmodulin dependent cAMP phosphodiesterase inhibition, docking, pharmacophore modeling and 3D QSAR studies.

    Science.gov (United States)

    Rajendra Prasad, V V S; Deepak Reddy, G; Appaji, D; Peters, G J; Mayur, Y C

    2013-03-01

    Calmodulin inhibitors have proved to play a significant role in sensitizing MDR cancer cells by interfering with cellular drug accumulation. The present investigation focuses on the evaluation of in vitro inhibitory efficacy of chloro acridones against calmodulin dependent cAMP phosphodiesterase (PDE1c). Moreover, molecular docking of acridones was performed with PDE1c in order to identify the possible protein ligand interactions and results thus obtained were compared with in vitro data. In addition an efficient pharmacophore model was developed from a set of 38 chemosensitizing acridones effective against doxorubicin resistant (HL-60/DX) cancer cell lines. Pharmacophoric features such as one hydrogen bond acceptor, one hydrophobic region, a positive ion group and three aromatic rings i.e., AHPRRR have been identified. Ligand based 3D-QSAR was also performed by employing partial least square regression analysis.

  10. 3D-QSAR Studies on a Series of Dihydroorotate Dehydrogenase Inhibitors: Analogues of the Active Metabolite of Leflunomide

    Directory of Open Access Journals (Sweden)

    Hong-Guang Du

    2011-05-01

    Full Text Available The active metabolite of the novel immunosuppressive agent leflunomide has been shown to inhibit the enzyme dihydroorotate dehydrogenase (DHODH. This enzyme catalyzes the fourth step in de novo pyrimidine biosynthesis. Self-organizing molecular field analysis (SOMFA, a simple three-dimensional quantitative structure-activity relationship (3D-QSAR method is used to study the correlation between the molecular properties and the biological activities of a series of analogues of the active metabolite. The statistical results, cross-validated rCV2 (0.664 and non cross-validated r2 (0.687, show a good predictive ability. The final SOMFA model provides a better understanding of DHODH inhibitor-enzyme interactions, and may be useful for further modification and improvement of inhibitors of this important enzyme.

  11. 3D QSAR modeling of 4-nerolidylcatechol derivatives and virtual screening for identification of potent plasmodium inhibitor

    Directory of Open Access Journals (Sweden)

    Dhrubajyoti Gogoi

    2014-08-01

    Full Text Available The present study was aim to develop a three dimensional quantitative structure–activity relationships (3D QSAR model based on the structure of 4-nerolidylcatechol (IC50=0.67 µM, a novel plant derived Plasmodium inhibitor and its derivatives for identification of efficient antimalarial lead. A statisti-cally validated Partial Least-Squares (PLS based Molecular Field Analysis (MFA model was built up using the training set of eight 4-nerolidylcatechol derivatives and their diverse conformers. A statistically reliable model with good predictive power (cross-validated correlation coefficient q2=0.769 was obtained. Hence, the generated model was used to screen a library of 30,000 compounds of chembridge database (http://www.chembridge.com. Results of drug likeness prediction and ADMET study has suggested six compounds as potential antimalarial/plasmodial lead.

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

    Directory of Open Access Journals (Sweden)

    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.

  13. Molecular docking and 3D-QSAR studies on triazolinone and pyridazinone, non-nucleoside inhibitor of HIV-1 reverse transcriptase.

    Science.gov (United States)

    Sivan, Sree Kanth; Manga, Vijjulatha

    2010-06-01

    Nonnucleoside reverse transcriptase inhibitors (NNRTIs) are allosteric inhibitors of the HIV-1 reverse transcriptase. Recently a series of Triazolinone and Pyridazinone were reported as potent inhibitors of HIV-1 wild type reverse transcriptase. In the present study, docking and 3D quantitative structure activity relationship (3D QSAR) studies involving comparative molecular field analysis (CoMFA) and comparative molecular similarity indices analysis (CoMSIA) were performed on 31 molecules. Ligands were built and minimized using Tripos force field and applying Gasteiger-Hückel charges. These ligands were docked into protein active site using GLIDE 4.0. The docked poses were analyzed; the best docked poses were selected and aligned. CoMFA and CoMSIA fields were calculated using SYBYL6.9. The molecules were divided into training set and test set, a PLS analysis was performed and QSAR models were generated. The model showed good statistical reliability which is evident from the r2 nv, q2 loo and r2 pred values. The CoMFA model provides the most significant correlation of steric and electrostatic fields with biological activities. The CoMSIA model provides a correlation of steric, electrostatic, acceptor and hydrophobic fields with biological activities. The information rendered by 3D QSAR model initiated us to optimize the lead and design new potential inhibitors.

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

    Science.gov (United States)

    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.

  15. 3D-QSAR study of 20 (S)-camptothecin analogs

    Institute of Scientific and Technical Information of China (English)

    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.

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

    Energy Technology Data Exchange (ETDEWEB)

    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.

  17. Global 3D-QSAR methods: MS-WHIM and autocorrelation

    Science.gov (United States)

    Gancia, Emanuela; Bravi, Gianpaolo; Mascagni, Paolo; Zaliani, Andrea

    2000-04-01

    The recently proposed MS-WHIM indices, a set of theoretical descriptors containing information about size, shape and electrostatic distribution of a molecule, have been further investigated. The main objectives of this work were: (i) to confirm the descriptive power of MS-WHIM in modelling specific biological interactions, (ii) to analyse the dependence of MS-WHIM on the type of atomic charges used for computing electrostatic potential and (iii) to compare the performances of MS-WHIM with those provided by other global 3D molecular descriptors. The spatial autocorrelation of atomic and molecular surface properties were selected for comparison purposes. WHIM-based and autocorrelation-based vectors were calculated for two molecular sets from the literature, namely a series of 18 HIV-1 reverse transcriptase inhibitors and a set of 36 sulphonamide endothelin inhibitors. PLS was adopted to derive statistical predictive models that were validated by means of cross-validation. The reported results confirmed that MS-WHIM indices are able to provide meaningful statistical correlations with biological activity. MS-WHIM descriptors are sensitive to the type of partial atomic charges applied and improved models were obtained using more accurate charges. Moreover for both the datasets, MS-WHIM results, in terms of fitting and predictive power of PLS models, were superior to those from autocorrelation. Finally, the strengths/weaknesses of global 3D-QSAR descriptors over local CoMFA-like methods, as well as the main differences between WHIM-based and autocorrelation-based vectors, are discussed.

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

    Science.gov (United States)

    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.

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

    Directory of Open Access Journals (Sweden)

    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.

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

    DEFF Research Database (Denmark)

    Hauser, Alexander Sebastian

    2014-01-01

    -dimensional quantitative structure–activity relationship (3D-QSAR) studies were carried out on a series of pyridine-2-carboxylic acid thiazol-2-ylamide-based MetAP inhibitors using comparative molecular field analysis (CoMFA) and comparative molecular similarity indices analysis (CoMSIA) techniques. The models were...... complexes, four new pyridine-2-carboxylic acid thiazol-2-ylamide analogs were designed. These analogs exhibit significantly better predicted activity than the reported molecules. The present work has implications for the development of novel antibiotics as potent MetAP inhibitors....

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

    Directory of Open Access Journals (Sweden)

    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

  2. 3D-QSAR modelling dataset of bioflavonoids for predicting the potential modulatory effect on P-glycoprotein activity

    Directory of Open Access Journals (Sweden)

    Pathomwat Wongrattanakamon

    2016-12-01

    Full Text Available 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, R2=0.927, Radj2=0.900, SEE=0.197, F=33.849 and q2=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.

  3. 2D-QSAR Using MLR and 3D-QSAR Using CoMSIA Studies on the Toxicity of Aromatic Hydrocarbons on Larval Sinonvaculina Constricta

    Institute of Scientific and Technical Information of China (English)

    WANG Cui-Hua; JIANG Mei; LI Xiao-Lin; SHEN Xin-Qiang; YU Hong-Xia; WU Yang

    2012-01-01

    Aromatic hydrocarbons,one of the persistent organic pollutants(POPs),has been usually found in mussels,accumulated for their hard mobility and activities in harbours and estuaries.In this study,based on the 96 hr-LC50 of 12 aromatic hydrocarbons with larval sinonvaculina constricta,three-dimensional quantitative structure-activity relationship(3D-QSAR) technique:comparative molecular similarity indices analysis(CoMSIA) and 2D-QSAR technique:multiple linear regression(MLR) were described to obtain more detailed insight into the structure-activity relationships between the molecular structure and bio-activity.The results show the MLR model based on density functional theory(DFT) calculation carried out at the B3LYP/6-311** level with Gaussian 03 program yielded a very good correlation with a coefficient squared R2 of 0.716 and a cross-validated Q2 of 0.874.The dipole moment and enthalpy,as the thermodynamic parameters,were two important factors influencing pLC50.Correspondingly,CoMSIA based on the partial least-squares(PLS) methodology with steric,electrostatic,hydrophobic,H-bond donor and acceptor fields contributing simultaneously were employed and the values of R2 and the cross validation with leave-One-Out(LOO) Q2LOO were 0.585 and 0.990,respectively,which reveals the structure features,such as the electronegative substituent(nitro-group),hydrophobic groups(the benzene ring) and H-bond(nitro-group),related to the toxicity.The results of 2D-QSAR employing MLR model and 3D-QSAR employing CoMSIA model provide the useful information for predicting the toxicity of other aromatic hydrocarbons by comparing the molecular structures of similar compounds.

  4. Predictive Modeling of Antioxidant Coumarin Derivatives Using Multiple Approaches: Descriptor-Based QSAR, 3D-Pharmacophore Mapping, and HQSAR

    Directory of Open Access Journals (Sweden)

    Indrani MITRA

    2016-09-01

    Full Text Available The inability of the systemic antioxidants to alleviate the exacerbation of free radical formation from metabolic outputs and environmental pollutants claims an urgent demand for the identification and design of new chemical entities with potent antioxidant activity. In the present work, different QSAR approaches have been utilized for identifying the essential structural attributes imparting a potential antioxidant activity profile of the coumarin derivatives. The descriptor-based QSAR model provides a quantitative outline regarding the structural prerequisites of the molecules, while 3D pharmacophore and HQSAR models emphasize the favourable spatial arrangement of the various chemical features and the crucial molecular fragments, respectively. All the models infer that the fused benzene ring and the oxygen atom of the pyran ring constituting the parent coumarin nucleus capture the prime pharmacophoric features, imparting superior antioxidant activity to the molecules. The developed models may serve as indispensable query tools for screening untested molecules belonging to the class of coumarin derivatives.

  5. Receptor-based modeling and 3D-QSAR for a quantitative production of the butyrylcholinesterase inhibitors based on genetic algorithm.

    Science.gov (United States)

    Zaheer-ul, Haq; Uddin, Reaz; Yuan, Hongbin; Petukhov, Pavel A; Choudhary, M Iqbal; Madura, Jeffry D

    2008-05-01

    Three-dimensional quantitative structure-activity relationship (3D-QSAR) models have been constructed using the comparative molecular field analysis (CoMFA) and comparative molecular similarity indices analysis (CoMSIA) for a series of structurally related steroidal alkaloids as butyrylcholinesterase (BuChE) inhibitors. Docking studies were employed to position the inhibitors into the BuChE active site to determine the most probable binding mode. The strategy was to explore multiple inhibitor conformations in producing a more reliable 3D-QSAR model. These multiple conformations were derived using the FlexS program. The conformation selection step for CoMFA was done by genetic algorithm. The genetic algorithm based CoMFA approach was found to be the best. Both CoMFA and CoMSIA yielded significant cross-validated q(2) values of 0.701 and 0.627 and the r(2) values of 0.979 and 0.982, respectively. These statistically significant models were validated by a test set of five compounds. Comparison of CoMFA and CoMSIA contour maps helped to identify structural requirements for the inhibitors and serves as a basis for the design of the next generation of the inhibitor analogues. The results demonstrate that the combination of ligand-based and receptor-based modeling with use of a genetic algorithm is a powerful approach to build 3D-QSAR models. These data can be used for the lead optimization process with respect to inhibition enhancement which is important for the drug discovery and development for Alzheimer's disease.

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

    Directory of Open Access Journals (Sweden)

    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

  7. Mechanistic Insights into the Binding of Class IIa HDAC Inhibitors toward Spinocerebellar Ataxia Type-2: A 3D-QSAR and Pharmacophore Modeling Approach.

    Science.gov (United States)

    Sinha, Siddharth; Goyal, Sukriti; Somvanshi, Pallavi; Grover, Abhinav

    2016-01-01

    Spinocerebellar ataxia (SCA-2) type-2 is a rare neurological disorder among the nine polyglutamine disorders, mainly caused by polyQ (CAG) trinucleotide repeats expansion within gene coding ataxin-2 protein. The expanded trinucleotide repeats within the ataxin-2 protein sequesters transcriptional cofactors i.e., CREB-binding protein (CBP), Ataxin-2 binding protein 1 (A2BP1) leading to a state of hypo-acetylation and transcriptional repression. Histone de-acetylases inhibitors (HDACi) have been reported to restore transcriptional balance through inhibition of class IIa HDAC's, that leads to an increased acetylation and transcription as demonstrated through in-vivo studies on mouse models of Huntington's. In this study, 61 di-aryl cyclo-propanehydroxamic acid derivatives were used for developing three dimensional (3D) QSAR and pharmacophore models. These models were then employed for screening and selection of anti-ataxia compounds. The chosen QSAR model was observed to be statistically robust with correlation coefficient (r(2)) value of 0.6774, cross-validated correlation coefficient (q(2)) of 0.6157 and co-relation coefficient for external test set (pred_r(2)) of 0.7570. A high F-test value of 77.7093 signified the robustness of the model. Two potential drug leads ZINC 00608101 (SEI) and ZINC 00329110 (ACI) were selected after a coalesce procedure of pharmacophore based screening using the pharmacophore model ADDRR.20 and structural analysis using molecular docking and dynamics simulations. The pharmacophore and the 3D-QSAR model generated were further validated for their screening and prediction ability using the enrichment factor (EF), goodness of hit (GH), and receiver operating characteristics (ROC) curve analysis. The compounds SEI and ACI exhibited a docking score of -10.097 and -9.182 kcal/mol, respectively. An evaluation of binding conformation of ligand-bound protein complexes was performed with MD simulations for a time period of 30 ns along with free

  8. Mechanistic Insights into the Binding of Class IIa HDAC Inhibitors toward Spinocerebellar Ataxia Type-2: A 3D-QSAR and Pharmacophore Modeling Approach

    Science.gov (United States)

    Sinha, Siddharth; Goyal, Sukriti; Somvanshi, Pallavi; Grover, Abhinav

    2017-01-01

    Spinocerebellar ataxia (SCA-2) type-2 is a rare neurological disorder among the nine polyglutamine disorders, mainly caused by polyQ (CAG) trinucleotide repeats expansion within gene coding ataxin-2 protein. The expanded trinucleotide repeats within the ataxin-2 protein sequesters transcriptional cofactors i.e., CREB-binding protein (CBP), Ataxin-2 binding protein 1 (A2BP1) leading to a state of hypo-acetylation and transcriptional repression. Histone de-acetylases inhibitors (HDACi) have been reported to restore transcriptional balance through inhibition of class IIa HDAC's, that leads to an increased acetylation and transcription as demonstrated through in-vivo studies on mouse models of Huntington's. In this study, 61 di-aryl cyclo-propanehydroxamic acid derivatives were used for developing three dimensional (3D) QSAR and pharmacophore models. These models were then employed for screening and selection of anti-ataxia compounds. The chosen QSAR model was observed to be statistically robust with correlation coefficient (r2) value of 0.6774, cross-validated correlation coefficient (q2) of 0.6157 and co-relation coefficient for external test set (pred_r2) of 0.7570. A high F-test value of 77.7093 signified the robustness of the model. Two potential drug leads ZINC 00608101 (SEI) and ZINC 00329110 (ACI) were selected after a coalesce procedure of pharmacophore based screening using the pharmacophore model ADDRR.20 and structural analysis using molecular docking and dynamics simulations. The pharmacophore and the 3D-QSAR model generated were further validated for their screening and prediction ability using the enrichment factor (EF), goodness of hit (GH), and receiver operating characteristics (ROC) curve analysis. The compounds SEI and ACI exhibited a docking score of −10.097 and −9.182 kcal/mol, respectively. An evaluation of binding conformation of ligand-bound protein complexes was performed with MD simulations for a time period of 30 ns along with free

  9. Identification of curcumin derivatives as human glyoxalase I inhibitors: A combination of biological evaluation, molecular docking, 3D-QSAR and molecular dynamics simulation studies.

    Science.gov (United States)

    Yuan, Minggui; Luo, Minxian; Song, Yao; Xu, Qiu; Wang, Xiaofeng; Cao, Yi; Bu, Xianzhang; Ren, Yanliang; Hu, Xiaopeng

    2011-02-01

    Several recent developments suggest that the human glyoxalase I (GLO I) is a potential target for anti-tumor drug development. In present study, a series of curcumin derivatives with high inhibitory activity against human GLO I were discovered. Inhibition constant (K(i)) values of compounds 8, 9, 10, 11 and 13 to GLO I are 4.600μM, 2.600μM, 3.200μM, 3.600μM and 3.600μM, respectively. To elucidate the structural features of potent inhibitors, docking-based three-dimensional structure-activity relationship (3D-QSAR) analyses were performed. Satisfactory agreement between experiment and theory suggests that comparative molecular similarity index analysis (CoMSIA) modeling exhibit much better correlation and predictive power. The cross-validated q(2) value is 0.638 while no-validation r(2) value is 0.930. Integrated with docking-based 3D-QSAR CoMSIA modeling, molecular surface property (electrostatic and steric) mapping and molecular dynamics simulation, a set of receptor-ligand binding models and bio-affinity predictive models for rational design of more potent inhibitors of GLO I are established.

  10. 3D-QSAR and Docking Studies of a Series of β-Carboline Derivatives as Antitumor Agents of PLK1

    Directory of Open Access Journals (Sweden)

    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.

  11. Synthesis, biological evaluation and 3D-QSAR studies of new chalcone derivatives as inhibitors of human P-glycoprotein.

    Science.gov (United States)

    Parveen, Zahida; Brunhofer, Gerda; Jabeen, Ishrat; Erker, Thomas; Chiba, Peter; Ecker, Gerhard F

    2014-04-01

    P-glycoprotein (P-gp) is an ATP-dependent multidrug resistance efflux transporter that plays an important role in anticancer drug resistance and in pharmacokinetics of medicines. Despite a large number of structurally and functionally diverse compounds, also flavonoids and chalcones have been reported as inhibitors of P-gp. The latter share some similarity with the well studied class of propafenones, but do not contain a basic nitrogen atom. Furthermore, due to their rigidity, they are suitable candidates for 3D-QSAR studies. In this study, a set of 22 new chalcone derivatives were synthesized and evaluated in a daunomycin efflux inhibition assay using the CCRF.CEM.VCR1000 cell line. The compound 10 showed the highest activity (IC50=42nM), which is one order of magnitude higher than the activity for an equilipohillic propafenone analogue. 2D- and 3D-QSAR studies indicate the importance of H-bond acceptors, methoxy groups, hydrophobic groups as well as the number of rotatable bonds as pharmacophoric features influencing P-gp inhibitory activity.

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

    Directory of Open Access Journals (Sweden)

    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.

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

    Science.gov (United States)

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

    2016-06-23

    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.

  14. 2D-QSAR and 3D-QSAR/CoMSIA Studies on a Series of (R)-2-((2-(1H-Indol-2-yl)ethyl)amino)-1-Phenylethan-1-ol with Human β₃-Adrenergic Activity.

    Science.gov (United States)

    Apablaza, Gastón; Montoya, Luisa; Morales-Verdejo, Cesar; Mellado, Marco; Cuellar, Mauricio; Lagos, Carlos F; Soto-Delgado, Jorge; Chung, Hery; Pessoa-Mahana, Carlos David; Mella, Jaime

    2017-03-05

    The β₃ adrenergic receptor is raising as an important drug target for the treatment of pathologies such as diabetes, obesity, depression, and cardiac diseases among others. Several attempts to obtain selective and high affinity ligands have been made. Currently, Mirabegron is the only available drug on the market that targets this receptor approved for the treatment of overactive bladder. However, the FDA (Food and Drug Administration) in USA and the MHRA (Medicines and Healthcare products Regulatory Agency) in UK have made reports of potentially life-threatening side effects associated with the administration of Mirabegron, casting doubts on the continuity of this compound. Therefore, it is of utmost importance to gather information for the rational design and synthesis of new β₃ adrenergic ligands. Herein, we present the first combined 2D-QSAR (two-dimensional Quantitative Structure-Activity Relationship) and 3D-QSAR/CoMSIA (three-dimensional Quantitative Structure-Activity Relationship/Comparative Molecular Similarity Index Analysis) study on a series of potent β₃ adrenergic agonists of indole-alkylamine structure. We found a series of changes that can be made in the steric, hydrogen-bond donor and acceptor, lipophilicity and molar refractivity properties of the compounds to generate new promising molecules. Finally, based on our analysis, a summary and a regiospecific description of the requirements for improving β₃ adrenergic activity is given.

  15. 2D-QSAR and 3D-QSAR/CoMSIA Studies on a Series of (R-2-((2-(1H-Indol-2-ylethylamino-1-Phenylethan-1-ol with Human β3-Adrenergic Activity

    Directory of Open Access Journals (Sweden)

    Gastón Apablaza

    2017-03-01

    Full Text Available The β3 adrenergic receptor is raising as an important drug target for the treatment of pathologies such as diabetes, obesity, depression, and cardiac diseases among others. Several attempts to obtain selective and high affinity ligands have been made. Currently, Mirabegron is the only available drug on the market that targets this receptor approved for the treatment of overactive bladder. However, the FDA (Food and Drug Administration in USA and the MHRA (Medicines and Healthcare products Regulatory Agency in UK have made reports of potentially life-threatening side effects associated with the administration of Mirabegron, casting doubts on the continuity of this compound. Therefore, it is of utmost importance to gather information for the rational design and synthesis of new β3 adrenergic ligands. Herein, we present the first combined 2D-QSAR (two-dimensional Quantitative Structure-Activity Relationship and 3D-QSAR/CoMSIA (three-dimensional Quantitative Structure-Activity Relationship/Comparative Molecular Similarity Index Analysis study on a series of potent β3 adrenergic agonists of indole-alkylamine structure. We found a series of changes that can be made in the steric, hydrogen-bond donor and acceptor, lipophilicity and molar refractivity properties of the compounds to generate new promising molecules. Finally, based on our analysis, a summary and a regiospecific description of the requirements for improving β3 adrenergic activity is given.

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

    Energy Technology Data Exchange (ETDEWEB)

    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.

  17. Studies of new fused benzazepine as selective dopamine D3 receptor antagonists using 3D-QSAR, molecular docking and molecular dynamics.

    Science.gov (United States)

    Liu, Jing; Li, Yan; Zhang, Shuwei; Xiao, Zhengtao; Ai, Chunzhi

    2011-02-18

    In recent years, great interest has been paid to the development of compounds with high selectivity for central dopamine (DA) D3 receptors, an interesting therapeutic target in the treatment of different neurological disorders. In the present work, based on a dataset of 110 collected benzazepine (BAZ) DA D3 antagonists with diverse kinds of structures, a variety of in silico modeling approaches, including comparative molecular field analysis (CoMFA), comparative similarity indices analysis (CoMSIA), homology modeling, molecular docking and molecular dynamics (MD) were carried out to reveal the requisite 3D structural features for activity. Our results show that both the receptor-based (Q(2) = 0.603, R(2) (ncv) = 0.829, R(2) (pre) = 0.690, SEE = 0.316, SEP = 0.406) and ligand-based 3D-QSAR models (Q(2) = 0.506, R(2) (ncv) =0.838, R(2) (pre) = 0.794, SEE = 0.316, SEP = 0.296) are reliable with proper predictive capacity. In addition, a combined analysis between the CoMFA, CoMSIA contour maps and MD results with a homology DA receptor model shows that: (1) ring-A, position-2 and R(3) substituent in ring-D are crucial in the design of antagonists with higher activity; (2) more bulky R(1) substituents (at position-2 of ring-A) of antagonists may well fit in the binding pocket; (3) hydrophobicity represented by MlogP is important for building satisfactory QSAR models; (4) key amino acids of the binding pocket are CYS101, ILE105, LEU106, VAL151, PHE175, PHE184, PRO254 and ALA251. To our best knowledge, this work is the first report on 3D-QSAR modeling of the new fused BAZs as DA D3 antagonists. These results might provide information for a better understanding of the mechanism of antagonism and thus be helpful in designing new potent DA D3 antagonists.

  18. 3D-QSAR study and design of 4-hydroxyamino α-pyranone carboxamide analogues as potential anti-HCV agents

    Science.gov (United States)

    Li, Wenlian; Xiao, Faqi; Zhou, Mingming; Jiang, Xuejin; Liu, Jun; Si, Hongzong; Xie, Meng; Ma, Xiuting; Duan, Yunbo; Zhai, Honglin

    2016-09-01

    The three dimensional-quantitative structure activity relationship (3D-QSAR) study was performed on a series of 4-hydroxyamino α-pyranone carboxamide analogues using comparative molecular similarity indices analysis (COMSIA). The purpose of the present study was to develop a satisfactory model providing a reliable prediction based on 4-hydroxyamino α-pyranone carboxamide analogues as anti-HCV (hepatitis C virus) inhibitors. The statistical results and the results of validation of this optimum COMSIA model were satisfactory. Furthermore, analysis of the contour maps helped to provide guidelines for finding structural requirement. Therefore, the satisfactory results from this study may provide useful guidelines for drug development of anti-HCV inhibitors.

  19. Evaluation and comparison of 3D-QSAR CoMSIA models for CDK1, CDK5, and GSK-3 inhibition by paullones

    DEFF Research Database (Denmark)

    Kunick, Conrad; Lauenroth, Kathrin; Wieking, Karen;

    2004-01-01

    With a view to the rational design of selective GSK-3beta inhibitors, 3D-QSAR CoMSIA models were developed for the inhibition of the three serine/threonine kinases CDK1/cyclin B, CDK5/p25, and GSK-3beta by compounds from the paullone inhibitor family. The models are based on the kinase inhibition...

  20. 3D-QSAR Design of New Escitalopram Derivatives for the Treatment of Major Depressive Disorders

    Science.gov (United States)

    Avram, Speranta; Buiu, Catalin; Duda-Seiman, Daniel M.; Duda-Seiman, Corina; Mihailescu, Dan

    2010-01-01

    Antidepressants are psychiatric agents used for the treatment of different types of depression being at present amongst the most commonly prescribed drug, while their effectiveness and adverse effects are the subject of many studies and competing claims. Having studied five QSAR models predicting the biological activities of 18 antidepressants, already approved for clinical treatment, in interaction with the serotonin transporter (SERT), we attempted to establish the membrane ions’ contributions (sodium, potassium, chlorine and calcium) supplied by donor/acceptor hydrogen bond character and electrostatic field to the antidepressant activity. Significant cross-validated correlation q2 (0.5–0.6) and the fitted correlation r2 (0.7–0.82) coefficients were obtained indicating that the models can predict the antidepressant activity of compounds. Moreover, considering the contribution of membrane ions (sodium, potassium and calcium) and hydrogen bond donor character, we have proposed a library of 24 new escitalopram structures, some of them probably with significantly improved antidepressant activity in comparison with the parent compound. PMID:21179345

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

    Institute of Scientific and Technical Information of China (English)

    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.

  2. 3D-QSAR and docking studies on 1-hydroxypyridin-2-one compounds as mutant isocitrate dehydrogenase 1 inhibitors

    Science.gov (United States)

    Wang, Zhenya; Chang, Yiqun; Han, Yushui; Liu, Kangjia; Hou, Jinsong; Dai, Chengli; Zhai, Yuanhao; Guo, Jialiang; Sun, Pinghua; Lin, Jing; Chen, Weimin

    2016-11-01

    Mutation of isocitrate dehydrogenase 1 (IDH1) which is frequently found in certain cancers such as glioma, sarcoma and acute myeloid leukemia, has been proven to be a potent drug target for cancer therapy. In silico methodologies such as 3D-QSAR and molecular docking were performed to explore compounds with better mutant isocitrate dehydrogenase 1 (MIDH1) inhibitory activity using a series of 40 newly reported 1-hydroxypyridin-2-one compounds as MIDH1 inhibitors. The satisfactory CoMFA and CoMSIA models obtained after internal and external cross-validation gave q2 values of 0.691 and 0.535, r2 values of 0.984 and 0.936, respectively. 3D contour maps generated from CoMFA and CoMSIA along with the docking results provided information about the structural requirements for better MIDH1 inhibitory activity. Based on the structure-activity relationship, 17 new potent molecules with better predicted activity than the most active compound in the literature have been designed.

  3. QSAR analysis for some β-carboline derivatives as anti-tumor

    Directory of Open Access Journals (Sweden)

    Ravindra Kumar Chourasiya

    2016-09-01

    Full Text Available β-Carboline moieties are important structural subunits which occur as components of many biologically interesting molecules for antitumor activity. Quantitative structure–activity relationship (QSAR studies have been performed on β-carboline derivatives to explore the structural necessities for antitumor activity. 3D QSAR studies were done using V-Life Sciences MDS 3.0 drug designing module to explain the structural requirements for the anti-tumor activity. The 3D-QSAR was performed using the Step Wise K Nearest Neighbour Molecular Field Analysis [(SW kNN MFA] technique with the partial least-square (PLS method on a database. Obtained best 3D-QSAR model having high predictive ability with q2 = 0.743, r2 = 0.721, pred_r2 = 0.708 and standard error = 0.346, explaining the majority of the variance in the data with partial least square (PLS components. The results of the present study may be useful on the designing of more potent compounds as antitumor drugs.

  4. 3D face modeling, analysis and recognition

    CERN Document Server

    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

  5. 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

    Directory of Open Access Journals (Sweden)

    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

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

    Science.gov (United States)

    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.

  7. Automated analysis of 3D echocardiography

    NARCIS (Netherlands)

    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

  8. Synthesis, activity evaluation and 3D-QSAR study of some novel derivatives of 4, 5, 6, 7-tetrahydrothieno [3,2-c] pyridine

    Institute of Scientific and Technical Information of China (English)

    Die Cheng; Deng Ke Liu; Mo Liu; Ying Liu; Wei Ren Xu; Chang Xiao Liu

    2008-01-01

    A series of novel derivatives of 4, 5, 6, 7-tetrahydrothieno [3,2-c] pyridine were synthesized and strucmrally characterized by 1H NMR and MS. Their in vivo anti-platelet aggregation activities were evaluated. A 3D-QSAR was performed using the CoMFA and the CoMSIA. This model provided useful guidelines for novel anti-platelet thienopyridines design.

  9. 3D QSAR, pharmacophore indentification studies on series of 1-(2-ethoxyethyl-1H-pyrazolo [4,3-d]pyrimidines as phosphodiesterase V inhibitors

    Directory of Open Access Journals (Sweden)

    Prafulla Choudhari

    2015-05-01

    Conclusion: The two different QSAR models are generated by using two different principles, both the models are showing similar results which indicate that this kNN-MFA technique can be utilized for cross validation of the results of multiple linear regression studies.

  10. 3D-QSAR Studies on Barbituric Acid Derivatives as Urease Inhibitors and the Effect of Charges on the Quality of a Model.

    Science.gov (United States)

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

    2016-04-30

    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.

  11. 3D-QSAR Studies on Barbituric Acid Derivatives as Urease Inhibitors and the Effect of Charges on the Quality of a Model

    Directory of Open Access Journals (Sweden)

    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.

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

    Directory of Open Access Journals (Sweden)

    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.

  13. 3D-QSAR and docking studies of estrogen compounds based on estrogen receptor β

    Institute of Scientific and Technical Information of China (English)

    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.

  14. 3D-QSAR and docking studies of estrogen compounds based on estrogen receptor β

    Institute of Scientific and Technical Information of China (English)

    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.

  15. SURVEY AND ANALYSIS OF 3D STEGANOGRAPHY

    Directory of Open Access Journals (Sweden)

    K .LAKSHMI

    2011-01-01

    Full Text Available Steganography is the science that involves communicating secret data in an appropriate multimedia carrier, eg., images, audio, and video files. The remarkable growth in computational power, increase in current security approaches and techniques are often used together to ensures security of the secret message. Steganography’s ultimate objectives, which are capacity and invisibility, are the main factors that separate it from related techniques. In this paper we focus on 3D models of steganography and conclude with some review analysis of high capacity data hiding and low-distortion 3D models.

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

    Directory of Open Access Journals (Sweden)

    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.

  17. A Mechanism-based 3D-QSAR Approach for Classification ...

    Science.gov (United States)

    Organophosphate (OP) and carbamate esters can inhibit acetylcholinesterase (AChE) by binding covalently to a serine residue in the enzyme active site, and their inhibitory potency depends largely on affinity for the enzyme and the reactivity of the ester. Despite this understanding, there has been no mechanism-based in silico approach for classification and prediction of the inhibitory potency of ether OPs or carbamates. This prompted us to develop a three dimensional prediction framework for OPs, carbamates, and their analogs. Inhibitory structures of a compound that can form the covalent bond were identified through analysis of docked conformations of the compound and its metabolites. Inhibitory potencies of the selected structures were then predicted using a previously developed three dimensional quantitative structure-active relationship. This approach was validated with a large number of structurally diverse OP and carbamate compounds encompassing widely used insecticides and structural analogs including OP flame retardants and thio- and dithiocarbamate pesticides. The modeling revealed that: (1) in addition to classical OP metabolic activation, the toxicity of carbamate compounds can be dependent on biotransformation, (2) OP and carbamate analogs such as OP flame retardants and thiocarbamate herbicides can act as AChEI, (3) hydrogen bonds at the oxyanion hole is critical for AChE inhibition through the covalent bond, and (4) π–π interaction with Trp86

  18. Combined 3D-QSAR, molecular docking, and molecular dynamics study of tacrine derivatives as potential acetylcholinesterase (AChE) inhibitors of Alzheimer's disease.

    Science.gov (United States)

    Zhou, An; Hu, Jianping; Wang, Lirong; Zhong, Guochen; Pan, Jian; Wu, Zeyu; Hui, Ailing

    2015-10-01

    Acetylcholinesterase (AChE) is one of the key targets of drugs for treating Alzheimer's disease (AD). Tacrine is an approved drug with AChE-inhibitory activity. In this paper, 3D-QSAR, molecular docking, and molecular dynamics were carried out in order to study 60 tacrine derivatives and their AChE-inhibitory activities. 3D-QSAR modeling resulted in an optimal CoMFA model with q(2) = 0.552 and r(2) = 0.983 and an optimal CoMSIA model with q(2) = 0.581 and r(2) = 0.989. These QSAR models also showed that the steric and H-bond fields of these compounds are important influences on their activities. The interactions between these inhibitors and AChE were further explored through molecular docking and molecular dynamics simulation. A few key residues (Tyr70, Trp84, Tyr121, Trp279, and Phe330) at the binding site of AChE were identified. The results of this study improve our understanding of the mechanisms of AChE inhibitors and afford valuable information that should aid the design of novel potential AChE inhibitors. Graphical Abstract Superposition of backbone atoms of the lowest-energy structure obtained from MD simulation (magenta) onto those of the structure of the initial molecular docking model (green).

  19. A combination of pharmacophore modeling, atom-based 3D-QSAR, molecular docking and molecular dynamics simulation studies on PDE4 enzyme inhibitors.

    Science.gov (United States)

    Tripuraneni, Naga Srinivas; Azam, Mohammed Afzal

    2016-11-01

    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 pyrazolopyridine and quinoline derivatives using Schrödinger suite 2014-3. A four-point pharmacophore model was developed using 74 molecules having pIC50 ranging from 10.1 to 4.5. The best four feature model consists of one hydrogen bond acceptor, two aromatic rings, and one hydrophobic group. The pharmacophore hypothesis yielded a statistically significant 3D-QSAR model, with a high correlation coefficient (R(2 )= .9949), cross validation coefficient (Q(2 )= .7291), and Pearson-r (.9107) at six component partial least square factor. The external validation indicated that our QSAR model possessed high predictive power with R(2) value of .88. The generated model was further validated by enrichment studies using the decoy test. Molecular docking, free energy calculation, and molecular dynamics (MD) simulation studies have been performed to explore the putative binding modes of these ligands. A 10-ns MD simulation confirmed the docking results of both stability of the 1XMU-ligand complex and the presumed active conformation. Outcomes of the present study provide insight in designing novel molecules with better PDE4 inhibitory activity.

  20. The discovery of a novel and selective inhibitor of PTP1B over TCPTP: 3D QSAR pharmacophore modeling, virtual screening, synthesis, and biological evaluation.

    Science.gov (United States)

    Ma, Ying; Jin, Yuan-Yuan; Wang, Ye-Liu; Wang, Run-Ling; Lu, Xin-Hua; Kong, De-Xin; Xu, Wei-Ren

    2014-06-01

    Given the special role of insulin and leptin signaling in various biological responses, protein-tyrosine phosphatase-1B (PTP1B) was regarded as a novel therapeutic target for treating type 2 diabetes and obesity. However, owing to the highly conserved (sequence identity of about 74%) in active pocket, targeting PTP1B for drug discovery is a great challenge. In this study, we employed the software package Discovery Studio to develop 3D QSAR pharmacophore models for PTP1B and TCPTP inhibitors. It was further validated by three methods (cost analysis, test set prediction, and Fisher's test) to show that the models can be used to predict the biological activities of compounds without costly and time-consuming synthesis. The criteria for virtual screening were also validated by testing the selective PTP1B inhibitors. Virtual screening experiments and subsequent in vitro evaluation of promising hits revealed a novel and selective inhibitor of PTP1B over TCPTP. After that, a most likely binding mode was proposed. Thus, the findings reported here may provide a new strategy in discovering selective PTP1B inhibitors.

  1. 3D object-oriented image analysis in 3D geophysical modelling

    DEFF Research Database (Denmark)

    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...

  2. Molecular modeling studies of [6,6,5] Tricyclic Fused Oxazolidinones as FXa inhibitors using 3D-QSAR, Topomer CoMFA, molecular docking and molecular dynamics simulations.

    Science.gov (United States)

    Xu, Cheng; Ren, Yujie

    2015-10-15

    Coagulation factor Xa (Factor Xa, FXa) is a particularly promising target for novel anticoagulant therapy. The first oral factor Xa inhibitor has been approved in the EU and Canada in 2008. In this work, 38 [6,6,5] Tricyclic Fused Oxazolidinones were studied using a combination of molecular modeling techniques including three-dimensional quantitative structure-activity relationship (3D-QSAR), molecular docking, molecular dynamics and Topomer CoMFA (comparative molecular field analysis) were used to build 3D-QSAR models. The results show that the best CoMFA model has q(2)=0.511 and r(2)=0.984, the best CoMSIA (comparative molecular similarity indices analysis) model has q(2)=0.700 and r(2)=0.993 and the Topomer CoMFA analysis has q(2)=0.377 and r(2)=0.886. The results indicated the steric, hydrophobic, H-acceptor and electrostatic fields play key roles in models. Molecular docking and molecular dynamics explored the binding relationship of the ligand and the receptor protein.

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

    Science.gov (United States)

    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.

  4. 3D-QSAR methods on the basis of ligand-receptor complexes. Application of COMBINE and GRID/GOLPE methodologies to a series of CYP1A2 ligands

    Science.gov (United States)

    Lozano, Juan José; Pastor, Manuel; Cruciani, Gabriele; Gaedt, Katrin; Centeno, Nuria B.; Gago, Federico; Sanz, Ferran

    2000-05-01

    Many heterocyclic amines (HCA) present in cooked food exert a genotoxic activity when they are metabolised (N-oxidated) by the human cytochrome P450 1A2 (CYP1A2h). In order to rationalize the observed differences in activity of this enzyme on a series of 12 HCA, 3D-QSAR methods were applied on the basis of models of HCA-CYP1A2h complexes. The CYP1A2h enzyme model has been previously reported and was built by homology modeling based on cytochrome P450 BM3. The complexes were automatically generated applying the AUTODOCK software and refined using AMBER. A COMBINE analysis on the complexes identified the most important enzyme-ligand interactions that account for the differences in activity within the series. A GRID/GOLPE analysis was then performed on just the ligands, in the conformations and orientations found in the modeled complexes. The results from both methods were concordant and confirmed the advantages of incorporating structural information from series of ligand-receptor complexes into 3D-QSAR methodologies.

  5. Combined Structure-Based Pharmacophore and 3D-QSAR Studies on Phenylalanine Series Compounds as TPH1 Inhibitors

    Directory of Open Access Journals (Sweden)

    Mingli Xiang

    2012-05-01

    Full Text Available Tryptophan hydroxylase-1 (TPH1 is a key enzyme in the synthesis of serotonin. As a neurotransmitter, serotonin plays important physiological roles both peripherally and centrally. In this study, a combination of ligand-based and structure-based methods is used to clarify the essential quantitative structure-activity relationship (QSAR of known TPH1 inhibitors. A multicomplex-based pharmacophore (MCBP guided method has been suggested to generate a comprehensive pharmacophore of TPH1 kinase based on three crystal structures of TPH1-inhibitor complex. This model has been successfully used to identify the bioactive conformation and align 32 structurally diverse substituted phenylalanine derivatives. The QSAR analyses have been performed on these TPH1 inhibitors based on the MCBP guided alignment. These results may provide important information for further design and virtual screening of novel TPH1 inhibitors.

  6. QSAR analysis of furanone derivatives as potential COX-2 inhibitors: kNN MFA approach

    Directory of Open Access Journals (Sweden)

    Ruchi Bhatiya

    2014-12-01

    Full Text Available A series of thirty-two furanone derivatives with their cyclooxygenase-2 inhibitory activity were subjected to quantitative structural–activity relationship analysis to derive a correlation between biological activity as a dependent variable and various descriptors as independent variables by using V-LIFE MDS3.5 software. The significant 2D QSAR model showed correlation coefficient (r2 = 0.840, standard error of estimation (SEE = 0.195, and a cross-validated squared correlation coefficient (q2 = 0.773. The descriptors involved in the building of 2D QSAR model are retention index for six membered rings, total number of oxygen connected with two single bonds, polar surface area excluding P and S plays a significant role in COX-2 inhibition. 3D-QSAR performed via Step Wise K Nearest Neighbor Molecular Field Analysis [(SW kNN MFA] with partial least-square (PLS technique showed high predictive ability (r2 = 0.7622, q2 = 0.7031 and standard error = 0.3660 explaining the majority of the variance in the data with two principle components. The results of the present study may be useful in the design of more potent furanone derivatives as COX-2 inhibitors.

  7. 3-D analysis of grain selection process

    Science.gov (United States)

    Arao, Tomoka; Esaka, Hisao; Shinozuka, Kei

    2012-07-01

    It is known that the grain selection plays an important role in the manufacturing process for turbine blades. There are some analytical or numerical models to treat the grain selection. However, the detailed mechanism of grain selection in 3-D is still uncertain. Therefore, an experimental research work using Al-Cu alloy has been carried out in order to understand the grain selection in 3-D.A mold made by Al2O3 was heated to 600 °C ( = liquids temperature of the alloy) and was set on a water-colded copper chill plate. Molten Al-20 wt%Cu alloy was cast into the mold and unidirectional solidified ingot was prepared. The size of ingot was approximately phi25×65H mm. To obtain the thermal history, 4 thermocouples were placed in the mold. It is confirmed that the alloy solidified unidirectionally from bottom to top. Solidified structure on a longitudinal cross section was observed and unidirectional solidification up to 40 mm was ensured. EBSD analysis has been performed on horizontal cross section at an interval of ca.200 μm. These observations were carried out 7-5 mm from the bottom surface. Crystallographic orientation of primary Al phase and size of solidified grains were characterized. A large solidified grain, the crystallographic orientation of which is approximately along heat flow direction, is observed near the lowest cross section. The area of grain decreased as solidification proceeded. On the other hand, it is found that the area of grain increased.

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

    Science.gov (United States)

    Gao, Xiaodong; Han, Liping; Ren, Yujie

    2016-05-05

    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.

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

    Directory of Open Access Journals (Sweden)

    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.

  10. 3D analysis of craniofacial growth and tooth eruption

    DEFF Research Database (Denmark)

    Kreiborg, Sven

    The 9th International Congress on Cleft Palate and Related Craniofacial Anomalies, 3D analysis, craniofacial growth, tooth eruption......The 9th International Congress on Cleft Palate and Related Craniofacial Anomalies, 3D analysis, craniofacial growth, tooth eruption...

  11. 3D QSAR studies, pharmacophore modeling, and virtual screening of diarylpyrazole-benzenesulfonamide derivatives as a template to obtain new inhibitors, using human carbonic anhydrase II as a model protein.

    Science.gov (United States)

    Entezari Heravi, Yeganeh; Sereshti, Hassan; Saboury, Ali Akbar; Ghasemi, Jahan; Amirmostofian, Marzieh; Supuran, Claudiu T

    2017-12-01

    A 3D-QSAR modeling was performed on a series of diarylpyrazole-benzenesulfonamide derivatives acting as inhibitors of the metalloenzyme carbonic anhydrase (CA, EC 4.2.1.1). The compounds were collected from two datasets with the same scaffold, and utilized as a template for a new pharmacophore model to screen the ZINC database of commercially available derivatives. The datasets were divided into training, test, and validation sets. As the first step, comparative molecular field analysis (CoMFA), CoMFA region focusing and comparative molecular similarity indices analysis (CoMSIA) in parallel with docking studies were applied to a set of 41 human (h) CA II inhibitors. The validity and the prediction capacity of the resulting models were evaluated by leave-one-out (LOO) cross-validation approach. The reliability of the model for the prediction of possibly new CA inhibitors was also tested.

  12. Combined pharmacophore and 3D-QSAR study on a series of Staphylococcus aureus Sortase A inhibitors.

    Science.gov (United States)

    Uddin, Reaz; Lodhi, Mazhar U; Ul-Haq, Zaheer

    2012-08-01

    Methicillin resistant Staphylococcus aureus has become a major health concern and it requires new therapeutic agents. Staphylococcus aureus Sortase A enzyme contributes in adherence of bacteria with the cell wall of host cell; consequently, inhibition of S. aureus Sortase A by small molecules could be employed as potential antibacterial agents against methicillin resistant S. aureus. Current study focused on the identification of 3D pharmacophoric features within a series of rhodanine, pyridazinone, and pyrazolethione analogs as S. aureus Sortase A inhibitors. Pharmacophore model was constructed employing representative molecules using Genetic Algorithm with Linear Assignment of Hypermolecular Alignment of Database. The identified pharmacophoric points were then utilized to create alignment hypothesis for three-dimensional quantitative structure-activity relationships. Outcome of comparative molecular field analysis and comparative molecular similarity indices analysis experiments were in good agreement (comparative molecular field analysis: q(2) = 0.562 and r(2) = 0.995, comparative molecular similarity indices analysis: q(2) = 0.549 and r(2) = 0.978) and capable of explaining the variance in biological activities coherently with respect to the structural features of compounds. The results were also found in concurrence with the outcome of pharmacophoric features.

  13. 3D-QSAR/CoMFA-Based Structure-Affinity/Selectivity Relationships of Aminoalkylindoles in the Cannabinoid CB1 and CB2 Receptors

    Directory of Open Access Journals (Sweden)

    Jaime Mella-Raipán

    2014-03-01

    Full Text Available A 3D-QSAR (CoMFA study was performed in an extensive series of aminoalkylindoles derivatives with affinity for the cannabinoid receptors CB1 and CB2. The aim of the present work was to obtain structure-activity relationships of the aminoalkylindole family in order to explain the affinity and selectivity of the molecules for these receptors. Major differences in both, steric and electrostatic fields were found in the CB1 and CB2 CoMFA models. The steric field accounts for the principal contribution to biological activity. These results provide a foundation for the future development of new heterocyclic compounds with high affinity and selectivity for the cannabinoid receptors with applications in several pathological conditions such as pain treatment, cancer, obesity and immune disorders, among others.

  14. Synthesis, biological evaluation and 3D-QSAR studies of novel 4,5-dihydro-1H-pyrazole niacinamide derivatives as BRAF inhibitors.

    Science.gov (United States)

    Li, Cui-Yun; Li, Qing-Shan; Yan, Li; Sun, Xiao-Guang; Wei, Ran; Gong, Hai-Bin; Zhu, Hai-Liang

    2012-06-15

    A series of novel 4,5-dihydropyrazole derivatives containing niacinamide moiety as potential V600E mutant BRAF kinase (BRAF(V600E)) inhibitors were designed and synthesized. Results of the bioassays against BRAF(V600E) and WM266.4 human melanoma cell line showed several compounds to be endowed potent activities with IC(50) and GI(50) value in low micromolar range, among which compound 27e, (5-(4-Chlorophenyl)-3-(4-methoxyphenyl)-4,5-dihydro-1H-pyrazol-1-yl)6-methylpyridin-3-yl methanone (IC(50)=0.20 μM, GI(50)=0.89 μM) was bearing the best bioactivity comparable with the positive control Sorafenib. Docking simulation was performed to determine the probable binding model and 3D-QSAR model was built to provide more pharmacophore understanding that could use to design new agents with more potent BRAF(V600E) inhibitory activity.

  15. 3D-QSAR/CoMFA-based structure-affinity/selectivity relationships of aminoalkylindoles in the cannabinoid CB1 and CB2 receptors.

    Science.gov (United States)

    Mella-Raipán, Jaime; Hernández-Pino, Santiago; Morales-Verdejo, César; Pessoa-Mahana, David

    2014-03-05

    A 3D-QSAR (CoMFA) study was performed in an extensive series of aminoalkylindoles derivatives with affinity for the cannabinoid receptors CB1 and CB2. The aim of the present work was to obtain structure-activity relationships of the aminoalkylindole family in order to explain the affinity and selectivity of the molecules for these receptors. Major differences in both, steric and electrostatic fields were found in the CB1 and CB2 CoMFA models. The steric field accounts for the principal contribution to biological activity. These results provide a foundation for the future development of new heterocyclic compounds with high affinity and selectivity for the cannabinoid receptors with applications in several pathological conditions such as pain treatment, cancer, obesity and immune disorders, among others.

  16. 3D face analysis for demographic biometrics

    Energy Technology Data Exchange (ETDEWEB)

    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.

  17. Multifractal modelling and 3D lacunarity analysis

    Energy Technology Data Exchange (ETDEWEB)

    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.

  18. 3D QSAR study of phytoestrogens:A combined molecular dockingand molecular dynamics simulation%基于对接的植物激素3D-QSAR和分子动力学模拟

    Institute of Scientific and Technical Information of China (English)

    蒙延娟; 易忠胜; 艾芳婷; 张爱茜

    2014-01-01

    In this study, molecular docking and molecular dynamics ( MD) simulation approaches were adopted to study the interactions between phytoestrogens compounds and estrogen receptor. The docking results reveal that the estrogenic activity ofphytoestrogens compounds is mainly affected by the hydrophobic and H-bond interactions at the active site of estrogen receptor. There are several H-bonds between the phytoestrogens compounds mainly with amino acid residues GLU353, ARG394, HIS524, LEU525. Furthermore, two 3D-QSAR models were established based on the docking conformations using comparative molecular field analysis ( CoMFA ) and comparative molecular similarity index analysis ( CoMSIA ) . The statistic parameters of two models ( CoMFA model with a cross-validation Q2 value of 0. 676 and a noncross-validation R2 value of 0. 994, a standard errors value of 0.143 and F statistics value of 342.115 and CoMSIA model with Q2=0.565, R2=0. 972, SEE=0. 286 and F=111. 480 ) show that CoMFA and CoMSIA models have good stability and prediction ability. Finally, the dynamics between small molecules and protein are studied by the MD simulation, and the results provide a reasonable validation of docking results.%采用分子对接和分子动力学( MD)模拟方法研究植物雌激素类化合物与雌激素受体的相互作用机制,对接结果表明,雌激素受体活性位点的疏水和氢键作用是影响植物雌激素化合物活性的主要原因,植物雌激素类化合物主要与氨基酸残基GLU353、ARG394、HIS524和LEU525之间形成氢键.然后以对接后的分子构象进行分子结构叠合,结合比较分子力场分析( CoMFA)和比较分子相似性指数分析( CoMSIA)方法建立了3D-QSAR模型.CoMFA模型的交叉验证相关系数(Q2)和非交叉验证相关系数(R2)值分别为0.676和0.994,标准估计误差SEE和F统计量分别为0.143和342.115;CoMSIA模型的Q2=0.565,R2=0.972,SEE=0.286

  19. 3D motion analysis via energy minimization

    Energy Technology Data Exchange (ETDEWEB)

    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

  20. 3D QSAR studies on binding affinities of coumarin natural products for glycosomal GAPDH of Trypanosoma cruzi

    Science.gov (United States)

    Menezes, Irwin R. A.; Lopes, Julio C. D.; Montanari, Carlos A.; Oliva, Glaucius; Pavão, Fernando; Castilho, Marcelo S.; Vieira, Paulo C.; Pupo, M.^onica T.

    2003-05-01

    Drug design strategies based on Comparative Molecular Field Analysis (CoMFA) have been used to predict the activity of new compounds. The major advantage of this approach is that it permits the analysis of a large number of quantitative descriptors and uses chemometric methods such as partial least squares (PLS) to correlate changes in bioactivity with changes in chemical structure. Because it is often difficult to rationalize all variables affecting the binding affinity of compounds using CoMFA solely, the program GRID was used to describe ligands in terms of their molecular interaction fields, MIFs. The program VolSurf that is able to compress the relevant information present in 3D maps into a few descriptors can treat these GRID fields. The binding affinities of a new set of compounds consisting of 13 coumarins, for one of which the three-dimensional ligand-enzyme bound structure is known, were studied. A final model based on the mentioned programs was independently validated by synthesizing and testing new coumarin derivatives. By relying on our knowledge of the real physical data (i.e., combining crystallographic and binding affinity results), it is also shown that ligand-based design agrees with structure-based design. The compound with the highest binding affinity was the coumarin chalepin, isolated from Rutaceae species, with an IC50 value of 55.5 μM towards the enzyme glyceraldehyde-3-phosphate dehydrogenase (gGAPDH) from glycosomes of the parasite Trypanosoma cruzi, the causative agent of Chagas' disease. The proposed models from GRID MIFs have revealed the importance of lipophilic interactions in modulating the inhibition, but without excluding the dependence on stereo-electronic properties as found from CoMFA fields.

  1. Reconstruction and analysis of shapes from 3D scans

    NARCIS (Netherlands)

    ter Haar, F.B.

    2009-01-01

    In this thesis we use 3D laser range scans for the acquisition, reconstruction, and analysis of 3D shapes. 3D laser range scanning has proven to be a fast and effective way to capture the surface of an object in a computer. Thousands of depth measurements represent a part of the surface geometry as

  2. Design, synthesis and 3D-QSAR studies of new diphenylamine containing 1,2,4-triazoles as potential antitubercular agents.

    Science.gov (United States)

    Mohan Krishna, K; Inturi, Bharathkumar; Pujar, Gurubasavaraj V; Purohit, Madhusudan N; Vijaykumar, G S

    2014-09-12

    A new series of new diphenylamine containing 1,2,4-triazoles were synthesized from 4-arylideneamino-5-[2-(2,6-dichlorophenylamino) benzyl]-2H-1,2,4-triazole-3(4H)-thiones 3a-f. The synthesized compounds were screened for in-vitro antimycobacterial and antibacterial activities. The synthesized compounds 4a, 4e and 4d have shown potential activity against Mycobacterium tuberculosis H37Rv strain with MIC of 0.2, 1.6 and 3.125 μM respectively. To investigate the SAR of diphenylamine containing 1,2,4-triazole derivatives in more details, CoMFA (q(2)-0.432, r(2)-0.902) and CoMSIA (q(2)-0.511, r(2)-0.953) models on M. tuberculosis H37Rv were established. The generated 3D-QSAR models are externally validated and have shown significant statistical results, and these models can be used for further rational design of novel diphenylamine containing 1,2,4-triazoles as potent antitubercular agents.

  3. 3D joint dynamics analysis of healthy children's gait

    OpenAIRE

    SAMSON, William; DESROCHES, Guillaume; Cheze, Laurence; Dumas, Raphaël

    2009-01-01

    The 3D joint moments and 2D joint powers have been largely explored in the literature of healthy children's gait, in particular to compare them with pathologic subjects' gait. However, no study reported on 3D joint power in children which could be due to the difficulties in interpreting the results. Recently, the analysis of the 3D angle between the joint moment and the joint angular velocity vectors has been proposed in order to help 3D joint power interpretation. Our hypothesis is that this...

  4. Development, evaluation and application of 3D QSAR Pharmacophore model in the discovery of potential human renin inhibitors

    Directory of Open Access Journals (Sweden)

    John Shalini

    2011-12-01

    Full Text Available Abstract Background Renin has become an attractive target in controlling hypertension because of the high specificity towards its only substrate, angiotensinogen. The conversion of angiotensinogen to angiotensin I is the first and rate-limiting step of renin-angiotensin system and thus designing inhibitors to block this step is focused in this study. Methods Ligand-based quantitative pharmacophore modeling methodology was used in identifying the important molecular chemical features present in the set of already known active compounds and the missing features from the set of inactive compounds. A training set containing 18 compounds including active and inactive compounds with a substantial degree of diversity was used in developing the pharmacophore models. A test set containing 93 compounds, Fischer randomization, and leave-one-out methods were used in the validation of the pharmacophore model. Database screening was performed using the best pharmacophore model as a 3D structural query. Molecular docking and density functional theory calculations were used to select the hit compounds with strong molecular interactions and favorable electronic features. Results The best quantitative pharmacophore model selected was made of one hydrophobic, one hydrogen bond donor, and two hydrogen bond acceptor features with high a correlation value of 0.944. Upon validation using an external test set of 93 compounds, Fischer randomization, and leave-one-out methods, this model was used in database screening to identify chemical compounds containing the identified pharmacophoric features. Molecular docking and density functional theory studies have confirmed that the identified hits possess the essential binding characteristics and electronic properties of potent inhibitors. Conclusion A quantitative pharmacophore model of predictive ability was developed with essential molecular features of a potent renin inhibitor. Using this pharmacophore model, two

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

    Directory of Open Access Journals (Sweden)

    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. Understanding the Molecular Determinant of Reversible Human Monoamine Oxidase B Inhibitors Containing 2H-chromen-2-One Core: Structure-Based and Ligand-Based Derived 3-D QSAR Predictive Models.

    Science.gov (United States)

    Mladenovic, Milan; Patsilinakos, Alexandros; Pirolli, Adele; Sabatino, Manuela; Ragno, Rino

    2017-03-14

    Monoamine oxidase B (MAO B) catalyzes the oxidative deamination of aryalkylamines neurotransmitters with concomitant reduction of oxygen to hydrogen peroxide. Consequently, the enzyme's malfunction can induce oxidative damage to mitochondrial DNA and mediates development of Parkinson's disease. Thus, MAO B emerges as a promising target for developing pharmaceuticals potentially useful to treat this vicious neurodegenerative condition. Aiming to contribute to the development of drugs with the reversible mechanism of MAO B inhibition only, herein, an extended in silico-in vitro procedure for the selection of novel MAO B inhibitors is demonstrated, including: (1) definition of optimized and validated structure-based (SB) 3-D QSAR models derived from available co-crystallized inhibitor-MAO B complexes; (2) elaboration of structure-activity relationships (SAR) features for either irreversible or reversible MAO B inhibitors to characterize and improve coumarin-based inhibitor activity (Protein Data Bank ID: 2V61) as the most potent reversible lead compound; (3) definition of structure-based (SB) and ligand-based (LB) alignment rules assessments by which virtually any untested potential MAO B inhibitor might be evaluated; (4) predictive ability validation of the best 3-D QSAR model through SB/LB modeling of four coumarin-based external test sets (267 compounds); (5) design and SB/LB alignment of novel coumarin-based scaffolds experimentally validated through synthesis and biological evaluation in vitro. Due to the wide range of molecular diversity within the 3-D QSARs training set and derived features, the selected N probe-derived 3-D QSAR model proves to be a valuable tool for virtual screening (VS) of novel MAO B inhibitors and a platform for design, synthesis and evaluation of novel active structures. Accordingly, six highly active and selective MAO B inhibitors (picomolar to low nanomolar range of activity) were disclosed as a result of rational SB/LB 3-D QSAR design

  7. Generalized Method of Variational Analysis for 3-D Flow

    Institute of Scientific and Technical Information of China (English)

    兰伟仁; 黄思训; 项杰

    2004-01-01

    The generalized method of variational analysis (GMVA) suggested for 2-D wind observations by Huang et al. is extended to 3-D cases. Just as in 2-D cases, the regularization idea is applied. But due to the complexity of the 3-D cases, the vertical vorticity is taken as a stable functional. The results indicate that wind observations can be both variationally optimized and filtered. The efficiency of GMVA is also checked in a numerical test. Finally, 3-D wind observations with random disturbances are manipulated by GMVA after being filtered.

  8. P38促细胞分裂蛋白酶活性抑制剂的分子对接及3D-QSAR研究%Docking and 3D-QSAR study on p38α MAP kinase inhibitors

    Institute of Scientific and Technical Information of China (English)

    沈勇; 王源丰; 吴景恒; 肖利民

    2012-01-01

    运用分子对接方法研究了26个以嘧啶基咪唑环为基底的一系列同源化合物与p38促细胞分裂蛋白酶晶体结构的结合模式.采用比较分子力场分析法(CoMFA)对选取的对接优势构象进行三维定量构效关系(3D-QSAR)研究.建立了3D-QSAR的CoMFA模型,其非交叉验证系数r2为0.986,交叉验证相关系数q2为0.755,外部验证的标准偏差(SD)为0.13,表明该模型合理、可信,并具有良好的预测能力.有趣的是, 配体与活性周围氨基酸残基4个距离之和与其活性之间具有良好的线性关系(R2=0.752),揭示了配体分子大小及与氨基酸残基结合的紧密程度对化合物的抑制活性起着主要的作用.最后,根据研究总结的规律设计了4个具有潜在高活性的嘧啶基咪唑衍生物.研究结果可为实验工作者合成新药提供理论有意义的理论参考.%A series of 26 pyridinylimidazole derivatives were docked to the X-ray structure of p38α MAP kinase,and their best docking conformations were analyzed by three-dimensional quantitative structure-activity relationship (3D-QSAR) studies.A robust 3D-QSAR model with high correlation coefficient (r2=0.986) and cross-validation coefficient (q2=0.755) has been established by comparative molecular field analysis (CoMFA).An external validation by the compounds with high activities shows the standard deviation (SD) between experimental and predicted pIC50 values is 0.13.Docking results show that different binding modes of pyridinylimidazole derivatives have a great impact on the inhibitory activity of inhibitors.Interestingly,the summation of the four distances measuring the interaction between the ligands and the protein show a good linear relation (R2 =0.752) with the inhibitory activity of the compounds.Finally,four new pyridinylimidazole derivatives with potent high p38α MAP kinase inhibitory activity have been theoretically designed.

  9. Analysis of temporal stability of autostereoscopic 3D displays

    Science.gov (United States)

    Rubiño, Manuel; Salas, Carlos; Pozo, Antonio M.; Castro, J. J.; Pérez-Ocón, Francisco

    2013-11-01

    An analysis has been made of the stability of the images generated by electronic autostereoscopic 3D displays, studying the time course of the photometric and colorimetric parameters. The measurements were made on the basis of the procedure recommended in the European guideline EN 61747-6 for the characterization of electronic liquid-crystal displays (LCD). The study uses 3 different models of autostereoscopic 3D displays of different sizes and numbers of pixels, taking the measurements with a spectroradiometer (model PR-670 SpectraScan of PhotoResearch). For each of the displays, the time course is shown for the tristimulus values and the chromaticity coordinates in the XYZ CIE 1931 system and values from the time periods required to reach stable values of these parameters are presented. For the analysis of how the procedure recommended in the guideline EN 61747-6 for 2D displays influenced the results, and for the adaption of the procedure to the characterization of 3D displays, the experimental conditions of the standard procedure were varied, making the stability analysis in the two ocular channels (RE and LE) of the 3D mode and comparing the results with those corresponding to the 2D. The results of our study show that the stabilization time of a autostereoscopic 3D display with parallax barrier technology depends on the tristimulus value analysed (X, Y, Z) as well as on the presentation mode (2D, 3D); furthermore, it was found that whether the 3D mode is used depends on the ocular channel evaluated (RE, LE).

  10. Accuracy of 3D Imaging Software in Cephalometric Analysis

    Science.gov (United States)

    2013-06-21

    orthodontic software program ( Dolphin 3D, mfg, city, state) used for measurement and analysis of craniofacial dimensions. Three-dimensional reconstructions...143(8), 899-902. Baik H, Jeon J, Lee H. (2007). Facial soft tissue analysis of Korean adults with normal occlusion using a 3-dimensional laser

  11. 3D Images of Materials Structures Processing and Analysis

    CERN Document Server

    Ohser, Joachim

    2009-01-01

    Taking and analyzing images of materials' microstructures is essential for quality control, choice and design of all kind of products. Today, the standard method still is to analyze 2D microscopy images. But, insight into the 3D geometry of the microstructure of materials and measuring its characteristics become more and more prerequisites in order to choose and design advanced materials according to desired product properties. This first book on processing and analysis of 3D images of materials structures describes how to develop and apply efficient and versatile tools for geometric analysis

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

    Science.gov (United States)

    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.

  13. 3D Regression Heat Map Analysis of Population Study Data.

    Science.gov (United States)

    Klemm, Paul; Lawonn, Kai; Glaßer, Sylvia; Niemann, Uli; Hegenscheid, Katrin; Völzke, Henry; Preim, Bernhard

    2016-01-01

    Epidemiological studies comprise heterogeneous data about a subject group to define disease-specific risk factors. These data contain information (features) about a subject's lifestyle, medical status as well as medical image data. Statistical regression analysis is used to evaluate these features and to identify feature combinations indicating a disease (the target feature). We propose an analysis approach of epidemiological data sets by incorporating all features in an exhaustive regression-based analysis. This approach combines all independent features w.r.t. a target feature. It provides a visualization that reveals insights into the data by highlighting relationships. The 3D Regression Heat Map, a novel 3D visual encoding, acts as an overview of the whole data set. It shows all combinations of two to three independent features with a specific target disease. Slicing through the 3D Regression Heat Map allows for the detailed analysis of the underlying relationships. Expert knowledge about disease-specific hypotheses can be included into the analysis by adjusting the regression model formulas. Furthermore, the influences of features can be assessed using a difference view comparing different calculation results. We applied our 3D Regression Heat Map method to a hepatic steatosis data set to reproduce results from a data mining-driven analysis. A qualitative analysis was conducted on a breast density data set. We were able to derive new hypotheses about relations between breast density and breast lesions with breast cancer. With the 3D Regression Heat Map, we present a visual overview of epidemiological data that allows for the first time an interactive regression-based analysis of large feature sets with respect to a disease.

  14. 3D-Aided-Analysis Tool for Lunar Rover

    Institute of Scientific and Technical Information of China (English)

    ZHANG Peng; LI Guo-peng; REN Xin; LIU Jian-jun; GAO Xing-ye; ZOU Xiao-duan

    2013-01-01

    3D-Aided-Analysis Tool (3DAAT) which is a virtual reality system is built up in this paper. 3DAAT is integrated with kinematics and dynamics model of rover as well as real lunar surface terrain mode. Methods of modeling which are proposed in this paper include constructing lunar surface, constructing 3D model of lander and rover, building up kinematic model of rover body. Photogrammetry technique and the remote sensing information are used to generate the terrain model of lunar surface. According to the implementation result, 3DAAT is an effective assist system for making exploration plan and analyzing the status of rover.

  15. AN ANALYSIS OF 3D FINITE CRACKED BODIES

    Institute of Scientific and Technical Information of China (English)

    Tao Weiming; Guo Yimu; Cao Zhiyuan

    2001-01-01

    The new-type traction boundary integral equations developed by Hu and with no hyper singular integral are applied to analysis of 3D finite cracked bodies. A numerical algorithm for general 3D problems and a semi-analytical one for axisymmetric problems are presented. Some examples of thick plates and cylindrical columns including penny-shaped crack(s), and rectangular plates including an elliptical crack normal to the surface are analyzed. The comparison between present results and those in literature shows the high accuracy and effectiveness of the present method.

  16. 3D Network Analysis for Indoor Space Applications

    Science.gov (United States)

    Tsiliakou, E.; Dimopoulou, E.

    2016-10-01

    Indoor space differs from outdoor environments, since it is characterized by a higher level of structural complexity, geometry, as well as topological relations. Indoor space can be considered as the most important component in a building's conceptual modelling, on which applications such as indoor navigation, routing or analysis are performed. Therefore, the conceptual meaning of sub spaces or the activities taking place in physical building boundaries (e.g. walls), require the comprehension of the building's indoor hierarchical structure. The scope of this paper is to perform 3D network analysis in a building's interior and is structured as follows: In Section 1 the definition of indoor space is provided and indoor navigation requirements are analysed. Section 2 describes the processes of indoor space modeling, as well as routing applications. In Section 3, a case study is examined involving a 3D building model generated in CityEngine (exterior shell) and ArcScene (interior parts), in which the use of commercially available software tools (ArcGIS, ESRI), in terms of indoor routing and 3D network analysis, are explored. The fundamentals of performing 3D analysis with the ArcGIS Network Analyst extension were tested. Finally a geoprocessing model was presented, which was specifically designed to be used to interactively find the best route in ArcScene. The paper ends with discussion and concluding remarks on Section 4.

  17. Descriptor Based Analysis of Digital 3D Shapes

    DEFF Research Database (Denmark)

    Welnicka, Katarzyna

    challenges. One such challenge, which is addressed in this thesis, is to develop computational methods for classifying shapes which are in agreement with the human way of understanding and classifying shapes. In this dissertation we first present a shape descriptor based on the process of diffusion......Analysis and processing of 3D digital shapes is a significant research area with numerous medical, industrial, and entertainment applications which has gained enormously in importance as optical scanning modalities have started to make acquired 3D geometry commonplace. The area holds many......, in conjunction with the method of Reeb graphs for skeletonization, it is an effective tool for generating scale dependent skeletons of shapes represented as 3D triangle meshes. The second part of the thesis aims at capturing the style phenomenon. The style of an object is easily recognized by humans...

  18. Discovery of potent and selective urea-based ROCK inhibitors: Exploring the inhibitor's potency and ROCK2/PKA selectivity by 3D-QSAR, molecular docking and molecular dynamics simulations.

    Science.gov (United States)

    Mei, Ding; Yin, Yan; Wu, Fanhong; Cui, Jiaxing; Zhou, Hong; Sun, Guofeng; Jiang, Yu; Feng, Yangbo

    2015-05-15

    An activity model and a selectivity model from 3D-QSAR studies were established by CoMFA and CoMSIA to explore the SAR. Then docking was used to study the binding modes between ligand and kinases (ROCK2 and PKA), and the molecular docking results were further validated by MD simulations. Computational results suggested that substitution containing positive charge attached to the middle phenyl ring, or electropositive group in urea linker was favored for both activity and ROCK2/PKA selectivity. Finally, three compounds were designed, and biological evaluation demonstrated that these molecular models were effective for guiding the design of potent and selective ROCK inhibitors.

  19. 3-D Experimental Fracture Analysis at High Temperature

    Energy Technology Data Exchange (ETDEWEB)

    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.

  20. Skeleton-Sectional Structural Analysis for 3D Printing

    Institute of Scientific and Technical Information of China (English)

    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.

  1. Prediction of eye irritation from organic chemicals using membrane-interaction QSAR analysis.

    Science.gov (United States)

    Kulkarni, A; Hopfinger, A J; Osborne, R; Bruner, L H; Thompson, E D

    2001-02-01

    Eye irritation potency of a compound or mixture has traditionally been evaluated using the Draize rabbit-eye test (Draize et al., 1944). In order to aid predictions of eye irritation and to explore possible corresponding mechanisms of eye irritation, a methodology termed "membrane-interaction QSAR analysis" (MI-QSAR) has been developed (Kulkarni and Hopfinger 1999). A set of Draize eye-irritation data established by the European Center for Ecotoxicology and Toxicology of Chemicals (ECETOC) (Bagley et al., 1992) was used as a structurally diverse training set in an MI-QSAR analysis. Significant QSAR models were constructed based primarily upon aqueous solvation-free energy of the solute and the strength of solute binding to a model phospholipid (DMPC) monolayer. The results demonstrate that inclusion of parameters to model membrane interactions of potentially irritating chemicals provides significantly better predictions of eye irritation for structurally diverse compounds than does modeling based solely on physiochemical properties of chemicals. The specific MI-QSAR models reported here are, in fact, close to the upper limit in both significance and robustness that can be expected for the variability inherent to the eye-irritation scores of the ECETOC training set. The MI-QSAR models can be used with high reliability to classify compounds of low- and high-predicted eye irritation scores. Thus, the models offer the opportunity to reduce animal testing for compounds predicted to fall into these two extreme eye-irritation score sets. The MI-QSAR paradigm may also be applicable to other toxicological endpoints, such as skin irritation, where interactions with cellular membranes are likely.

  2. 3D Guided Wave Motion Analysis on Laminated Composites

    Science.gov (United States)

    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.

  3. Advanced computational tools for 3-D seismic analysis

    Energy Technology Data Exchange (ETDEWEB)

    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.

  4. Quantitative nanoscale analysis in 3D using electron tomography

    Energy Technology Data Exchange (ETDEWEB)

    Kuebel, Christian [Karlsruhe Institute of Technology, INT, 76344 Eggenstein-Leopoldshafen (Germany)

    2011-07-01

    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.

  5. Advancements in 3D Structural Analysis of Geothermal Systems

    Energy Technology Data Exchange (ETDEWEB)

    Siler, Drew L [Nevada Bureau of Mines and Geology, University of Nevada, Reno; Faulds, James E [Nevada Bureau of Mines and Geology, University of Nevada, Reno; Mayhew, Brett [Nevada Bureau of Mines and Geology, University of Nevada, Reno; McNamara, David [Department of Geothermal Science, GNS Science, NZ

    2013-06-23

    Robust geothermal activity in the Great Basin, USA is a product of both anomalously high regional heat flow and active fault-controlled extension. Elevated permeability associated with some fault systems provides pathways for circulation of geothermal fluids. Constraining the local-scale 3D geometry of these structures and their roles as fluid flow conduits is crucial in order to mitigate both the costs and risks of geothermal exploration and to identify blind (no surface expression) geothermal resources. Ongoing studies have indicated that much of the robust geothermal activity in the Great Basin is associated with high density faulting at structurally complex fault intersection/interaction areas, such as accommodation/transfer zones between discrete fault systems, step-overs or relay ramps in fault systems, intersection zones between faults with different strikes or different senses of slip, and horse-tailing fault terminations. These conceptualized models are crucial for locating and characterizing geothermal systems in a regional context. At the local scale, however, pinpointing drilling targets and characterizing resource potential within known or probable geothermal areas requires precise 3D characterization of the system. Employing a variety of surface and subsurface data sets, we have conducted detailed 3D geologic analyses of two Great Basin geothermal systems. Using EarthVision (Dynamic Graphics Inc., Alameda, CA) we constructed 3D geologic models of both the actively producing Brady’s geothermal system and a ‘greenfield’ geothermal prospect at Astor Pass, NV. These 3D models allow spatial comparison of disparate data sets in 3D and are the basis for quantitative structural analyses that can aid geothermal resource assessment and be used to pinpoint discrete drilling targets. The relatively abundant data set at Brady’s, ~80 km NE of Reno, NV, includes 24 wells with lithologies interpreted from careful analysis of cuttings and core, a 1

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

    Energy Technology Data Exchange (ETDEWEB)

    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)

  7. The development of a 3D risk analysis method.

    Science.gov (United States)

    I, Yet-Pole; Cheng, Te-Lung

    2008-05-01

    Much attention has been paid to the quantitative risk analysis (QRA) research in recent years due to more and more severe disasters that have happened in the process industries. Owing to its calculation complexity, very few software, such as SAFETI, can really make the risk presentation meet the practice requirements. However, the traditional risk presentation method, like the individual risk contour in SAFETI, is mainly based on the consequence analysis results of dispersion modeling, which usually assumes that the vapor cloud disperses over a constant ground roughness on a flat terrain with no obstructions and concentration fluctuations, which is quite different from the real situations of a chemical process plant. All these models usually over-predict the hazardous regions in order to maintain their conservativeness, which also increases the uncertainty of the simulation results. On the other hand, a more rigorous model such as the computational fluid dynamics (CFD) model can resolve the previous limitations; however, it cannot resolve the complexity of risk calculations. In this research, a conceptual three-dimensional (3D) risk calculation method was proposed via the combination of results of a series of CFD simulations with some post-processing procedures to obtain the 3D individual risk iso-surfaces. It is believed that such technique will not only be limited to risk analysis at ground level, but also be extended into aerial, submarine, or space risk analyses in the near future.

  8. Somatotyping using 3D anthropometry: a cluster analysis.

    Science.gov (United States)

    Olds, Tim; Daniell, Nathan; Petkov, John; David Stewart, Arthur

    2013-01-01

    Somatotyping is the quantification of human body shape, independent of body size. Hitherto, somatotyping (including the most popular method, the Heath-Carter system) has been based on subjective visual ratings, sometimes supported by surface anthropometry. This study used data derived from three-dimensional (3D) whole-body scans as inputs for cluster analysis to objectively derive clusters of similar body shapes. Twenty-nine dimensions normalised for body size were measured on a purposive sample of 301 adults aged 17-56 years who had been scanned using a Vitus Smart laser scanner. K-means Cluster Analysis with v-fold cross-validation was used to determine shape clusters. Three male and three female clusters emerged, and were visualised using those scans closest to the cluster centroid and a caricature defined by doubling the difference between the average scan and the cluster centroid. The male clusters were decidedly endomorphic (high fatness), ectomorphic (high linearity), and endo-mesomorphic (a mixture of fatness and muscularity). The female clusters were clearly endomorphic, ectomorphic, and the ecto-mesomorphic (a mixture of linearity and muscularity). An objective shape quantification procedure combining 3D scanning and cluster analysis yielded shape clusters strikingly similar to traditional somatotyping.

  9. Predicting MDCK cell permeation coefficients of organic molecules using membrane-interaction QSAR analysis

    Institute of Scientific and Technical Information of China (English)

    Li-li CHEN; Jia YAO; Jian-bo YANG; Jie YANG

    2005-01-01

    Aim: To use membrane-interaction quantitative structure-activity relationship analysis (MI-QSAR) to develop predictive models of partitioning of organic compounds in gastrointestinal cells. Methods: A training set of 22 structurally diverse compounds, whose apparent permeability accross cellular membranes of MadinDarby canine kidney (MDCK) cells were measured, were used to construct MIQSAR models. Molecular dynamic simulations were used to determine the explicit interaction of each test compound (solute) with a dimyristoyl-phosphatidyl-choline monolayer membrane model. An additional set of intramolecular solute descriptors were computed and considered in the trial pool of descriptors for building MI-QSAR models. The QSAR models were optimized using multidimensional linear regression fitting and the stepwise method. A test set of 8 compounds were evaluated using the MI-QSAR models as part of a validation process. Results:MI-QSAR models of the gastrointestinal absorption process were constructed.The descriptors found in the best MI-QSAR models are as follows: 1) ClogP (the logarithm of the 1-octanol/water partition coefficient); 2) EHOMO (the highest occupied molecular orbital energy); 3) Es (stretch energy); 4) PMY (the principal moment of inertia Y, the inertia along the y axis in the rectangular coordinates; 5) Ct(total connectivity); and 6) Enb (the energy of interactions between all of the nonbonded atoms). The most important descriptor in the models is ClogP. Conclusion:Permeability is not only determined by the properties of drug molecules, but is also very much influenced by the molecule-membrane interaction process.

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

    OpenAIRE

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

  11. 3D Massive MIMO Systems: Modeling and Performance Analysis

    KAUST Repository

    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.

  12. Reconstruction and Analysis of Shapes from 3D Scans

    NARCIS (Netherlands)

    Haar, F.B. ter

    2009-01-01

    In this thesis, we measure 3D shapes with the use of 3D laser technology, a recent technology that combines physics, mathematics, and computer science to acquire the surface geometry of 3D shapes in the computer. We use this surface geometry to fully reconstruct real world shapes as computer models,

  13. Uncertainty Analysis of RELAP5-3D

    Energy Technology Data Exchange (ETDEWEB)

    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.

  14. Comparative visual analysis of 3D urban wind simulations

    Science.gov (United States)

    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.

  15. Physically based analysis of deformations in 3D images

    Science.gov (United States)

    Nastar, Chahab; Ayache, Nicholas

    1993-06-01

    We present a physically based deformable model which can be used to track and to analyze the non-rigid motion of dynamic structures in time sequences of 2-D or 3-D medical images. The model considers an object undergoing an elastic deformation as a set of masses linked by springs, where the natural lengths of the springs is set equal to zero, and is replaced by a set of constant equilibrium forces, which characterize the shape of the elastic structure in the absence of external forces. This model has the extremely nice property of yielding dynamic equations which are linear and decoupled for each coordinate, whatever the amplitude of the deformation. It provides a reduced algorithmic complexity, and a sound framework for modal analysis, which allows a compact representation of a general deformation by a reduced number of parameters. The power of the approach to segment, track, and analyze 2-D and 3-D images is demonstrated by a set of experimental results on various complex medical images.

  16. QSAR modeling for quinoxaline derivatives using genetic algorithm and simulated annealing based feature selection.

    Science.gov (United States)

    Ghosh, P; Bagchi, M C

    2009-01-01

    With a view to the rational design of selective quinoxaline derivatives, 2D and 3D-QSAR models have been developed for the prediction of anti-tubercular activities. Successful implementation of a predictive QSAR model largely depends on the selection of a preferred set of molecular descriptors that can signify the chemico-biological interaction. Genetic algorithm (GA) and simulated annealing (SA) are applied as variable selection methods for model development. 2D-QSAR modeling using GA or SA based partial least squares (GA-PLS and SA-PLS) methods identified some important topological and electrostatic descriptors as important factor for tubercular activity. Kohonen network and counter propagation artificial neural network (CP-ANN) considering GA and SA based feature selection methods have been applied for such QSAR modeling of Quinoxaline compounds. Out of a variable pool of 380 molecular descriptors, predictive QSAR models are developed for the training set and validated on the test set compounds and a comparative study of the relative effectiveness of linear and non-linear approaches has been investigated. Further analysis using 3D-QSAR technique identifies two models obtained by GA-PLS and SA-PLS methods leading to anti-tubercular activity prediction. The influences of steric and electrostatic field effects generated by the contribution plots are discussed. The results indicate that SA is a very effective variable selection approach for such 3D-QSAR modeling.

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

    Energy Technology Data Exchange (ETDEWEB)

    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.

  18. 3D-QSAR studies of triazolopyrimidine derivatives of Plasmodium falciparum dihydroorotate dehydrogenase inhibitors using a combination of molecular dynamics, docking, and genetic algorithm-based methods.

    Science.gov (United States)

    Shah, Priyanka; Kumar, Sumit; Tiwari, Sunita; Siddiqi, Mohammad Imran

    2012-07-01

    A series of 35 triazolopyrimidine analogues reported as Plasmodium falciparum dihydroorotate dehydrogenase (PfDHODH) inhibitors were optimized using quantum mechanics methods, and their binding conformations were studied by docking and 3D quantitative structure-activity relationship studies. Genetic algorithm-based criteria was adopted for selection of training and test sets while maintaining structural diversity of training and test sets, which is also very crucial for model development and validation. Both the comparative molecular field analyses ([Formula: see text], [Formula: see text]) and comparative molecular similarity indices analyses ([Formula: see text], [Formula: see text]) show excellent correlation and high predictive power. Furthermore, molecular dynamics simulations were performed to explore the binding mode of the two of the most active compounds of the series, 10 and 14. Harmonization in the two simulation results validate the analysis and therefore applicability of docking parameters based on crystallographic conformation of compound 14 bound to receptor molecule. This work provides useful information about the inhibition mechanism of this class of molecules and will assist in the design of more potent inhibitors of PfDHODH.

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

    Science.gov (United States)

    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.

  20. 3D Finite Element Analysis of Particle-Reinforced Aluminum

    Science.gov (United States)

    Shen, H.; Lissenden, C. J.

    2002-01-01

    Deformation in particle-reinforced aluminum has been simulated using three distinct types of finite element model: a three-dimensional repeating unit cell, a three-dimensional multi-particle model, and two-dimensional multi-particle models. The repeating unit cell model represents a fictitious periodic cubic array of particles. The 3D multi-particle (3D-MP) model represents randomly placed and oriented particles. The 2D generalized plane strain multi-particle models were obtained from planar sections through the 3D-MP model. These models were used to study the tensile macroscopic stress-strain response and the associated stress and strain distributions in an elastoplastic matrix. The results indicate that the 2D model having a particle area fraction equal to the particle representative volume fraction of the 3D models predicted the same macroscopic stress-strain response as the 3D models. However, there are fluctuations in the particle area fraction in a representative volume element. As expected, predictions from 2D models having different particle area fractions do not agree with predictions from 3D models. More importantly, it was found that the microscopic stress and strain distributions from the 2D models do not agree with those from the 3D-MP model. Specifically, the plastic strain distribution predicted by the 2D model is banded along lines inclined at 45 deg from the loading axis while the 3D model prediction is not. Additionally, the triaxial stress and maximum principal stress distributions predicted by 2D and 3D models do not agree. Thus, it appears necessary to use a multi-particle 3D model to accurately predict material responses that depend on local effects, such as strain-to-failure, fracture toughness, and fatigue life.

  1. 3-D Image Analysis of Fluorescent Drug Binding

    Directory of Open Access Journals (Sweden)

    M. Raquel Miquel

    2005-01-01

    Full Text Available Fluorescent ligands provide the means of studying receptors in whole tissues using confocal laser scanning microscopy and have advantages over antibody- or non-fluorescence-based method. Confocal microscopy provides large volumes of images to be measured. Histogram analysis of 3-D image volumes is proposed as a method of graphically displaying large amounts of volumetric image data to be quickly analyzed and compared. The fluorescent ligand BODIPY FL-prazosin (QAPB was used in mouse aorta. Histogram analysis reports the amount of ligand-receptor binding under different conditions and the technique is sensitive enough to detect changes in receptor availability after antagonist incubation or genetic manipulations. QAPB binding was concentration dependent, causing concentration-related rightward shifts in the histogram. In the presence of 10 μM phenoxybenzamine (blocking agent, the QAPB (50 nM histogram overlaps the autofluorescence curve. The histogram obtained for the 1D knockout aorta lay to the left of that of control and 1B knockout aorta, indicating a reduction in 1D receptors. We have shown, for the first time, that it is possible to graphically display binding of a fluorescent drug to a biological tissue. Although our application is specific to adrenergic receptors, the general method could be applied to any volumetric, fluorescence-image-based assay.

  2. Analysis of User Requirements in Interactive 3D Video Systems

    Directory of Open Access Journals (Sweden)

    Haiyue Yuan

    2012-01-01

    Full Text Available The recent development of three dimensional (3D display technologies has resulted in a proliferation of 3D video production and broadcasting, attracting a lot of research into capture, compression and delivery of stereoscopic content. However, the predominant design practice of interactions with 3D video content has failed to address its differences and possibilities in comparison to the existing 2D video interactions. This paper presents a study of user requirements related to interaction with the stereoscopic 3D video. The study suggests that the change of view, zoom in/out, dynamic video browsing, and textual information are the most relevant interactions with stereoscopic 3D video. In addition, we identified a strong demand for object selection that resulted in a follow-up study of user preferences in 3D selection using virtual-hand and ray-casting metaphors. These results indicate that interaction modality affects users’ decision of object selection in terms of chosen location in 3D, while user attitudes do not have significant impact. Furthermore, the ray-casting-based interaction modality using Wiimote can outperform the volume-based interaction modality using mouse and keyboard for object positioning accuracy.

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

    Science.gov (United States)

    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. Analysis of Alignment Influence on 3-D Anthropometric Statistics

    Institute of Scientific and Technical Information of China (English)

    CAI Xiuwen; LI Zhizhong; CHANG Chien-Chi; DEMPSEY Patrick

    2005-01-01

    Three-dimensional (3-D) surface anthropometry can provide much more useful information for many applications such as ergonomic product design than traditional individual body dimension measurements. However, the traditional definition of the percentile calculation is designed only for 1-D anthropometric data estimates. The same approach cannot be applied directly to 3-D anthropometric statistics otherwise it could lead to misinterpretations. In this paper, the influence of alignment references on 3-D anthropometric statistics is analyzed mathematically, which shows that different alignment reference points (for example, landmarks) for translation alignment could result in different object shapes if 3-D anthropometric data are processed for percentile values based on coordinates and that dimension percentile calculations based on coordinate statistics are incompatible with those traditionally based on individual dimensions.

  5. Quantitative analysis of autophagy using advanced 3D fluorescence microscopy.

    Science.gov (United States)

    Changou, Chun A; Wolfson, Deanna L; Ahluwalia, Balpreet Singh; Bold, Richard J; Kung, Hsing-Jien; Chuang, Frank Y S

    2013-05-03

    Prostate cancer is the leading form of malignancies among men in the U.S. While surgery carries a significant risk of impotence and incontinence, traditional chemotherapeutic approaches have been largely unsuccessful. Hormone therapy is effective at early stage, but often fails with the eventual development of hormone-refractory tumors. We have been interested in developing therapeutics targeting specific metabolic deficiency of tumor cells. We recently showed that prostate tumor cells specifically lack an enzyme (argininosuccinate synthase, or ASS) involved in the synthesis of the amino acid arginine(1). This condition causes the tumor cells to become dependent on exogenous arginine, and they undergo metabolic stress when free arginine is depleted by arginine deiminase (ADI)(1,10). Indeed, we have shown that human prostate cancer cells CWR22Rv1 are effectively killed by ADI with caspase-independent apoptosis and aggressive autophagy (or macroautophagy)(1,2,3). Autophagy is an evolutionarily-conserved process that allows cells to metabolize unwanted proteins by lysosomal breakdown during nutritional starvation(4,5). Although the essential components of this pathway are well-characterized(6,7,8,9), many aspects of the molecular mechanism are still unclear - in particular, what is the role of autophagy in the death-response of prostate cancer cells after ADI treatment? In order to address this question, we required an experimental method to measure the level and extent of autophagic response in cells - and since there are no known molecular markers that can accurately track this process, we chose to develop an imaging-based approach, using quantitative 3D fluorescence microscopy(11,12). Using CWR22Rv1 cells specifically-labeled with fluorescent probes for autophagosomes and lysosomes, we show that 3D image stacks acquired with either widefield deconvolution microscopy (and later, with super-resolution, structured-illumination microscopy) can clearly capture the early

  6. 3-D Printed Ultem 9085 Testing and Analysis

    Science.gov (United States)

    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.

  7. Digital holography microscopy in 3D biologic samples analysis

    Energy Technology Data Exchange (ETDEWEB)

    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.

  8. Reliability of 3D upper limb motion analysis in children with obstetric brachial plexus palsy.

    Science.gov (United States)

    Mahon, Judy; Malone, Ailish; Kiernan, Damien; Meldrum, Dara

    2017-03-01

    Kinematics, measured by 3D upper limb motion analysis (3D-ULMA), can potentially increase understanding of movement patterns by quantifying individual joint contributions. Reliability in children with obstetric brachial plexus palsy (OBPP) has not been established.

  9. Yield and Cost Analysis or 3D Stacked ICs

    NARCIS (Netherlands)

    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

  10. A Texture Analysis of 3D Radar Images

    NARCIS (Netherlands)

    Deiana, D.; Yarovoy, A.

    2009-01-01

    In this paper a texture feature coding method to be applied to high-resolution 3D radar images in order to improve target detection is developed. An automatic method for image segmentation based on texture features is proposed. The method has been able to automatically detect weak targets which fail

  11. Xanthone as Antimalarial: QSAR Analysis, Synthesis, Molecular Docking and In-vitro Antimalarial Evaluation

    Directory of Open Access Journals (Sweden)

    Jufrizal Syahri

    2017-02-01

    Full Text Available The rational design of eighteen new antimalarial compounds from xanthone derivatives has been conducted based on Quantitative Structure-Activity Relationship(QSAR calculation using semi-empirical AM1 methods. The best equation model obtained from QSAR calculation was Log pIC50 = 2.997 - 29.256 (qO8 - 138.234 (qC9 - 6.882 (qC12 - 107.836 (qC14 + 48.764 (qO15. Among the designed compounds, 3,6-dihydroxy-9H-xanthen-9-one (26 and 3,4,6-trihydroxy-9H-xanthen-9-one (27 have been synthesized and investigated their in-vitro antimalarial activities against the chloroquine-sensitive 3D7 strain. An in-vitro antimalarial activity of compound 26 and 27 showed to be highly potential as antimalarial compounds with IC50 of 0.71 and 0.11 µM respectively. Molecular docking studies of compound 26 and 27 showed the formation of a binding interaction between the compounds with the amino acids Ala16, Ser108, Phe58, Asp54 and Leu46, which is the crucial amino acids for antimalarial activity based on the protein-ligand co-crystal structure of WR99210(1,3,5-triazine, a pre-clinical molecule as P. falciparum DHFR-TS inhibitor.

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

    Energy Technology Data Exchange (ETDEWEB)

    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.

  13. Molecular field analysis (MFA) and other QSAR techniques in development of phosphatase inhibitors.

    Science.gov (United States)

    Nair, Pramod C

    2011-01-01

    Phosphatases are well known drug targets for diseases such as diabetes, obesity and other autoimmune diseases. Their role in cancer is due to unusual expression patterns in different types of cancer. However, there is strong evidence for selective targeting of phosphatases in cancer therapy. Several experimental and in silico techniques have been attempted for design of phosphatase inhibitors, with focus on diseases such as diabetes, inflammation and obesity. Their utility for cancer therapy is limited and needs to be explored vastly. Quantitative Structure Activity relationship (QSAR) is well established in silico ligand based drug design technique, used by medicinal chemists for prediction of ligand binding affinity and lead design. These techniques have shown promise for subsequent optimization of already existing lead compounds, with an aim of increased potency and pharmacological properties for a particular drug target. Furthermore, their utility in virtual screening and scaffold hopping is highlighted in recent years. This review focuses on the recent molecular field analysis (MFA) and QSAR techniques, directed for design and development of phosphatase inhibitors and their potential use in cancer therapy. In addition, this review also addresses issues concerning the binding orientation and binding conformation of ligands for alignment sensitive QSAR approaches.

  14. Analysis of 3-D Propagation Effects Due to Environmental Variability

    Science.gov (United States)

    2014-09-30

    presence of 3-D environmental variations, especially shelf break canyons . Work was also performed in support of 2-D propagation in shallow water to...propagation in the Monterey Bay Canyon . This was motivated by observations of highly variable directional features in measured acoustic vector data...Rev. 8-98) Prescribed by ANSI Std Z39-18 2 the Monterey Bay Canyon were used as inputs to the model, and broadband calculations were performed

  15. 3D-QSAR Studies on Diacylurea Derivatives Containing Furan Moiety%含呋喃环双酰脲类衍生物的三维定量构效关系研究

    Institute of Scientific and Technical Information of China (English)

    崔紫宁; 张莉; 黄娟; 李映; 凌云; 杨新玲

    2008-01-01

    采用比较分子力场分析法(CoMFA)和比较分子相似性指数分析法(CoMSIA),对27个新型双酰基脲类化合物的杀蚊幼虫(Aedes aegypti L.)活性进行三维定量构效关系(3D-QSAR)研究.在CoMFA研究中,考察了网格点步长对统计结果的影响.在CoMSIA研究中,系统考察了各种分子场组合、网格点步长和衰减因子对模型统计结果的影响,发现立体场和氢键供体场的组合得到最佳模型.所建立的CoMFA和CoMSIA模型的非交叉验证相关系数r2值分别为0.828和0.841,并都具有较强的预测能力.CoMFA和CoMSIA模型的三维等值图不仅直观地解释了结构与活性的关系,而且为后续优化该系列化合物提供了理论依据.

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

    DEFF Research Database (Denmark)

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

    2014-01-01

    to 3D models using Sketchup and Designing Reality. Finally, panoramic photography is discussed as a 2D alternative to 3D. Sketchup is a free-ware 3D drawing program and Designing Reality is a commercial program, which uses Structure from motion. For each program/method, the same comparative analysis...

  17. 3D Massive MIMO Systems: Channel Modeling and Performance Analysis

    KAUST Repository

    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

  18. 3D CFD analysis of a twin screw expander

    OpenAIRE

    Kovacevic, A.; S Rane

    2013-01-01

    Twin screw machines can be used as expanders for variety of applications. This paper describes how the performance of an oil free twin screw air expander of 3/5 lobe configuration was estimated by use of full 3D Computational Fluid Dynamics (CFD) applying a procedure similar to that used for screw compressors. The grid generator SCORG© was employed for pre-processing of the moving domains between the rotors while the stationary grids for the ports were derived from a commercial grid generator...

  19. Point Cluster Analysis Using a 3D Voronoi Diagram with Applications in Point Cloud Segmentation

    Directory of Open Access Journals (Sweden)

    Shen Ying

    2015-08-01

    Full Text Available Three-dimensional (3D point analysis and visualization is one of the most effective methods of point cluster detection and segmentation in geospatial datasets. However, serious scattering and clotting characteristics interfere with the visual detection of 3D point clusters. To overcome this problem, this study proposes the use of 3D Voronoi diagrams to analyze and visualize 3D points instead of the original data item. The proposed algorithm computes the cluster of 3D points by applying a set of 3D Voronoi cells to describe and quantify 3D points. The decompositions of point cloud of 3D models are guided by the 3D Voronoi cell parameters. The parameter values are mapped from the Voronoi cells to 3D points to show the spatial pattern and relationships; thus, a 3D point cluster pattern can be highlighted and easily recognized. To capture different cluster patterns, continuous progressive clusters and segmentations are tested. The 3D spatial relationship is shown to facilitate cluster detection. Furthermore, the generated segmentations of real 3D data cases are exploited to demonstrate the feasibility of our approach in detecting different spatial clusters for continuous point cloud segmentation.

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

    Science.gov (United States)

    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.

  1. Metrological analysis of the human foot: 3D multisensor exploration

    Science.gov (United States)

    Muñoz Potosi, A.; Meneses Fonseca, J.; León Téllez, J.

    2011-08-01

    In the podiatry field, many of the foot dysfunctions are mainly generated due to: Congenital malformations, accidents or misuse of footwear. For the treatment or prevention of foot disorders, the podiatrist diagnoses prosthesis or specific adapted footwear, according to the real dimension of foot. Therefore, it is necessary to acquire 3D information of foot with 360 degrees of observation. As alternative solution, it was developed and implemented an optical system of threedimensional reconstruction based in the principle of laser triangulation. The system is constituted by an illumination unit that project a laser plane into the foot surface, an acquisition unit with 4 CCD cameras placed around of axial foot axis, an axial moving unit that displaces the illumination and acquisition units in the axial axis direction and a processing and exploration unit. The exploration software allows the extraction of distances on three-dimensional image, taking into account the topography of foot. The optical system was tested and their metrological performances were evaluated in experimental conditions. The optical system was developed to acquire 3D information in order to design and make more appropriate footwear.

  2. 3D numerical simulation and analysis of railgun gouging mechanism

    Institute of Scientific and Technical Information of China (English)

    Jin-guo WU; Bo TANG; Qing-hua LIN; Hai-yuan LI; Bao-ming LI

    2016-01-01

    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.

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

    Directory of Open Access Journals (Sweden)

    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.

  4. 3D object-oriented image analysis in 3D geophysical modelling: Analysing the central part of the East African Rift System

    Science.gov (United States)

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

    2015-03-01

    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 interactive modelling environment IGMAS+, and their density contrast values were calculated using an object-based inversion technique to calculate the forward signal of the objects and compare it with the measured satellite gravity. Thus, a new object-based approach was implemented to interpret and extract the 3D subsurface objects from 3D geophysical data. We also introduce a new approach to constrain the interpretation of the satellite gravity measurements that can be applied using any 3D geophysical model.

  5. The importance of molecular structures, endpoints' values, and predictivity parameters in QSAR research: QSAR analysis of a series of estrogen receptor binders.

    Science.gov (United States)

    Li, Jiazhong; Gramatica, Paola

    2010-11-01

    Quantitative structure-activity relationship (QSAR) methodology aims to explore the relationship between molecular structures and experimental endpoints, producing a model for the prediction of new data; the predictive performance of the model must be checked by external validation. Clearly, the qualities of chemical structure information and experimental endpoints, as well as the statistical parameters used to verify the external predictivity have a strong influence on QSAR model reliability. Here, we emphasize the importance of these three aspects by analyzing our models on estrogen receptor binders (Endocrine disruptor knowledge base (EDKB) database). Endocrine disrupting chemicals, which mimic or antagonize the endogenous hormones such as estrogens, are a hot topic in environmental and toxicological sciences. QSAR shows great values in predicting the estrogenic activity and exploring the interactions between the estrogen receptor and ligands. We have verified our previously published model for additional external validation on new EDKB chemicals. Having found some errors in the used 3D molecular conformations, we redevelop a new model using the same data set with corrected structures, the same method (ordinary least-square regression, OLS) and DRAGON descriptors. The new model, based on some different descriptors, is more predictive on external prediction sets. Three different formulas to calculate correlation coefficient for the external prediction set (Q2 EXT) were compared, and the results indicated that the new proposal of Consonni et al. had more reasonable results, consistent with the conclusions from regression line, Williams plot and root mean square error (RMSE) values. Finally, the importance of reliable endpoints values has been highlighted by comparing the classification assignments of EDKB with those of another estrogen receptor binders database (METI): we found that 16.1% assignments of the common compounds were opposite (20 among 124 common

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

    Institute of Scientific and Technical Information of China (English)

    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.

  7. QSAR study and VolSurf characterization of anti-HIV quinolone library

    Science.gov (United States)

    Filipponi, Enrica; Cruciani, Gabriele; Tabarrini, Oriana; Cecchetti, Violetta; Fravolini, Arnaldo

    2001-03-01

    Antiviral quinolones are promising compounds in the search for new therapeutically effective agents for the treatment of AIDS. To rationalize the SAR for this new interesting class of anti-HIV derivatives, we performed a 3D-QSAR study on a library of 101 6-fluoro and 6-desfluoroquinolones, taken either from the literature or synthesized by us. The chemometric procedure involved a fully semiempirical minimization of the molecular structures by the AMSOL program, which takes into account the solvatation effect, and their 3D characterization by the VolSurf/GRID program. The QSAR analysis, based on PCA and PLS methods, shows the key structural features responsible for the antiviral activity.

  8. 3D thermo-chemical-mechanical analysis of the pultrusion process

    DEFF Research Database (Denmark)

    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...

  9. DYNA3D analysis of the DT-20 shipping container

    Energy Technology Data Exchange (ETDEWEB)

    Logan, R.W.; Lovejoy, S.C.

    1991-08-22

    A DYNA3D model of the DT-20 shipping container was constructed. Impact onto a rigid steel surface at a velocity of 44 ft/sec (30 foot gravity drop) was studied. The orientation of most interest was a side-drop, but end and corner drops were also studied briefly. The assembly for the baseline side impact contained a 150 lb. payload. During this drop, the outer drum sustains plastic strains of up to 0.15, with most the deformation near the rim. The plywood/Celotex packing is crushed about 3 inches. The inner sealed can sees significant stresses, but barely reaches the onset of yielding in some local areas. Based on hand calculations, the bolts joining the can halves could see stresses near 50 ksi. It is felt that overall, the container should survive this drop. However, detailed modeling of the rim closure and the center bolted joint was not possible due to time constraints. Furthermore, better material models and properties are needed for the Celotex, plywood, and honeycomb in particular. 39 figs., 1 tab.

  10. 3-D acquisition geometry analysis: Incorporating information from multiples

    NARCIS (Netherlands)

    Kumar, A.; Blacquiere, G.; Verschuur, D.J.

    2014-01-01

    Recent advances in survey design have led to conventional common-midpoint-based analysis being replaced by the subsurface-based seismic acquisition analysis and design, with the emphasis on advance techniques of illumination analysis. Amongst them are wave-equation-based seismic illumination analyse

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

    Directory of Open Access Journals (Sweden)

    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.

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

    Directory of Open Access Journals (Sweden)

    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.

  13. A mechanism-based 3D-QSAR approach for classification and prediction of acetylcholinesterase inhibitory potency of organophosphate and carbamate analogs

    Science.gov (United States)

    Lee, Sehan; Barron, Mace G.

    2016-04-01

    Organophosphate (OP) and carbamate esters can inhibit acetylcholinesterase (AChE) by binding covalently to a serine residue in the enzyme active site, and their inhibitory potency depends largely on affinity for the enzyme and the reactivity of the ester. Despite this understanding, there has been no mechanism-based in silico approach for classification and prediction of the inhibitory potency of ether OPs or carbamates. This prompted us to develop a three dimensional prediction framework for OPs, carbamates, and their analogs. Inhibitory structures of a compound that can form the covalent bond were identified through analysis of docked conformations of the compound and its metabolites. Inhibitory potencies of the selected structures were then predicted using a previously developed three dimensional quantitative structure-active relationship. This approach was validated with a large number of structurally diverse OP and carbamate compounds encompassing widely used insecticides and structural analogs including OP flame retardants and thio- and dithiocarbamate pesticides. The modeling revealed that: (1) in addition to classical OP metabolic activation, the toxicity of carbamate compounds can be dependent on biotransformation, (2) OP and carbamate analogs such as OP flame retardants and thiocarbamate herbicides can act as AChEI, (3) hydrogen bonds at the oxyanion hole is critical for AChE inhibition through the covalent bond, and (4) π-π interaction with Trp86 is necessary for strong inhibition of AChE. Our combined computation approach provided detailed understanding of the mechanism of action of OP and carbamate compounds and may be useful for screening a diversity of chemical structures for AChE inhibitory potency.

  14. Inverse Multifractal Analysis of Different Frame Types of Multiview 3D Video

    Directory of Open Access Journals (Sweden)

    A. Zeković

    2014-11-01

    Full Text Available In this paper, the results of multifractal characterization of multiview 3D video are presented. Analyses are performed for different views of multiview video and for different frame types of video. Multifractal analysis is performed by the histogram method. Due to the advantages of the selected method for determining the spectrum, the inverse multifractal analysis of multiview 3D video was also possible. A discussion of the results obtained by the inverse multifractal analysis of multiview 3D video is presented, taking into account the frame type and whether the original frames belong to the left or right view of multiview 3D video. In the analysis, publicly available multiview 3D video traces were used.

  15. Limit Analysis of 3D Reinforced Concrete Beam Elements

    DEFF Research Database (Denmark)

    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 th...

  16. Analysis of information for cerebrovascular disorders obtained by 3D MR imaging

    Energy Technology Data Exchange (ETDEWEB)

    Yoshikawa, Kohki [Tokyo Univ. (Japan). Inst. of Medical Science; Yoshioka, Naoki; Watanabe, Fumio; Shiono, Takahiro; Sugishita, Morihiro; Umino, Kazunori

    1995-12-01

    Recently, it becomes easy to analyze information obtained by 3D MR imaging due to remarkable progress of fast MR imaging technique and analysis tool. Six patients suffered from aphasia (4 cerebral infarctions and 2 bleedings) were performed 3D MR imaging (3D FLASH-TR/TE/flip angle; 20-50 msec/6-10 msec/20-30 degrees) and their volume information were analyzed by multiple projection reconstruction (MPR), surface rendering 3D reconstruction, and volume rendering 3D reconstruction using Volume Design PRO (Medical Design Co., Ltd.). Four of them were diagnosed as Broca`s aphasia clinically and their lesions could be detected around the cortices of the left inferior frontal gyrus. Another 2 patients were diagnosed as Wernicke`s aphasia and the lesions could be detected around the cortices of the left supramarginal gyrus. This technique for 3D volume analyses would provide quite exact locational information about cerebral cortical lesions. (author).

  17. Stereo Scene Flow for 3D Motion Analysis

    CERN Document Server

    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

  18. High Resolution Krylov Space 3-D Wavenumber-Frequency Analysis

    Science.gov (United States)

    2007-04-01

    wavenumber-frequency distri- bution of signal modes. That is, PPER (k, f, t) = eH(k) R̂[f, t] e(k). (3) Different from eq.(2), here R̂[f, t] is a time... PPER (k, f, t) frequency f w av en um be r k Capon wavenumber frequency analysis 0.4 0.5 0.6 0.7 0.8 0.9 1 0.5 0.4 0.3 0.2 0.1 0 0.1 0.2 0.3 0.4 0.5 30

  19. Evaluation of stereoscopic 3D displays for image analysis tasks

    Science.gov (United States)

    Peinsipp-Byma, E.; Rehfeld, N.; Eck, R.

    2009-02-01

    In many application domains the analysis of aerial or satellite images plays an important role. The use of stereoscopic display technologies can enhance the image analyst's ability to detect or to identify certain objects of interest, which results in a higher performance. Changing image acquisition from analog to digital techniques entailed the change of stereoscopic visualisation techniques. Recently different kinds of digital stereoscopic display techniques with affordable prices have appeared on the market. At Fraunhofer IITB usability tests were carried out to find out (1) with which kind of these commercially available stereoscopic display techniques image analysts achieve the best performance and (2) which of these techniques achieve a high acceptance. First, image analysts were interviewed to define typical image analysis tasks which were expected to be solved with a higher performance using stereoscopic display techniques. Next, observer experiments were carried out whereby image analysts had to solve defined tasks with different visualization techniques. Based on the experimental results (performance parameters and qualitative subjective evaluations of the used display techniques) two of the examined stereoscopic display technologies were found to be very good and appropriate.

  20. Solar Burst Analysis with 3D Loop Models

    CERN Document Server

    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...

  1. Sub aquatic 3D visualization and temporal analysis utilizing ArcGIS online and 3D applications

    Science.gov (United States)

    We used 3D Visualization tools to illustrate some complex water quality data we’ve been collecting in the Great Lakes. These data include continuous tow data collected from our research vessel the Lake Explorer II, and continuous water quality data collected from an autono...

  2. Influence of the structural diversity of data sets on the statistical quality of three-dimensional quantitative structure-activity relationship (3D-QSAR) models: predicting the estrogenic activity of xenoestrogens.

    Science.gov (United States)

    Yu, Seong Jae; Keenan, Susan M; Tong, Weida; Welsh, William J

    2002-10-01

    Federal legislation has resulted in the two-tiered in vitro and in vivo screening of some 80 000 structurally diverse chemicals for possible endocrine disrupting effects. To maximize efficiency and minimize expense, prioritization of these chemicals with respect to their estrogenic disrupting potential prior to this time-consuming and labor-intensive screening process is essential. Computer-based quantitative structure-activity relationship (QSAR) models, such as those obtained using comparative molecular field analysis (CoMFA), have been demonstrated as useful for risk assessment in this application. In general, however, CoMFA models to predict estrogenicity have been developed from data sets with limited structural diversity. In this study, we constructed CoMFA models based on biological data for a structurally diverse set of compounds spanning eight chemical families. We also compared two standard alignment schemes employed in CoMFA, namely, atom-fit and flexible field-fit, with respect to the predictive capabilities of their respective models for structurally diverse data sets. The present analysis indicates that flexible field-fit alignment fares better than atom-fit alignment as the structural diversity of the data set increases. Values of log(RP), where RP = relative potency, predicted by the final flexible field-fit CoMFA models are in good agreement with the corresponding experimental values. These models should be effective for predicting the endocrine disrupting potential of existing chemicals as well as prospective and newly prepared chemicals before they enter the environment.

  3. 3D Reacting Flow Analysis of LANTR Nozzles

    Science.gov (United States)

    Stewart, Mark E. M.; Krivanek, Thomas M.; Hemminger, Joseph A.; Bulman, M. J.

    2006-01-01

    This paper presents performance predictions for LANTR nozzles and the system implications for their use in a manned Mars mission. The LANTR concept is rocket thrust augmentation by injecting Oxygen into the nozzle to combust the Hydrogen exhaust of a Nuclear Thermal Rocket. The performance predictions are based on three-dimensional reacting flow simulations using VULCAN. These simulations explore a range of O2/H2 mixture ratios, injector configurations, and concepts. These performance predictions are used for a trade analysis within a system study for a manned Mars mission. Results indicate that the greatest benefit of LANTR will occur with In-Situ Resource Utilization (ISRU). However, Hydrogen propellant volume reductions may allow greater margins for fitting tanks within the launch vehicle where packaging issues occur.

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

    Institute of Scientific and Technical Information of China (English)

    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.

  5. Detailed 3-D nuclear analysis of ITER blanket modules

    Energy Technology Data Exchange (ETDEWEB)

    Bohm, T.D., E-mail: tdbohm@wisc.edu [University of Wisconsin-Madison, Madison, WI (United States); Sawan, M.E.; Marriott, E.P.; Wilson, P.P.H. [University of Wisconsin-Madison, Madison, WI (United States); Ulrickson, M.; Bullock, J. [Sandia National Laboratories, Albuquerque, NM (United States)

    2014-10-15

    In ITER, the blanket modules (BM) are arranged around the plasma to provide thermal and nuclear shielding for the vacuum vessel (VV), magnets, and other components. As a part of the BM design process, nuclear analysis is required to determine the level of nuclear heating, helium production, and radiation damage in the BM. Additionally, nuclear heating in the VV is also important for assessing the BM design. We used the CAD based DAG-MCNP5 transport code to analyze detailed models inserted into a 40-degree partially homogenized ITER global model. The regions analyzed include BM01, the neutral beam injection (NB) region, and the upper port region. For BM01, the results show that He production meets the limit necessary for re-welding, and the VV heating behind BM01 is acceptable. For the NBI region, the VV nuclear heating behind the NB region exceeds the design limit by a factor of two. For the upper port region, the nuclear heating of the VV exceeds the design limit by up to 20%. The results presented in this work are being used to modify the BM design in the cases where limits are exceeded.

  6. Compatibility analysis of 3D printer resin for biological applications

    KAUST Repository

    Sivashankar, Shilpa

    2016-08-30

    The salient features of microfluidics such as reduced cost, handling small sample and reagent volumes and less time required to fabricate the devices has inspired the present work. The incompatibility of three-dimensional printer resins in their native form and the method to improve their compatibility to many biological processes via surface modification are reported. The compatibility of the material to build microfluidic devices was evaluated in three different ways: (i) determining if the ultraviolet (UV) cured resin inhibits the polymerase chain reaction (PCR), i.e. testing devices for PCR compatibility; (ii) observing agglutination complex formed on the surface of the UV cured resin when anti-C-reactive protein (CRP) antibodies and CRP proteins were allowed to agglutinate; and (iii) by culturing human embryonic kidney cell line cells and testing for its attachment and viability. It is shown that only a few among four in its native form could be used for fabrication of microchannels and that had the least effect on biological molecules that could be used for PCR and protein interactions and cells, whereas the others were used after treating the surface. Importance in building lab-on-chip/micrototal analysis systems and organ-on-chip devices is found.

  7. 3D nuclear track analysis by digital holographic microscopy

    Energy Technology Data Exchange (ETDEWEB)

    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.

  8. Global stability analysis of turbulent 3D wakes

    Science.gov (United States)

    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.

  9. Detailed 3-D nuclear analysis of ITER outboard blanket modules

    Energy Technology Data Exchange (ETDEWEB)

    Bohm, Tim, E-mail: tdbohm@wisc.edu [Fusion Technology Institute, University of Wisconsin-Madison, Madison, WI (United States); Davis, Andrew; Sawan, Mohamed; Marriott, Edward; Wilson, Paul [Fusion Technology Institute, University of Wisconsin-Madison, Madison, WI (United States); Ulrickson, Michael; Bullock, James [Formerly, Fusion Technology, Sandia National Laboratories, Albuquerque, NM (United States)

    2015-10-15

    Highlights: • Nuclear analysis was performed on detailed CAD models placed in a 40 degree model of ITER. • The regions examined include BM09, the upper ELM coil region (BM11–13), the neutral beam (NB) region (BM13–16), and BM18. • The results show that VV nuclear heating exceeds limits in the NB and upper ELM coil regions. • The results also show that the level of He production in parts of BM18 exceeds limits. • These calculations are being used to modify the design of the ITER blanket modules. - Abstract: In the ITER design, the blanket modules (BM) provide thermal and nuclear shielding for the vacuum vessel (VV), magnets, and other components. We used the CAD based DAG-MCNP5 transport code to analyze detailed models inserted into a 40 degree partially homogenized ITER global model. The regions analyzed include BM09, BM16 near the heating neutral beam injection (HNB) region, BM11–13 near the upper ELM coil region, and BM18. For the BM16 HNB region, the VV nuclear heating behind the NB region exceeds the design limit by up to 80%. For the BM11–13 region, the nuclear heating of the VV exceeds the design limit by up to 45%. For BM18, the results show that He production does not meet the limit necessary for re-welding. The results presented in this work are being used by the ITER Organization Blanket and Tokamak Integration groups to modify the BM design in the cases where limits are exceeded.

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

    Science.gov (United States)

    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.

  11. Advanced Visualization and Analysis of Climate Data using DV3D and UV-CDAT

    Science.gov (United States)

    Maxwell, T. P.

    2012-12-01

    This paper describes DV3D, a Vistrails package of high-level modules for the Ultra-scale Visualization Climate Data Analysis Tools (UV-CDAT) interactive visual exploration system that enables exploratory analysis of diverse and rich data sets stored in the Earth System Grid Federation (ESGF). DV3D provides user-friendly workflow interfaces for advanced visualization and analysis of climate data at a level appropriate for scientists. The application builds on VTK, an open-source, object-oriented library, for visualization and analysis. DV3D provides the high-level interfaces, tools, and application integrations required to make the analysis and visualization power of VTK readily accessible to users without exposing burdensome details such as actors, cameras, renderers, and transfer functions. It can run as a desktop application or distributed over a set of nodes for hyperwall or distributed visualization applications. DV3D is structured as a set of modules which can be linked to create workflows in Vistrails. Figure 1 displays a typical DV3D workflow as it would appear in the Vistrails workflow builder interface of UV-CDAT and, on the right, the visualization spreadsheet output of the workflow. Each DV3D module encapsulates a complex VTK pipeline with numerous supporting objects. Each visualization module implements a unique interactive 3D display. The integrated Vistrails visualization spreadsheet offers multiple synchronized visualization displays for desktop or hyperwall. The currently available displays include volume renderers, volume slicers, 3D isosurfaces, 3D hovmoller, and various vector plots. The DV3D GUI offers a rich selection of interactive query, browse, navigate, and configure options for all displays. All configuration operations are saved as Vistrails provenance. DV3D's seamless integration with UV-CDAT's climate data management system (CDMS) and other climate data analysis tools provides a wide range of climate data analysis operations, e

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

    Science.gov (United States)

    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.

  13. 3D BUILDING MODELS SEGMENTATION BASED ON K-MEANS++ CLUSTER ANALYSIS

    Directory of Open Access Journals (Sweden)

    C. Zhang

    2016-10-01

    Full Text Available 3D mesh model segmentation is drawing increasing attentions from digital geometry processing field in recent years. The original 3D mesh model need to be divided into separate meaningful parts or surface patches based on certain standards to support reconstruction, compressing, texture mapping, model retrieval and etc. Therefore, segmentation is a key problem for 3D mesh model segmentation. In this paper, we propose a method to segment Collada (a type of mesh model 3D building models into meaningful parts using cluster analysis. Common clustering methods segment 3D mesh models by K-means, whose performance heavily depends on randomized initial seed points (i.e., centroid and different randomized centroid can get quite different results. Therefore, we improved the existing method and used K-means++ clustering algorithm to solve this problem. Our experiments show that K-means++ improves both the speed and the accuracy of K-means, and achieve good and meaningful results.

  14. Model and numerical analysis of 3D corrosion layer of reinforced concrete structure

    Institute of Scientific and Technical Information of China (English)

    李永和; 葛修润

    2003-01-01

    Under the assumption that the corrosion at the end of steel bolt or steel bar is shaped like the contour line of ellipsoid, a mathematic model and formulas of calculating the thickness of corrosion layer at arbitrary point are presented in this paper. Then regarding the arbitrary points of 3D corrosion layer as patch element model of fictitious displacement discontinuity, we propose the basic solution of 3D problem of the patch element acting on discontinuous displacement. With three basic assumptions of the corrosion layer, we set up the 3D numerical discreted model, and derive the stress boundary equation for fictitious corrosion layer of 3D numerical analysis. We also make the numerical stimulating calculation of the shotcrete structure at some lane using 3D finite element method. The results show that this method is effective and reasonable.

  15. Suspected feigned knee extensor weakness: usefulness of 3D gait analysis. Case report.

    Science.gov (United States)

    Chaler, Joaquim; Müller, Bertram; Maiques, Anna; Pujol, Eduard

    2010-07-01

    The purpose of the present case report is to show the potential for use of 3D gait analysis as an assessment method of feigned muscle weakness. We describe a patient complaining of right leg pain and weakness. Physical examination showed severe quadriceps muscle weakness in a highly abnormal gait pattern context. Conventional diagnostic workup did not show any relevant findings. Three-dimensional (3D) gait analysis was performed with a 3D motion capture system. Joint angles, internal moments and powers were computed from the motion data. Lower leg muscle surface-electromyography was also performed. During the late stance phase, flexor moment and negative power peaks (indicating eccentric knee extensor activity) were generated in the knee, together with relevant Rectus femoris activity. All findings were highly inconsistent with true quadriceps weakness and gave objective ground to suspect insincerity of patient complaints. 3D gait analysis might be a valuable clinical assessment tool in suspected feigned lower limb muscle weakness.

  16. Automated quantification and integrative analysis of 2D and 3D mitochondrial shape and network properties.

    Directory of Open Access Journals (Sweden)

    Julie Nikolaisen

    Full Text Available Mitochondrial morphology and function are coupled in healthy cells, during pathological conditions and (adaptation to endogenous and exogenous stress. In this sense mitochondrial shape can range from small globular compartments to complex filamentous networks, even within the same cell. Understanding how mitochondrial morphological changes (i.e. "mitochondrial dynamics" are linked to cellular (patho physiology is currently the subject of intense study and requires detailed quantitative information. During the last decade, various computational approaches have been developed for automated 2-dimensional (2D analysis of mitochondrial morphology and number in microscopy images. Although these strategies are well suited for analysis of adhering cells with a flat morphology they are not applicable for thicker cells, which require a three-dimensional (3D image acquisition and analysis procedure. Here we developed and validated an automated image analysis algorithm allowing simultaneous 3D quantification of mitochondrial morphology and network properties in human endothelial cells (HUVECs. Cells expressing a mitochondria-targeted green fluorescence protein (mitoGFP were visualized by 3D confocal microscopy and mitochondrial morphology was quantified using both the established 2D method and the new 3D strategy. We demonstrate that both analyses can be used to characterize and discriminate between various mitochondrial morphologies and network properties. However, the results from 2D and 3D analysis were not equivalent when filamentous mitochondria in normal HUVECs were compared with circular/spherical mitochondria in metabolically stressed HUVECs treated with rotenone (ROT. 2D quantification suggested that metabolic stress induced mitochondrial fragmentation and loss of biomass. In contrast, 3D analysis revealed that the mitochondrial network structure was dissolved without affecting the amount and size of the organelles. Thus, our results demonstrate

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

    Institute of Scientific and Technical Information of China (English)

    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.

  18. Mobile 3D quality of experience evaluation: a hybrid data collection and analysis approach

    Science.gov (United States)

    Utriainen, Timo; Häyrynen, Jyrki; Jumisko-Pyykkö, Satu; Boev, Atanas; Gotchev, Atanas; Hannuksela, Miska M.

    2011-02-01

    The paper presents a hybrid approach to study the user's experienced quality of 3D visual content on mobile autostereoscopic displays. It combines extensive subjective tests with collection and objective analysis of eye-tracked data. 3D cues which are significant for mobiles are simulated in the generated 3D test content. The methodology for conducting subjective quality evaluation includes hybrid data-collection of quantitative quality preferences, qualitative impressions, and binocular eye-tracking. We present early results of the subjective tests along with eye movement reaction times, areas of interest and heatmaps obtained from raw eye-tracked data after statistical analysis. The study contributes to the question what is important to be visualized on portable auto-stereoscopic displays and how to maintain and visually enhance the quality of 3D content for such displays.

  19. A 3D sparse motion field filtering for quantitative analysis of fascial layers mobility based on 3D ultrasound scans.

    Science.gov (United States)

    Turini, G; Condino, S; Stecco, A; Ferrari, V; Ferrari, M; Gesi, M

    2015-08-01

    In the last few years, there has been an increasing interest in the role of deep fascia mobility in musculoskeletal dynamics and chronic pain mechanisms. In a previous paper we presented an innovative semiautomatic approach to evaluate the 3D motion of the fascia using ultrasound (US) imaging, generating a sparse deformation vector field. This paper presents an improvement of our original method, focusing on the filtering of the sparse vector field and its validation. Moreover, in order to evaluate the performance of the algorithm, a method is proposed to generate synthetic deformation vector fields, including: expansion, rotation, horizontal shear, and oblique shear components. Preliminary tests on the final synthetic deformation vector fields showed promising results. Further experiments are required in order to optimize the tuning of the algorithm.

  20. 3D texture analysis in renal cell carcinoma tissue image grading.

    Science.gov (United States)

    Kim, Tae-Yun; Cho, Nam-Hoon; Jeong, Goo-Bo; Bengtsson, Ewert; Choi, Heung-Kook

    2014-01-01

    One of the most significant processes in cancer cell and tissue image analysis is the efficient extraction of features for grading purposes. This research applied two types of three-dimensional texture analysis methods to the extraction of feature values from renal cell carcinoma tissue images, and then evaluated the validity of the methods statistically through grade classification. First, we used a confocal laser scanning microscope to obtain image slices of four grades of renal cell carcinoma, which were then reconstructed into 3D volumes. Next, we extracted quantitative values using a 3D gray level cooccurrence matrix (GLCM) and a 3D wavelet based on two types of basis functions. To evaluate their validity, we predefined 6 different statistical classifiers and applied these to the extracted feature sets. In the grade classification results, 3D Haar wavelet texture features combined with principal component analysis showed the best discrimination results. Classification using 3D wavelet texture features was significantly better than 3D GLCM, suggesting that the former has potential for use in a computer-based grading system.

  1. 3D Texture Analysis in Renal Cell Carcinoma Tissue Image Grading

    Directory of Open Access Journals (Sweden)

    Tae-Yun Kim

    2014-01-01

    Full Text Available One of the most significant processes in cancer cell and tissue image analysis is the efficient extraction of features for grading purposes. This research applied two types of three-dimensional texture analysis methods to the extraction of feature values from renal cell carcinoma tissue images, and then evaluated the validity of the methods statistically through grade classification. First, we used a confocal laser scanning microscope to obtain image slices of four grades of renal cell carcinoma, which were then reconstructed into 3D volumes. Next, we extracted quantitative values using a 3D gray level cooccurrence matrix (GLCM and a 3D wavelet based on two types of basis functions. To evaluate their validity, we predefined 6 different statistical classifiers and applied these to the extracted feature sets. In the grade classification results, 3D Haar wavelet texture features combined with principal component analysis showed the best discrimination results. Classification using 3D wavelet texture features was significantly better than 3D GLCM, suggesting that the former has potential for use in a computer-based grading system.

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

    Science.gov (United States)

    Di Simone, Alessio

    2016-06-25

    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.

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

    Directory of Open Access Journals (Sweden)

    Alessio Di Simone

    2016-06-01

    Full Text Available 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.

  4. 2D vs 3D gamma analysis: Establishment of comparable clinical action limits

    Directory of Open Access Journals (Sweden)

    Kiley B Pulliam

    2014-03-01

    Full Text Available Purpose: As clinics begin to use 3D metrics for intensity-modulated radiation therapy (IMRT quality assurance; these metrics will often produce results different from those produced by their 2D counterparts. 3D and 2D gamma analyses would be expected to produce different values, because of the different search space available. We compared the results of 2D and 3D gamma analysis (where both datasets were generated the same way for clinical treatment plans.                    Methods: 50 IMRT plans were selected from our database and recalculated using Monte Carlo. Treatment planning system-calculated (“evaluated” and Monte Carlo-recalculated (“reference” dose distributions were compared using 2D and 3D gamma analysis. This analysis was performed using a variety of dose-difference (5%, 3%, 2%, and 1% and distance-to-agreement (5, 3, 2, and 1 mm acceptance criteria, low-dose thresholds (5%, 10%, and 15% of the prescription dose, and data grid sizes (1.0, 1.5, and 3.0 mm. Each comparison was evaluated to determine the average 2D and 3D gamma and percentage of pixels passing gamma.Results: Average gamma and percentage of passing pixels for each acceptance criterion demonstrated better agreement for 3D than for 2D analysis for every plan comparison. Average difference in the percentage of passing pixels between the 2D and 3D analyses with no low-dose threshold ranged from 0.9% to 2.1%. Similarly, using a low-dose threshold resulted in a differences ranging from 0.8% to 1.5%. No appreciable differences in gamma with changes in the data density (constant difference: 0.8% for 2D vs. 3D were observed.Conclusion: We found that 3D gamma analysis resulted in up to 2.9% more pixels passing than 2D analysis.  Factors such as inherent dosimeter differences may be an important additional consideration to the extra dimension of available data that was evaluated in this study.------------------------------------Cite this article as

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

    DEFF Research Database (Denmark)

    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...

  6. 3D video analysis of the novel object recognition test in rats.

    Science.gov (United States)

    Matsumoto, Jumpei; Uehara, Takashi; Urakawa, Susumu; Takamura, Yusaku; Sumiyoshi, Tomiki; Suzuki, Michio; Ono, Taketoshi; Nishijo, Hisao

    2014-10-01

    The novel object recognition (NOR) test has been widely used to test memory function. We developed a 3D computerized video analysis system that estimates nose contact with an object in Long Evans rats to analyze object exploration during NOR tests. The results indicate that the 3D system reproducibly and accurately scores the NOR test. Furthermore, the 3D system captures a 3D trajectory of the nose during object exploration, enabling detailed analyses of spatiotemporal patterns of object exploration. The 3D trajectory analysis revealed a specific pattern of object exploration in the sample phase of the NOR test: normal rats first explored the lower parts of objects and then gradually explored the upper parts. A systematic injection of MK-801 suppressed changes in these exploration patterns. The results, along with those of previous studies, suggest that the changes in the exploration patterns reflect neophobia to a novel object and/or changes from spatial learning to object learning. These results demonstrate that the 3D tracking system is useful not only for detailed scoring of animal behaviors but also for investigation of characteristic spatiotemporal patterns of object exploration. The system has the potential to facilitate future investigation of neural mechanisms underlying object exploration that result from dynamic and complex brain activity.

  7. 2D and 3D stability analysis of slurry trench in frictional/cohesive soil

    Institute of Scientific and Technical Information of China (English)

    Chang-yu HAN; Jin-jian CHEN; Jian-hua WANG; Xiao-he XIA

    2013-01-01

    A 2D and 3D kinematically admissible rotational failure mechanism is presented for homogeneous slurry trenches in frictional/cohesive soils.Analytical approaches are derived to obtain the upper bounds on slurry trench stability in the strict framework of limit analysis.It is shown that the factor of safety from a 3D analysis will be greater than that from a 2D analysis.Compared with the limit equilibrium method,the limit analysis method yields an unconservative estimate on the safety factors.A set of examples are presented in a wide range of parameters for 2D and 3D homogeneous slurry trenches.The factor of safety increases with increasing slurry and soil bulk density ratio,cohesion,friction angle,and with decreasing slurry level depth and trench depth ratio,trench width and depth ratio.It is convenient to assess the safety for the homogeneous slurry trenches in practical applications.

  8. 3D finite element analysis of porous Ti-based alloy prostheses.

    Science.gov (United States)

    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.

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

    Directory of Open Access Journals (Sweden)

    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.

  10. A detailed 3D finite element analysis of the peeling behaviour of a gecko spatula

    NARCIS (Netherlands)

    Sauer, R.A.; Holl, M.

    2013-01-01

    This paper presents a detailed finite element analysis of the adhesion of a gecko spatula. The gecko spatulae form the tips of the gecko foot hairs that transfer the adhesional and frictional forces between substrate and foot. The analysis is based on a parameterised description of the 3D geometry o

  11. Multi-Layer Identification of Highly-Potent ABCA1 Up-Regulators Targeting LXRβ Using Multiple QSAR Modeling, Structural Similarity Analysis, and Molecular Docking

    Directory of Open Access Journals (Sweden)

    Meimei Chen

    2016-11-01

    Full Text Available In this study, in silico approaches, including multiple QSAR modeling, structural similarity analysis, and molecular docking, were applied to develop QSAR classification models as a fast screening tool for identifying highly-potent ABCA1 up-regulators targeting LXRβ based on a series of new flavonoids. Initially, four modeling approaches, including linear discriminant analysis, support vector machine, radial basis function neural network, and classification and regression trees, were applied to construct different QSAR classification models. The statistics results indicated that these four kinds of QSAR models were powerful tools for screening highly potent ABCA1 up-regulators. Then, a consensus QSAR model was developed by combining the predictions from these four models. To discover new ABCA1 up-regulators at maximum accuracy, the compounds in the ZINC database that fulfilled the requirement of structural similarity of 0.7 compared to known potent ABCA1 up-regulator were subjected to the consensus QSAR model, which led to the discovery of 50 compounds. Finally, they were docked into the LXRβ binding site to understand their role in up-regulating ABCA1 expression. The excellent binding modes and docking scores of 10 hit compounds suggested they were highly-potent ABCA1 up-regulators targeting LXRβ. Overall, this study provided an effective strategy to discover highly potent ABCA1 up-regulators.

  12. Visualization and analysis of 3D gene expression patterns in zebrafish using web services

    Science.gov (United States)

    Potikanond, D.; Verbeek, F. J.

    2012-01-01

    The analysis of patterns of gene expression patterns analysis plays an important role in developmental biology and molecular genetics. Visualizing both quantitative and spatio-temporal aspects of gene expression patterns together with referenced anatomical structures of a model-organism in 3D can help identifying how a group of genes are expressed at a certain location at a particular developmental stage of an organism. In this paper, we present an approach to provide an online visualization of gene expression data in zebrafish (Danio rerio) within 3D reconstruction model of zebrafish in different developmental stages. We developed web services that provide programmable access to the 3D reconstruction data and spatial-temporal gene expression data maintained in our local repositories. To demonstrate this work, we develop a web application that uses these web services to retrieve data from our local information systems. The web application also retrieve relevant analysis of microarray gene expression data from an external community resource; i.e. the ArrayExpress Atlas. All the relevant gene expression patterns data are subsequently integrated with the reconstruction data of the zebrafish atlas using ontology based mapping. The resulting visualization provides quantitative and spatial information on patterns of gene expression in a 3D graphical representation of the zebrafish atlas in a certain developmental stage. To deliver the visualization to the user, we developed a Java based 3D viewer client that can be integrated in a web interface allowing the user to visualize the integrated information over the Internet.

  13. Spatial and temporal analysis of DIII-D 3D magnetic diagnostic data

    Science.gov (United States)

    Strait, E. J.; King, J. D.; Hanson, J. M.; Logan, N. C.

    2016-11-01

    An extensive set of magnetic diagnostics in DIII-D is aimed at measuring non-axisymmetric "3D" features of tokamak plasmas, with typical amplitudes ˜10-3 to 10-5 of the total magnetic field. We describe hardware and software techniques used at DIII-D to condition the individual signals and analysis to estimate the spatial structure from an ensemble of discrete measurements. Applications of the analysis include detection of non-rotating MHD instabilities, plasma control, and validation of MHD stability and 3D equilibrium models.

  14. Statistical 2D and 3D shape analysis using Non-Euclidean Metrics

    DEFF Research Database (Denmark)

    Larsen, Rasmus; Hilger, Klaus Baggesen; Wrobel, Mark Christoph

    2002-01-01

    We address the problem of extracting meaningful, uncorrelated biological modes of variation from tangent space shape coordinates in 2D and 3D using non-Euclidean metrics. We adapt the maximum autocorrelation factor analysis and the minimum noise fraction transform to shape decomposition. Furtherm......We address the problem of extracting meaningful, uncorrelated biological modes of variation from tangent space shape coordinates in 2D and 3D using non-Euclidean metrics. We adapt the maximum autocorrelation factor analysis and the minimum noise fraction transform to shape decomposition...

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

    Directory of Open Access Journals (Sweden)

    S. Tavani

    2010-12-01

    Full Text Available In this work we present the Open Plot Project, a software for structural data analysis including a 3-D environment. This first alpha release represents a stand-alone toolkit for structural data analysis and, due to many import/export facilities and to the presence of a 3-D environment, also candidates as a tool to be incorporated in workflows for 3-D geological modelling.

    The software (for both Windows and Linux O.S., the User Manual, a set of example movies, and the source code are provided as Supplement. It is our purpose that the publication of the source code sets the base for the development of a public and free software that, hopefully, the structural geologists community will use, modify, and implement. The creation of additional public controls/tools is strongly encouraged.

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

    CERN Document Server

    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 ...

  17. 3D texture analysis for classification of second harmonic generation images of human ovarian cancer

    Science.gov (United States)

    Wen, Bruce; Campbell, Kirby R.; Tilbury, Karissa; Nadiarnykh, Oleg; Brewer, Molly A.; Patankar, Manish; Singh, Vikas; Eliceiri, Kevin. W.; Campagnola, Paul J.

    2016-10-01

    Remodeling of the collagen architecture in the extracellular matrix (ECM) has been implicated in ovarian cancer. To quantify these alterations we implemented a form of 3D texture analysis to delineate the fibrillar morphology observed in 3D Second Harmonic Generation (SHG) microscopy image data of normal (1) and high risk (2) ovarian stroma, benign ovarian tumors (3), low grade (4) and high grade (5) serous tumors, and endometrioid tumors (6). We developed a tailored set of 3D filters which extract textural features in the 3D image sets to build (or learn) statistical models of each tissue class. By applying k-nearest neighbor classification using these learned models, we achieved 83-91% accuracies for the six classes. The 3D method outperformed the analogous 2D classification on the same tissues, where we suggest this is due the increased information content. This classification based on ECM structural changes will complement conventional classification based on genetic profiles and can serve as an additional biomarker. Moreover, the texture analysis algorithm is quite general, as it does not rely on single morphological metrics such as fiber alignment, length, and width but their combined convolution with a customizable basis set.

  18. Analysis of 3-D images of dental imprints using computer vision

    Science.gov (United States)

    Aubin, Michele; Cote, Jean; Laurendeau, Denis; Poussart, Denis

    1992-05-01

    This paper addressed two important aspects of dental analysis: (1) location and (2) identification of the types of teeth by means of 3-D image acquisition and segmentation. The 3-D images of both maxillaries are acquired using a wax wafer as support. The interstices between teeth are detected by non-linear filtering of the 3-D and grey-level data. Two operators are presented: one for the detection of the interstices between incisors, canines, and premolars and one for those between molars. Teeth are then identified by mapping the imprint under analysis on the computer model of an 'ideal' imprint. For the mapping to be valid, a set of three reference points is detected on the imprint. Then, the points are put in correspondence with similar points on the model. Two such points are chosen based on a least-squares fit of a second-order polynomial of the 3-D data in the area of canines. This area is of particular interest since the canines show a very characteristic shape and are easily detected on the imprint. The mapping technique is described in detail in the paper as well as pre-processing of the 3-D profiles. Experimental results are presented for different imprints.

  19. Application of multi-resolution 3D techniques in crime scene documentation with bloodstain pattern analysis.

    Science.gov (United States)

    Hołowko, Elwira; Januszkiewicz, Kamil; Bolewicki, Paweł; Sitnik, Robert; Michoński, Jakub

    2016-10-01

    In forensic documentation with bloodstain pattern analysis (BPA) it is highly desirable to obtain non-invasively overall documentation of a crime scene, but also register in high resolution single evidence objects, like bloodstains. In this study, we propose a hierarchical 3D scanning platform designed according to the top-down approach known from the traditional forensic photography. The overall 3D model of a scene is obtained via integration of laser scans registered from different positions. Some parts of a scene being particularly interesting are documented using midrange scanner, and the smallest details are added in the highest resolution as close-up scans. The scanning devices are controlled using developed software equipped with advanced algorithms for point cloud processing. To verify the feasibility and effectiveness of multi-resolution 3D scanning in crime scene documentation, our platform was applied to document a murder scene simulated by the BPA experts from the Central Forensic Laboratory of the Police R&D, Warsaw, Poland. Applying the 3D scanning platform proved beneficial in the documentation of a crime scene combined with BPA. The multi-resolution 3D model enables virtual exploration of a scene in a three-dimensional environment, distance measurement, and gives a more realistic preservation of the evidences together with their surroundings. Moreover, high-resolution close-up scans aligned in a 3D model can be used to analyze bloodstains revealed at the crime scene. The result of BPA such as trajectories, and the area of origin are visualized and analyzed in an accurate model of a scene. At this stage, a simplified approach considering the trajectory of blood drop as a straight line is applied. Although the 3D scanning platform offers a new quality of crime scene documentation with BPA, some of the limitations of the technique are also mentioned.

  20. 3D intrathoracic region definition and its application to PET-CT analysis

    Science.gov (United States)

    Cheirsilp, Ronnarit; Bascom, Rebecca; Allen, Thomas W.; Higgins, William E.

    2014-03-01

    Recently developed integrated PET-CT scanners give co-registered multimodal data sets that offer complementary three-dimensional (3D) digital images of the chest. PET (positron emission tomography) imaging gives highly specific functional information of suspect cancer sites, while CT (X-ray computed tomography) gives associated anatomical detail. Because the 3D CT and PET scans generally span the body from the eyes to the knees, accurate definition of the intrathoracic region is vital for focusing attention to the central-chest region. In this way, diagnostically important regions of interest (ROIs), such as central-chest lymph nodes and cancer nodules, can be more efficiently isolated. We propose a method for automatic segmentation of the intrathoracic region from a given co-registered 3D PET-CT study. Using the 3D CT scan as input, the method begins by finding an initial intrathoracic region boundary for a given 2D CT section. Next, active contour analysis, driven by a cost function depending on local image gradient, gradient-direction, and contour shape features, iteratively estimates the contours spanning the intrathoracic region on neighboring 2D CT sections. This process continues until the complete region is defined. We next present an interactive system that employs the segmentation method for focused 3D PET-CT chest image analysis. A validation study over a series of PET-CT studies reveals that the segmentation method gives a Dice index accuracy of less than 98%. In addition, further results demonstrate the utility of the method for focused 3D PET-CT chest image analysis, ROI definition, and visualization.

  1. Development of 3D Chromatin Texture Analysis Using Confocal Laser Scanning Microscopy

    Directory of Open Access Journals (Sweden)

    André Huisman

    2005-01-01

    Full Text Available Introduction: Analysis of nuclear texture features as a measure of nuclear chromatin changes has been proven to be useful when measured on thin (5–6 μm tissue sections using conventional 2D bright field microscopy. The drawback of this approach is that most nuclei are not intact because of those thin sections. Confocal laser scanning microscopy (CLSM allows measurements of texture in 3D reconstructed nuclei. The aim of this study was to develop 3D texture features that quantitatively describe changes in chromatin architecture associated with malignancy using CLSM images. Methods: Thirty-five features thoughtfully chosen from 4 categories of 3D texture features (discrete texture features, Markovian features, fractal features, grey value distribution features were selected and tested for invariance properties (rotation and scaling using artificial images with a known grey value distribution. The discriminative power of the 3D texture features was tested on artificially constructed benign and malignant 3D nuclei with increasing nucleolar size and advancing chromatin margination towards the periphery of the nucleus. As a clinical proof of principle, the discriminative power of the texture features was assessed on 10 benign and 10 malignant human prostate nuclei, evaluating also whether there was more texture information in 3D whole nuclei compared to a single 2D plane from the middle of the nucleus. Results: All texture features showed the expected invariance properties. Almost all features were sensitive to variations in the nucleolar size and to the degree of margination of chromatin. Fourteen texture features from different categories had high discriminative power for separating the benign and malignant nuclei. The discrete texture features performed less than expected. There was more information on nuclear texture in 3D than in 2D. Conclusion: A set of 35 3D nuclear texture features was used successfully to assess nuclear chromatin patterns

  2. Critical body residues linked to octanol-water partitioning, organism composition, and LC50 QSARs: meta-analysis and model.

    Science.gov (United States)

    Hendriks, A Jan; Traas, Theo P; Huijbregts, Mark A J

    2005-05-01

    To protect thousands of species from thousands of chemicals released in the environment, various risk assessment tools have been developed. Here, we link quantitative structure-activity relationships (QSARs) for response concentrations in water (LC50) to critical concentrations in organisms (C50) by a model for accumulation in lipid or non-lipid phases versus water Kpw. The model indicates that affinity for neutral body components such as storage fat yields steep Kpw-Kow relationships, whereas slopes for accumulation in polar phases such as proteins are gentle. This pattern is confirmed by LC50 QSARs for different modes of action, such as neutral versus polar narcotics and organochlorine versus organophosphor insecticides. LC50 QSARs were all between 0.00002 and 0.2Kow(-1). After calibrating the model with the intercepts and, for the first time also, with the slopes of the LC50 QSARs, critical concentrations in organisms C50 are calculated and compared to an independent validation data set. About 60% of the variability in lethal body burdens C50 is explained by the model. Explanations for differences between estimated and measured levels for 11 modes of action are discussed. In particular, relationships between the critical concentrations in organisms C50 and chemical (Kow) or species (lipid content) characteristics are specified and tested. The analysis combines different models proposed before and provides a substantial extension of the data set in comparison to previous work. Moreover, the concept is applied to species (e.g., plants, lean animals) and substances (e.g., specific modes of action) that were scarcely studied quantitatively so far.

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

    Directory of Open Access Journals (Sweden)

    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.

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

    Directory of Open Access Journals (Sweden)

    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.

  5. New technologies of 2-D and 3-D modeling for analysis and management of natural resources

    Science.gov (United States)

    Cheremisina, E. N.; Lyubimova, A. V.; Kirpicheva, E. Yu.

    2016-09-01

    For ensuring technological support of research and administrative activity in the sphere of environmental management a specialized modular program complex was developed. The special attention in developing a program complex is focused to creation of convenient and effective tools for creation and visualization 2d and 3D models providing the solution of tasks of the analysis and management of natural resources.

  6. A 3D contact analysis approach for the visualization of the electrical contact asperities

    Science.gov (United States)

    Swingler, Jonathan

    2017-01-01

    The electrical contact is an important phenomenon that should be given into consideration to achieve better performance and long term reliability for the design of devices. Based upon this importance, the electrical contact interface has been visualized as a ‘‘3D Contact Map’’ and used in order to investigate the contact asperities. The contact asperities describe the structures above and below the contact spots (the contact spots define the 3D contact map) to the two conductors which make the contact system. The contact asperities require the discretization of the 3D microstructures of the contact system into voxels. A contact analysis approach has been developed and introduced in this paper which shows the way to the 3D visualization of the contact asperities of a given contact system. For the discretization of 3D microstructure of contact system into voxels, X-ray Computed Tomography (CT) method is used in order to collect the data of a 250 V, 16 A rated AC single pole rocker switch which is used as a contact system for investigation. PMID:28105383

  7. Finite element analysis of 3D elastic-plastic frictional contact problem for Cosserat materials

    Science.gov (United States)

    Zhang, S.; Xie, Z. Q.; Chen, B. S.; Zhang, H. W.

    2013-06-01

    The objective of this paper is to develop a finite element model for 3D elastic-plastic frictional contact problem of Cosserat materials. Because 3D elastic-plastic frictional contact problems belong to the unspecified boundary problems with nonlinearities in both material and geometric forms, a large number of calculations are needed to obtain numerical results with high accuracy. Based on the parametric variational principle and the corresponding quadratic programming method for numerical simulation of frictional contact problems, a finite element model is developed for 3D elastic-plastic frictional contact analysis of Cosserat materials. The problems are finally reduced to linear complementarity problems (LCP). Numerical examples show the feasibility and importance of the developed model for analyzing the contact problems of structures with materials which have micro-polar characteristics.

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

    Science.gov (United States)

    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.

  9. 3D city models for CAAD-supported analysis and design of urban areas

    Science.gov (United States)

    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.

  10. A 3-D model of superfluid helium suitable for numerical analysis

    CERN Document Server

    Darve, C; Van Sciver, S W

    2009-01-01

    The two-fluid description is a very successful phenomenological representation of the properties of Helium II. A 3-D model suitable for numerical analysis based on the Landau-Khalatnikov description of Helium II is proposed. In this paper we introduce a system of partial differential equations that is both complete and consistent as well as practical, to be used for a 3-D solution of the flow of Helium II. The development of a 3-D numerical model for Helium II is motivated by the need to validate experimental results obtained by observing the normal component velocity distribution in a Helium II thermal counter-flow using the Particle Image Velocimetry (PIV) technique.

  11. PROP3D: A Program for 3D Euler Unsteady Aerodynamic and Aeroelastic (Flutter and Forced Response) Analysis of Propellers. Version 1.0

    Science.gov (United States)

    Srivastava, R.; Reddy, T. S. R.

    1996-01-01

    This guide describes the input data required, for steady or unsteady aerodynamic and aeroelastic analysis of propellers and the output files generated, in using PROP3D. The aerodynamic forces are obtained by solving three dimensional unsteady, compressible Euler equations. A normal mode structural analysis is used to obtain the aeroelastic equations, which are solved using either time domain or frequency domain solution method. Sample input and output files are included in this guide for steady aerodynamic analysis of single and counter-rotation propellers, and aeroelastic analysis of single-rotation propeller.

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

    Energy Technology Data Exchange (ETDEWEB)

    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.

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

    Energy Technology Data Exchange (ETDEWEB)

    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.

  14. Multivoxel pattern analysis reveals 3D place information in the human hippocampus.

    Science.gov (United States)

    Kim, Misun; Jeffery, Kate J; Maguire, Eleanor A

    2017-03-20

    The spatial world is three-dimensional (3D), and humans and other animals move both horizontally and vertically within it. Extant neuroscientific studies have typically investigated spatial navigation on a horizontal two-dimensional plane, leaving much unknown about how 3D spatial information is represented in the brain. Specifically, horizontal and vertical information may be encoded in the same or different neural structures with equal or unequal sensitivity. Here, we investigated these possibilities using functional MRI (fMRI) while participants were passively moved within a 3D lattice structure as if riding a rollercoaster. Multivoxel pattern analysis was used to test for the existence of information relating to where and in which direction participants were heading in this virtual environment. Behaviorally, participants had similarly accurate memory for vertical and horizontal locations, and the right anterior hippocampus expressed place information that was sensitive to changes along both horizontal and vertical axes. This is suggestive of isotropic 3D place encoding. By contrast, participants indicated their heading direction faster and more accurately when they were heading in a tilted-up or tilted-down direction. This direction information was expressed in the right retrosplenial cortex and posterior hippocampus, and was only sensitive to vertical pitch, which could reflect the importance of the vertical (gravity) axis as a reference frame. Overall, our findings extend previous knowledge of how we represent the spatial world and navigate within it, by taking into account the important third dimension.SIGNIFICANCE STATEMENTThe spatial world is three-dimensional (3D) -- we can move horizontally across surfaces, but also vertically, going up slopes or stairs. Little is known about how the brain supports representations of 3D space. A key question is whether or not horizontal and vertical information is equally well represented. Here we measured functional MRI

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

    Institute of Scientific and Technical Information of China (English)

    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.

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

    Science.gov (United States)

    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.

  17. 3D analysis of vortical structures in an abdominal aortic aneurysm by stereoscopic PIV

    Science.gov (United States)

    Deplano, Valérie; Guivier-Curien, Carine; Bertrand, Eric

    2016-11-01

    The present work presents an experimental in vitro three-dimensional analysis of the flow dynamics in an abdominal aortic aneurysm (AAA) through stereoscopic particle image velocimetry (SPIV) measurements. The experimental set-up mimics the pathophysiological context involving a shear thinning blood analogue fluid, compliant AAA and aorto-iliac bifurcation walls and controlled inlet and outlet flow rate and pressure waveforms as well as working fluid temperature. SPIV was carefully calibrated and conducted to assess the three velocity components in the AAA volume. For the first time in the literature, the 3D vortex ring genesis, propagation, and vanishing in the AAA bulge are experimentally described and quantified. In comparison with classical 2-component PIV measurements (2C PIV), the third component of the velocity vector was shown to be of importance in such a geometry, especially, during the deceleration phase of the flow rate. The 3D velocity magnitude reached up more than 20 % of the 2D one showing that 2C PIV are definitively not accurate enough to provide a complete description of flow behaviour in an AAA. In addition to potential clinical implications of a full 3D vortex ring description in AAA evolution, the 3D in vitro experimental quantification of the flow dynamics carried out in the present study offers an interesting tool for the validation of fluid-structure interaction numerical studies dealing with AAA.

  18. 3D DIGITIZATION OF AN HERITAGE MASTERPIECE - A CRITICAL ANALYSIS ON QUALITY ASSESSMENT

    Directory of Open Access Journals (Sweden)

    F. Menna

    2016-06-01

    Full Text Available Despite being perceived as interchangeable when properly applied, close-range photogrammetry and range imaging have both their pros and limitations that can be overcome using suitable procedures. Even if the two techniques have been frequently cross-compared, critical analysis discussing all sub-phases of a complex digitization project are quite rare. Comparisons taking into account the digitization of a cultural masterpiece, such as the Etruscan Sarcophagus of the Spouses (Figure 1 discussed in this paper, are even less common. The final 3D model of the Sarcophagus shows impressive spatial and texture resolution, in the order of tenths of millimetre for both digitization techniques, making it a large 3D digital model even though the physical size of the artwork is quite limited. The paper presents the survey of the Sarcophagus, a late 6th century BC Etruscan anthropoid Sarcophagus. Photogrammetry and laser scanning were used for its 3D digitization in two different times only few days apart from each other. The very short time available for the digitization was a crucial constraint for the surveying operations (due to constraints imposed us by the museum curators. Despite very high-resolution and detailed 3D models have been produced, a metric comparison between the two models shows intrinsic limitations of each technique that should be overcome through suitable onsite metric verification procedures as well as a proper processing workflow.

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

    Science.gov (United States)

    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.

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

    Directory of Open Access Journals (Sweden)

    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.

  1. Optical properties of 3d-ions in crystals spectroscopy and crystal field analysis

    CERN Document Server

    Brik, Mikhail

    2013-01-01

    "Optical Properties of 3d-Ions in Crystals: Spectroscopy and Crystal Field Analysis" discusses spectral, vibronic and magnetic properties of 3d-ions in a wide range of crystals, used as active media for solid state lasers and potential candidates for this role. Crystal field calculations (including first-principles calculations of energy levels and absorption spectra) and their comparison with experimental spectra, the Jahn-Teller effect, analysis of vibronic spectra, materials science applications are systematically presented. The book is intended for researchers and graduate students in crystal spectroscopy, materials science and optical applications. Dr. N.M. Avram is an Emeritus Professor at the Physics Department, West University of Timisoara, Romania; Dr. M.G. Brik is a Professor at the Institute of Physics, University of Tartu, Estonia.

  2. A Method for Sectioning and Immunohistochemical Analysis of Stem Cell-Derived 3-D Organoids.

    Science.gov (United States)

    Wiley, Luke A; Beebe, David C; Mullins, Robert F; Stone, Edwin M; Tucker, Budd A

    2016-05-12

    This unit describes a protocol for embedding, sectioning, and immunocytochemical analysis of pluripotent stem cell-derived 3-D organoids. Specifically, we describe a method to embed iPSC-derived retinal cups in low-melt agarose, acquire thick sections using a vibratome tissue slicer, and perform immunohistochemical analysis. This method includes an approach for antibody labeling that minimizes the amount of antibody needed for individual experiments and that utilizes large-volume washing to increase the signal-to-noise ratio, allowing for clean, high-resolution imaging of developing cell types. The universal methods described can be employed regardless of the type of pluripotent stem cell used and 3-D organoid generated. © 2016 by John Wiley & Sons, Inc.

  3. Optical parametric oscillators in isotropic photonic crystals and cavities: 3D time domain analysis

    OpenAIRE

    Conti, Claudio; Di Falco, Andrea; Assanto, Gaetano

    2004-01-01

    We investigate optical parametric oscillations through four-wave mixing in resonant cavities and photonic crystals. The theoretical analysis underlines the relevant features of the phenomenon and the role of the density of states. Using fully vectorial 3D time-domain simulations, including both dispersion and nonlinear polarization, for the first time we address this process in a face centered cubic lattice and in a photonic crystal slab. The results lead the way to the development of novel p...

  4. Analysis, Modeling and Dynamic Optimization of 3D Time-of-Flight Imaging Systems

    OpenAIRE

    Schmidt, Mirko

    2011-01-01

    The present thesis is concerned with the optimization of 3D Time-of-Flight (ToF) imaging systems. These novel cameras determine range images by actively illuminating a scene and measuring the time until the backscattered light is detected. Depth maps are constructed from multiple raw images. Usually two of such raw images are acquired simultaneously using special correlating sensors. This thesis covers four main contributions: A physical sensor model is presented which enables the analysis a...

  5. Strategy and software for the statistical spatial analysis of 3D intracellular distributions.

    Science.gov (United States)

    Biot, Eric; Crowell, Elizabeth; Burguet, Jasmine; Höfte, Herman; Vernhettes, Samantha; Andrey, Philippe

    2016-07-01

    The localization of proteins in specific domains or compartments in the 3D cellular space is essential for many fundamental processes in eukaryotic cells. Deciphering spatial organization principles within cells is a challenging task, in particular because of the large morphological variations between individual cells. We present here an approach for normalizing variations in cell morphology and for statistically analyzing spatial distributions of intracellular compartments from collections of 3D images. The method relies on the processing and analysis of 3D geometrical models that are generated from image stacks and that are used to build representations at progressively increasing levels of integration, ultimately revealing statistical significant traits of spatial distributions. To make this methodology widely available to end-users, we implemented our algorithmic pipeline into a user-friendly, multi-platform, and freely available software. To validate our approach, we generated 3D statistical maps of endomembrane compartments at subcellular resolution within an average epidermal root cell from collections of image stacks. This revealed unsuspected polar distribution patterns of organelles that were not detectable in individual images. By reversing the classical 'measure-then-average' paradigm, one major benefit of the proposed strategy is the production and display of statistical 3D representations of spatial organizations, thus fully preserving the spatial dimension of image data and at the same time allowing their integration over individual observations. The approach and software are generic and should be of general interest for experimental and modeling studies of spatial organizations at multiple scales (subcellular, cellular, tissular) in biological systems.

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

    Science.gov (United States)

    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

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

    Energy Technology Data Exchange (ETDEWEB)

    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.

  8. Application of 3D Spatio-Temporal Data Modeling, Management, and Analysis in DB4GEO

    Science.gov (United States)

    Kuper, P. V.; Breunig, M.; Al-Doori, M.; Thomsen, A.

    2016-10-01

    Many of todaýs world wide challenges such as climate change, water supply and transport systems in cities or movements of crowds need spatio-temporal data to be examined in detail. Thus the number of examinations in 3D space dealing with geospatial objects moving in space and time or even changing their shapes in time will rapidly increase in the future. Prominent spatio-temporal applications are subsurface reservoir modeling, water supply after seawater desalination and the development of transport systems in mega cities. All of these applications generate large spatio-temporal data sets. However, the modeling, management and analysis of 3D geo-objects with changing shape and attributes in time still is a challenge for geospatial database architectures. In this article we describe the application of concepts for the modeling, management and analysis of 2.5D and 3D spatial plus 1D temporal objects implemented in DB4GeO, our service-oriented geospatial database architecture. An example application with spatio-temporal data of a landfill, near the city of Osnabrück in Germany demonstrates the usage of the concepts. Finally, an outlook on our future research focusing on new applications with big data analysis in three spatial plus one temporal dimension in the United Arab Emirates, especially the Dubai area, is given.

  9. The three-dimensional elemental distribution based on the surface topography by confocal 3D-XRF analysis

    Energy Technology Data Exchange (ETDEWEB)

    Yi, Longtao; Qin, Min; Wang, Kai; Peng, Shiqi; Sun, Tianxi; Liu, Zhiguo [Beijing Normal University, College of Nuclear Science and Technology, Beijing (China); Lin, Xue [Northwest University, School of Cultural Heritage, Xi' an (China)

    2016-09-15

    Confocal three-dimensional micro-X-ray fluorescence (3D-XRF) is a good surface analysis technology widely used to analyse elements and elemental distributions. However, it has rarely been applied to analyse surface topography and 3D elemental mapping in surface morphology. In this study, a surface adaptive algorithm using the progressive approximation method was designed to obtain surface topography. A series of 3D elemental mapping analyses in surface morphology were performed in laboratories to analyse painted pottery fragments from the Majiayao Culture (3300-2900 BC). To the best of our knowledge, for the first time, sample surface topography and 3D elemental mapping were simultaneously obtained. Besides, component and depth analyses were also performed using synchrotron radiation confocal 3D-XRF and tabletop confocal 3D-XRF, respectively. The depth profiles showed that the sample has a layered structure. The 3D elemental mapping showed that the red pigment, black pigment, and pottery coat contain a large amount of Fe, Mn, and Ca, respectively. From the 3D elemental mapping analyses at different depths, a 3D rendering was obtained, clearly showing the 3D distributions of the red pigment, black pigment, and pottery coat. Compared with conventional 3D scanning, this method is time-efficient for analysing 3D elemental distributions and hence especially suitable for samples with non-flat surfaces. (orig.)

  10. The three-dimensional elemental distribution based on the surface topography by confocal 3D-XRF analysis

    Science.gov (United States)

    Yi, Longtao; Qin, Min; Wang, Kai; Lin, Xue; Peng, Shiqi; Sun, Tianxi; Liu, Zhiguo

    2016-09-01

    Confocal three-dimensional micro-X-ray fluorescence (3D-XRF) is a good surface analysis technology widely used to analyse elements and elemental distributions. However, it has rarely been applied to analyse surface topography and 3D elemental mapping in surface morphology. In this study, a surface adaptive algorithm using the progressive approximation method was designed to obtain surface topography. A series of 3D elemental mapping analyses in surface morphology were performed in laboratories to analyse painted pottery fragments from the Majiayao Culture (3300-2900 BC). To the best of our knowledge, for the first time, sample surface topography and 3D elemental mapping were simultaneously obtained. Besides, component and depth analyses were also performed using synchrotron radiation confocal 3D-XRF and tabletop confocal 3D-XRF, respectively. The depth profiles showed that the sample has a layered structure. The 3D elemental mapping showed that the red pigment, black pigment, and pottery coat contain a large amount of Fe, Mn, and Ca, respectively. From the 3D elemental mapping analyses at different depths, a 3D rendering was obtained, clearly showing the 3D distributions of the red pigment, black pigment, and pottery coat. Compared with conventional 3D scanning, this method is time-efficient for analysing 3D elemental distributions and hence especially suitable for samples with non-flat surfaces.

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

    Energy Technology Data Exchange (ETDEWEB)

    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.

  12. Microstructure analysis of the secondary pulmonary lobules by 3D synchrotron radiation CT

    Science.gov (United States)

    Fukuoka, Y.; Kawata, Y.; Niki, N.; Umetani, K.; Nakano, Y.; Ohmatsu, H.; Moriyama, N.; Itoh, H.

    2014-03-01

    Recognition of abnormalities related to the lobular anatomy has become increasingly important in the diagnosis and differential diagnosis of lung abnormalities at clinical routines of CT examinations. This paper aims a 3-D microstructural analysis of the pulmonary acinus with isotropic spatial resolution in the range of several micrometers by using micro CT. Previously, we demonstrated the ability of synchrotron radiation micro CT (SRμCT) using offset scan mode in microstructural analysis of the whole part of the secondary pulmonary lobule. In this paper, we present a semiautomatic method to segment the acinar and subacinar airspaces from the secondary pulmonary lobule and to track small vessels running inside alveolar walls in human acinus imaged by the SRμCT. The method beains with and segmentation of the tissues such as pleural surface, interlobular septa, alveola wall, or vessel using a threshold technique and 3-D connected component analysis. 3-D air space are then conustructed separated by tissues and represented branching patterns of airways and airspaces distal to the terminal bronchiole. A graph-partitioning approach isolated acini whose stems are interactively defined as the terminal bronchiole in the secondary pulmonary lobule. Finally, we performed vessel tracking using a non-linear sate space which captures both smoothness of the trajectories and intensity coherence along vessel orientations. Results demonstrate that the proposed method can extract several acinar airspaces from the 3-D SRμCT image of secondary pulmonary lobule and that the extracted acinar airspace enable an accurate quantitative description of the anatomy of the human acinus for interpretation of the basic unit of pulmonary structure and function.

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

    Directory of Open Access Journals (Sweden)

    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.

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

    Energy Technology Data Exchange (ETDEWEB)

    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

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

    Science.gov (United States)

    Vrtovec, Tomaz; Likar, Bostjan; Pernus, Franjo

    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 CA

  16. Metabolic biotransformation half-lives in fish: QSAR modeling and consensus analysis.

    Science.gov (United States)

    Papa, Ester; van der Wal, Leon; Arnot, Jon A; Gramatica, Paola

    2014-02-01

    Bioaccumulation in fish is a function of competing rates of chemical uptake and elimination. For hydrophobic organic chemicals bioconcentration, bioaccumulation and biomagnification potential are high and the biotransformation rate constant is a key parameter. Few measured biotransformation rate constant data are available compared to the number of chemicals that are being evaluated for bioaccumulation hazard and for exposure and risk assessment. Three new Quantitative Structure-Activity Relationships (QSARs) for predicting whole body biotransformation half-lives (HLN) in fish were developed and validated using theoretical molecular descriptors that seek to capture structural characteristics of the whole molecule and three data set splitting schemes. The new QSARs were developed using a minimal number of theoretical descriptors (n=9) and compared to existing QSARs developed using fragment contribution methods that include up to 59 descriptors. The predictive statistics of the models are similar thus further corroborating the predictive performance of the different QSARs; Q(2)ext ranges from 0.75 to 0.77, CCCext ranges from 0.86 to 0.87, RMSE in prediction ranges from 0.56 to 0.58. The new QSARs provide additional mechanistic insights into the biotransformation capacity of organic chemicals in fish by including whole molecule descriptors and they also include information on the domain of applicability for the chemical of interest. Advantages of consensus modeling for improving overall prediction and minimizing false negative errors in chemical screening assessments, for identifying potential sources of residual error in the empirical HLN database, and for identifying structural features that are not well represented in the HLN dataset to prioritize future testing needs are illustrated.

  17. Analysis of uncertainty and repeatability of a low-cost 3D laser scanner.

    Science.gov (United States)

    Polo, María-Eugenia; Felicísimo, Angel M

    2012-01-01

    Portable 3D laser scanners are a valuable tool for compiling elaborate digital collections of archaeological objects and analysing the shapes and dimensions of pieces. Although low-cost desktop 3D laser scanners have powerful capacities, it is important to know their limitations. This paper performs an analysis of the uncertainty and repeatability of the NextEngine™ portable low-cost 3D laser scanner by scanning an object 20 times in two different resolution modes-Macro and Wide. Some dimensions of the object were measured using a digital calliper, and these results were used as the "true" or control data. In comparing the true and the scanned data, we verified that the mean uncertainty in the Macro Mode is approximately half that of the Wide Mode, at ± 0.81 mm and ± 1.66 mm, respectively. These experimental results are significantly higher than the accuracy specifications provided by the manufacturer. An analysis of repeatability shows that the successive replicates do not match in the same position. The results are better in Macro Mode than in Wide Mode; it is observed that the repeatability factor is slightly larger than the corresponding mode accuracy, with ± 0.84 vs. ± 0.81 mm in Macro Mode and ± 1.82 vs. ± 1.66 mm in Wide Mode. We suggest several improvements, such as adding an external reference scale or providing a calibrated object to allow for a self-calibration operation of the scanner.

  18. 3D wind-induced response analysis of a cable-membrane structure

    Institute of Scientific and Technical Information of China (English)

    Jun-jie LUO; Da-jian HAN

    2009-01-01

    Wind loading is a dominant factor for design of a cable-membrane structure. Three orthogonal turbulent components, including the longitudinal, lateral and vertical wind velocities, should be taken into account for the wind loads. In this study, a stochastic 3D coupling wind field model is derived by the spectral representation theory, The coherence functions of the three orthognnal turbulent components are considered in this model. Then the model is applied to generate the three correlated wind turbulent components. After that, formulae are proposed to transform the velocities into wind loads, and to introduce the modified wind pressure force. Finally, a wind-induced time-history response analysis is conducted for a 3D cable-membrane structure. Analytical results indicate that responses induced by the proposed wind load model are 10%--25% larger than those by the con-ventionai uncorrelated model, and that the responses are not quite influenced by the modified wind pressure force. Therefore, we concluded that, in the time-history response analysis, the coherences of the three orthogonal turbulent components are necessary for a 3D cable-membrane structure, but the modified wind pressure force can be ignored.

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

    Science.gov (United States)

    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.

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

    Directory of Open Access Journals (Sweden)

    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.

  1. Quasimodes instability analysis of uncertain asymmetric rotor system based on 3D solid element model

    Science.gov (United States)

    Zuo, Yanfei; Wang, Jianjun; Ma, Weimeng

    2017-03-01

    Uncertainties are considered in the equation of motion of an asymmetric rotor system. Based on Hill's determinant method, quasimodes stability analysis with uncertain parameters is used to get stochastic boundaries of unstable regions. Firstly, A 3D finite element rotor model was built in rotating frame with four parameterized coefficients, which is assumed as random parameters representing the uncertainties existing in the rotor system. Then the influences of uncertain coefficients on the distribution of the unstable region boundaries are analyzed. The results show that uncertain parameters have various influences on the size, boundary and number of unstable regions. At last, the statistic results of the minimum and maximum spin speeds of unstable regions were got by Monte Carlo simulation. The used method is suitable for real engineering rotor system, because arbitrary configuration of rotors can be modeled by 3D finite element.

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

    Directory of Open Access Journals (Sweden)

    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.

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

    Science.gov (United States)

    Germaneau, A.; Doumalin, P.; Dupré, J. C.; Brèque, C.; Brémand, F.; D'Houtaud, S.; Rigoard, P.

    2010-06-01

    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.

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

    CERN Document Server

    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...

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

    Institute of Scientific and Technical Information of China (English)

    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.

  6. QSAR analysis on benzodithiazine derivatives as HIV-1 in-tegrase inhibitors

    Institute of Scientific and Technical Information of China (English)

    Ravichandran V; Jain A; Mourya VK; Agrawal RK

    2009-01-01

    Objective:Inhibition of HIV-1 integrase is an important strategy for the treatment of HIV and AIDS.There-fore,HIV-1 integrase inhibitory activity of 3-aroyl-1,1-dioxo-1,4,2-benzodithiazines has been analyzed with different physicochemical parameters.Methods:In the present work,quantitative structure activity relation-ship studies were performed on a series of benzodithiazines as HIV-1 integrase inhibitors using the modeling software Win CAChe version 6.1.Multiple linear regression analysis was performed to derive quantitative structure activity relationship models which were further evaluated for statistical significance and predictive power by internal and external validation.Results:The best QSAR models were having good correlation coeffi-cient (r)with low standard error of estimation (SEE)and cross validated square of correlation coefficient (q2 ).The robustness of the models was checked by Y-randomization test and they were identified as good pre-dictive models.The model for HIV integrase (wt)inhibitory activity of benzodithiazines suggest that the in-crease of dipole moment (Z)of molecules leads to reduce 3'processing and strand transfer inhibitory activity, substitution with high electro positive groups is conducive for the 3'processing inhibitory activity,and the in-crease in heat of formation is favorable for 3'-processing and strand transfer inhibitory activity.Conclusion:The model for HIV integrase (C65s)inhibitory activity of benzodithiazines suggest that the increase of dipole moment (X)of molecules leads to reduce 3'processing and strand transfer inhibitory activity,and the substitu-tion with high hydrophobic groups is conducive for the 3'processing and strand transfer inhibitory.

  7. Depth migration and de-migration for 3-D migration velocity analysis; Migration profondeur et demigration pour l'analyse de vitesse de migration 3D

    Energy Technology Data Exchange (ETDEWEB)

    Assouline, F.

    2001-07-01

    3-D seismic imaging of complex geologic structures requires the use of pre-stack imaging techniques, the post-stack ones being unsuitable in that case. Indeed, pre-stack depth migration is a technique which allows to image accurately complex structures provided that we have at our disposal a subsurface velocity model accurate enough. The determination of this velocity model is thus a key element for seismic imaging, and to this end, migration velocity analysis methods have met considerable interest. The SMART method is a specific migration velocity analysis method: the singularity of this method is that it does not rely on any restrictive assumptions on the complexity of the velocity model to determine. The SMART method uses a detour through the pre-stack depth migrated domain for extracting multi-offset kinematic information hardly accessible in the time domain. Once achieved the interpretation of the pre-stack depth migrated seismic data, a kinematic de-migration technique of the interpreted events enables to obtain a consistent kinematic database (i.e. reflection travel-times). Then, the inversion of these travel-times, by means of reflection tomography, allows the determination of an accurate velocity model. To be able to really image geologic structures for which the 3-D feature is predominant, we have studied the implementation of migration velocity analysis in 3-D in the context of the SMART method, and more generally, we have developed techniques allowing to overcome the intrinsic difficulties in the 3-D aspects of seismic imaging. Indeed, although formally the SMART method can be directly applied to the case of 3-D complex structures, the feasibility of its implementation requires to choose well the imaging domain. Once this choice done, it is also necessary to conceive a method allowing, via the associated de-migration, to obtain the reflection travel-times. We first consider the offset domain which constitutes, still today, the strategy most usually used

  8. 3D strain map of axially loaded mouse tibia: a numerical analysis validated by experimental measurements.

    Science.gov (United States)

    Stadelmann, Vincent A; Hocke, Jean; Verhelle, Jensen; Forster, Vincent; Merlini, Francesco; Terrier, Alexandre; Pioletti, Dominique P

    2009-02-01

    A combined experimental/numerical study was performed to calculate the 3D octahedral shear strain map in a mouse tibia loaded axially. This study is motivated by the fact that the bone remodelling analysis, in this in vivo mouse model should be performed at the zone of highest mechanical stimulus to maximise the measured effects. Accordingly, it is proposed that quantification of bone remodelling should be performed at the tibial crest and at the distal diaphysis. The numerical model could also be used to furnish a more subtle analysis as a precise correlation between local strain and local biological response can be obtained with the experimentally validated numerical model.

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

    Science.gov (United States)

    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

  10. Action Sport Cameras as an Instrument to Perform a 3D Underwater Motion Analysis.

    Science.gov (United States)

    Bernardina, Gustavo R D; Cerveri, Pietro; Barros, Ricardo M L; Marins, João C B; Silvatti, Amanda P

    2016-01-01

    Action sport cameras (ASC) are currently adopted mainly for entertainment purposes but their uninterrupted technical improvements, in correspondence of cost decreases, are going to disclose them for three-dimensional (3D) motion analysis in sport gesture study and athletic performance evaluation quantitatively. Extending this technology to sport analysis however still requires a methodologic step-forward to making ASC a metric system, encompassing ad-hoc camera setup, image processing, feature tracking, calibration and 3D reconstruction. Despite traditional laboratory analysis, such requirements become an issue when coping with both indoor and outdoor motion acquisitions of athletes. In swimming analysis for example, the camera setup and the calibration protocol are particularly demanding since land and underwater cameras are mandatory. In particular, the underwater camera calibration can be an issue affecting the reconstruction accuracy. In this paper, the aim is to evaluate the feasibility of ASC for 3D underwater analysis by focusing on camera setup and data acquisition protocols. Two GoPro Hero3+ Black (frequency: 60Hz; image resolutions: 1280×720/1920×1080 pixels) were located underwater into a swimming pool, surveying a working volume of about 6m3. A two-step custom calibration procedure, consisting in the acquisition of one static triad and one moving wand, carrying nine and one spherical passive markers, respectively, was implemented. After assessing camera parameters, a rigid bar, carrying two markers at known distance, was acquired in several positions within the working volume. The average error upon the reconstructed inter-marker distances was less than 2.5mm (1280×720) and 1.5mm (1920×1080). The results of this study demonstrate that the calibration of underwater ASC is feasible enabling quantitative kinematic measurements with accuracy comparable to traditional motion capture systems.

  11. 3D Finite element analysis of functionally graded multilayered dental ceramic cores.

    Science.gov (United States)

    Al-Maqtari, Ali Abdullah; Razak, Abdul Aziz Abdul; Hamdi, Mohd

    2014-01-01

    This study aimed at investigating and establishing stress distributions in graded multilayered zirconia/alumina ceramic cores and at veneer-core-cement-dentin interfaces, using finite element analysis (FEA), to facilitate the structural design of ceramic cores through computer modeling. An intact maxillary premolar was digitized using CT scanning. An imaging software, Mimics, was used to reconstruct 3D models based on computed tomography (CT) data saved in DICOM format. Eight different 3D models were created for FEA, where each 3D model was meshed and its bottom boundaries constrained. A static load was applied in the oblique direction. The materials were assumed to be isotropic and homogeneous. Highest von Mises stress values were found in areas directly below the load application point, and stress gradually decreased in occlusal loading direction from the external surface toward the dentin. Stress levels occurring at veneer-ceramic core-cement-dentin interfaces were shown to be lower in multilayered ceramic cores than in single-layer models.

  12. Performance Analysis of 3D Massive MIMO Cellular Systems with Collaborative Base Station

    Directory of Open Access Journals (Sweden)

    Xingwang Li

    2014-01-01

    Full Text Available Massive MIMO have drawn considerable attention as they enable significant capacity and coverage improvement in wireless cellular network. However, pilot contamination is a great challenge in massive MIMO systems. Under this circumstance, cooperation and three-dimensional (3D MIMO are emerging technologies to eliminate the pilot contamination and to enhance the performance relative to the traditional interference-limited implementations. Motivated by this, we investigate the achievable sum rate performance of MIMO systems in the uplink employing cooperative base station (BS and 3D MIMO systems. In our model, we consider the effects of both large-scale and small-scale fading, as well as the spatial correlation and indoor-to-outdoor high-rise propagation environment. In particular, we investigate the cooperative communication model based on 3D MIMO and propose a closed-form lower bound on the sum rate. Utilizing this bound, we pursue a “large-system” analysis and provide the asymptotic expression when the number of antennas at the BS grows large, and when the numbers of antennas at transceiver grow large with a fixed ratio. We demonstrate that the lower bound is very tight and becomes exact in the massive MIMO system limits. Finally, under the sum rate maximization condition, we derive the optimal number of UTs to be served.

  13. Analysis of 3d Magnetotelluric Measurements Over the Coso Geothermal Field

    Science.gov (United States)

    Newman, G. A.; Gasperikova, E.; Hoversten, M.

    2007-12-01

    We have carried out an investigation of the Coso Geothermal field utilizing a dense grid of magnetotelluric (MT) stations plus a single line of contiguous bipole array profiling over the east flank of the field. Motivation for this study is that electrical resistivity/conductivity mapping can contribute to better understanding of enhanced geothermal systems (EGS) by imaging the geometry, bounds and controlling structures in existing production, and by monitoring changes in the underground resistivity properties in the vicinity of injection due to fracture porosity enhancement. Initial analysis of the Coso MT data was carried out using 2D MT imaging technology to construct a starting 3D resistivity model from a series of 2D resistivity images obtained using the inline electric field measurements (Zxy impedance elements) along different measurement transects. This model was then refined through a 3D inversion process. The 3D resisitivity model clearly showed the controlling geological structures influencing well production at Coso and shows correlations with mapped surface features such as faults and regional geoelectric strike. We have also correlated the model with an acoustic and shear velocity model of the field to show that the near-vertical high conductivity (low resistivity) structure on the eastern flank of the producing field is also a zone of increase acoustic velocity and increased Vp/Vs ratio.

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

    Directory of Open Access Journals (Sweden)

    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. 3D distribution of interstellar medium in the Galaxy: Preparation for analysis of Gaia observations

    Energy Technology Data Exchange (ETDEWEB)

    Puspitarini, Lucky, E-mail: rosine.lallement@obspm.fr [GEPI Observatoire de Paris, CNRS, Paris Diderot University, 5 Place Jules Janssen, 92190, Meudon (France); Bosscha Observatory and Department of Astronomy, FMIPA, Institut Teknologi Bandung, Jl. Ganesha 10, Bandung 40132 (Indonesia); Lallement, Rosine, E-mail: rosine.lallement@obspm.fr [GEPI Observatoire de Paris, CNRS, Paris Diderot University, 5 Place Jules Janssen, 92190, Meudon (France)

    2015-09-30

    Accurate and detailed three-dimensional (3D) maps of Galactic interstellar medium (ISM) are still lacking. One way to obtain such 3D descriptions is to record a large set of individual absorption or reddening measurements toward target stars located at various known distances and directions. The inversion of these measurements using a tomographic method can produce spatial distribution of the ISM. Until recently absorption data were very limited and distances to the target stars are still uncertain, but the situation will greatly improve thanks to current and future massive stellar surveys from ground, and to Gaia mission. To prepare absorption data for inversion from a huge number of stellar spectra, automated tools are needed. We have developed various spectral analysis tools adapted to different type of spectra, early- or late- type star. We also have used diffuse interstellar bands (DIBs) to trace IS structures and kinematics. Although we do not know yet their carriers, they can be a promising tool to trace distant interstellar clouds or Galactic arms. We present some examples of the interstellar fitting and show the potentiality of DIBs in tracing the ISM. We will also briefly show and comment the latest 3D map of the local ISM which reveal nearby cloud complexes and cavities.

  16. Modeling and validation of a 3D premolar for finite element analysis

    Directory of Open Access Journals (Sweden)

    Letícia Brandão DURAND

    Full Text Available Abstract Introduction The development and validation of mathematical models is an important step of the methodology of finite element studies. Objective This study aims to describe the development and validation of a three-dimensional numerical model of a maxillary premolar for finite element analysis. Material and method The 3D model was based on standardized photographs of sequential slices of an intact premolar and generated with the use of SolidWorks Software (Dassault, France. In order to validate the model, compression and numerical tests were performed. The load versus displacement graphs of both tests were visually compared, the percentage of error calculated and homogeneity of regression coefficients tested. Result An accurate 3D model was developed and validated since the graphs were visually similar, the percentage error was within acceptable limits, and the straight lines were considered parallel. Conclusion The modeling procedures and validation described allows the development of accurate 3D dental models with biomechanical behavior similar to natural teeth. The methods may be applied in development and validation of new models and computer-aided simulations using FEM.

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

    Directory of Open Access Journals (Sweden)

    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.

  18. A Method for 3D Histopathology Reconstruction Supporting Mouse Microvasculature Analysis.

    Directory of Open Access Journals (Sweden)

    Yiwen Xu

    Full Text Available Structural abnormalities of the microvasculature can impair perfusion and function. Conventional histology provides good spatial resolution with which to evaluate the microvascular structure but affords no 3-dimensional information; this limitation could lead to misinterpretations of the complex microvessel network in health and disease. The objective of this study was to develop and evaluate an accurate, fully automated 3D histology reconstruction method to visualize the arterioles and venules within the mouse hind-limb. Sections of the tibialis anterior muscle from C57BL/J6 mice (both normal and subjected to femoral artery excision were reconstructed using pairwise rigid and affine registrations of 5 µm-thick, paraffin-embedded serial sections digitized at 0.25 µm/pixel. Low-resolution intensity-based rigid registration was used to initialize the nucleus landmark-based registration, and conventional high-resolution intensity-based registration method. The affine nucleus landmark-based registration was developed in this work and was compared to the conventional affine high-resolution intensity-based registration method. Target registration errors were measured between adjacent tissue sections (pairwise error, as well as with respect to a 3D reference reconstruction (accumulated error, to capture propagation of error through the stack of sections. Accumulated error measures were lower (p < 0.01 for the nucleus landmark technique and superior vasculature continuity was observed. These findings indicate that registration based on automatic extraction and correspondence of small, homologous landmarks may support accurate 3D histology reconstruction. This technique avoids the otherwise problematic "banana-into-cylinder" effect observed using conventional methods that optimize the pairwise alignment of salient structures, forcing them to be section-orthogonal. This approach will provide a valuable tool for high-accuracy 3D histology tissue

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

    Directory of Open Access Journals (Sweden)

    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. 3D TRANSIENT COUPLED THERMO-ELASTIC-PLASTIC CONTACT SEALING ANALYSIS OF REACTOR PRESSURE VESSEL

    Institute of Scientific and Technical Information of China (English)

    Du Xuesong; Li Runfang; Lin Tengjiao

    2005-01-01

    Sealing analysis of sealing system in reactor pressure vessels is relevant with multiple nonlinear coupled-field effects, so even large-scale commercial finite element software cannot finish the complicated analysis. A fmite element method of 3D transient coupled thermo-elastic-plastic contact sealing analysis for reactor pressure vessels is presented, in which the surface nonlinearity,material nonlinearity, transient heat transfer nonlinearity and multiple coupled effect are taken into account and the sealing equation is coupling solved in iterative procedure. At the same time, a computational analysis program is developed, which is applied in the sealing analysis of experimental reactor pressure vessel, and the numerical results are in good coincidence with the experimental results. This program is also successful in analyzing the practical problem in engineering.

  1. Semi-automated 3D leaf reconstruction and analysis of trichome patterning from light microscopic images.

    Directory of Open Access Journals (Sweden)

    Henrik Failmezger

    2013-04-01

    Full Text Available Trichomes are leaf hairs that are formed by single cells on the leaf surface. They are known to be involved in pathogen resistance. Their patterning is considered to emerge from a field of initially equivalent cells through the action of a gene regulatory network involving trichome fate promoting and inhibiting factors. For a quantitative analysis of single and double mutants or the phenotypic variation of patterns in different ecotypes, it is imperative to statistically evaluate the pattern reliably on a large number of leaves. Here we present a method that enables the analysis of trichome patterns at early developmental leaf stages and the automatic analysis of various spatial parameters. We focus on the most challenging young leaf stages that require the analysis in three dimensions, as the leaves are typically not flat. Our software TrichEratops reconstructs 3D surface models from 2D stacks of conventional light-microscope pictures. It allows the GUI-based annotation of different stages of trichome development, which can be analyzed with respect to their spatial distribution to capture trichome patterning events. We show that 3D modeling removes biases of simpler 2D models and that novel trichome patterning features increase the sensitivity for inter-accession comparisons.

  2. Depth migration and de-migration for 3-D migration velocity analysis; Migration profondeur et demigration pour l'analyse de vitesse de migration 3D

    Energy Technology Data Exchange (ETDEWEB)

    Assouline, F.

    2001-07-01

    3-D seismic imaging of complex geologic structures requires the use of pre-stack imaging techniques, the post-stack ones being unsuitable in that case. Indeed, pre-stack depth migration is a technique which allows to image accurately complex structures provided that we have at our disposal a subsurface velocity model accurate enough. The determination of this velocity model is thus a key element for seismic imaging, and to this end, migration velocity analysis methods have met considerable interest. The SMART method is a specific migration velocity analysis method: the singularity of this method is that it does not rely on any restrictive assumptions on the complexity of the velocity model to determine. The SMART method uses a detour through the pre-stack depth migrated domain for extracting multi-offset kinematic information hardly accessible in the time domain. Once achieved the interpretation of the pre-stack depth migrated seismic data, a kinematic de-migration technique of the interpreted events enables to obtain a consistent kinematic database (i.e. reflection travel-times). Then, the inversion of these travel-times, by means of reflection tomography, allows the determination of an accurate velocity model. To be able to really image geologic structures for which the 3-D feature is predominant, we have studied the implementation of migration velocity analysis in 3-D in the context of the SMART method, and more generally, we have developed techniques allowing to overcome the intrinsic difficulties in the 3-D aspects of seismic imaging. Indeed, although formally the SMART method can be directly applied to the case of 3-D complex structures, the feasibility of its implementation requires to choose well the imaging domain. Once this choice done, it is also necessary to conceive a method allowing, via the associated de-migration, to obtain the reflection travel-times. We first consider the offset domain which constitutes, still today, the strategy most usually used

  3. 3D visualisation and analysis of single and coalescing tracks in Solid state Nuclear Track Detectors

    Science.gov (United States)

    Wertheim, David; Gillmore, Gavin; Brown, Louise; Petford, Nick

    2010-05-01

    Exposure to radon gas (222Rn) and associated ionising decay products can cause lung cancer in humans (1). Solid state Nuclear Track Detectors (SSNTDs) can be used to monitor radon concentrations (2). Radon particles form tracks in the detectors and these tracks can be etched in order to enable 2D surface image analysis. We have previously shown that confocal microscopy can be used for 3D visualisation of etched SSNTDs (3). The aim of the study was to further investigate track angles and patterns in SSNTDs. A 'LEXT' confocal laser scanning microscope (Olympus Corporation, Japan) was used to acquire 3D image datasets of five CR-39 plastic SSNTD's. The resultant 3D visualisations were analysed by eye and inclination angles assessed on selected tracks. From visual assessment, single isolated tracks as well as coalescing tracks were observed on the etched detectors. In addition varying track inclination angles were observed. Several different patterns of track formation were seen such as single isolated and double coalescing tracks. The observed track angles of inclination may help to assess the angle at which alpha particles hit the detector. Darby, S et al. Radon in homes and risk of lung cancer : collaborative analysis of individual data from 13 European case-control studies. British Medical Journal 2005; 330, 223-226. Phillips, P.S., Denman, A.R., Crockett, R.G.M., Gillmore, G., Groves-Kirkby, C.J., Woolridge, A., Comparative Analysis of Weekly vs. Three monthly radon measurements in dwellings. DEFRA Report No., DEFRA/RAS/03.006. (2004). Wertheim D, Gillmore G, Brown L, and Petford N. A new method of imaging particle tracks in Solid State Nuclear Track Detectors. Journal of Microscopy 2010; 237: 1-6.

  4. 3-D inelastic analysis methods for hot section components. Volume 2: Advanced special functions models

    Science.gov (United States)

    Wilson, R. B.; Banerjee, P. K.

    1987-01-01

    This Annual Status Report presents the results of work performed during the third year of the 3-D Inelastic Analysis Methods for Hot Sections Components program (NASA Contract NAS3-23697). The objective of the program is to produce a series of computer codes that permit more accurate and efficient three-dimensional analyses of selected hot section components, i.e., combustor liners, turbine blades, and turbine vanes. The computer codes embody a progression of mathematical models and are streamlined to take advantage of geometrical features, loading conditions, and forms of material response that distinguish each group of selected components.

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

    CERN Document Server

    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.

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

    Science.gov (United States)

    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

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

    Science.gov (United States)

    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.

  8. THEORETICAL ANALYSIS OF COORDINATES MEASUREMENT BY FLEXIBLE 3D MEASURING SYSTEM

    Institute of Scientific and Technical Information of China (English)

    ZHANG Guoyu; SUN Tianxiang; WANG Lingyun; XU Xiping

    2007-01-01

    The system mathematical model of flexible 3D measuring system is built by theoretical analysis, and the theoretical formula for measuring space point coordinate is also derived.Frog-jumping based coordinate transform method is put forward in order to solve measuring problem for large size parts. The flog-jumping method is discussed, and the coordinate transform mathematical model is method of the space point coordinate compared to original value, and an advanced method is provided. Form the space point coordinate transform formula can derive the calculation measuring method for measuring large size parts.

  9. High Resolution 3D Earth Observation Data Analysis for Safeguards Activities

    OpenAIRE

    d'Angelo, Pablo; Rossi, Cristian; Minet, Christian; Eineder, Michael; Flory, Michael; Niemeyer, Irmgard

    2014-01-01

    This paper provides an overview of the investigations performed at DLR with respect to the application of high resolution SAR and optical data for 3D analysis in the context of Safeguards. The Research Center Jülich and the adjacent open cut mines were used as main test sites, and a comprehensive stack of ascending and descending TerraSAR data was acquired over two years. TerraSAR data acquisition was performed, and various ways to visualize and analyze stacks of radar images w...

  10. ANALYSIS OF THE POSSIBILITIES OF USING LOW-COST SCANNING SYSTEM IN 3D MODELING

    Directory of Open Access Journals (Sweden)

    M. Kedzierski

    2016-06-01

    Full Text Available 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

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

    DEFF Research Database (Denmark)

    Couturier, Philippe; Krenk, Steen

    2014-01-01

    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...... an 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....

  12. 3D Simulation of Storm Surge Disaster Based on Scenario Analysis

    Institute of Scientific and Technical Information of China (English)

    王晓玲; 孙小沛; 张胜利; 孙蕊蕊; 李瑞金; 朱泽彪

    2016-01-01

    The occurrence of storm surge disaster is often accompanied with floodplain, overflow, dike breach and other complex phenomena, while current studies on storm surge flooding are more concentrated on the 1D/2D numerical simulation of single disaster scenario (floodplain, overflow or dike breach), ignoring the composite ef-fects of various phenomena. Therefore, considering the uncertainty in the disaster process of storm surge, scenario analysis was firstly proposed to identify the composite disaster scenario including multiple phenomena by analyzing key driving forces, building scenario matrix and deducing situation logic. Secondly, by combining the advantages of k-ωand k-εmodels in the wall treatment, a shear stress transmission k-ωmodel coupled with VOF was proposed to simulate the 3D flood routing for storm surge disaster. Thirdly, risk degree was introduced to make the risk analysis of storm surge disaster. Finally, based on the scenario analysis, four scenarios with different storm surge intensity (100-year and 200-year frequency) were identified in Tianjin Binhai New Area. Then, 3D numerical simulation and risk map were made for the case.

  13. Modification, biological evaluation and 3D QSAR studies of novel 2-(1,3-diaryl- 4,5-dihydro-1H-pyrazol-5-ylphenol derivatives as inhibitors of B-Raf kinase.

    Directory of Open Access Journals (Sweden)

    Yu-Shun Yang

    Full Text Available A series of novel 2-(1,3-diaryl- 4,5-dihydro-1H-pyrazol-5-ylphenol derivatives (C1-C24 have been synthesized. The B-Raf inhibitory activity and anti-proliferation activity of these compounds have been tested. Compound C6 displayed the most potent biological activity against B-RafV600E (IC50 = 0.15 µM and WM266.4 human melanoma cell line (GI50 = 1.75 µM, being comparable with the positive control (Vemurafenib and Erlotinib and more potent than our previous best compounds. The docking simulation was performed to analyze the probable binding models and poses while the QSAR model was built to check the previous work as well as to introduce new directions. This work aimed at seeking more potent inhibitors as well as discussing some previous findings. As a result, the introduction of ortho-hydroxyl group on 4,5-dihydro-1H-pyrazole skeleton did reinforce the anti-tumor activity while enlarging the group on N-1 of pyrazoline was also helpful.

  14. The usefulness of 3D quantitative analysis with using MRI for measuring osteonecrosis of the femoral head

    Energy Technology Data Exchange (ETDEWEB)

    Hwang, Ji Young; Lee, Sun Wha [Ewha Womans University College of Medicine, Seoul (Korea, Republic of); Park, Youn Soo [Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul (Korea, Republic of)

    2006-11-15

    We wanted to evaluate the usefulness of MRI 3D quantitative analysis for measuring osteonecrosis of the femoral head in comparison with MRI 2D quantitative analysis and quantitative analysis of the specimen. For 3 months at our hospital, 14 femoral head specimens with osteonecrosis were obtained after total hip arthroplasty. The patients preoperative MRIs were retrospectively reviewed for quantitative analysis of the size of the necrosis. Each necrotic fraction of the femoral head was measured by 2D quantitative analysis with using mid-coronal and mid-sagittal MRIs, and by 3D quantitative analysis with using serial continuous coronal MRIs and 3D reconstruction software. The necrotic fraction of the specimen was physically measured by the fluid displacement method. The necrotic fraction according to MRI 2D or 3D quantitative analysis was compared with that of the specimen by using Spearman's correlation test. On the correlative analysis, the necrotic fraction by MRI 2D quantitative analysis and quantitative analysis of the specimen showed moderate correlation (r = 0.657); on the other hand, the necrotic fraction by MRI 3D quantitative analysis and quantitative analysis of the specimen demonstrated a strong correlation (r = 0.952) ({rho} < 0.05). MRI 3D quantitative analysis was more accurate than 2D quantitative analysis using MRI for measuring osteonecrosis of the femoral head. Therefore, it may be useful for predicting the clinical outcome and deciding the proper treatment option.

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

    Data.gov (United States)

    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. Corotational formulation for 3d solids. An analysis of geometrically nonlinear foam deformation

    CERN Document Server

    Kaczmarczyk, Łukasz; Pearce, Chris J

    2011-01-01

    This paper presents theory for the Lagrange co-rotational (CR) formulation of finite elements in the geometrically nonlinear analysis of 3D structures. In this paper strains are assumed to be small while the magnitude of rotations from the reference configuration is not restricted. A new best fit rotator and consistent spin filter are derived. Lagrange CR formulation is applied with Hybrid Trefftz Stress elements, although presented methodology can be applied to arbitrary problem formulation and discretization technique, f.e. finite volume methods and lattice models, discreet element methods. Efficiency of CR formulation can be utilized in post-buckling stability analysis, damage and fracture mechanics, modelling of dynamic fragmentation of bodies made from quasi-brittle materials, solid fluid interactions and analysis of post-stressed structures, discreet body dynamics.

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

    Science.gov (United States)

    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.

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

    Directory of Open Access Journals (Sweden)

    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.

  19. 3D finite element model of the diabetic neuropathic foot: a gait analysis driven approach.

    Science.gov (United States)

    Guiotto, Annamaria; Sawacha, Zimi; Guarneri, Gabriella; Avogaro, Angelo; Cobelli, Claudio

    2014-09-22

    Diabetic foot is an invalidating complication of diabetes that can lead to foot ulcers. Three-dimensional (3D) finite element analysis (FEA) allows characterizing the loads developed in the different anatomical structures of the foot in dynamic conditions. The aim of this study was to develop a subject specific 3D foot FE model (FEM) of a diabetic neuropathic (DNS) and a healthy (HS) subject, whose subject specificity can be found in term of foot geometry and boundary conditions. Kinematics, kinetics and plantar pressure (PP) data were extracted from the gait analysis trials of the two subjects with this purpose. The FEM were developed segmenting bones, cartilage and skin from MRI and drawing a horizontal plate as ground support. Materials properties were adopted from previous literature. FE simulations were run with the kinematics and kinetics data of four different phases of the stance phase of gait (heel strike, loading response, midstance and push off). FEMs were then driven by group gait data of 10 neuropathic and 10 healthy subjects. Model validation focused on agreement between FEM-simulated and experimental PP. The peak values and the total distribution of the pressures were compared for this purpose. Results showed that the models were less robust when driven from group data and underestimated the PP in each foot subarea. In particular in the case of the neuropathic subject's model the mean errors between experimental and simulated data were around the 20% of the peak values. This knowledge is crucial in understanding the aetiology of diabetic foot.

  20. 3D thermal-hydraulic analysis of two irregular field joints for the ITER vacuum vessel

    Energy Technology Data Exchange (ETDEWEB)

    Savoldi, Laura, E-mail: laura.savoldi@polito.it [Dipartimento Energia, Politecnico di Torino, I-10129 Torino (Italy); Bonifetto, Roberto [Dipartimento Energia, Politecnico di Torino, I-10129 Torino (Italy); Izquierdo, Jesus [Fusion for Energy, ES-08019 Barcelona (Spain); Le Barbier, Robin; Utin, Yuri [ITER Organization, Route de Vinon sur Verdon, CS 90 046, 13067 Saint Paul Lez Durance Cedex (France); Zanino, Roberto [Dipartimento Energia, Politecnico di Torino, I-10129 Torino (Italy)

    2015-10-15

    Highlights: • ITER vacuum vessel irregular field joints analyzed with ANSYS-FLUENT. • Steady-state thermal-hydraulic performance evaluated with 3D analysis. • Pressure drop comparable to that of regular field joints. • Acceptable hot spots on the inner shell and ports. • Heat transfer coefficient above the target value of 500 W/m{sup 2} K on the inner shell. - Abstract: In ITER, so-called “Irregular” Field Joints (IFJs) are foreseen at the interface between irregular sectors of the Vacuum Vessel (VV), which is located inside the cryostat and houses the in-vessel components. In the IFJs, a peculiar design of the equatorial port, with respect to that adopted in the Regular Field Joints (RFJs), accommodates the irregularities of the adjacent VV sectors. The IFJs are subject to nuclear heating and actively cooled by sub-cooled pressurized water flowing in a dedicated hydraulic loop, which includes the space left open by the borated In-Wall Shielding (IWS). Here we perform the 3D steady state thermal-hydraulic analysis of two different IFJs using the Computational Fluid Dynamics (CFD) software ANSYS-FLUENT{sup ®}. The water flow field, the pressure drop and the temperature maps are computed. The thermal performance of the IFJs in nominal operation is compared to that of an RFJ and it is shown that also in this case enough cooling capability is available to avoid hot spots above the design limits, while the pressure drop remains acceptably low.

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

    Science.gov (United States)

    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.

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

    Directory of Open Access Journals (Sweden)

    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.

  3. [Application of PARAFAC method and 3-D fluorescence spectra in petroleum pollutant measurement and analysis].

    Science.gov (United States)

    Pan, Zhao; Wang, Yu-tian; Shao, Xiao-qing; Wu, Xi-jun; Yang, Li-li

    2012-03-01

    A method for identification and concentration measurement of petroleum pollutant by combining three-dimensional (3-D) fluorescence spectra with parallel factor analysis (PARAFAC) was proposed. The main emphasis of research was the measurement of coexisting different kinds of petroleum. The CCl4 solutions of a 0# diesel sample, a 97# gasoline sample, and a kerosene sample were used as measurement objects. The condition of multiple petroleum coexistence was simulated by petroleum solutions with different mixed ratios. The character of PARAFAC in complex mixture coexisting system analysis was studied. The spectra of three kinds of solutions and the spectra of gasoline-diesel mixed samples, diesel-kerosene mixed samples, and gas oline-diesel mixed with small counts of kerosene interference samples were analyzed respectively. The core consistency diagnostic method and residual sum of squares method were applied to calculate the number of factors in PARAFAC. In gasoline-diesel experiment, gasoline or diesel can be identified and measured as a whole respectively by 2-factors parallel factors analysis. In diesel-kerosene experiment, 2-factors parallel factors analysis can only obtain the characters of diesel, and the 3rd factor is needed to separate the kerosene spectral character from the mixture spectrum. When small counts of kerosene exist in gasoline-diesel solution, gasoline and diesel still can be identified and measured as principal components by a 2-factors parallel factor analysis, and the effect of interference on qualitative analysis is not significant. The experiment verified that the PARAFAC method can obtain characteristic spectrum of each kind of petroleum, and the concentration of petroleum in solutions can be predicted simultaneously, with recoveries shown in the paper. The results showed the possibility of petroleum pollutant identification and concentration measurement based on the 3-D fluorescence spectra and PARAFAC.

  4. Mechanical analysis of single myocyte contraction in a 3-D elastic matrix.

    Directory of Open Access Journals (Sweden)

    John Shaw

    Full Text Available BACKGROUND: Cardiac myocytes experience mechanical stress during each heartbeat. Excessive mechanical stresses under pathological conditions cause functional and structural remodeling that lead to heart diseases, yet the precise mechanisms are still incompletely understood. To study the cellular and molecular level mechanotransduction mechanisms, we developed a new 'cell-in-gel' experimental system to exert multiaxial (3-D stresses on a single myocyte during active contraction. METHODS: Isolated myocytes are embedded in an elastic hydrogel to simulate the mechanical environment in myocardium (afterload. When electrically stimulated, the in-gel myocyte contracts while the matrix resists shortening and broadening of the cell, exerting normal and shear stresses on the cell. Here we provide a mechanical analysis, based on the Eshelby inclusion problem, of the 3-D strain and stress inside and outside the single myocyte during contraction in an elastic matrix. RESULTS: (1 The fractional shortening of the myocyte depends on the cell's geometric dimensions and the relative stiffness of the cell to the gel. A slender or softer cell has less fractional shortening. A myocyte of typical dimensions embedded in a gel of similar elastic stiffness can contract only 20% of its load-free value. (2 The longitudinal stress inside the cell is about 15 times the transverse stress level. (3 The traction on the cell surface is highly non-uniform, with a maximum near its ends, showing 'hot spots' at the location of intercalated disks. (4 The mechanical energy expenditure of the myocyte increases with the matrix stiffness in a monotonic and nonlinear manner. CONCLUSION: Our mechanical analyses provide analytic solutions that readily lend themselves to parametric studies. The resulting 3-D mapping of the strain and stress states serve to analyze and interpret ongoing cell-in-gel experiments, and the mathematical model provides an essential tool to decipher and quantify

  5. Robust object tracking techniques for vision-based 3D motion analysis applications

    Science.gov (United States)

    Knyaz, Vladimir A.; Zheltov, Sergey Y.; Vishnyakov, Boris V.

    2016-04-01

    Automated and accurate spatial motion capturing of an object is necessary for a wide variety of applications including industry and science, virtual reality and movie, medicine and sports. For the most part of applications a reliability and an accuracy of the data obtained as well as convenience for a user are the main characteristics defining the quality of the motion capture system. Among the existing systems for 3D data acquisition, based on different physical principles (accelerometry, magnetometry, time-of-flight, vision-based), optical motion capture systems have a set of advantages such as high speed of acquisition, potential for high accuracy and automation based on advanced image processing algorithms. For vision-based motion capture accurate and robust object features detecting and tracking through the video sequence are the key elements along with a level of automation of capturing process. So for providing high accuracy of obtained spatial data the developed vision-based motion capture system "Mosca" is based on photogrammetric principles of 3D measurements and supports high speed image acquisition in synchronized mode. It includes from 2 to 4 technical vision cameras for capturing video sequences of object motion. The original camera calibration and external orientation procedures provide the basis for high accuracy of 3D measurements. A set of algorithms as for detecting, identifying and tracking of similar targets, so for marker-less object motion capture is developed and tested. The results of algorithms' evaluation show high robustness and high reliability for various motion analysis tasks in technical and biomechanics applications.

  6. 3D geometry analysis of the medial meniscus--a statistical shape modeling approach.

    Science.gov (United States)

    Vrancken, A C T; Crijns, S P M; Ploegmakers, M J M; O'Kane, C; van Tienen, T G; Janssen, D; Buma, P; Verdonschot, N

    2014-10-01

    The geometry-dependent functioning of the meniscus indicates that detailed knowledge on 3D meniscus geometry and its inter-subject variation is essential to design well functioning anatomically shaped meniscus replacements. Therefore, the aim of this study was to quantify 3D meniscus geometry and to determine whether variation in medial meniscus geometry is size- or shape-driven. Also we performed a cluster analysis to identify distinct morphological groups of medial menisci and assessed whether meniscal geometry is gender-dependent. A statistical shape model was created, containing the meniscus geometries of 35 subjects (20 females, 15 males) that were obtained from MR images. A principal component analysis was performed to determine the most important modes of geometry variation and the characteristic changes per principal component were evaluated. Each meniscus from the original dataset was then reconstructed as a linear combination of principal components. This allowed the comparison of male and female menisci, and a cluster analysis to determine distinct morphological meniscus groups. Of the variation in medial meniscus geometry, 53.8% was found to be due to primarily size-related differences and 29.6% due to shape differences. Shape changes were most prominent in the cross-sectional plane, rather than in the transverse plane. Significant differences between male and female menisci were only found for principal component 1, which predominantly reflected size differences. The cluster analysis resulted in four clusters, yet these clusters represented two statistically different meniscal shapes, as differences between cluster 1, 2 and 4 were only present for principal component 1. This study illustrates that differences in meniscal geometry cannot be explained by scaling only, but that different meniscal shapes can be distinguished. Functional analysis, e.g. through finite element modeling, is required to assess whether these distinct shapes actually influence

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

    Science.gov (United States)

    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

  8. Nonlinear coupling analysis of coal seam floor during mining based on FLAC3D

    Institute of Scientific and Technical Information of China (English)

    YAO Duo-xi; XU Ji-ying; LU Hai-feng

    2011-01-01

    Based on the hydro-geological conditions of 1028 mining face in Suntuan Coal Mine, mining seepage strain mechanism of seam floor was simulated by a nonlinear coupling method, which applied fluid-solid coupling analysis module of FLAC3D. The results indicate that the permeability coefficient of adjoining rock changes a lot due to mining. The maximum value reaches 1 379.9 times to the original value, where it is at immediate roof of the mined-out area. According to the analysis on the seepage field, mining does not destroy water resistance of the floor aquiclude. The mining fissure does not conduct lime-stone aquifer, and it is less likely to form damage. The plastic zone does not exactly correspond to the seepage area, and the scope of the altered seepage area is much larger than the plastic zone.

  9. ANALYSIS OF SLAB EDGING BY A 3-D RIGID VISCO-PLASTIC FINITE ELEMENT METHOD

    Institute of Scientific and Technical Information of China (English)

    2002-01-01

    3-D rigid visco-plastic finite element method (FEM) is used in the analysis of metal forming processes, including strip and plate rolling, shape rolling, slab edging, special strip rolling. The shifted incomplete Cholesky decomposition of the stiffness matrix with the solution of the equations for velocity increment by the conjugate gradient method is combined. This technique, termed the shifted ICCG method, is then employed to solve the slab edging problem. The performance of this algorithm in terms of the number of iterations, friction variation, shifted parameter ( and the results of simulation for processing parameters are analysed. Numerical tests and application of this technique verify the efficiency and stability of the shifted ICCG method in the analysis of slab edging.

  10. Shakedown Analysis of 3-D Structures Using the Boundary Element Method Based on the Static Theorem

    Institute of Scientific and Technical Information of China (English)

    张晓峰; 刘应华; 岑章志

    2003-01-01

    The static shakedown theorem was reformulated for the boundary element method (BEM) rather than the finite element method with Melan's theorem, then used to develop a numerical solution procedure for shakedown analysis. The self-equilibrium stress field was constructed by a linear combination of several basis self-equilibrium stress fields with undetermined parameters. These basis self-equilibrium stress fields were expressed as elastic responses of the body to imposed permanent strains obtained using a 3-D BEM elastic-plastic incremental analysis. The lower bound for the shakedown load was obtained from a series of nonlinear mathematical programming problems solved using the Complex method. Numerical examples verified the precision of the present method.

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

    CERN Document Server

    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...

  12. On the Parallel Design and Analysis for 3-D ADI Telegraph Problem with MPI

    Directory of Open Access Journals (Sweden)

    Simon Uzezi Ewedafe

    2014-05-01

    Full Text Available In this paper we describe the 3-D Telegraph Equation (3-DTEL with the use of Alternating Direction Implicit (ADI method on Geranium Cadcam Cluster (GCC with Message Passing Interface (MPI parallel software. The algorithm is presented by the use of Single Program Multiple Data (SPMD technique. The implementation is discussed by means of Parallel Design and Analysis with the use of Domain Decomposition (DD strategy. The 3-DTEL with ADI scheme is implemented on the GCC cluster, with an objective to evaluate the overhead it introduces, with ability to exploit the inherent parallelism of the computation. Results of the parallel experiments are presented. The Speedup and Efficiency from the experiments on different block sizes agree with the theoretical analysis.

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

    Science.gov (United States)

    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

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

    Directory of Open Access Journals (Sweden)

    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.

  15. Novel 3D/VR interactive environment for MD simulations, visualization and analysis.

    Science.gov (United States)

    Doblack, Benjamin N; Allis, Tim; Dávila, Lilian P

    2014-12-18

    The increasing development of computing (hardware and software) in the last decades has impacted scientific research in many fields including materials science, biology, chemistry and physics among many others. A new computational system for the accurate and fast simulation and 3D/VR visualization of nanostructures is presented here, using the open-source molecular dynamics (MD) computer program LAMMPS. This alternative computational method uses modern graphics processors, NVIDIA CUDA technology and specialized scientific codes to overcome processing speed barriers common to traditional computing methods. In conjunction with a virtual reality system used to model materials, this enhancement allows the addition of accelerated MD simulation capability. The motivation is to provide a novel research environment which simultaneously allows visualization, simulation, modeling and analysis. The research goal is to investigate the structure and properties of inorganic nanostructures (e.g., silica glass nanosprings) under different conditions using this innovative computational system. The work presented outlines a description of the 3D/VR Visualization System and basic components, an overview of important considerations such as the physical environment, details on the setup and use of the novel system, a general procedure for the accelerated MD enhancement, technical information, and relevant remarks. The impact of this work is the creation of a unique computational system combining nanoscale materials simulation, visualization and interactivity in a virtual environment, which is both a research and teaching instrument at UC Merced.

  16. Transient Thermal Analysis of 3-D Integrated Circuits Packages by the DGTD Method

    KAUST Repository

    Li, Ping

    2017-03-11

    Since accurate thermal analysis plays a critical role in the thermal design and management of the 3-D system-level integration, in this paper, a discontinuous Galerkin time-domain (DGTD) algorithm is proposed to achieve this purpose. Such as the parabolic partial differential equation (PDE), the transient thermal equation cannot be directly solved by the DGTD method. To address this issue, the heat flux, as an auxiliary variable, is introduced to reduce the Laplace operator to a divergence operator. The resulting PDE is hyperbolic, which can be further written into a conservative form. By properly choosing the definition of the numerical flux used for the information exchange between neighboring elements, the hyperbolic thermal PDE can be solved by the DGTD together with the auxiliary differential equation. The proposed algorithm is a kind of element-level domain decomposition method, which is suitable to deal with multiscale geometries in 3-D integrated systems. To verify the accuracy and robustness of the developed DGTD algorithm, several representative examples are benchmarked.

  17. Analysis of 3D Printed Diopside Scaffolds Properties for Tissue Engineering

    Directory of Open Access Journals (Sweden)

    Tingting LIU

    2015-11-01

    Full Text Available Diopside exhibits favorable potential for bone repair on account of the good mechanical performance, bioactivity and biocompatibility. In this paper, diopside scaffolds with high pore interconnectivity were successfully fabricated by laser three-dimensional (3D printing. The microstructure and mechanical performance of the diopside scaffolds were studied. The experimental analysis indicated that diopside particles gradually fused together until a dense structure was built with an energy density increasing in the range between 2.4 and 4.8 J·mm-2. Meanwhile, compressive strength and fracture toughness increased gradually from 5.96 ± 0.88 MPa to 10.87 ± 0.55 MPa. However, mechanical properties decreased due to the appearance of voids when energy density were 5.4 and 6 J·mm-2. Simulated body fluid (SBF tests showed that apatite crystals formed on the diopside scaffolds surface, and the apatite crystals increased with soaking time. Cell culture tests indicated the scaffolds supported the adhesion and growth of MG-63 cells. The study suggested that diopside scaffolds fabricated by laser 3D printing are promising candidates for bone tissue engineering.DOI: http://dx.doi.org/10.5755/j01.ms.21.4.9845

  18. Multispectral polarization viewing angle analysis of circular polarized stereoscopic 3D displays

    Science.gov (United States)

    Boher, Pierre; Leroux, Thierry; Bignon, Thibault; Collomb-Patton, Véronique

    2010-02-01

    In this paper we propose a method to characterize polarization based stereoscopic 3D displays using multispectral Fourier optics viewing angle measurements. Full polarization analysis of the light emitted by the display in the full viewing cone is made at 31 wavelengths in the visible range. Vertical modulation of the polarization state is observed and explained by the position of the phase shift filter into the display structure. In addition, strong spectral dependence of the ellipticity and polarization degree is observed. These features come from the strong spectral dependence of the phase shift film and introduce some imperfections (color shifts and reduced contrast). Using the measured transmission properties of the two glasses filters, the resulting luminance across each filter is computed for left and right eye views. Monocular contrast for each eye and binocular contrasts are performed in the observer space, and Qualified Monocular and Binocular Viewing Spaces (QMVS and QBVS) can be deduced in the same way as auto-stereoscopic 3D displays allowing direct comparison of the performances.

  19. Promoting best practice design intent in 3D CAD for engineers through a task analysis

    Directory of Open Access Journals (Sweden)

    Keelin Leahy

    2013-01-01

    Full Text Available Assessment encompasses a range of methods and techniques. At the University of Limerick, Ireland, it is an affirmed obligation to facilitate timely and useful feedback for both formative (for learning and summative (of learning assessment. However, the effectiveness of this feedback has raised concern and has a wide-ranging review of research findings. This paper presents research findings to build a picture of the extent to which the impact of feedback as a constructivist paradigm of teaching and learning can promote best practice design intent in 3D CAD Modelling. The resulting data set, comprised of 114 higher education students, is used to discuss the impact of assessment and feedback, comparing semesters Spring 2011/12 and Spring 2012/13. The 2012/13 cohort received formative assessment feedback from a task analysis. This evidenced an upsurge in understanding in best practice design intent in 3D CAD parametric modelling, supported by an effect size of 0.534.

  20. Evolution of residual stress and crack morphologies during 3D FIB tomographic analysis of alumina.

    Science.gov (United States)

    Elfallagh, F; Inkson, B J

    2008-05-01

    Three-dimensional focused ion beam (FIB) tomography is increasingly being used for 3D characterization of microstructures in the 50 nm-20 microm range. FIB tomography is a destructive, invasive process, and microstructural changes may potentially occur during the analysis process. Here residual stress and crack morphologies in single-crystal sapphire samples have been concurrently analyzed using Cr3+ fluorescence spectroscopy and FIB tomography. Specifically, maps of surface residual stress have been obtained from optically polished single-crystal alumina [surface orientation (1 ī 0 2)], from FIB milled surface trenches, from Vickers micro-indentation sites (loads 50 g-300 g), and from Vickers micro-indentation sites during FIB serial sectioning. The residual stress maps clearly show that FIB sputtering generates residual stress changes. For the case of the Vickers micro-indentations, FIB sputtering causes significant changes in residual stress during the FIB tomographic serial sectioning. 3D reconstruction of the crack distribution around micro-indentation sites shows that the cracks observed are influenced by the location of the FIB milled surface trenches due to localized stress changes.

  1. Deterioration estimation of paintings by means of combined 3D and hyperspectral data analysis

    Science.gov (United States)

    Granero-Montagud, Luís.; Portalés, Cristina; Pastor-Carbonell, Begoña.; Ribes-Gómez, Emilio; Gutiérrez-Lucas, Antonio; Tornari, Vivi; Papadakis, Vassilis; Groves, Roger M.; Sirmacek, Beril; Bonazza, Alessandra; Ozga, Izabela; Vermeiren, Jan; van der Zanden, Koen; Föster, Matthias; Aswendt, Petra; Borreman, Albert; Ward, Jon D.; Cardoso, António; Aguiar, Luís.; Alves, Filipa; Ropret, Polonca; Luzón-Nogué, José María.; Dietz, Christian

    2013-05-01

    Deterioration of artwork, in particular paintings, can be produced by environmental factors such as temperature fluctuations, relative humidity variations, ultraviolet radiation and biological factors among others. The effects of these parameters produce changes in both the painting structure and chemical composition. While well established analytical methodologies, such as those based in Raman Spectroscopy and FTIR Spectroscopy require the extraction of a sample for its inspection, other approaches such as hyperspectral imaging and 3D scanning present advantages for in-situ, noninvasive analysis of artwork. In this paper we introduce a novel system and the related methodology to acquire process, generate and analyze 4D data of paintings. Our system is based on non-contact techniques and is used to develop analytical tools which extract rich 3D and hyperspectral maps of the objects, which are processed to obtain accurate quantitative estimations of the deterioration and degradation present in the piece of art. In particular, the construction of 4D data allows the identification of risk maps on the painting representation, which can allow the curators and restorers in the task of painting state evaluation and prioritize intervention actions.

  2. 3D Analysis of Porosity in a Ceramic Coating Using X-ray Microscopy

    Science.gov (United States)

    Klement, Uta; Ekberg, Johanna; Kelly, Stephen T.

    2017-02-01

    Suspension plasma spraying (SPS) is a new, innovative plasma spray technique using a feedstock consisting of fine powder particles suspended in a liquid. Using SPS, ceramic coatings with columnar microstructures have been produced which are used as topcoats in thermal barrier coatings. The microstructure contains a wide pore size range consisting of inter-columnar spacings, micro-pores and nano-pores. Hence, determination of total porosity and pore size distribution is a challenge. Here, x-ray microscopy (XRM) has been applied for describing the complex pore space of the coatings because of its capability to image the (local) porosity within the coating in 3D at a resolution down to 50 nm. The possibility to quantitatively segment the analyzed volume allows analysis of both open and closed porosity. For an yttria-stabilized zirconia coating with feathery microstructure, both open and closed porosity were determined and it could be revealed that 11% of the pore volumes (1.4% of the total volume) are closed pores. The analyzed volume was reconstructed to illustrate the distribution of open and closed pores in 3D. Moreover, pore widths and pore volumes were determined. The results on the complex pore space obtained by XRM are discussed in connection with other porosimetry techniques.

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

    Directory of Open Access Journals (Sweden)

    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.

  4. 3D Finite Element Analysis of PWA-Oil Sand Terrain System Interaction

    Directory of Open Access Journals (Sweden)

    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.

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

    Energy Technology Data Exchange (ETDEWEB)

    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.)

  6. Laser Scanning for 3D Object Characterization: Infrastructure for Exploration and Analysis of Vegetation Signatures

    Science.gov (United States)

    Koenig, K.; Höfle, B.

    2012-04-01

    Mapping and characterization of the three-dimensional nature of vegetation is increasingly gaining in importance. Deeper insight is required for e.g. forest management, biodiversity assessment, habitat analysis, precision agriculture, renewable energy production or the analysis of interaction between biosphere and atmosphere. However the potential of 3D vegetation characterization has not been exploited so far and new technologies are needed. Laser scanning has evolved into the state-of-the-art technology for highly accurate 3D data acquisition. By now several studies indicated a high value of 3D vegetation description by using laser data. The laser sensors provide a detailed geometric presentation (geometric information) of scanned objects as well as a full profile of laser energy that was scattered back to the sensor (radiometric information). In order to exploit the full potential of these datasets, profound knowledge on laser scanning technology for data acquisition, geoinformation technology for data analysis and object of interest (e.g. vegetation) for data interpretation have to be joined. A signature database is a collection of signatures of reference vegetation objects acquired under known conditions and sensor parameters and can be used to improve information extraction from unclassified vegetation datasets. Different vegetation elements (leaves, branches, etc.) at different heights above ground with different geometric composition contribute to the overall description (i.e. signature) of the scanned object. The developed tools allow analyzing tree objects according to single features (e.g. echo width and signal amplitude) and to any relation of features and derived statistical values (e.g. ratio of laser point attributes). For example, a single backscatter cross section value does not allow for tree species determination, whereas the average echo width per tree segment can give good estimates. Statistical values and/or distributions (e.g. Gaussian

  7. A customized model for 3D human segmental kinematic coupling analysis by optoelectronic stereophotogrammetry

    Institute of Scientific and Technical Information of China (English)

    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

  8. Feasibility analysis of high resolution tissue image registration using 3-D synthetic data

    Directory of Open Access Journals (Sweden)

    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.

  9. NODAL3 Sensitivity Analysis for NEACRP 3D LWR Core Transient Benchmark (PWR

    Directory of Open Access Journals (Sweden)

    Surian Pinem

    2016-01-01

    Full Text Available This paper reports the results of sensitivity analysis of the multidimension, multigroup neutron diffusion NODAL3 code for the NEACRP 3D LWR core transient benchmarks (PWR. The code input parameters covered in the sensitivity analysis are the radial and axial node sizes (the number of radial node per fuel assembly and the number of axial layers, heat conduction node size in the fuel pellet and cladding, and the maximum time step. The output parameters considered in this analysis followed the above-mentioned core transient benchmarks, that is, power peak, time of power peak, power, averaged Doppler temperature, maximum fuel centerline temperature, and coolant outlet temperature at the end of simulation (5 s. The sensitivity analysis results showed that the radial node size and maximum time step give a significant effect on the transient parameters, especially the time of power peak, for the HZP and HFP conditions. The number of ring divisions for fuel pellet and cladding gives negligible effect on the transient solutions. For productive work of the PWR transient analysis, based on the present sensitivity analysis results, we recommend NODAL3 users to use 2×2 radial nodes per assembly, 1×18 axial layers per assembly, the maximum time step of 10 ms, and 9 and 1 ring divisions for fuel pellet and cladding, respectively.

  10. Using SAR and QSAR analysis to model the activity and structure of the quinolone-DNA complex.

    Science.gov (United States)

    Llorente, B; Leclerc, F; Cedergren, R

    1996-01-01

    A set of 78 quinolone derivatives were used in a structure-activity study to identify structural features correlating with antibacterial activity. Distinct combinations of functional properties were identified for Gram-negative and Gram-positive bacteria. 3-D Quantitative structure-activity relationship (QSAR) studies identified specific hydrophobic, topologic and electronic properties of the molecules for both in vitro and in vivo activities. From these results, a three-dimensional model of a DNA-quinolone complex was built using molecular modeling techniques. It was based on the intercalation of quinolone into the double helix of DNA. We conclude that the intercalation model is consistent with most available data on the structure of the quinolone complex. This predicted structure is stabilized by the binding of magnesium ion with the sp2 oxygens present in quinolone, a phosphate and a purine base of the DNA. Substituents R1 and R7 are predicted to make hydrophobic interactions in the major and minor groove of DNA, respectively. R7 could also form hydrogen bonds with amino groups of guanines and the aspartic acid residue at position 87 in DNA gyrase subunit A.

  11. Development of QSAR Model of substituted Benzene Sulphonamide using Multiple Regression Analysis

    Directory of Open Access Journals (Sweden)

    R.G.Varma

    2014-01-01

    Full Text Available In continuation of our earlier work in this paper we studied 50 substituted Benzenesulphonamide using substituent nanofluorobutyl sulphonyl chloride (C4F9SO2Cl and pentafluoro benzene sulphonyl chloride (C6F5SO2Cl Accordingly we have development QSAR model of studied compounds. These models were derived using the parameters Balaban Index, Balaban-type index,(Jhetz, Jhetm, Jhetv, Jhete, Jhetp Balaban related index (F,G. and Randic connectivity index (χ1. The best suitable model is predicted on the basis of Maximum-R2 (R-squared.

  12. Inlining 3d Reconstruction, Multi-Source Texture Mapping and Semantic Analysis Using Oblique Aerial Imagery

    Science.gov (United States)

    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

  13. [Upper airway's 3D analysis of patients with obstructive sleep apnea using tomographic cone beam].

    Science.gov (United States)

    Bruwier, A; Poirrier, A L; Limme, M; Poirrier, R

    2014-12-01

    The progress of medical imaging over the last decades has led to a better understanding of the upper airway structure in sleep-disordered patients. The Obstructive Sleep Apnea Syndrome (OSA) is attributed to a functional narrowing of the upper airway, particularly of the oropharynx, during sleep. This narrowing is multifactorial. We have shown that in 60% cases, the maxilla (nasal pyramid) seems too narrow. A mandible retroposition may also play a dominant role in 30% of the cases. Both scenarios can be combined. Cone Beam Computed Tomography (CBCT) is a new medical imaging technique that permits to visualize the upper airway with less ionizing radiation than the conventional scanner. To date, only five authors have performed an upper airway's 3D analysis of sleep apnea patients with cone beam. A better understanding of the affected segment of the upper airway should help refine treatment options.

  14. Micromechanical analysis of nanocomposites using 3D voxel based material model

    DEFF Research Database (Denmark)

    Mishnaevsky, Leon

    2012-01-01

    A computational study on the effect of nanocomposite structures on the elastic properties is carried out with the use of the 3D voxel based model of materials and the combined Voigt–Reuss method. A hierarchical voxel based model of a material reinforced by an array of exfoliated and intercalated...... nanoclay platelets surrounded by interphase layers is developed. With this model, the elastic properties of the interphase layer are estimated using the inverse analysis. The effects of aspect ratio, intercalation and orientation of nanoparticles on the elastic properties of the nanocomposites are analyzed....... For modeling the damage in nanocomposites with intercalated structures, “four phase” model is suggested, in which the strength of “intrastack interphase” is lower than that of “outer” interphase around the nanoplatelets. Analyzing the effect of nanoreinforcement in the matrix on the failure probability...

  15. 3D Finite Elements Modelling for Design and Performance Analysis of UO Pellets

    Directory of Open Access Journals (Sweden)

    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.

  16. Noise analysis for near field 3-D FM-CW radar imaging systems

    Energy Technology Data Exchange (ETDEWEB)

    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.

  17. Object Extraction from Architecture Scenes through 3D Local Scanned Data Analysis

    Directory of Open Access Journals (Sweden)

    NING, X.

    2012-08-01

    Full Text Available Terrestrial laser scanning becomes a standard way for acquiring 3D data of complex outdoor objects. The processing of huge number of points and recognition of different objects inside become a new challenge, especially in the case where objects are included. In this paper, a new approach is proposed to classify objects through an analysis on shape information of the point cloud data. The scanned scene is constructed using k Nearest Neighboring (k-NN, and then similarity measurement between points is defined to cluster points with similar primitive shapes. Moreover, we introduce a combined geometrical criterion to refine the over-segmented results. To achieve more detail information, a residual based segmentation is adopted to refine the segmentation of architectural objects into more parts with different shape properties. Experimental results demonstrate that this approach can be used as a robust way to extract different objects in the scenes.

  18. Analysis of 3D curve expansion of conical cam with oscillating tapered roller follower

    Institute of Scientific and Technical Information of China (English)

    2007-01-01

    This paper focuses on the analysis of running conditions and machining processes of conical cam with oscillating follower. We point out the common errors existing in the design and machining of the widely used plane expansion method of conical cam trough-out line. We show that the motion can be divided into two parts, i.e. the oscillating motion of oscillating bar and the rotary motion of oscillating bar relative to the conical cam. By increasing the rotary motion of oscillating bar, the motion path of tapered roller on oscillating bar (i.e. contour surface of conical cam) can be expanded on the cylinder. Based on these analyses,we present a creative and effective designing and machining method for 3D curve expansion of conical cam with oscillating follower.

  19. 3D thermal analysis of rectangular microscale inorganic light-emitting diodes in a pulsed operation

    Science.gov (United States)

    Cui, Y.; Bian, Z.; Li, Y.; Xing, Y.; Song, J.

    2016-10-01

    Microscale inorganic light-emitting diodes (µ-ILEDs) have attracted much attention due to their excellent performance in biointegrated applications such as optogenetics. The thermal behaviors of µ-ILEDs are critically important since a certain temperature increase may degrade the LED performance and cause tissue lesion. The µ-ILEDs in a pulsed operation offer an advantage in thermal management. In this paper, a 3D analytic model, as validated by finite element analysis, is developed to study the thermal response of rectangular µ-ILEDs in a pulsed operation. A scaling law for the maximum normalized temperature increase of rectangular µ-ILEDs in terms of non-dimensional parameters is established. The influences of geometric (i.e. shape factor) and loading parameters (e.g. duty cycle and period) on the temperature increase are systematically investigated. These results are very helpful in designing µ-ILEDs by providing guidelines to avoid adverse thermal effects.

  20. The 3D EdgeRunner Pipeline: a novel shape-based analysis for neoplasms characterization

    Science.gov (United States)

    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.

  1. Thoracic cavity definition for 3D PET/CT analysis and visualization.

    Science.gov (United States)

    Cheirsilp, Ronnarit; Bascom, Rebecca; Allen, Thomas W; Higgins, William E

    2015-07-01

    X-ray computed tomography (CT) and positron emission tomography (PET) serve as the standard imaging modalities for lung-cancer management. CT gives anatomical details on diagnostic regions of interest (ROIs), while PET gives highly specific functional information. During the lung-cancer management process, a patient receives a co-registered whole-body PET/CT scan pair and a dedicated high-resolution chest CT scan. With these data, multimodal PET/CT ROI information can be gleaned to facilitate disease management. Effective image segmentation of the thoracic cavity, however, is needed to focus attention on the central chest. We present an automatic method for thoracic cavity segmentation from 3D CT scans. We then demonstrate how the method facilitates 3D ROI localization and visualization in patient multimodal imaging studies. Our segmentation method draws upon digital topological and morphological operations, active-contour analysis, and key organ landmarks. Using a large patient database, the method showed high agreement to ground-truth regions, with a mean coverage=99.2% and leakage=0.52%. Furthermore, it enabled extremely fast computation. For PET/CT lesion analysis, the segmentation method reduced ROI search space by 97.7% for a whole-body scan, or nearly 3 times greater than that achieved by a lung mask. Despite this reduction, we achieved 100% true-positive ROI detection, while also reducing the false-positive (FP) detection rate by >5 times over that achieved with a lung mask. Finally, the method greatly improved PET/CT visualization by eliminating false PET-avid obscurations arising from the heart, bones, and liver. In particular, PET MIP views and fused PET/CT renderings depicted unprecedented clarity of the lesions and neighboring anatomical structures truly relevant to lung-cancer assessment.

  2. ADVANCED 3D LASER MICROSCOPY FOR MEASUREMENTS AND ANALYSIS OF VITRIFIED BONDED ABRASIVE TOOLS

    Directory of Open Access Journals (Sweden)

    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.

  3. 3D analysis of the reactivity insertion accident in VVER-1000

    Energy Technology Data Exchange (ETDEWEB)

    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)

  4. 3D structure determination of protein using TEM single particle analysis.

    Science.gov (United States)

    Sato, Chikara; Mio, Kazuhiro; Kawata, Masaaki; Ogura, Toshihiko

    2014-11-01

    Proteins play important roles in cell functions such as enzymes, cell trafficking, neurotransmission, muscle contraction and hormone secretion. However, some proteins are very difficult to be crystallized and their structures are undetermined. Several techniques have been developed to elucidate the structure of macromolecules; X-ray or electron crystallography, nuclear magnetic resonance spectroscopy, and high-resolution electron microscopy. Among them, electron microscopy based single particle reconstruction (SPA) technique is a computer-aided structure determination method. This method reconstructs the 3D structure from projection images of dispersed protein. A large number of two-dimensional particle images are picked up from EM films, aligned and classified to generate 2D averages, and used to reconstruct the 3D structure by assigning the Euler angle of each 2D average. Due to the necessity of elaborate collaboration between the classical biology and the innovative information technology including parallel computing, scientists needed to break unseen barriers to get a start of this analysis. However, recent progresses in electron microscopes, mathematical algorithms, and computational abilities greatly reduced the height of barriers and expanded targets that are considered to be primarily addressable using single particle analysis. Membrane proteins are one of these targets to which the single particle analysis is successfully applied for the understanding of their 3D structures. For this purpose, we have developed various SPA methods [1-5] and applied them to different proteins [6-8].Here, we introduce reconstructed proteins, and discuss the availability of this technique. The intramembrane-cleaving proteases (I-CLiPs) that sever the transmembrane domains of their substrates have been identified in a range of organisms and play a variety of roles in biological conditions. I-CLiPs have been classified into three groups: serine-, aspartyl- and metalloprotease

  5. RETRAN-3D Analysis Of The OECD/NRC Peach Bottom 2 Turbine Trip Benchmark

    Energy Technology Data Exchange (ETDEWEB)

    Barten, W.; Coddington, P

    2003-03-01

    This paper presents the PSI results on the different Phases of the Peach Bottom BWR Turbine Trip Benchmark using the RETRAN-3D code. In the first part of the paper, the analysis of Phase 1 is presented, in which the system pressure is predicted based on a pre-defined core power distribution. These calculations demonstrate the importance of accurate modelling of the non-equilibrium effects within the steam separator region. In the second part, a selection of the RETRAN-3D results for Phase 2 are given, where the power is predicted using a 3-D core with pre-defined core flow and pressure boundary conditions. A comparison of calculations using the different (Benchmark-specified) boundary conditions illustrates the sensitivity of the power maximum on the various resultant system parameters. In the third part of the paper, the results of the Phase 3 calculation are presented. This phase, which is a combination of the analytical work of Phases 1 and 2, gives good agreement with the measured data. The coupling of the pressure and flow oscillations in the steam line, the mass balance in the core, the (void) reactivity and the core power are all discussed. It is shown that the reactivity effects resulting from the change in the core void can explain the overall behaviour of the transient prior to the reactor scram. The time-dependent, normalized power for different thermal-hydraulic channels in the core is discussed in some detail. Up to the time of reactor scram, the power change was similar in all channels, with differences of the order of only a few percent. The axial shape of the channel powers at the time of maximum (overall) power increased in the core centre (compared with the shape at time zero). These changes occur as a consequence of the relative change in the channel void, which is largest in the region of the onset of boiling, and the influence on the different fuel assemblies of the complex ring pattern of the control rods. (author)

  6. Femoral curvature in Neanderthals and modern humans: a 3D geometric morphometric analysis.

    Science.gov (United States)

    De Groote, Isabelle

    2011-05-01

    Since their discovery, Neanderthals have been described as having a marked degree of anteroposterior curvature of the femoral shaft. Although initially believed to be pathological, subsequent discoveries of Neanderthal remains lead femoral curvature to be considered as a derived Neanderthal feature. A recent study on Neanderthals and middle and early Upper Palaeolithic modern humans found no differences in femoral curvature, but did not consider size-corrected curvature. Therefore, the objectives of this study were to use 3D morphometric landmark and semi-landmark analysis to quantify relative femoral curvature in Neanderthals, Upper Palaeolithic and recent modern humans, and to compare adult bone curvature as part of the overall femoral morphology among these populations. Comparisons among populations were made using geometric morphometrics (3D landmarks) and standard multivariate methods. Comparative material involved all available complete femora from Neanderthal and Upper Palaeolithic modern human, archaeological (Mesolithic, Neolithic, Medieval) and recent human populations representing a wide geographical and lifestyle range. There are significant differences in the anatomy of the femur between Neanderthals and modern humans. Neanderthals have more curved femora than modern humans. Early modern humans are most similar to recent modern humans in their anatomy. Femoral curvature is a good indicator of activity level and habitual loading of the lower limb, indicating higher activity levels in Neanderthals than modern humans. These differences contradict robusticity studies and the archaeological record, and would suggest that femoral morphology, and curvature in particular, in Neanderthals may not be explained by adult behavior alone and could be the result of genetic drift, natural selection or differences in behavior during ontogeny.

  7. A novel asymptotic expansion homogenization analysis for 3-D composite with relieved periodicity in the thickness direction

    KAUST Repository

    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.

  8. An analysis of postoperative complications and efficacy of 3-D miniplates in fixation of mandibular fractures

    Directory of Open Access Journals (Sweden)

    Sadhasivam Gokkulakrishnan

    2012-01-01

    Conclusions: It was seen that 3-D titanium miniplates were effective in the treatment of mandibular fractures and overall complication rates were lesser. In symphysis and parasymphysis regions, 3-D plating system uses lesser foreign material than the conventional miniplates using Champy′s principle.

  9. Localization of spots in FISH images of breast cancer using 3-D shape analysis.

    Science.gov (United States)

    Les, T; Markiewicz, T; Osowski, S; Jesiotr, M; Kozlowski, W

    2016-06-01

    The fluorescence in situ (FISH) belongs to the most often used molecular cytogenetic techniques, applied in many areas of diagnosis and research. The analysis of FISH images relies on localization and counting the red and green spots in order to determine HER2 status of the breast cancer samples. The algorithm of spot localization presented in the paper is based on 3-D shape analysis of the image objects. The subsequent regions of the image are matched to the reference pattern and the results of this matching influence localization of spots. The paper compares different shapes of the reference pattern and their efficiency in spot localization. The numerical experiments have been performed on the basis of 12 cases (patients), each represented by three images. Few thousands of cells have been analysed. The quantitative analyses comparing different versions of algorithm are presented and compared to the expert results. The best version of the procedure provides the absolute relative difference to the expert results smaller than 3%. These results confirm high efficiency of the proposed approach to the spot identification. The proposed method of FISH image analysis improves the efficiency of detecting fluorescent signals in FISH images. The evaluation results are encouraging for further testing of the developed automatic system directed to application in medical practice.

  10. Earthscape, a Multi-Purpose Interactive 3d Globe Viewer for Hybrid Data Visualization and Analysis

    Science.gov (United States)

    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.

  11. EARTHSCAPE, A MULTI-PURPOSE INTERACTIVE 3D GLOBE VIEWER FOR HYBRID DATA VISUALIZATION AND ANALYSIS

    Directory of Open Access Journals (Sweden)

    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.

  12. 3D Survey and instability’s analysis of Romena parish

    Directory of Open Access Journals (Sweden)

    Stefano Bertocci

    2015-01-01

    Full Text Available The Romanesque parish church San Pietro a Romena is located in the municipal district of Pratovecchio, in the Casentino valley. It was built, due to a inscription chiselled on a capital, in 1152 d.C. probably wanted byMatilde di Canossa, who has promoted the construction of a lot of churches in this area. We don’t have many informations about the first church, probably destroyed by an earthquake, event that frequently has hit the valley. We based our research on what the DM 01/2008 requests, so our analysis was made following some steps of knowledge: firstly an accurated research in the archive of the Fiesole diocese, to suppose how the buildinghas evolved during the ages, then a 3D laser scanner survey. Thanks to the accurate point cluod we could draw our sections of the church, integrating the material analysis, the orthophotos and the degradation analysis. In parallel has been developed the stratigraphic analysisof the building, which is useful to understand how it has been costructed and how it has grown, so that a coherent restoration project can be efficiently designed.

  13. Technology to the king or the content first——An analysis of China's 3D movie%技术为王还是内容至上——浅析中国3D 电影

    Institute of Scientific and Technical Information of China (English)

    袁淑芸

    2012-01-01

      3D film has now become the mainstream Hollywood productions, created a film market visual revolution."Afanda" hot makes mainland China taking advantage of a global 3D screen second market.In China, the United States 3D tracts in the global and Chinese film market performance of the market for the research background, around the "content" and "technology" two elements of the Chinese film market analysis of 3D, 3D film on the key factors in the development of a classification and analysis, with a view to China 3D film industry at home and abroad to obtain how can a space for one person and give some advice on.%  3D 电影如今已经成为好莱坞大制作的主流,引发了一场电影市场的视觉革命。《阿凡达》的火爆使得中国内地借势成为全球3D 银幕数第二多的市场。以中国、美国3D 大片在全球及中国电影市场上的市场表现为研究背景,围绕“内容”和“技术”两要素对中国3D 电影市场展开分析,就3D 电影发展的关键因素做一梳理和解读,以期为中国3D 电影业如何能在海内外取得一席之地提出参考性建议。

  14. Deformation analysis of 3D tagged cardiac images using an optical flow method

    Directory of Open Access Journals (Sweden)

    Gorman Robert C

    2010-03-01

    Full Text Available Abstract Background This study proposes and validates a method of measuring 3D strain in myocardium using a 3D Cardiovascular Magnetic Resonance (CMR tissue-tagging sequence and a 3D optical flow method (OFM. Methods Initially, a 3D tag MR sequence was developed and the parameters of the sequence and 3D OFM were optimized using phantom images with simulated deformation. This method then was validated in-vivo and utilized to quantify normal sheep left ventricular functions. Results Optimizing imaging and OFM parameters in the phantom study produced sub-pixel root-mean square error (RMS between the estimated and known displacements in the x (RMSx = 0.62 pixels (0.43 mm, y (RMSy = 0.64 pixels (0.45 mm and z (RMSz = 0.68 pixels (1 mm direction, respectively. In-vivo validation demonstrated excellent correlation between the displacement measured by manually tracking tag intersections and that generated by 3D OFM (R ≥ 0.98. Technique performance was maintained even with 20% Gaussian noise added to the phantom images. Furthermore, 3D tracking of 3D cardiac motions resulted in a 51% decrease in in-plane tracking error as compared to 2D tracking. The in-vivo function studies showed that maximum wall thickening was greatest in the lateral wall, and increased from both apex and base towards the mid-ventricular region. Regional deformation patterns are in agreement with previous studies on LV function. Conclusion A novel method was developed to measure 3D LV wall deformation rapidly with high in-plane and through-plane resolution from one 3D cine acquisition.

  15. Analysis of the KROTOS KFC test by coupling X-Ray image analysis and MC3D calculations

    Energy Technology Data Exchange (ETDEWEB)

    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)

  16. Segmentation of vascular structures and hematopoietic cells in 3D microscopy images and quantitative analysis

    Science.gov (United States)

    Mu, Jian; Yang, Lin; Kamocka, Malgorzata M.; Zollman, Amy L.; Carlesso, Nadia; Chen, Danny Z.

    2015-03-01

    In this paper, we present image processing methods for quantitative study of how the bone marrow microenvironment changes (characterized by altered vascular structure and hematopoietic cell distribution) caused by diseases or various factors. We develop algorithms that automatically segment vascular structures and hematopoietic cells in 3-D microscopy images, perform quantitative analysis of the properties of the segmented vascular structures and cells, and examine how such properties change. In processing images, we apply local thresholding to segment vessels, and add post-processing steps to deal with imaging artifacts. We propose an improved watershed algorithm that relies on both intensity and shape information and can separate multiple overlapping cells better than common watershed methods. We then quantitatively compute various features of the vascular structures and hematopoietic cells, such as the branches and sizes of vessels and the distribution of cells. In analyzing vascular properties, we provide algorithms for pruning fake vessel segments and branches based on vessel skeletons. Our algorithms can segment vascular structures and hematopoietic cells with good quality. We use our methods to quantitatively examine the changes in the bone marrow microenvironment caused by the deletion of Notch pathway. Our quantitative analysis reveals property changes in samples with deleted Notch pathway. Our tool is useful for biologists to quantitatively measure changes in the bone marrow microenvironment, for developing possible therapeutic strategies to help the bone marrow microenvironment recovery.

  17. Comparative abilities of Microsoft Kinect and Vicon 3D motion capture for gait analysis.

    Science.gov (United States)

    Pfister, Alexandra; West, Alexandre M; Bronner, Shaw; Noah, Jack Adam

    2014-07-01

    Biomechanical analysis is a powerful tool in the evaluation of movement dysfunction in orthopaedic and neurologic populations. Three-dimensional (3D) motion capture systems are widely used, accurate systems, but are costly and not available in many clinical settings. The Microsoft Kinect™ has the potential to be used as an alternative low-cost motion analysis tool. The purpose of this study was to assess concurrent validity of the Kinect™ with Brekel Kinect software in comparison to Vicon Nexus during sagittal plane gait kinematics. Twenty healthy adults (nine male, 11 female) were tracked while walking and jogging at three velocities on a treadmill. Concurrent hip and knee peak flexion and extension and stride timing measurements were compared between Vicon and Kinect™. Although Kinect measurements were representative of normal gait, the Kinect™ generally under-estimated joint flexion and over-estimated extension. Kinect™ and Vicon hip angular displacement correlation was very low and error was large. Kinect™ knee measurements were somewhat better than hip, but were not consistent enough for clinical assessment. Correlation between Kinect™ and Vicon stride timing was high and error was fairly small. Variability in Kinect™ measurements was smallest at the slowest velocity. The Kinect™ has basic motion capture capabilities and with some minor adjustments will be an acceptable tool to measure stride timing, but sophisticated advances in software and hardware are necessary to improve Kinect™ sensitivity before it can be implemented for clinical use.

  18. Computer-assisted 3D kinematic analysis of all leg joints in walking insects.

    Directory of Open Access Journals (Sweden)

    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.

  19. Statistical Analysis of Detailed 3-D CFD LES Simulations with Regard to CCV Modeling

    Directory of Open Access Journals (Sweden)

    Vítek Oldřich

    2016-06-01

    Full Text Available The paper deals with statistical analysis of large amount of detailed 3-D CFD data in terms of cycle-to-cycle variations (CCVs. These data were obtained by means of LES calculations of many consecutive cycles. Due to non-linear nature of Navier-Stokes equation set, there is a relatively significant CCV. Hence, every cycle is slightly different – this leads to requirement to perform statistical analysis based on ensemble averaging procedure which enables better understanding of CCV in ICE including its quantification. The data obtained from the averaging procedure provides results on different space resolution levels. The procedure is applied locally, i.e., in every cell of the mesh. Hence there is detailed CCV information on local level – such information can be compared with RANS simulations. Next, volume/mass averaging provides information at specific locations – e.g., gap between electrodes of a spark plug. Finally, volume/mass averaging of the whole combustion chamber leads to global information which can be compared with experimental data or results of system simulation tools (which are based on 0-D/1-D approach.

  20. Knee cartilage extraction and bone-cartilage interface analysis from 3D MRI data sets

    Science.gov (United States)

    Tamez-Pena, Jose G.; Barbu-McInnis, Monica; Totterman, Saara

    2004-05-01

    This works presents a robust methodology for the analysis of the knee joint cartilage and the knee bone-cartilage interface from fused MRI sets. The proposed approach starts by fusing a set of two 3D MR images the knee. Although the proposed method is not pulse sequence dependent, the first sequence should be programmed to achieve good contrast between bone and cartilage. The recommended second pulse sequence is one that maximizes the contrast between cartilage and surrounding soft tissues. Once both pulse sequences are fused, the proposed bone-cartilage analysis is done in four major steps. First, an unsupervised segmentation algorithm is used to extract the femur, the tibia, and the patella. Second, a knowledge based feature extraction algorithm is used to extract the femoral, tibia and patellar cartilages. Third, a trained user corrects cartilage miss-classifications done by the automated extracted cartilage. Finally, the final segmentation is the revisited using an unsupervised MAP voxel relaxation algorithm. This final segmentation has the property that includes the extracted bone tissue as well as all the cartilage tissue. This is an improvement over previous approaches where only the cartilage was segmented. Furthermore, this approach yields very reproducible segmentation results in a set of scan-rescan experiments. When these segmentations were coupled with a partial volume compensated surface extraction algorithm the volume, area, thickness measurements shows precisions around 2.6%

  1. QUALITY ANALYSIS OF 3D SURFACE RECONSTRUCTION USING MULTI-PLATFORM PHOTOGRAMMETRIC SYSTEMS

    Directory of Open Access Journals (Sweden)

    Z. Lari

    2016-06-01

    Full Text Available In recent years, the necessity of accurate 3D surface reconstruction has been more pronounced for a wide range of mapping, modelling, and monitoring applications. The 3D data for satisfying the needs of these applications can be collected using different digital imaging systems. Among them, photogrammetric systems have recently received considerable attention due to significant improvements in digital imaging sensors, emergence of new mapping platforms, and development of innovative data processing techniques. To date, a variety of techniques haven been proposed for 3D surface reconstruction using imagery collected by multi-platform photogrammetric systems. However, these approaches suffer from the lack of a well-established quality control procedure which evaluates the quality of reconstructed 3D surfaces independent of the utilized reconstruction technique. Hence, this paper aims to introduce a new quality assessment platform for the evaluation of the 3D surface reconstruction using photogrammetric data. This quality control procedure is performed while considering the quality of input data, processing procedures, and photo-realistic 3D surface modelling. The feasibility of the proposed quality control procedure is finally verified by quality assessment of the 3D surface reconstruction using images from different photogrammetric systems.

  2. In vivo analysis of the human superficial cerebral venous anatomy by using 3D-MRI

    Energy Technology Data Exchange (ETDEWEB)

    Fujinaga, Yasunari [Kanazawa Univ. (Japan). School of Medicine

    1997-12-01

    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)

  3. Wide area 2D/3D imaging development, analysis and applications

    CERN Document Server

    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

  4. Analysis of 3D-printed metal for rapid-prototyped reflective terahertz optics

    Science.gov (United States)

    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.

  5. Tensile Behavior Analysis on Different Structures of 3D Glass Woven Perform for Fibre Reinforced Composites

    Directory of Open Access Journals (Sweden)

    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.

  6. Analysis of 3D-printed metal for rapid-prototyped reflective terahertz optics

    CERN Document Server

    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.

  7. 3D tumor spheroids: an overview on the tools and techniques used for their analysis.

    Science.gov (United States)

    Costa, Elisabete C; Moreira, André F; de Melo-Diogo, Duarte; Gaspar, Vítor M; Carvalho, Marco P; Correia, Ilídio J

    2016-12-01

    In comparison with 2D cell culture models, 3D spheroids are able to accurately mimic some features of solid tumors, such as their spatial architecture, physiological responses, secretion of soluble mediators, gene expression patterns and drug resistance mechanisms. These unique characteristics highlight the potential of 3D cellular aggregates to be used as in vitro models for screening new anticancer therapeutics, both at a small and large scale. Nevertheless, few reports have focused on describing the tools and techniques currently available to extract significant biological data from these models. Such information will be fundamental to drug and therapeutic discovery process using 3D cell culture models. The present review provides an overview of the techniques that can be employed to characterize and evaluate the efficacy of anticancer therapeutics in 3D tumor spheroids.

  8. 3D automatic quantification applied to optically sectioned images to improve microscopy analysis

    Directory of Open Access Journals (Sweden)

    JE Diaz-Zamboni

    2009-08-01

    Full Text Available New fluorescence microscopy techniques, such as confocal or digital deconvolution microscopy, allow to easily obtain three-dimensional (3D information from specimens. However, there are few 3D quantification tools that allow extracting information of these volumes. Therefore, the amount of information acquired by these techniques is difficult to manipulate and analyze manually. The present study describes a model-based method, which for the first time shows 3D visualization and quantification of fluorescent apoptotic body signals, from optical serial sections of porcine hepatocyte spheroids correlating them to their morphological structures. The method consists on an algorithm that counts apoptotic bodies in a spheroid structure and extracts information from them, such as their centroids in cartesian and radial coordinates, relative to the spheroid centre, and their integrated intensity. 3D visualization of the extracted information, allowed us to quantify the distribution of apoptotic bodies in three different zones of the spheroid.

  9. 3-D gravity analysis of the Dniepr Donets Basin and Donbas Foldbelt, Ukraine

    Science.gov (United States)

    Yegorova, T. P.; Stephenson, R. A.; Kozlenko, V. G.; Starostenko, V. I.; Legostaeva, O. V.

    1999-11-01

    The Dniepr-Donets Basin (DDB) is a linear, NW-SE trending, late Palaeozoic and younger sedimentary basin on the East European Platform separating the Ukrainian Shield from the Voronezh Massif. Its northwestern (Dniepr) segment has the characteristics of a typical rift basin. To the southeast, through a transition zone of approximately 200 km length, the DDB is progressively uplifted and compressionally deformed into the correlatable Donbas Foldbelt (DF). Along the axis of the Dniepr segment a series of gravity highs has been previously explained by high-density crystalline crust beneath the axis of the basin caused by intrusion of mafic and ultramafic rocks. In this paper, the results of a 3-D gravity analysis, using a gravity backstripping technique, is described that investigates the crustal and upper mantle structure in the region of the DDB-DF transition zone and DF. A residual gravity field I, obtained by subtracting the gravity influence of the sedimentary succession of the DDB from the observed field, reveals a distinct positive anomaly along the axis of the rift basin increasing in amplitude to the southeast in concert with increasing sedimentary thickness. A residual gravity field II, derived by removing the gravity effects of a modelled homogeneous crystalline crust from residual field I, reaches 200 and 100 mGal amplitude in the DF for two respective Moho models based on different interpretations of the published crust and upper mantle seismic velocity models. The first of these (model A) assumes crustal thickening beneath the transition zone and DF (to a Moho depth up to 50 km) whereas the second (model B) assumes a Moho shallowing (to depths in the range 35-37 km) along the whole basin axis. For each residual anomaly II, the best-fitting 3-D distribution of average density in the crystalline crust has been computed. Both models indicate the existence of a high-density body in the crystalline crust along the DDB axis, increasing in density from the

  10. Design and mechanical analysis of a 3D-printed biodegradable biomimetic micro air vehicle wing

    Science.gov (United States)

    Salami, E.; Ganesan, P. B.; Ward, T. A.; Viyapuri, R.; Romli, F. I.

    2016-10-01

    The biomimetic micro air vehicles (BMAV) are unmanned, micro-scaled aircraft that are bio-inspired from flying organisms to achieve the lift and thrust by flapping their wings. There are still many technological challenges involved with designing the BMAV. One of these is designing the ultra-lightweight materials and structures for the wings that have enough mechanical strength to withstand continuous flapping at high frequencies. Insects achieve this by having chitin-based, wing frame structures that encompass a thin, film membrane. The main objectives of this study are to design a biodegradable BMAV wing (inspired from the dragonfly) and analyze its mechanical properties. The dragonfly-like wing frame structure was bio-mimicked and fabricated using a 3D printer. A chitosan nanocomposite film membrane was applied to the BMAV wing frames through casting method. Its mechanical performance was analyzed using universal testing machine (UTM). This analysis indicates that the tensile strength and Young's modulus of the wing with a membrane is nearly double that of the wing without a membrane, which allow higher wing beat frequencies and deflections that in turn enable a greater lifting performance.

  11. CCTV Coverage Index Based on Surveillance Resolution and Its Evaluation Using 3D Spatial Analysis

    Directory of Open Access Journals (Sweden)

    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.

  12. Analysis of heterogeneous boron dilution transients during outages with APROS 3D nodal core model

    Energy Technology Data Exchange (ETDEWEB)

    Kuopanportti, Jaakko [Fortum Power and Heat Ltd, Nuclear Production, Fortum (Finland)

    2015-09-15

    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.

  13. Electrical performance analysis of HTS synchronous motor based on 3D FEM

    Science.gov (United States)

    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.

  14. Comprehensive analysis of photonic nanojets in 3D dielectric cuboids excited by surface plasmons

    Energy Technology Data Exchange (ETDEWEB)

    Pacheco-Pena, Victor [Antennas Group - TERALAB, Universidad Publica de Navarra, Campus Arrosadia, 31006, Pamplona (Spain); Minin, Igor V.; Minin, Oleg V. [National Research Tomsk State University, Lenina Ave., 36, Tomsk, 634050 (Russian Federation); Beruete, Miguel [Antennas Group - TERALAB, Universidad Publica de Navarra, Campus Arrosadia, 31006, Pamplona (Spain); Institute of Smart Cities, Public University of Navarra, 31006, Pamplona (Spain)

    2016-10-15

    In this paper we study the excitation of photonic nanojets (PNJ) in 3D dielectric cuboids by surface plasmons at telecommunication wavelengths. The analysis is done using the effective refractive index approach. It is shown that the refractive index contrast between the regions with and without cuboid should be roughly less than 2 in order to generate jets at the output of the cuboid. The best performance at λ{sub 0} = 1550 nm is obtained when the height of the cuboid is 160 nm producing a jet just at the output interface with a subwavelength resolution of 0.68λ{sub 0} and a high intensity enhancement (x 5) at the focus. The multi-wavelength response is also studied demonstrating that it is possible to use the proposed structure at different wavelengths. Finally, the backscattering enhancement is numerically evaluated by inserting a metal particle within the PNJ region, demonstrating a maximum value of ∝2.44 dB for a gold sphere of radius 0.1λ{sub 0}. (copyright 2016 by WILEY-VCH Verlag GmbH and Co. KGaA, Weinheim)

  15. Cycle graph analysis for 3D roof structure modelling: Concepts and performance

    Science.gov (United States)

    Perera, Gamage Sanka Nirodha; Maas, Hans-Gerd

    2014-07-01

    The paper presents a cycle graph analysis approach to the automatic reconstruction of 3D roof models from airborne laser scanner data. The nature of convergences of topological relations of plane adjacencies, allowing for the reconstruction of roof corner geometries with preserved topology, can be derived from cycles in roof topology graphs. The topology between roof adjacencies is defined in terms of ridge-lines and step-edges. In the proposed method, the input point cloud is first segmented and roof topology is derived while extracting roof planes from identified non-terrain segments. Orientation and placement regularities are applied on weakly defined edges using a piecewise regularization approach prior to the reconstruction, which assists in preserving symmetries in building geometry. Roof corners are geometrically modelled using the shortest closed cycles and the outermost cycle derived from roof topology graph in which external target graphs are no longer required. Based on test results, we show that the proposed approach can handle complexities with nearly 90% of the detected roof faces reconstructed correctly. The approach allows complex height jumps and various types of building roofs to be firmly reconstructed without prior knowledge of primitive building types.

  16. Braking Distance Prediction by Hydroplaning Analysis of 3-D Patterned Tire Model

    Science.gov (United States)

    Cho, Jin-Rae; Choi, Joo-Hyoung; Lee, Hong-Woo; Woo, Jong-Shik; Yoo, Wan-Suk

    In this paper, we present a wet-road braking distance estimate for the vehicles equipped with ABS (Anti-lock Brake System). In order to effectively compute the interval-wise braking times and the resulting total braking distance, we divide the entire speed interval at braking into finite number of uniform sub-intervals and apply the energy conservation law to individual sub-intervals. The proposed method is based on a numerical-analytical approach such that the frictional energy loss of the patterned tire is computed by 3-D hydroplaning analysis while the other at the disc pad is analytically derived. The hydroplaning simulation is performed by generally coupling an Eulerian finite volume method and an explicit Lagrangian finite element method. The operation of ABS is numerically implemented by controlling the tire angular velocity such that the preset tire slip ratio on the wet road is maintained. Numerical results are presented to illustrative and verify the the proposed numerical estimate.

  17. Filtered chorochronic interface as a capability for 3-D unsteady throughflow analysis of multistage turbomachinery

    Science.gov (United States)

    Gerolymos, G. A.

    2013-02-01

    This note reviews the widely used phased-lagged [Erdos, J. L., E. Alzner, and W. McNally. 1977. AIAA Journal 15: 1559-68.] approach and corresponding chorochronic interface relations [Gerolymos G. A., G. J. Michon, and J. Neubauer. 2002. Journal of Propulsion and Power 18: 1139-52.] and explores its potential extension to the approximate unsteady throughflow analysis of multistage turbomachinery. The basic relations pertaining to the binary blade-row interaction case, for which chorochronic periodicity is exact in a phase-averaged rans framework, are briefly formulated, and selected computational examples illustrate the application of the method. Then, the filtered chorochronic interface is defined as the unsteady counterpart of the well-known mixing-plane concept. This interface takes into account only those tθ-waves which are compatible with the interaction of the immediately upstream and downstream blade-rows. The concept, which is similar to the decomposition-and-superposition method [Li, H. D., and L. He. 2005. ASME J ournal of Turbomachinery 127: 589-98.], is illustrated by 3-D computations of a ½-stage transonic compressor.

  18. 3D Finite Element Analysis of a Man Hip Joint Femur under Impact Loads

    Institute of Scientific and Technical Information of China (English)

    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.

  19. 3D depth image analysis for indoor fall detection of elderly people

    Directory of Open Access Journals (Sweden)

    Lei Yang

    2016-02-01

    Full Text Available This paper presents a new fall detection method of elderly people in a room environment based on shape analysis of 3D depth images captured by a Kinect sensor. Depth images are pre-processed by a median filter both for background and target. The silhouette of moving individual in depth images is achieved by a subtraction method for background frames. The depth images are converted to disparity map, which is obtained by the horizontal and vertical projection histogram statistics. The initial floor plane information is obtained by V disparity map, and the floor plane equation is estimated by the least square method. Shape information of human subject in depth images is analyzed by a set of moment functions. Coefficients of ellipses are calculated to determine the direction of individual. The centroids of the human body are calculated and the angle between the human body and the floor plane is calculated. When both the distance from the centroids of the human body to the floor plane and the angle between the human body and the floor plane are lower than some thresholds, fall incident will be detected. Experiments with different falling direction are performed. Experimental results show that the proposed method can detect fall incidents effectively.

  20. Large deformation inelastic analysis of impact for shipping casks. [DYNA3D Code

    Energy Technology Data Exchange (ETDEWEB)

    Charman, C.M.; Grenier, R.M. (General Atomic Co., San Diego, CA (USA)); Nickell, R.E. (Applied Science and Technology, Poway, CA (USA))

    1982-09-01

    This paper describes the use of two- and three-dimensional nonlinear finite element computer programs to design a radioative material transportation cask to withstand a drop of 30 feet onto an unyielding surface. Because of recent advancement in the area of non-linear finite element code development, the use of such codes for an iterative design process is becoming practicable. The paper begins with a section dealing with a two-dimensional side drop analysis and is followed by a discussion of the general capabilities of DYNA3D and a brief discussion of the implementation of the code on a computational mainframe unlike any for which the developer had intended. Then, a section on three-dimensional models of center-of-gravity over a corner impact follows, which introduces design features such as bolted closures, internal impact limiter, seals and shear rings. Figs. showing the deformed model grids are included. Stress and strain results are given in the subsequent section. Finally, we interpret these results in terms of possible rules being developed by the American Society of Mechanical Engineers (ASME) Boiler and Pressure Vessel Code committees.

  1. Analysis and modeling of 3D complex modulus tests on hot and warm bituminous mixtures

    Science.gov (United States)

    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.

  2. STATICS ANALYSIS AND OPENGL BASED 3D SIMULATION OF COLLABORATIVE RECONFIGURABLE PLANETARY ROBOTS

    Institute of Scientific and Technical Information of China (English)

    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.

  3. An amalgamation of 3D city models in urban air quality modelling for improving visual impact analysis

    DEFF Research Database (Denmark)

    Ujang, U.; Anton, F.; Ariffin, A.

    2015-01-01

    Geographical Information Systems (GISs) can be seen as a common tool to map and visualize the air quality index based on geographical locations. However, in urban areas, the area resolution for air quality models is less than 2 kilometres.Since the main emissions agent in urban areas...... as physical data input. The Level of Details (LoD) in 3D city models (i.e. LoD1 and LoD2) ascertains the potentials of implementing air quality modelling for urban areas. Therefore, this research is focused towards investigating the integration of 3D city models in air quality modelling for urban areas....... The results presented show the simplicity of using 3D city models as a physical data input in air quality modelling and the 3D air quality will improve insight for visual impact analysis (i.e. analysing the immersion of are circulation zone). The results are advantageous for city planners, architects...

  4. Analysis and Visualization of 3D Motion Data for UPDRS Rating of Patients with Parkinson's Disease.

    Science.gov (United States)

    Piro, Neltje E; Piro, Lennart K; Kassubek, Jan; Blechschmidt-Trapp, Ronald A

    2016-06-21

    Remote monitoring of Parkinson's Disease (PD) patients with inertia sensors is a relevant method for a better assessment of symptoms. We present a new approach for symptom quantification based on motion data: the automatic Unified Parkinson Disease Rating Scale (UPDRS) classification in combination with an animated 3D avatar giving the neurologist the impression of having the patient live in front of him. In this study we compared the UPDRS ratings of the pronation-supination task derived from: (a) an examination based on video recordings as a clinical reference; (b) an automatically classified UPDRS; and (c) a UPDRS rating from the assessment of the animated 3D avatar. Data were recorded using Magnetic, Angular Rate, Gravity (MARG) sensors with 15 subjects performing a pronation-supination movement of the hand. After preprocessing, the data were classified with a J48 classifier and animated as a 3D avatar. Video recording of the movements, as well as the 3D avatar, were examined by movement disorder specialists and rated by UPDRS. The mean agreement between the ratings based on video and (b) the automatically classified UPDRS is 0.48 and with (c) the 3D avatar it is 0.47. The 3D avatar is similarly suitable for assessing the UPDRS as video recordings for the examined task and will be further developed by the research team.

  5. Intelligent Autonomous Primary 3D Feature Extraction in Vehicle System Dynamics' Analysis: Theory and Application

    Directory of Open Access Journals (Sweden)

    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.

  6. DiAna, an ImageJ tool for object-based 3D co-localization and distance analysis

    OpenAIRE

    2016-01-01

    International audience; We present a new plugin for ImageJ called DiAna, for Distance Analysis, which comes with a user-friendly interface. DiAna proposes robust and accurate 3D segmentation for object extraction. The plugin performs automated object-based co-localization and distance analysis. DiAna offers an in-depth analysis of co-localization between objects and retrieves 3D measurements including co-localizing volumes and surfaces of contact. It also computes the distribution of distance...

  7. 3-D segmentation and quantitative analysis of inner and outer walls of thrombotic abdominal aortic aneurysms

    Science.gov (United States)

    Lee, Kyungmoo; Yin, Yin; Wahle, Andreas; Olszewski, Mark E.; Sonka, Milan

    2008-03-01

    An abdominal aortic aneurysm (AAA) is an area of a localized widening of the abdominal aorta, with a frequent presence of thrombus. A ruptured aneurysm can cause death due to severe internal bleeding. AAA thrombus segmentation and quantitative analysis are of paramount importance for diagnosis, risk assessment, and determination of treatment options. Until now, only a small number of methods for thrombus segmentation and analysis have been presented in the literature, either requiring substantial user interaction or exhibiting insufficient performance. We report a novel method offering minimal user interaction and high accuracy. Our thrombus segmentation method is composed of an initial automated luminal surface segmentation, followed by a cost function-based optimal segmentation of the inner and outer surfaces of the aortic wall. The approach utilizes the power and flexibility of the optimal triangle mesh-based 3-D graph search method, in which cost functions for thrombus inner and outer surfaces are based on gradient magnitudes. Sometimes local failures caused by image ambiguity occur, in which case several control points are used to guide the computer segmentation without the need to trace borders manually. Our method was tested in 9 MDCT image datasets (951 image slices). With the exception of a case in which the thrombus was highly eccentric, visually acceptable aortic lumen and thrombus segmentation results were achieved. No user interaction was used in 3 out of 8 datasets, and 7.80 +/- 2.71 mouse clicks per case / 0.083 +/- 0.035 mouse clicks per image slice were required in the remaining 5 datasets.

  8. Mutational analysis of the complement receptor type 2 (CR2/CD21)-C3d interaction reveals a putative charged SCR1 binding site for C3d.

    Science.gov (United States)

    Hannan, Jonathan P; Young, Kendra A; Guthridge, Joel M; Asokan, Rengasamy; Szakonyi, Gerda; Chen, Xiaojiang S; Holers, V Michael

    2005-02-25

    We have characterized the interaction between the first two short consensus repeats (SCR1-2) of complement receptor type 2 (CR2, CD21) and C3d in solution, by utilising the available crystal structures of free and C3d-bound forms of CR2 to create a series of informative mutations targeting specific areas of the CR2-C3d complex. Wild-type and mutant forms of CR2 were expressed on the surface of K562 erythroleukemia cells and their binding ability assessed using C3dg-biotin tetramers complexed to fluorochrome conjugated streptavidin and measured by flow cytometry. Mutations directed at the SCR2-C3d interface (R83A, R83E, G84Y) were found to strongly disrupt C3dg binding, supporting the conclusion that the SCR2 interface reflected in the crystal structure is correct. Previous epitope and peptide mapping studies have also indicated that the PILN11GR13IS sequence of the first inter-cysteine region of SCR1 is essential for the binding of iC3b. Mutations targeting residues within or in close spatial proximity to this area (N11A, N11E, R13A, R13E, Y16A, S32A, S32E), and a number of other positively charged residues located primarily on a contiguous face of SCR1 (R28A, R28E, R36A, R36E, K41A, K41E, K50A, K50E, K57A, K57E, K67A, K67E), have allowed us to reassess those regions on SCR1 that are essential for CR2-C3d binding. The nature of this interaction and the possibility of a direct SCR1-C3d association are discussed extensively. Finally, a D52N mutant was constructed introducing an N-glycosylation sequence at an area central to the CR2 dimer interface. This mutation was designed to disrupt the CR2-C3d interaction, either directly through steric inhibition, or indirectly through disruption of a physiological dimer. However, no difference in C3dg binding relative to wild-type CR2 could be observed for this mutant, suggesting that the dimer may only be found in the crystal form of CR2.

  9. Analysis of Intensity-Modulated Radiation Therapy (IMRT), Proton and 3D Conformal Radiotherapy (3D-CRT) for Reducing Perioperative Cardiopulmonary Complications in Esophageal Cancer Patients

    Energy Technology Data Exchange (ETDEWEB)

    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.

  10. Difference in performance between 3D and 4D CBCT for lung imaging: a dose and image quality analysis.

    Science.gov (United States)

    Thengumpallil, Sheeba; Smith, Kathleen; Monnin, Pascal; Bourhis, Jean; Bochud, François; Moeckli, Raphaël

    2016-11-08

    The study was to describe and to compare the performance of 3D and 4D CBCT imaging modalities by measuring and analyzing the delivered dose and the image quality. The 3D (Chest) and 4D (Symmetry) CBCT Elekta XVI lung IGRT protocols were analyzed. Dose profiles were measured with TLDs inside a dedicated phantom. The dosimetric indicator cone-beam dose index (CBDI) was evaluated. The image quality analysis was performed by assessing the contrast transfer function (CTF), the noise power spectrum (NPS) and the noise-equivalent quanta (NEQ). Artifacts were also evaluated by simulating irregular breathing variations. The two imaging modalities showed different dose distributions within the phantom. At the center, the 3D CBCT delivered twice the dose of the 4D CBCT. The CTF was strongly reduced by motion compared to static conditions, resulting in a CTF reduction of 85% for the 3D CBCT and 65% for the 4D CBCT. The amplitude of the NPS was two times higher for the 4D CBCT than for the 3D CBCT. In the presence of motion, the NEQ of the 4D CBCT was 50% higher than the 3D CBCT. In the presence of breathing irregularities, the 4D CBCT protocol was mainly affected by view-aliasing artifacts, which were typically cone-beam artifacts, while the 3D CBCT protocol was mainly affected by duplication artifacts. The results showed that the 4D CBCT ensures a reasonable dose and better image quality when mov-ing targets are involved compared to 3D CBCT. Therefore, 4D CBCT is a reliable imaging modality for lung free-breathing radiation therapy.

  11. 3D numerical analysis of crack propagation of heterogeneous notched rock under uniaxial tension

    Science.gov (United States)

    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.

  12. 3D FACE RECOGNITION FROM RANGE IMAGES BASED ON CURVATURE ANALYSIS

    Directory of Open Access Journals (Sweden)

    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.

  13. 3D Hand Gesture Analysis Through a Real-time Gesture Search Engine

    Directory of Open Access Journals (Sweden)

    Shahrouz Yousefi

    2015-06-01

    Full Text Available 3D gesture recognition and tracking are highly desired features of interaction design in future mobile and smart environments. Specifically, in virtual/augmented reality applications, intuitive interaction with the physical space seems unavoidable and 3D gestural interaction might be the most effective alternative for the current input facilities such as touchscreens. In this paper, we introduce a novel solution for real-time 3D gesture-based interaction by finding the best match from an extremely large gesture database. This database includes images of various articulated hand gestures with the annotated 3D position/orientation parameters of the hand joints. Our unique matching algorithm is based on the hierarchical scoring of the low-level edge-orientation features between the query frames and database and retrieving the best match. Once the best match is found from the database in each moment, the pre-recorded 3D motion parameters can instantly be used for natural interaction. The proposed bare-hand interaction technology performs in real time with high accuracy using an ordinary camera.

  14. Seepage Analysis of Upper Gotvand Dam Concerning Gypsum Karstification (2D and 3D Approaches)

    DEFF Research Database (Denmark)

    Sadrekarimi, Jamshid; Kiyani, Majid; Fakhri, Behnam;

    2011-01-01

    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...... 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...

  15. Evaluation by quantitative image analysis of anticancer drug activity on multicellular spheroids grown in 3D matrices

    Science.gov (United States)

    Gomes, Aurélie; Russo, Adrien; Vidal, Guillaume; Demange, Elise; Pannetier, Pauline; Souguir, Zied; Lagarde, Jean-Michel; Ducommun, Bernard; Lobjois, Valérie

    2016-01-01

    Pharmacological evaluation of anticancer drugs using 3D in vitro models provides invaluable information for predicting in vivo activity. Artificial matrices are currently available that scale up and increase the power of such 3D models. The aim of the present study was to propose an efficient and robust imaging and analysis pipeline to assess with quantitative parameters the efficacy of a particular cytotoxic drug. HCT116 colorectal adenocarcinoma tumor cell multispheres were grown in a 3D physiological hyaluronic acid matrix. 3D microscopy was performed with structured illumination, whereas image processing and feature extraction were performed with custom analysis tools. This procedure makes it possible to automatically detect spheres in a large volume of matrix in 96-well plates. It was used to evaluate drug efficacy in HCT116 spheres treated with different concentrations of topotecan, a DNA topoisomerase inhibitor. Following automatic detection and quantification, changes in cluster size distribution with a topotecan concentration-dependent increase of small clusters according to drug cytotoxicity were observed. Quantitative image analysis is thus an effective means to evaluate and quantify the cytotoxic and cytostatic activities of anticancer drugs on 3D multicellular models grown in a physiological matrix. PMID:28105152

  16. A procedure for the evaluation of 2D radiographic texture analysis to assess 3D bone micro-architecture

    Science.gov (United States)

    Apostol, Lian; Peyrin, Francoise; Yot, Sophie; Basset, Olivier; Odet, Christophe; Tabary, Joachim; Dinten, Jean-Marc; Boller, Elodie; Boudousq, Vincent; Kotzki, Pierre-Olivier

    2004-05-01

    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 s-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 betweeen 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 imagees 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-occurence, spectrum, fractal...). First results of the statistical analysis between 2D and 3D parameters allowed identfying the most relevant 2D texture parameters.

  17. 3D analysis of condylar remodelling and skeletal relapse following bilateral sagittal split advancement osteotomies.

    Science.gov (United States)

    Xi, Tong; Schreurs, Ruud; van Loon, Bram; de Koning, Martien; Bergé, Stefaan; Hoppenreijs, Theo; Maal, Thomas

    2015-05-01

    A major concern in mandibular advancement surgery using bilateral sagittal split osteotomies (BSSO) is potential postoperative relapse. Although the role of postoperative changes in condylar morphology on skeletal relapse was reported in previous studies, no study so far has objectified the precise changes of the condylar volume. The aim of the present study was to quantify the postoperative volume changes of condyles and its role on skeletal stability following BSSO mandibular advancement surgery. A total of 56 patients with mandibular hypoplasia who underwent BSSO advancement surgery were prospectively enrolled into the study. A cone beam computed tomography (CBCT) scan was acquired preoperatively, at 1 week postoperatively and at 1 year postoperatively. After the segmentation of the facial skeleton and condyles, three-dimensional cephalometry and condylar volume analysis were performed. The mean mandibular advancement was 4.6 mm, and the mean postoperative relapse was 0.71 mm. Of 112 condyles, 55% showed a postoperative decrease in condylar volume, with a mean reduction of 105 mm(3) (6.1% of the original condylar volume). The magnitude of condylar remodelling (CR) was significantly correlated with skeletal relapse (p = 0.003). Patients with a CR greater than 17% of the original condylar volume exhibited relapse as seen in progressive condylar resorption. Female patients with a high mandibular angle who exhibited postoperative CR were particularly at risk for postoperative relapse. Gender, preoperative condylar volume, and downward displacement of pogonion at surgery were prognostic factors for CR (r(2) = 21%). It could be concluded that the condylar volume can be applied as a useful 3D radiographic parameter for the diagnosis and follow-up of postoperative skeletal relapse and progressive condylar resorption.

  18. Analysis of Hyoid-Larynx Complex Using 3D Geometric Morphometrics.

    Science.gov (United States)

    Loth, Anthony; Corny, Julien; Santini, Laure; Dahan, Laurie; Dessi, Patrick; Adalian, Pascal; Fakhry, Nicolas

    2015-06-01

    The aim of this study was to obtain a quantitative anatomical description of the hyoid bone-larynx complex using modern 3D reconstruction tools. The study was conducted on 104 bones from CT scan images of living adult subjects. Three-dimensional reconstructions were created from CT scan images using AVIZO 6.2 software package. A study of this complex was carried out using metric and morphological analyses. Characteristics of the hyoid bone and larynx were highly heterogeneous and were closely linked with the sex, height, and weight of the individuals. Height and width of larynx were significantly greater in men than in women (24.99 vs. 17.3 mm, p ≤ 0.05 and 46.75 vs. 41.07, p ≤ 0.05), whereas the thyroid angle was larger in females (81.12° vs. 74.48°, p ≤ 0.05). There was a significant correlation between the height and weight of subjects and different measurements of the hyoid-larynx complex. (Pearson's coefficient correlation r = 0.42, p ≤ 0.05 between the height of thyroid ala and the height of subjects and r = 0.1, p ≤ 0.05 between the height of thyroid ala and the weight of subjects). Shape and size analysis of the hyoid-larynx complex showed the existence of a significant sexual dimorphism and high interindividual heterogeneity depending to patient morphology. These results encourage us to go further with functional and imaging correlations.

  19. Laser Welding Analysis for 3D Printed Thermoplastic and Poly-acetate Polymers

    Energy Technology Data Exchange (ETDEWEB)

    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.

  20. Modeling of 3-D Losses and Deviations in a Throughflow Analysis Tool

    Institute of Scientific and Technical Information of China (English)

    Jean-Francois Simon; Olivier Léonard

    2007-01-01

    This contribution is dedicated to the modeling of the end-wall flows in a throughflow model for turbomachinery applications. The throughflow model is based on the Euler or Navier-Stokes equations solved by a Finite-Volume technique. Two approaches are presented for the end-wall modeling. The first one is based on an inviscid formulation with dedicated 3-D distributions of loss coefficient and deviation in the end-wall regions. The second approach is directly based on a viscous formulation with no-slip boundary condition along the annular end-walls and blade force modification in the region close to the end-walls. The throughflow results are compared to a series of 3-D Navier-Stokes calculations averaged in the circumferential direction. These 3-D calculations were performed on the three rotors of a low pressure axial compressor, for a series of tip clearance values.

  1. 3D Numerical Simulation Analysis of Passive Drag near Free Surface in Swimming

    Institute of Scientific and Technical Information of China (English)

    詹杰民; 李天赠; 陈学彬; 李毓湘; 韦永康

    2015-01-01

    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-εturbulence 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.

  2. 3D numerical simulation analysis of passive drag near free surface in swimming

    Science.gov (United States)

    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.

  3. 3-D Finite Element Analysis of Induction Logging in a Dipping Formation

    Energy Technology Data Exchange (ETDEWEB)

    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.

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

    DEFF Research Database (Denmark)

    Jørgensen, Peter Stanley

    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...... task of manually delineating structures within each image slice or the quality of manual and automatic segmentation schemes. To solve this, a framework for the automatic segmentation of 3D image data is developed. The technique is based on a level set method and uses numerical approximations to partial...... differential equations to evolve a 3D surface to capture the phase boundaries. Vector fields derived from the experimentally acquired data are used as the driving forces. The framework performs the segmentation in 3D rather than on a slice by slice basis. It naturally supplies sub-voxel accuracy of segmented...

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

    Directory of Open Access Journals (Sweden)

    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

  6. Structural optimization of wind turbine rotor blades by multilevel sectional/multibody/3D-FEM analysis

    DEFF Research Database (Denmark)

    Bottasso, C. L.; Campagnolo, F.; Croce, A.;

    2014-01-01

    model fully-populated cross sectional stiffness matrices. Next, a "fine"-level 3D FEM model is used for the refinement of the coarse-level solution. Improved results obtained at the level of the 3D model are utilized at the following coarse-level iteration through a heuristic modification of the design...... level. At first, a "coarse"-level constrained design optimization is performed by using a 1D spatial geometrically exact beam model for aero-servo-elastic multibody analysis and load calculation, integrated with a 2D FEM cross sectional model for stress/strain analysis, and the evaluation of the 1D...

  7. Analysis of 3D and multiview extensions of the emerging HEVC standard

    Science.gov (United States)

    Vetro, Anthony; Tian, Dong

    2012-10-01

    Standardization of a new set of 3D formats has been initiated with the goal of improving the coding of stereo and multiview video, and also facilitating the generation of multiview output needed for auto-stereoscopic displays. Part of this effort will develop 3D and multiview extensions of the emerging standard for High Efficiency Video Coding (HEVC). This paper outlines some of the key technologies and architectures being considered for standardization, and analyzes the viability, benefits and drawbacks of different codec designs.

  8. Preprocessing Methods with AVA Analysis of 3D VSP Data%3D VSP资料AVA分析预处理方法

    Institute of Scientific and Technical Information of China (English)

    乔玉雷

    2010-01-01

    3D VSP数据与地面地震数据相比接收噪音少、反射角信息比较丰富,更能直接反映波的运动学和动力学特征,因此,利用3D VSP AVO/AVA分析推测地层岩性和含油气性,为隐蔽性油气藏勘探提供有效技术手段.但是,用于AVA分析的VSP资料必须进行严格的振幅保持、地表一致性和角道集提取等精细预处理.本文采用全波场振幅补偿、两步法统计子波反褶积和直射线路径近似角度道集转换等适于3D VSP资料特点的精细预处理方法,最大程度地消除影响振幅的各种主要非地质因素,确保从角道集上得到的AVA响应是地下真实的AVA反映,取得了很好的处理效果.

  9. 3D P-wave velocity structure of the deep Galicia rifted margin: A first analysis of the Galicia 3D wide-angle seismic dataset

    Science.gov (United States)

    Bayrakci, Gaye; Minshull, Timothy A.; Davy, Richard G.; Karplus, Marianne S.; Kaeschen, Dirk; Papenberg, Cord; Krabbenhoeft, Anne; Sawyer, Dale; Reston, Timothy J.; Shillington, Donna J.; Ranero, César R.

    2014-05-01

    Galicia 3D, a reflection-refraction and long offset seismic experiment was carried out from May through September 2013, at the Galicia rifted margin (in the northeast Atlantic Ocean, west of Spain) as a collaboration between US, UK, German and Spanish groups. The 3D multichannel seismic acquisition conducted by R/V Marcus Langseth covered a 64 km by 20 km (1280 km2) zone where the main geological features are the Peridotite Ridge (PR), composed of serpentinized peridotite and thought be upper mantle exhumed to the seafloor during rifting, and the S reflector which has been interpreted to be a low angle detachment fault overlain by fault bounded, rotated, continental crustal blocks. In the 3D box, two airgun arrays of 3300 cu.in. were fired alternately (in flip-flop configuration) every 37.5 m. All shots are recorded by 44 short period four component ocean bottom seismometers (OBS) and 26 ocean bottom hydrophones (OBH) deployed and recovered by R/V Poseidon, as well as four 6 km hydrophone streamers with 12.5 m channel spacing towed by R/V Marcus Langseth. We present the preliminary results of the first arrival time tomography study which is carried out with a subset of the wide-angle dataset, in order to generate a 3D P-wave velocity volume for the entire depth sampled by the reflection data. After the relocation of OBSs and OBHs, an automatic first-arrival time picking approach is applied to a subset of the dataset, which comprises more than 5.5 million source-receiver pairs. Then, the first-arrival times are checked visually, in 3-dimensions. The a priori model used for the first-arrival time tomography is built up using information from previous seismic surveys carried out at the Galicia margin (e.g. ISE, 1997). The FAST algorithm of Zelt and Barton (1998) is used for the first-arrival time inversion. The 3D P-wave velocity volume can be used in interpreting the reflection dataset, as a starting point for migration, to quantify the thinning of the crustal layers

  10. 3D DVH-based metric analysis versus per-beam planar analysis in IMRT pretreatment verification

    Energy Technology Data Exchange (ETDEWEB)

    Carrasco, Pablo; Jornet, Nuria; Latorre, Artur; Eudaldo, Teresa; Ruiz, Agusti; Ribas, Montserrat [Servei de Radiofisica i Radioproteccio, Hospital de la Santa Creu i Sant Pau, Sant Antoni Maria Claret, 167, 08025 Barcelona (Spain)

    2012-08-15

    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 (D{sub 98} and D{sub 95}) 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

  11. Automated Clustering Analysis of Immunoglobulin Sequences in Chronic Lymphocytic Leukemia Based on 3D Structural Descriptors

    DEFF Research Database (Denmark)

    Marcatili, Paolo; Mochament, Konstantinos; Agathangelidis, Andreas

    2016-01-01

    Imunoglobulins (Igs) are crucial for the defense against pathogens, but they are also important in many clinical and biotechnological applications. Their characteristics, and ultimately their function, depend on their three-dimensional (3D) structure; however, the procedures to experimentally det...

  12. Tolerance Analysis of 3d-MJM parts according to IT grade

    Science.gov (United States)

    Kitsakis, K.; Kechagias, J.; Vaxevanidis, N.; Giagkopoulos, D.

    2016-11-01

    In this study we investigate the dimensional accuracy of 3D printed objects and define the International Tolerance (IT) Grade for the linear sizes of parallel opposite surfaces and the diameter of a cylinder. Eight (8) exact parts were printed by an Objet Eden250 3D printer using the Multi Jet Modelling (MJM) process. The printed objects were measured and their dimensions analysed to define the IT grade of the specific process. MJM is an Additive Manufacturing (AM) or 3D Printing manufacturing process that can be used in place of CNC to save weeks of lead time, allows us to create parts with a superior strength to weight ratio and can significantly improve the efficiency of the completed system. MJM process is used for a great variety of applications on concept models to model performance parts as functional prototypes, jigs and fixtures, manufacturing tooling and sometimes even production parts. The result of this investigation is that the MJM 3D printing process can produce objects with IT11 grade or better, which classify it to the Fits area of IT grades.

  13. A 3D elasto-plastic soil model for lateral buckling analysis

    DEFF Research Database (Denmark)

    Hededal, Ole; Strandgaard, Torsten

    2008-01-01

    Modeling the lay-down of pipelines and subsequently the in- service conditions for a pipeline involves definition of a pipe-soil interaction model. A generalized true 3D elasto-plastic spring element based on an anisotropic hardening/degradation model for sliding is presented. The basis for the m...

  14. Recording and analysis of locomotion in dairy cows with 3D accelerometers

    NARCIS (Netherlands)

    Mol, de R.M.; Lammers, R.J.H.; Pompe, J.C.A.M.; Ipema, A.H.; Hogewerf, P.H.

    2009-01-01

    An automated method for lameness detection can be an alternative for detection by regular observations. Accelerometers attached to a leg of the dairy cow can be used to record the locomotion of a dairy cow. In an experiment the 3D acceleration of the right hind leg during walking of three dairy cows

  15. A Critical Analysis of a Hand Orthosis Reverse Engineering and 3D Printing Process.

    Science.gov (United States)

    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.

  16. Evaluation and Performance Analysis of 3D Printing Technique for Ka-Band Antenna Production

    DEFF Research Database (Denmark)

    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...

  17. A Critical Analysis of a Hand Orthosis Reverse Engineering and 3D Printing Process

    Directory of Open Access Journals (Sweden)

    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.

  18. Oxygen mask fit analysis in F-16 fighter pilots using 3D imaging

    NARCIS (Netherlands)

    Schreinemakers, J.R.C.; Oudenhuijzen, A.J.K.; Amerongen, P.C.G.M. van; Kon, M.

    2013-01-01

    Background: The majority of Dutch F-16 pilots experience in-flight oxygen mask related nasal discomfort and injury. We aimed to analyze the fit of the oxygen mask. Methods: We successfully scanned 35 pilots with a 3D scanner to measure the distance between the contact area on the nose and the oxygen

  19. A Critical Analysis of a Hand Orthosis Reverse Engineering and 3D Printing Process

    Science.gov (United States)

    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

  20. PRONTO3D users` instructions: A transient dynamic code for nonlinear structural analysis

    Energy Technology Data Exchange (ETDEWEB)

    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.

  1. Full Waveform Analysis for Long-Range 3D Imaging Laser Radar

    Directory of Open Access Journals (Sweden)

    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.

  2. Some Methods of Applied Numerical Analysis to 3d Facial Reconstruction Software

    Science.gov (United States)

    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.

  3. A 3D multilevel model of damage and strength of wood: Analysis of microstructural effects

    DEFF Research Database (Denmark)

    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...

  4. BER Analysis Using Beat Probability Method of 3D Optical CDMA Networks with Double Balanced Detection

    Directory of Open Access Journals (Sweden)

    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.

  5. Structure analysis of solution to equations of quasi 3-D accretion disk model

    Institute of Scientific and Technical Information of China (English)

    2001-01-01

    In this paper we discuss the problems contained in the solution to the equations of quasi 3-D accretion disk model, and point out that the angular momentum equation should not be integrated directly. Finally, we develop a criterion of the existence of a disconnected solution to this model.

  6. Fatigue of multiscale composites with secondary nanoplatelet reinforcement: 3D computational analysis

    DEFF Research Database (Denmark)

    Dai, Gaoming; Mishnaevsky, Leon, Jr.

    2014-01-01

    3D numerical simulations of fatigue damage of multiscale fiber reinforced polymer composites with secondary nanoclay reinforcement are carried out. Macro–micro FE models of the multiscale composites are generated automatically using Python based software. The effect of the nanoclay reinforcement...

  7. Rigorous analysis of an electric-field-driven liquid crystal lens for 3D displays

    Energy Technology Data Exchange (ETDEWEB)

    Kim, Bong-Sik; Lee, Seung-Chul; Park, Woo-Sang [Inha University, Incheon (Korea, Republic of)

    2014-08-15

    We numerically analyzed the optical performance of an electric field driven liquid crystal (ELC) lens adopted for 3-dimensional liquid crystal displays (3D-LCDs) through rigorous ray tracing. For the calculation, we first obtain the director distribution profile of the liquid crystals by using the Erickson-Leslie motional equation; then, we calculate the transmission of light through the ELC lens by using the extended Jones matrix method. The simulation was carried out for a 9 view 3D-LCD with a diagonal of 17.1 inches, where the ELC lens was slanted to achieve natural stereoscopic images. The results show that each view exists separately according to the viewing position at an optimum viewing distance of 80 cm. In addition, our simulation results provide a quantitative explanation for the ghost or blurred images between views observed from a 3D-LCD with an ELC lens. The numerical simulations are also shown to be in good agreement with the experimental results. The present simulation method is expected to provide optimum design conditions for obtaining natural 3D images by rigorously analyzing the optical functionalities of an ELC lens.

  8. Feature aware Digital Surface Model analysis and generalization based on the 3D Medial Axix Transform

    NARCIS (Netherlands)

    Peters, R.Y.

    2014-01-01

    Modern Digital Surface Models (DSMs) are highly detailed and cover large areas. This brings great advantages for applications such as flood modeling, crisis management and 3D city modeling. Unfor- tunately, and despite recent developments on this subject, current methods are unable to fully take ad-

  9. Error analysis of 3D shearography using finite-element modelling

    NARCIS (Netherlands)

    Goto, D.T.; Groves, R.M.

    2010-01-01

    This paper describes the development of an opto-mechanical simulation of a complete shearography system, including the shearography instrument, the samples and the test environment. This simulation is applied to the measurement of 3D strains in engineering samples. The samples are a cylinder loaded

  10. Analysis and 3D inversion of magnetotelluric crooked profile data from central Svalbard for geothermal application

    Science.gov (United States)

    Beka, Thomas I.; Smirnov, Maxim; Birkelund, Yngve; Senger, Kim; Bergh, Steffen G.

    2016-08-01

    Broadband (0.001-1000 s) magnetotelluric (MT) data along a crooked profile collected to investigate the geothermal potential on Spitsbergen could not be fully explained by two-dimensional (2D) models; hence we interpret the data with three-dimensional (3D) inversion herein. To better accommodate 3D features and nearby off profile resistivity structures, the full MT impedance tensor data together with the tipper were inverted. As a model control, a detailed bathymetry is systematically incorporated in the inversion. Our results from testing different inversion settings emphasised that appropriately choosing and tuning the starting model, data error floor and the model regularization together are crucial to obtain optimum benefit from MT field data. Through the 3D inversion, we reproduced out of quadrant impedance components and obtained an overall satisfactory data fit (RMS = 1.05). The final 3D resistivity model displays a complex geology of the near surface region (fault systems and igneous intrusions in the Mesozoic platform cover deposits. The Billefjorden fault zone is revealed as a consistent and deep rooted (> 2 km) conductive anomaly, confirming the regional nature of the fault. The fault zone is positioned between two uplifted basement blocks (> 1000 Ωm) of presumably pre-Devonian (Caledonian) metamorphic rocks, and the fault may have been responsible for deformation in the overlying Paleozoic-Mesozoic unit. Upper crustal conductive anomalies (3D model are interpreted as part of a Devonian basin fill. These conductors are laterally and vertically bounded by resistive rocks, suggesting a conducive environment for deep geothermal heat storage. Having this scenario in an area of a known high heat-flow, deep faults and a thinned lithosphere makes the hypothesis on finding a technologically exploitable geothermal resource close to human settlement in the area stronger.

  11. Quantitative analysis of vascular heterogeneity in breast lesions using contrast-enhanced 3-D harmonic and subharmonic ultrasound imaging.

    Science.gov (United States)

    Sridharan, Anush; Eisenbrey, John R; Machado, Priscilla; Ojeda-Fournier, Haydee; Wilkes, Annina; Sevrukov, Alexander; Mattrey, Robert F; Wallace, Kirk; Chalek, Carl L; Thomenius, Kai E; Forsberg, Flemming

    2015-03-01

    Ability to visualize breast lesion vascularity and quantify the vascular heterogeneity using contrast-enhanced 3-D harmonic (HI) and subharmonic (SHI) ultrasound imaging was investigated in a clinical population. Patients (n = 134) identified with breast lesions on mammography were scanned using power Doppler imaging, contrast-enhanced 3-D HI, and 3-D SHI on a modified Logiq 9 scanner (GE Healthcare). A region of interest corresponding to ultrasound contrast agent flow was identified in 4D View (GE Medical Systems) and mapped to raw slice data to generate a map of time-intensity curves for the lesion volume. Time points corresponding to baseline, peak intensity, and washout of ultrasound contrast agent were identified and used to generate and compare vascular heterogeneity plots for malignant and benign lesions. Vascularity was observed with power Doppler imaging in 84 lesions (63 benign and 21 malignant). The 3-D HI showed flow in 8 lesions (5 benign and 3 malignant), whereas 3-D SHI visualized flow in 68 lesions (49 benign and 19 malignant). Analysis of vascular heterogeneity in the 3-D SHI volumes found benign lesions having a significant difference in vascularity between central and peripheral sections (1.71 ± 0.96 vs. 1.13 ± 0.79 dB, p < 0.001, respectively), whereas malignant lesions showed no difference (1.66 ± 1.39 vs. 1.24 ± 1.14 dB, p = 0.24), indicative of more vascular coverage. These preliminary results suggest quantitative evaluation of vascular heterogeneity in breast lesions using contrast-enhanced 3-D SHI is feasible and able to detect variations in vascularity between central and peripheral sections for benign and malignant lesions.

  12. 3D NLTE analysis of the most iron-deficient star, SMSS0313-6708

    Science.gov (United States)

    Nordlander, T.; Amarsi, A. M.; Lind, K.; Asplund, M.; Barklem, P. S.; Casey, A. R.; Collet, R.; Leenaarts, J.

    2017-01-01

    Context. Models of star formation in the early universe require a detailed understanding of accretion, fragmentation and radiative feedback in metal-free molecular clouds. Different simulations predict different initial mass functions of the first stars, ranging from predominantly low-mass (0.1-10 M⊙), to massive (10-100 M⊙), or even supermassive (100-1000 M⊙). The mass distribution of the first stars should lead to unique chemical imprints on the low-mass second and later generation metal-poor stars still in existence. The chemical composition of SMSS0313-6708, which has the lowest abundances of Ca and Fe of any star known, indicates it was enriched by a single massive supernova. Aims: The photospheres of metal-poor stars are relatively transparent in the UV, which may lead to large three-dimensional (3D) effects as well as departures from local thermodynamical equilibrium (LTE), even for weak spectral lines. If 3D effects and departures from LTE (NLTE) are ignored or treated incorrectly, errors in the inferred abundances may significantly bias the inferred properties of the polluting supernovae. We redetermine the chemical composition of SMSS0313-6708by means of the most realistic methods available, and compare the results to predicted supernova yields. Methods: A 3D hydrodynamical Staggermodel atmosphere and 3D NLTE radiative transfer were applied to obtain accurate abundances for Li, Na, Mg, Al, Ca and Fe. The model atoms employ realistic collisional rates, with no calibrated free parameters. Results: We find significantly higher abundances in 3D NLTE than 1D LTE by 0.8 dex for Fe, and 0.5 dex for Mg, Al and Ca, while Li and Na are unaffected to within 0.03 dex. In particular, our upper limit for [Fe/H] is now a factor ten larger, at [Fe/H] < -6.53 (3σ), than previous estimates based on ⟨ 3D ⟩NLTE (i.e., using averaged 3D models). This higher estimate is due to a conservative upper limit estimation, updated NLTE data, and 3D-⟨ 3D

  13. Fixed versus Removable Appliance for Palatal Expansion; A 3D Analysis Using the Finite Element Method.

    Directory of Open Access Journals (Sweden)

    Allahyar Geramy

    2014-02-01

    Full Text Available Several appliances have been used for palatal expansion for treatment of posterior cross bite. The purpose of this study was to evaluate the stress induced in the apical and crestal alveolar bone and the pattern of tooth displacement following expansion via removable expansion plates or fixed-banded palatal expander using the finite element method (FEM analysis.Two 3D FEM models were designed from a mesio-distal slice of the maxilla containing the upper first molars, their periodontium and alveolar bone. Two palatal expanders (removable and fixed were modeled. The models were designed in SolidWorks 2006 and then transferred to ANSYS Workbench. The appliance halves were displaced 0.1 mm laterally. The von Mises stress in the apical, crestal, and PDL areas and also the vertical displacement of the cusps (palatal and buccal was were evaluated.The total PDL stress was 0.40003 MPa in the removable appliance (RA model and 4.88e-2 MPa in the fixed appliance (FA model and the apical stress was 9.9e-2 and 1.17e-2 MPa, respectively. The crestal stress was 2.99e-1 MPa in RA and 7.62e-2 MPa in the FA. The stress in the cortical bone crest was 0.30327 and 7.9244e-2 MPa for RA and FA, respectively and 3.7271 and 7.4373e-2 MPa in crestal area of spongy bone, respectively. The vertical displacement of the buccal cusp and palatal cusp was 1.64e-2 and 5.90e-2 mm in RA and 1.05e-4 and 1.7e-4 mm in FA, respectively.The overall stress as well as apical and crestal stress in periodontium of anchor teeth was higher in RA than FA; RA elicited higher stress in both cortical and spongy bone. The vertical displacement of molar cusps was more in removable than fixed palatal expander model.

  14. Uncertainty analysis in 3D global models: Aerosol representation in MOZART-4

    Science.gov (United States)

    Gasore, J.; Prinn, R. G.

    2012-12-01

    The Probabilistic Collocation Method (PCM) has been proven to be an efficient general method of uncertainty analysis in atmospheric models (Tatang et al 1997, Cohen&Prinn 2011). However, its application has been mainly limited to urban- and regional-scale models and chemical source-sink models, because of the drastic increase in computational cost when the dimension of uncertain parameters increases. Moreover, the high-dimensional output of global models has to be reduced to allow a computationally reasonable number of polynomials to be generated. This dimensional reduction has been mainly achieved by grouping the model grids into a few regions based on prior knowledge and expectations; urban versus rural for instance. As the model output is used to estimate the coefficients of the polynomial chaos expansion (PCE), the arbitrariness in the regional aggregation can generate problems in estimating uncertainties. To address these issues in a complex model, we apply the probabilistic collocation method of uncertainty analysis to the aerosol representation in MOZART-4, which is a 3D global chemical transport model (Emmons et al., 2010). Thereafter, we deterministically delineate the model output surface into regions of homogeneous response using the method of Principal Component Analysis. This allows the quantification of the uncertainty associated with the dimensional reduction. Because only a bulk mass is calculated online in Mozart-4, a lognormal number distribution is assumed with a priori fixed scale and location parameters, to calculate the surface area for heterogeneous reactions involving tropospheric oxidants. We have applied the PCM to the six parameters of the lognormal number distributions of Black Carbon, Organic Carbon and Sulfate. We have carried out a Monte-Carlo sampling from the probability density functions of the six uncertain parameters, using the reduced PCE model. The global mean concentration of major tropospheric oxidants did not show a

  15. 3D-analysis of the spay test 101 in the TOSQAN facility using GASFLOW II

    Energy Technology Data Exchange (ETDEWEB)

    Lee, Un-Jang; Kim, Jong-Tae; Kim, Sang-Baik; Kim, Hee-Dong [Korea Atomic Energy Research Institute, Taejon (Korea, Republic of); Park, Goon-Cherl [Seoul National Univ., Seoul (Korea, Republic of)

    2006-07-01

    During the course of a hypothetical severe accident in a PWR, hydrogen can be produced by the reactor core oxidation and distributed into the reactor containment according to convection flows and water steam wall condensation. In order to prevent the over pressures in the event of a steam break, spray systems are used in the containment. However, the effect of a spray could even increase the risk of hydrogen explosion by condensing steam and therefore locally enriches hydrogen in gaseous mixtures. Thus, detailed understanding of the 3D thermal hydraulic conditions inside the containment is of high relevance for all aspects of accident management and mitigation. The computer code GASFLOW II has demonstrated its ability in the past to calculate the important thermal hydraulic processes during such severe accident sequences. GASFLOW gives a time dependent solution of the 3D Navier Stokes equations in cylindrical or cartesian coordinates. The validation of the code with scenario related 3D experimental data is required to use this code as a predictive tool for the simulation of such accidents in real reactor containments and for the design and verification of mitigation measures. Validation is therefore an essential part of code development.The validation of GASFLOW have focused on more recent experiments in the new containment test facilities ThAI, TOSQAN, and MISTRA. They have innovative 3D instrumentation for the validation of results from 3D CFD simulations. GASFLOW blindly predicted the pressure and temperature distribution for a MISTRA experiment and for the ThAI benchmark experiment TH7 quite well. The 3D experiment TH7 was performed without hydrogen release in a multi compartment geometry of the ThAI facility and involved a sequence of eccentric steam injections at high and low injection points followed by a heating phase. Also, the-state-of-art tests of the open TOSQAN benchmark (ISP 47) was analyzed with GASFLOW in a 2-D cylindrical geometry. Recently the

  16. A new method to create depth information based on lighting analysis for 2D/3D conversion

    Institute of Scientific and Technical Information of China (English)

    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.

  17. A unified and efficient framework for court-net sports video analysis using 3D camera modeling

    Science.gov (United States)

    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%.

  18. Evaluation of AN Integrated Gis-Based Crime Analysis & 3d Modelling for Izmir-Konak Municipality

    Science.gov (United States)

    Tarhan, C.; Deniz, D.

    2011-08-01

    GIS integrated 3D modelling is crucial for the city planning and design processes because urban modelling is a tool used in virtual environments, and provides convenience to work. Although, the creation and display of 3D city models for large regions is difficult it is vital for planning and designing safer cities, as well as public places. Today, crime is a significant problem in Turkey. When it was compared by years of crime rates, population growth and urbanization rate, an increasing more than in parallel has been observed. This paper aims to discuss GIS integrated 3D modelling affects in urban planning and design, explaining Turkish planning processes with GIS and 3D modelling. To do that, it presents a case study for Izmir Konak Municipality about GIS integrated crime analysis and 3D models of the crime scenes. Izmir crime records has been obtained from Izmir Police Department belonging to 2003-2004 and 2005 (D. Deniz, 2007) are used for districts' crime map. In the light of these data, the highest rate crime district, Konak, is analyzed between 2001 and 2005 data.

  19. Automated detection, 3D segmentation and analysis of high resolution spine MR images using statistical shape models

    Science.gov (United States)

    Neubert, A.; Fripp, J.; Engstrom, C.; Schwarz, R.; Lauer, L.; Salvado, O.; Crozier, S.

    2012-12-01

    Recent advances in high resolution magnetic resonance (MR) imaging of the spine provide a basis for the automated assessment of intervertebral disc (IVD) and vertebral body (VB) anatomy. High resolution three-dimensional (3D) morphological information contained in these images may be useful for early detection and monitoring of common spine disorders, such as disc degeneration. This work proposes an automated approach to extract the 3D segmentations of lumbar and thoracic IVDs and VBs from MR images using statistical shape analysis and registration of grey level intensity profiles. The algorithm was validated on a dataset of volumetric scans of the thoracolumbar spine of asymptomatic volunteers obtained on a 3T scanner using the relatively new 3D T2-weighted SPACE pulse sequence. Manual segmentations and expert radiological findings of early signs of disc degeneration were used in the validation. There was good agreement between manual and automated segmentation of the IVD and VB volumes with the mean Dice scores of 0.89 ± 0.04 and 0.91 ± 0.02 and mean absolute surface distances of 0.55 ± 0.18 mm and 0.67 ± 0.17 mm respectively. The method compares favourably to existing 3D MR segmentation techniques for VBs. This is the first time IVDs have been automatically segmented from 3D volumetric scans and shape parameters obtained were used in preliminary analyses to accurately classify (100% sensitivity, 98.3% specificity) disc abnormalities associated with early degenerative changes.

  20. NUMERICAL SIMULATION OF 3-D TURBULENT FLOWS IN A CUT-OFF VALVE AND ANALYSIS OF FLOW CHARACTERISTICS IN PIPE

    Institute of Scientific and Technical Information of China (English)

    He Zhi-guo; Mao Gen-hai; Yuan Xing-ming

    2003-01-01

    The 3-D turbulent flows in a valve pipe were described by the incompressible Reynolds-averaged Navier-Stokes equations with an RNG k-ε turbulence model. With the finite volume method and a body-fitted coordinate system, the discretised equations were solved by the SIMPLEST algorithm. The numerical result of a cut-off valve with curved inlet shows the flow characteristics and the main cause of energy loss when fluid flows through a valve. And then, the boundaries of valve were modified in order to reduce the energy loss. The computational results of modified valve show that the numerical value of turbulent kinetic energy is lower, and that the modified design of the 3-D valve boundaries is much better. The analysis of the result also shows that RNG k-ε turbulence model can successfully be used to predict the 3-D turbulent separated flows and the secondary flow inside valve pipes.

  1. An experimental analysis for the impact of 3D variation assi- milation of satellite data on typhoon track simulation

    Institute of Scientific and Technical Information of China (English)

    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.

  2. Developing a 3D constrained variational analysis method to obtain accurate gridded atmospheric vertical velocity and horizontal advections

    Science.gov (United States)

    Tang, S.; Zhang, M.

    2013-12-01

    Based on the constrained variational analysis (CVA) algorithm developed by Zhang and Lin (1997), a 3-dimensional (3D) version of CVA is developed. The new algorithm used gridded surface and TOA observations as constraints to adjust atmospheric state variables in each grid point to satisfy column-integrated mass, moisture and static energy conservation. From the process of adjustment a set of high-quality 3D large-scale forcing data (vertical velocity and horizontal advections) can be derived to drive Single-Column models (SCM), Cloud-Resolving Models (CRM) and Large-Eddy Simulations (LES) to evaluate and improve parameterizations. Since the 3D CVA can adjust gridded state variables from any data source with observed precipitation, radiation and surface fluxes, it also gives a potential possibility to use this algorithm in data assimilation system to assimilate precipitation and radiation data.

  3. Identifying fault segments from 3D fault drag analysis (Vienna Basin, Austria)

    Science.gov (United States)

    Spahić, Darko; Grasemann, Bernhard; Exner, Ulrike

    2013-10-01

    The segmented growth of the Markgrafneusiedl normal fault in the late Miocene clastic sediments of the central Vienna Basin (Austria) was investigated by construction of a detailed three-dimensional (3D) structural model. Using high resolution 3D seismic data, the fault surface and marker horizons in the hanging wall and the footwall of the Markgrafneusiedl Fault were mapped and orientation, displacement and morphology of the fault surface were quantified. Individual, fault segments were identified by direct mapping of the deflection of the marker horizons close to the fault surface. Correlating the size of the identified segments with the magnitude of fault drag and displacement distribution showed that fault evolution progressed in several stages. The proposed method allows the detection of segments that are not recorded by the magnitude of displacement or fault morphology. Most importantly, detailed mapping of marker deflections in the hanging wall could help to constrain equivalent structures in the footwall, which may represent potential hydrocarbon traps.

  4. 3D RECONSTRUCTION AND ANALYSIS OF THE FRAGMENTED GRAINS IN A COMPOSITE MATERIAL

    Directory of Open Access Journals (Sweden)

    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.

  5. FRICTIONAL CONTACT MULTIPOLE-BEM AND 3-D ANALYSIS OF SCREWPAIRS

    Institute of Scientific and Technical Information of China (English)

    Chen Xiumin; Shen Guangxian; Liu Deyi

    2004-01-01

    The 3-D traction field in the pressure screw-pair of a 3 500 heavy and medium plate mill press down system is successfully calculated by applying the 3-D frictional contact multipole-BEM and the corresponding program that has been developed. The computing results show the medium diameter orientation is unreliable, especially under the interference of an outer force couple. Under such working conditions, the circumferential traction distribution on the screw teeth is extremely uneven, which is the main reason for the destruction and short life time of screw-pairs. When utilizing the same precision (the relative tolerance is 10×10-5),the mltipole-BEM uses almost the CPU time as used by the FEM,but the needed computer menory size is only one eighieth of that needed by the FEM(10 MB vs.800 MB).The multipole-BEM is well suited for computing large-scale engineering problems.

  6. Automated Rock Detection and Shape Analysis from Mars Rover Imagery and 3D Point Cloud Data

    Institute of Scientific and Technical Information of China (English)

    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.

  7. Semantic segmentation of 3D textured meshes for urban scene analysis

    Science.gov (United States)

    Rouhani, Mohammad; Lafarge, Florent; Alliez, Pierre

    2017-01-01

    Classifying 3D measurement data has become a core problem in photogrammetry and 3D computer vision, since the rise of modern multiview geometry techniques, combined with affordable range sensors. We introduce a Markov Random Field-based approach for segmenting textured meshes generated via multi-view stereo into urban classes of interest. The input mesh is first partitioned into small clusters, referred to as superfacets, from which geometric and photometric features are computed. A random forest is then trained to predict the class of each superfacet as well as its similarity with the neighboring superfacets. Similarity is used to assign the weights of the Markov Random Field pairwise-potential and to account for contextual information between the classes. The experimental results illustrate the efficacy and accuracy of the proposed framework.

  8. A 3D tomographic EBSD analysis of a CVD diamond thin film

    Directory of Open Access Journals (Sweden)

    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.

  9. A Multimodal Discourse Analysis of the First Movie Poster of Titanic (3D)

    Institute of Scientific and Technical Information of China (English)

    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.

  10. Development of direct-inverse 3-D methods for applied aerodynamic design and analysis

    Science.gov (United States)

    Carlson, Leland A.

    1988-01-01

    Several inverse methods have been compared and initial results indicate that differences in results are primarily due to coordinate systems and fuselage representations and not to design procedures. Further, results from a direct-inverse method that includes 3-D wing boundary layer effects, wake curvature, and wake displacement are presented. These results show that boundary layer displacements must be included in the design process for accurate results.

  11. Seepage-Based Factor of Safety Analysis Using 3D Groundwater Simulation Results

    Science.gov (United States)

    2014-08-01

    Hydraulics Engineering Technical Note (CHETN) is to document techniques for computing Factors of Safety (FoS) for seepage-related soil instability...topography, geology, sources or sinks , and boundary conditions along the length of the soil structure. If these conditions exist, a 3D model may be needed... hydraulic gradient, and iv is the exit gradient at the point of interest. The critical, stable, and unstable conditions are thus defined as FoS = 1, FoS

  12. ERROR ANALYSIS OF 3D DETECTING SYSTEM BASED ON WHOLE-FIELD PARALLEL CONFOCAL MICROSCOPE

    Institute of Scientific and Technical Information of China (English)

    Wang Yonghong; Yu Xiaofen

    2005-01-01

    Compared with the traditional scanning confocal microscopy, the effect of various factors on characteristic in multi-beam parallel confocal system is discussed, the error factors in multi-beam parallel confocal system are analyzed. The factors influencing the characteristics of the multi-beam parallel confocal system are discussed. The construction and working principle of the non-scanning 3D detecting system is introduced, and some experiment results prove the effect of various factors on the detecting system.

  13. Geoarchaeological site documentation and analysis of 3D data derived by terrestrial laser scanning

    Science.gov (United States)

    Hoffmeister, D.; Zellmann, S.; Kindermann, K.; Pastoors, A.; Lang, U.; Bubenzer, O.; Weniger, G.-C.; Bareth, G.

    2014-05-01

    Terrestrial laser scanning was conducted to document and analyse sites of geoarchaeological interest in Jordan, Egypt and Spain. In those cases, the terrestrial laser scanner LMS-Z420i from Riegl was used in combination with an accurate RTK-GPS for georeferencing of the point clouds. Additionally, local surveying networks were integrated by established transformations and used for indirect registration purposes. All data were integrated in a workflow that involves different software and according results. The derived data were used for the documentation of the sites by accurate plans and cross-sections. Furthermore, the 3D data were analysed for geoarchaeological research problems, such as volumetric determinations, the ceiling thickness of a cave and lighting simulations based on path tracing. The method was reliable in harsh environmental conditions, but the weight of the instrument, the measuring time and the minimum measurement distance were a drawback. However, generally an accurate documentation of the sites was possible. Overall, the integration in a 3D GIS is easily possible by the accurate georeference of the derived data. In addition, local survey results are also implemented by the established transformations. Enhanced analyses based on the derived 3D data shows promising results.

  14. 3D endobronchial ultrasound reconstruction and analysis for multimodal image-guided bronchoscopy

    Science.gov (United States)

    Zang, Xiaonan; Bascom, Rebecca; Gilbert, Christopher R.; Toth, Jennifer W.; Higgins, William E.

    2014-03-01

    State-of-the-art image-guided intervention (IGI) systems for lung-cancer management draw upon high-resolution three-dimensional multi-detector computed-tomography (MDCT) images and bronchoscopic video. An MDCT scan provides a high-resolution three-dimensional (3D) image of the chest that is used for preoperative procedure planning, while bronchoscopy gives live intraoperative video of the endobronchial airway tree structure. However, because neither source provides live extraluminal information on suspect nodules or lymph nodes, endobronchial ultrasound (EBUS) is often introduced during a procedure. Unfortunately, existing IGI systems provide no direct synergistic linkage between the MDCT/video data and EBUS data. Hence, EBUS proves difficult to use and can lead to inaccurate interpretations. To address this drawback, we present a prototype of a multimodal IGI system that brings together the various image sources. The system enables 3D reconstruction and visualization of structures depicted in the 2D EBUS video stream. It also provides a set of graphical tools that link the EBUS data directly to the 3D MDCT and bronchoscopic video. Results using phantom and human data indicate that the new system could potentially enable smooth natural incorporation of EBUS into the system-level work flow of bronchoscopy.

  15. Analysis of Uncertainty in a Middle-Cost Device for 3D Measurements in BIM Perspective.

    Science.gov (United States)

    Sánchez, Alonso; Naranjo, José-Manuel; Jiménez, Antonio; González, Alfonso

    2016-09-22

    Medium-cost devices equipped with sensors are being developed to get 3D measurements. Some allow for generating geometric models and point clouds. Nevertheless, the accuracy of these measurements should be evaluated, taking into account the requirements of the Building Information Model (BIM). This paper analyzes the uncertainty in outdoor/indoor three-dimensional coordinate measures and point clouds (using Spherical Accuracy Standard (SAS) methods) for Eyes Map, a medium-cost tablet manufactured by e-Capture Research & Development Company, Mérida, Spain. To achieve it, in outdoor tests, by means of this device, the coordinates of targets were measured from 1 to 6 m and cloud points were obtained. Subsequently, these were compared to the coordinates of the same targets measured by a Total Station. The Euclidean average distance error was 0.005-0.027 m for measurements by Photogrammetry and 0.013-0.021 m for the point clouds. All of them satisfy the tolerance for point cloud acquisition (0.051 m) according to the BIM Guide for 3D Imaging (General Services Administration); similar results are obtained in the indoor tests, with values of 0.022 m. In this paper, we establish the optimal distances for the observations in both, Photogrammetry and 3D Photomodeling modes (outdoor) and point out some working conditions to avoid in indoor environments. Finally, the authors discuss some recommendations for improving the performance and working methods of the device.

  16. Analysis of discriminants for experimental 3D SAR imagery of human targets

    Science.gov (United States)

    Chan, Brigitte; Sévigny, Pascale; DiFilippo, David D. J.

    2014-10-01

    Development of a prototype 3-D through-wall synthetic aperture radar (SAR) system is currently underway at Defence Research and Development Canada. The intent is to map out building wall layouts and to detect targets of interest and their location behind walls such as humans, arms caches, and furniture. This situational awareness capability can be invaluable to the military working in an urban environment. Tools and algorithms are being developed to exploit the resulting 3-D imagery. Current work involves analyzing signatures of targets behind a wall and understanding the clutter and multipath signals in a room of interest. In this paper, a comprehensive study of 3-D human target signature metrics in free space is presented. The aim is to identify features for discrimination of the human target from other targets. Targets used in this investigation include a human standing, a human standing with arms stretched out, a chair, a table, and a metallic plate. Several features were investigated as potential discriminants and five which were identified as good candidates are presented in this paper. Based on this study, no single feature could be used to fully discriminate the human targets from all others. A combination of at least two different features is required to achieve this.

  17. Design and Stability Analysis of a 3D Rimless Wheel with Flat Feet and Ankle Springs

    Science.gov (United States)

    Narukawa, Terumasa; Takahashi, Masaki; Yoshida, Kazuo

    A two-dimensional rimless wheel provides a simple model of bipedal walking. The motion of the rimless wheel is stable, and this particular property has clarified the fundamental role of a swing leg in planar bipedal walking that addresses the problem of falling forward. In this paper, a three-dimensional rimless wheel is investigated as a simple model of three-dimensional bipedal walking. The 3D rimless wheel model is useful in understanding the essential dynamics of 3D bipedal locomotion. The model consists of two rimless wheels connected by a link at the center of the wheels, and flat feet connected to the spokes with springs. The first numerical stability studies indicated that the motion of the 3D rimless wheel could be unstable; however, numerical simulations and experimental results showed that for a given slope and physical parameters, including the spring constant at the ankles, a stable motion is obtained. This indicates the usefulness of ankle springs in providing stable bipedal locomotion in three-dimensions.

  18. Quality Analysis on 3d Buidling Models Reconstructed from Uav Imagery

    Science.gov (United States)

    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.

  19. Analysis of Uncertainty in a Middle-Cost Device for 3D Measurements in BIM Perspective

    Science.gov (United States)

    Sánchez, Alonso; Naranjo, José-Manuel; Jiménez, Antonio; González, Alfonso

    2016-01-01

    Medium-cost devices equipped with sensors are being developed to get 3D measurements. Some allow for generating geometric models and point clouds. Nevertheless, the accuracy of these measurements should be evaluated, taking into account the requirements of the Building Information Model (BIM). This paper analyzes the uncertainty in outdoor/indoor three-dimensional coordinate measures and point clouds (using Spherical Accuracy Standard (SAS) methods) for Eyes Map, a medium-cost tablet manufactured by e-Capture Research & Development Company, Mérida, Spain. To achieve it, in outdoor tests, by means of this device, the coordinates of targets were measured from 1 to 6 m and cloud points were obtained. Subsequently, these were compared to the coordinates of the same targets measured by a Total Station. The Euclidean average distance error was 0.005–0.027 m for measurements by Photogrammetry and 0.013–0.021 m for the point clouds. All of them satisfy the tolerance for point cloud acquisition (0.051 m) according to the BIM Guide for 3D Imaging (General Services Administration); similar results are obtained in the indoor tests, with values of 0.022 m. In this paper, we establish the optimal distances for the observations in both, Photogrammetry and 3D Photomodeling modes (outdoor) and point out some working conditions to avoid in indoor environments. Finally, the authors discuss some recommendations for improving the performance and working methods of the device. PMID:27669245

  20. GISAXS analysis of 3D nanoparticle assemblies--effect of vertical nanoparticle ordering.

    Science.gov (United States)

    Vegso, K; Siffalovic, P; Benkovicova, M; Jergel, M; Luby, S; Majkova, E; Capek, I; Kocsis, T; Perlich, J; Roth, S V

    2012-02-03

    We report on grazing-incidence small-angle x-ray scattering (GISAXS) study of 3D nanoparticle arrays prepared by two different methods from colloidal solutions-layer-by-layer Langmuir-Schaefer deposition and spontaneous self-assembling during the solvent evaporation. GISAXS results are evaluated within the distorted wave Born approximation (DWBA) considering the multiple scattering effects and employing a simplified multilayer model to reduce the computing time. In the model, particular layers are represented by nanoparticle chains where the positions of individual nanoparticles are generated following a model of cumulative disorder. The nanoparticle size dispersion is considered as well. Three model ca