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Sample records for 3d molecular modeling

  1. 3D Printing of Molecular Models

    ERIC Educational Resources Information Center

    Gardner, Adam; Olson, Arthur

    2016-01-01

    Physical molecular models have played a valuable role in our understanding of the invisible nano-scale world. We discuss 3D printing and its use in producing models of the molecules of life. Complex biomolecular models, produced from 3D printed parts, can demonstrate characteristics of molecular structure and function, such as viral self-assembly,…

  2. 3D Printing of Molecular Potential Energy Surface Models

    ERIC Educational Resources Information Center

    Lolur, Phalgun; Dawes, Richard

    2014-01-01

    Additive manufacturing, commonly known as 3D printing, is gaining popularity in a variety of applications and has recently become routinely available. Today, 3D printing services are not only found in engineering design labs and through online companies, but also in university libraries offering student access. In addition, affordable options for…

  3. Molecular interaction study of flavonoid derivative 3d with human serum albumin using multispectroscopic and molecular modeling approach.

    PubMed

    Wei, Juntong; Jin, Feng; Wu, Qin; Jiang, Yuyang; Gao, Dan; Liu, Hongxia

    2014-08-01

    Human serum albumin (HSA) has been developed as a model protein to study drug-protein interaction. In the present work, the interaction between our synthesized flavonoid derivative 3d (possessing potent antitumor activity against HepG2 cells) and HSA was investigated using fluorescence spectroscopy, circular dichroism spectroscopy, UV-vis spectroscopy and molecular modeling approach. Fluorescence spectroscopy showed that the fluorescence of HSA can be quenched remarkably by 3d under physiological condition with a slight shift of maximum fluorescence emission bands from 360nm to 363nm. Calculated results from Stern-Volmer equation and modified Stern-Volmer equation indicated that the fluorescence was quenched by static quenching processing with association constant 5.26±0.04×10(4)L mol(-1) at 298K. After comprehensive consideration of the free energy change ΔG, enthalpy change ΔH and entropy change ΔS, electrostatic interactions were confirmed as the main factor that participate in stabilizing the 3d-HSA complex. Both dichroism spectroscopy and UV-vis spectroscopy indicated conformational change of HSA after binding to 3d. Moreover, the structure of HSA was loosened and the percentage of α-helix decreased with increasing concentration of 3d. Molecular modeling results demonstrated that 3d could bind to HSA well into subdomain IIA, which is related to its capability of deposition and delivery. Three cation-π interactions and three hydrogen bonds occurred between 3d and amino acid residuals ARG218, ARG222 and LYS199. In conclusion, flavonoid derivative 3d can bind to HSA with noncovalent bond in a relatively stable way, so it can be delivered by HSA in a circulatory system.

  4. An in-depth spectroscopic examination of molecular bands from 3D hydrodynamical model atmospheres. II. Carbon-enhanced metal-poor 3D model atmospheres

    NASA Astrophysics Data System (ADS)

    Gallagher, A. J.; Caffau, E.; Bonifacio, P.; Ludwig, H.-G.; Steffen, M.; Homeier, D.; Plez, B.

    2017-02-01

    Context. Tighter constraints on metal-poor stars we observe are needed to better understand the chemical processes of the early Universe. Computing a stellar spectrum in 3D allows one to model complex stellar behaviours, which cannot be replicated in 1D. Aims: We examine the effect that the intrinsic CNO abundances have on a 3D model structure and the resulting 3D spectrum synthesis. Methods: Model atmospheres were computed in 3D for three distinct CNO chemical compositions using the CO5BOLD model atmosphere code, and their internal structures were examined. Synthetic spectra were computed from these models using Linfor3D and they were compared. New 3D abundance corrections for the G-band and a selection of UV OH lines were also computed. Results: The varying CNO abundances change the metal content of the 3D models. This had an effect on the model structure and the resulting synthesis. However, it was found that the C/O ratio had a larger effect than the overall metal content of a model. Conclusions: Our results suggest that varying the C/O ratio has a substantial impact on the internal structure of the 3D model, even in the hot turn-off star models explored here. This suggests that bespoke 3D models, for specific CNO abundances should be sought. Such effects are not seen in 1D at these temperature regimes.

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

    NASA Astrophysics Data System (ADS)

    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.

  6. 3D-QSAR and molecular modeling of HIV-1 integrase inhibitors

    NASA Astrophysics Data System (ADS)

    Makhija, Mahindra T.; Kulkarni, Vithal M.

    2002-03-01

    Three-dimensional quantitative structure-activity relationship (3D QSAR) methods were applied on a series of inhibitors of HIV-1 integrase with respect to their inhibition of 3'-processing and 3'-end joining steps in vitro.The training set consisted of 27 compounds belonging to the class of thiazolothiazepines. The predictive ability of each model was evaluated using test set I consisting of four thiazolothiazepines and test set II comprised of seven compounds belonging to an entirely different structural class of coumarins. Maximum Common Substructure (MCS) based method was used to align the molecules and this was compared with other known methods of alignment. Two methods of 3D QSAR: comparative molecular field analysis (CoMFA) and comparative molecular similarity indices analysis (CoMSIA) were analyzed in terms of their predictive abilities. CoMSIA produced significantly better results for all correlations. The results indicate a strong correlation between the inhibitory activity of these compounds and the steric and electrostatic fields around them. CoMSIA models with considerable internal as well as external predictive ability were obtained. A poor correlation obtained with hydrophobic field indicates that the binding of thiazolothiazepines to HIV-1 integrase is mainly enthalpic in nature. Further the most active compound of the series was docked into the active site using the crystal structure of integrase. The binding site was formed by the amino acid residues 64-67, 116, 148, 151-152, 155-156, and 159. The comparison of coefficient contour maps with the steric and electrostatic properties of the receptor shows high level of compatibility.

  7. Can molecular dynamics simulations help in discriminating correct from erroneous protein 3D models?

    PubMed Central

    Taly, Jean-François; Marin, Antoine; Gibrat, Jean-François

    2008-01-01

    Background Recent approaches for predicting the three-dimensional (3D) structure of proteins such as de novo or fold recognition methods mostly rely on simplified energy potential functions and a reduced representation of the polypeptide chain. These simplifications facilitate the exploration of the protein conformational space but do not permit to capture entirely the subtle relationship that exists between the amino acid sequence and its native structure. It has been proposed that physics-based energy functions together with techniques for sampling the conformational space, e.g., Monte Carlo or molecular dynamics (MD) simulations, are better suited to the task of modelling proteins at higher resolutions than those of models obtained with the former type of methods. In this study we monitor different protein structural properties along MD trajectories to discriminate correct from erroneous models. These models are based on the sequence-structure alignments provided by our fold recognition method, FROST. We define correct models as being built from alignments of sequences with structures similar to their native structures and erroneous models from alignments of sequences with structures unrelated to their native structures. Results For three test sequences whose native structures belong to the all-α, all-β and αβ classes we built a set of models intended to cover the whole spectrum: from a perfect model, i.e., the native structure, to a very poor model, i.e., a random alignment of the test sequence with a structure belonging to another structural class, including several intermediate models based on fold recognition alignments. We submitted these models to 11 ns of MD simulations at three different temperatures. We monitored along the corresponding trajectories the mean of the Root-Mean-Square deviations (RMSd) with respect to the initial conformation, the RMSd fluctuations, the number of conformation clusters, the evolution of secondary structures and the

  8. Non-Newtonian models for molecular viscosity and wall shear stress in a 3D reconstructed human left coronary artery.

    PubMed

    Soulis, Johannes V; Giannoglou, George D; Chatzizisis, Yiannis S; Seralidou, Kypriani V; Parcharidis, George E; Louridas, George E

    2008-01-01

    The capabilities and limitations of various molecular viscosity models, in the left coronary arterial tree, were analyzed via: molecular viscosity, local and global non-Newtonian importance factors, wall shear stress (WSS) and wall shear stress gradient (WSSG). The vessel geometry was acquired using geometrically correct 3D intravascular ultrasound (3D IVUS). Seven non-Newtonian molecular viscosity models, plus the Newtonian one, were compared. The WSS distribution yielded a consistent LCA pattern for nearly all non-Newtonian models. High molecular viscosity, low WSS and low WSSG values occurred at the outer walls of the major bifurcation in proximal LCA regions. The Newtonian blood flow was found to be a good approximation at mid- and high-strain rates. The non-Newtonian Power Law, Generalized Power Law, Carreau and Casson and Modified Cross blood viscosity models gave comparable molecular viscosity, WSS and WSSG values. The Power Law and Walburn-Schneck models over-estimated the non-Newtonian global importance factor I(G) and under-estimated the area averaged WSS and WSSG values. The non-Newtonian Power Law and the Generalized Power Law blood viscosity models were found to approximate the molecular viscosity and WSS calculations in a more satisfactory way.

  9. Receptor Surface Models in the Classroom: Introducing Molecular Modeling to Students in a 3-D World

    ERIC Educational Resources Information Center

    Geldenhuys, Werner J.; Hayes, Michael; Van der Schyf, Cornelis J.; Allen, David D.; Malan, Sarel F.

    2007-01-01

    A simple, novel and generally applicable method to demonstrate structure-activity associations of a group of biologically interesting compounds in relation to receptor binding is described. This method is useful for undergraduates and graduate students in medicinal chemistry and computer modeling programs.

  10. Teaching Molecular 3-D Literacy

    ERIC Educational Resources Information Center

    Richardson, David C.; Richardson, Jane S.

    2002-01-01

    This article describes how the use of interactive molecular graphics makes a unique and important contribution to student learning of biochemistry and molecular biology at any level. These authors developed the concept of the kinemage (from "kinetic image"), a different way of organizing computer graphics that is aimed explicitly at the…

  11. Identifying cell and molecular stress after radiation in a three-dimensional (3-D) model of oral mucositis

    SciTech Connect

    Lambros, Maria Polikandritou; Parsa, Cyrus; Mulamalla, HariChandana; Orlando, Robert; Lau, Bernard; Huang, Ying; Pon, Doreen; Chow, Moses

    2011-02-04

    Research highlights: {yields} We irradiated a 3-D human oral cell culture of keratinocytes and fibroblasts with 12 and 2 Gy. {yields} 6 h after irradiation the histopathology and apoptosis of the 3-D culture were evaluated. Microarrays were used to assess the gene expression in the irradiated 3-D tissue. {yields} 12 Gy induced significant histopathologic changes and cellular apoptosis. {yields} 12 Gy significantly affected genes of the NF-kB pathway, inflammatory cytokines and DAMPs. -- Abstract: Mucositis is a debilitating adverse effect of chemotherapy and radiation treatment. It is important to develop a simple and reliable in vitro model, which can routinely be used to screen new drugs for prevention and treatment of mucositis. Furthermore, identifying cell and molecular stresses especially in the initiation phase of mucositis in this model will help towards this end. We evaluated a three-dimensional (3-D) human oral cell culture that consisted of oral keratinocytes and fibroblasts as a model of oral mucositis. The 3-D cell culture model was irradiated with 12 or 2 Gy. Six hours after the irradiation we evaluated microscopic sections of the cell culture for evidence of morphologic changes including apoptosis. We used microarrays to compare the expression of several genes from the irradiated tissue with identical genes from tissue that was not irradiated. We found that irradiation with 12 Gy induced significant histopathologic effects including cellular apoptosis. Irradiation significantly affected the expression of several genes of the NF-kB pathway and several inflammatory cytokines, such as IL-1B, 1L-8, NF-kB1, and FOS compared to tissue that was not irradiated. We identified significant upregulation of several genes that belong to damage-associated molecular patterns (DAMPs) such as HMB1, S100A13, SA10014, and SA10016 in the 3-D tissues that received 12 Gy but not in tissues that received 2 Gy. In conclusion, this model quantifies radiation damage and this

  12. Identifying cell and molecular stress after radiation in a three-dimensional (3-D) model of oral mucositis.

    PubMed

    Lambros, Maria Polikandritou; Parsa, Cyrus; Mulamalla, HariChandana; Orlando, Robert; Lau, Bernard; Huang, Ying; Pon, Doreen; Chow, Moses

    2011-02-04

    Mucositis is a debilitating adverse effect of chemotherapy and radiation treatment. It is important to develop a simple and reliable in vitro model, which can routinely be used to screen new drugs for prevention and treatment of mucositis. Furthermore, identifying cell and molecular stresses especially in the initiation phase of mucositis in this model will help towards this end. We evaluated a three-dimensional (3-D) human oral cell culture that consisted of oral keratinocytes and fibroblasts as a model of oral mucositis. The 3-D cell culture model was irradiated with 12 or 2 Gy. Six hours after the irradiation we evaluated microscopic sections of the cell culture for evidence of morphologic changes including apoptosis. We used microarrays to compare the expression of several genes from the irradiated tissue with identical genes from tissue that was not irradiated. We found that irradiation with 12 Gy induced significant histopathologic effects including cellular apoptosis. Irradiation significantly affected the expression of several genes of the NF-kB pathway and several inflammatory cytokines, such as IL-1B, 1L-8, NF-kB1, and FOS compared to tissue that was not irradiated. We identified significant upregulation of several genes that belong to damage-associated molecular patterns (DAMPs) such as HMB1, S100A13, SA10014, and SA10016 in the 3-D tissues that received 12 Gy but not in tissues that received 2 Gy. In conclusion, this model quantifies radiation damage and this is an important first step towards the development 3-D tissue as a screening tool.

  13. Pharmacophore modeling, 3D-QSAR and molecular docking studies of benzimidazole derivatives as potential FXR agonists.

    PubMed

    Sindhu, Thangaraj; Srinivasan, Pappu

    2014-08-01

    Farnesoid X receptor (FXR) is a potential therapeutic target for the treatment of diabetes mellitus. Atom-based three-dimensional quantitative structure activity relationship (3D-QSAR) models were developed for a series of 48 benzimidazole-based agonists of FXR. A total of five pharmacophore hypotheses were generated based on the survival score to build QSAR models. HHHRR was considered as a best model that consisted of three hydrophobic features (H) and two aromatic rings (R). The best hypothesis, HHHRR yielded a 3D-QSAR model with good statistical value (R(2)) of 0.8974 for a training set of 39 compounds and also showed good predictive power with correlation coefficient (Q(2)) of 0.7559 for a test set of nine compounds. Furthermore, molecular docking simulation was performed to understand the binding affinity of 48 benzimidazole-based compounds against the active site of human FXR protein. Docking results revealed that both the most active and least active compounds showed similar binding mode to the experimentally observed binding mode of co-crystallized ligand. The generated 3D contour maps revealed the structure activity relationship of the compounds. Substitution effects at different positions of benzimidazole derivatives would lead to the discovery of new agonists against human FXR protein.

  14. A Molecular Perspective of Inter-filament Bonding in Fused Deposition Modeling 3-D Printing

    NASA Astrophysics Data System (ADS)

    Duranty, Edward; Spradlin, Brandon; Dadmun, Mark

    2015-03-01

    Fused deposition 3D printing is an important tool for low-cost and rapid prototyping of objects with complex geometries. 3D printed materials are composed of many filaments deposited on a heated substrate, requiring the bonding of neighboring filaments during the deposition process. Filament deposition often creates voids between filaments, which requires necking between them to create a robust sample. Therefore the amount of interfacial contact and interdiffusion between filaments become important parameters that control the macroscopic physical properties of the printed prototype. Our research focuses on quantifying the interfacial adhesion between ABS filaments and its impact on structural properties. The time evolution of the temperature profile near the heated substrate demonstrates that the deposited filaments are repeatedly heated above the Tg of ABS allowing interpenetration of the polymer chains between adjacent filaments. Results of DMA experiments on samples of different geometries have been correlated to microphotography that monitors the degree of necking between filaments and the thermal history. Results indicate that interfacial contact area between filaments and increased thermal energy are crucial to their mechanical properties.

  15. Modeling cellular processes in 3D.

    PubMed

    Mogilner, Alex; Odde, David

    2011-12-01

    Recent advances in photonic imaging and fluorescent protein technology offer unprecedented views of molecular space-time dynamics in living cells. At the same time, advances in computing hardware and software enable modeling of ever more complex systems, from global climate to cell division. As modeling and experiment become more closely integrated we must address the issue of modeling cellular processes in 3D. Here, we highlight recent advances related to 3D modeling in cell biology. While some processes require full 3D analysis, we suggest that others are more naturally described in 2D or 1D. Keeping the dimensionality as low as possible reduces computational time and makes models more intuitively comprehensible; however, the ability to test full 3D models will build greater confidence in models generally and remains an important emerging area of cell biological modeling.

  16. Making Inexpensive 3-D Models

    ERIC Educational Resources Information Center

    Manos, Harry

    2016-01-01

    Visual aids are important to student learning, and they help make the teacher's job easier. Keeping with the "TPT" theme of "The Art, Craft, and Science of Physics Teaching," the purpose of this article is to show how teachers, lacking equipment and funds, can construct a durable 3-D model reference frame and a model gravity…

  17. Synthesis, structure determination and 3D molecular modeling of some novel manganese(II) complexes

    NASA Astrophysics Data System (ADS)

    Hari Kumaran Nair, M. L.; Lalitha, K. P.

    2013-06-01

    Some novel manganese(II) complexes with the ligand (z)-4-((2-hydroxy-4-methoxyphenyl)diazenyl)-1,5-dimethyl-2-phenyl-1H-pyrazol-3(2H)-one, MPAAP, 3-methoxy phenol azoantipyrine, L1, having the formulae [Mn(L1)2(X)2], [Mn(L1)2(Y)2], where X = Cl- / Br-; Y = NCS- were synthesized and characterized by elemental analysis, molar conductance and magnetic susceptibility measurements, spectral (IR, UV-Visible, EPR, FAB mass) studies, thermogravimetric analysis, powder XRD and cyclic voltammetric studies and by SEM image. An octahedral structure is tentatively proposed for the complexes with respect to the above studies. The [Mn(L1)2(Y)2] was subjected to γ-ray irradiation and the internal changes accompanied were evaluated. The energy minimized configuration of the complex [Mn(L1)2(Y)2] was made with CHEM Bio 3D Ultra 11.0 and the respective parameters are computed. The ligand and its complex [Mn(L1)2(Y)2] were screened for their possible antimicrobial activities.

  18. Mammalian olfactory receptors: molecular mechanisms of odorant detection, 3D-modeling, and structure-activity relationships.

    PubMed

    Persuy, Marie-Annick; Sanz, Guenhaël; Tromelin, Anne; Thomas-Danguin, Thierry; Gibrat, Jean-François; Pajot-Augy, Edith

    2015-01-01

    This chapter describes the main characteristics of olfactory receptor (OR) genes of vertebrates, including generation of this large multigenic family and pseudogenization. OR genes are compared in relation to evolution and among species. OR gene structure and selection of a given gene for expression in an olfactory sensory neuron (OSN) are tackled. The specificities of OR proteins, their expression, and their function are presented. The expression of OR proteins in locations other than the nasal cavity is regulated by different mechanisms, and ORs display various additional functions. A conventional olfactory signal transduction cascade is observed in OSNs, but individual ORs can also mediate different signaling pathways, through the involvement of other molecular partners and depending on the odorant ligand encountered. ORs are engaged in constitutive dimers. Ligand binding induces conformational changes in the ORs that regulate their level of activity depending on odorant dose. When present, odorant binding proteins induce an allosteric modulation of OR activity. Since no 3D structure of an OR has been yet resolved, modeling has to be performed using the closest G-protein-coupled receptor 3D structures available, to facilitate virtual ligand screening using the models. The study of odorant binding modes and affinities may infer best-bet OR ligands, to be subsequently checked experimentally. The relationship between spatial and steric features of odorants and their activity in terms of perceived odor quality are also fields of research that development of computing tools may enhance.

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

    PubMed Central

    Choi, Light; Woo Lee, Keun

    2016-01-01

    Bruton’s tyrosine kinase (BTK) is a cytoplasmic, non-receptor tyrosine kinase which is expressed in most of the hematopoietic cells and plays an important role in many cellular signaling pathways. B cell malignancies are dependent on BCR signaling, thus making BTK an efficient therapeutic target. Over the last few years, significant efforts have been made in order to develop BTK inhibitors to treat B-cell malignancies, and autoimmunity or allergy/hypersensitivity but limited success has been achieved. Here in this study, 3D QSAR pharmacophore models were generated for Btk based on known IC50 values and experimental energy scores with extensive validations. The five features pharmacophore model, Hypo1, includes one hydrogen bond acceptor lipid, one hydrogen bond donor, and three hydrophobic features, which has the highest correlation coefficient (0.98), cost difference (112.87), and low RMS (1.68). It was further validated by the Fisher’s randomization method and test set. The well validated Hypo1 was used as a 3D query to search novel Btk inhibitors with different chemical scaffold using high throughput virtual screening technique. The screened compounds were further sorted by applying ADMET properties, Lipinski’s rule of five and molecular docking studies to refine the retrieved hits. Furthermore, molecular dynamic simulation was employed to study the stability of docked conformation and to investigate the binding interactions in detail. Several important hydrogen bonds with Btk were revealed, which includes the gatekeeper residues Glu475 and Met 477 at the hinge region. Overall, this study suggests that the proposed hits may be more effective inhibitors for cancer and autoimmune therapy. PMID:26784025

  20. Making Inexpensive 3-D Models

    NASA Astrophysics Data System (ADS)

    Manos, Harry

    2016-03-01

    Visual aids are important to student learning, and they help make the teacher's job easier. Keeping with the TPT theme of "The Art, Craft, and Science of Physics Teaching," the purpose of this article is to show how teachers, lacking equipment and funds, can construct a durable 3-D model reference frame and a model gravity well tailored to specific class lessons. Most of the supplies are readily available in the home or at school: rubbing alcohol, a rag, two colors of spray paint, art brushes, and masking tape. The cost of these supplies, if you don't have them, is less than 20.

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

    PubMed

    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.

  2. Crowdsourcing Based 3d Modeling

    NASA Astrophysics Data System (ADS)

    Somogyi, A.; Barsi, A.; Molnar, B.; Lovas, T.

    2016-06-01

    Web-based photo albums that support organizing and viewing the users' images are widely used. These services provide a convenient solution for storing, editing and sharing images. In many cases, the users attach geotags to the images in order to enable using them e.g. in location based applications on social networks. Our paper discusses a procedure that collects open access images from a site frequently visited by tourists. Geotagged pictures showing the image of a sight or tourist attraction are selected and processed in photogrammetric processing software that produces the 3D model of the captured object. For the particular investigation we selected three attractions in Budapest. To assess the geometrical accuracy, we used laser scanner and DSLR as well as smart phone photography to derive reference values to enable verifying the spatial model obtained from the web-album images. The investigation shows how detailed and accurate models could be derived applying photogrammetric processing software, simply by using images of the community, without visiting the site.

  3. Molecular modeling study of CP-690550 derivatives as JAK3 kinase inhibitors through combined 3D-QSAR, molecular docking, and dynamics simulation techniques.

    PubMed

    Wang, Jing Li; Cheng, Li Ping; Wang, Tian Chi; Deng, Wei; Wu, Fan Hong

    2017-03-01

    To develop more potent JAK3 kinase inhibitors, a series of CP-690550 derivatives were investigated using combined molecular modeling techniques, such as 3D-QSAR, molecular docking and molecular dynamics (MD). The leave-one-out correlation (q(2)) and non-cross-validated correlation coefficient (r(2)) of the best CoMFA model are 0.715 and 0.992, respectively. The q(2) and r(2) values of the best CoMSIA model are 0.739 and 0.995, respectively. The steric, electrostatic, and hydrophobic fields played important roles in determining the inhibitory activity of CP-690550 derivatives. Some new JAK3 kinase inhibitors were designed. Some of them have better inhibitory activity than the most potent Tofacitinib (CP-690550). Molecular docking was used to identify some key amino acid residues at the active site of JAK3 protein. 10ns MD simulations were successfully performed to confirm the detailed binding mode and validate the rationality of docking results. The calculation of the binding free energies by MMPBSA method gives a good correlation with the predicted biological activity. To our knowledge, this is the first report on MD simulations and free energy calculations for this series of compounds. The combination results of this study will be valuable for the development of potent and novel JAK3 kinase inhibitors.

  4. A mechanistic approach to explore novel HDAC1 inhibitor using pharmacophore modeling, 3D- QSAR analysis, molecular docking, density functional and molecular dynamics simulation study.

    PubMed

    Choubey, Sanjay K; Jeyaraman, Jeyakanthan

    2016-11-01

    Deregulated epigenetic activity of Histone deacetylase 1 (HDAC1) in tumor development and carcinogenesis pronounces it as promising therapeutic target for cancer treatment. HDAC1 has recently captured the attention of researchers owing to its decisive role in multiple types of cancer. In the present study a multistep framework combining ligand based 3D-QSAR, molecular docking and Molecular Dynamics (MD) simulation studies were performed to explore potential compound with good HDAC1 binding affinity. Four different pharmacophore hypotheses Hypo1 (AADR), Hypo2 (AAAH), Hypo3 (AAAR) and Hypo4 (ADDR) were obtained. The hypothesis Hypo1 (AADR) with two hydrogen bond acceptors (A), one hydrogen bond donor (D) and one aromatics ring (R) was selected to build 3D-QSAR model on the basis of statistical parameter. The pharmacophore hypothesis produced a statistically significant QSAR model, with co-efficient of correlation r(2)=0.82 and cross validation correlation co-efficient q(2)=0.70. External validation result displays high predictive power with r(2) (o) value of 0.88 and r(2) (m) value of 0.58 to carry out further in silico studies. Virtual screening result shows ZINC70450932 as the most promising lead where HDAC1 interacts with residues Asp99, His178, Tyr204, Phe205 and Leu271 forming seven hydrogen bonds. A high docking score (-11.17kcal/mol) and lower docking energy -37.84kcal/mol) displays the binding efficiency of the ligand. Binding free energy calculation was done using MM/GBSA to access affinity of ligands towards protein. Density Functional Theory was employed to explore electronic features of the ligands describing intramolcular charge transfer reaction. Molecular dynamics simulation studies at 50ns display metal ion (Zn)-ligand interaction which is vital to inhibit the enzymatic activity of the protein.

  5. Molecular Modeling Studies of 11β-Hydroxysteroid Dehydrogenase Type 1 Inhibitors through Receptor-Based 3D-QSAR and Molecular Dynamics Simulations.

    PubMed

    Qian, Haiyan; Chen, Jiongjiong; Pan, Youlu; Chen, Jianzhong

    2016-09-19

    11β-Hydroxysteroid dehydrogenase type 1 (11β-HSD1) is a potential target for the treatment of numerous human disorders, such as diabetes, obesity, and metabolic syndrome. In this work, molecular modeling studies combining molecular docking, 3D-QSAR, MESP, MD simulations and free energy calculations were performed on pyridine amides and 1,2,4-triazolopyridines as 11β-HSD1 inhibitors to explore structure-activity relationships and structural requirement for the inhibitory activity. 3D-QSAR models, including CoMFA and CoMSIA, were developed from the conformations obtained by docking strategy. The derived pharmacophoric features were further supported by MESP and Mulliken charge analyses using density functional theory. In addition, MD simulations and free energy calculations were employed to determine the detailed binding process and to compare the binding modes of inhibitors with different bioactivities. The binding free energies calculated by MM/PBSA showed a good correlation with the experimental biological activities. Free energy analyses and per-residue energy decomposition indicated the van der Waals interaction would be the major driving force for the interactions between an inhibitor and 11β-HSD1. These unified results may provide that hydrogen bond interactions with Ser170 and Tyr183 are favorable for enhancing activity. Thr124, Ser170, Tyr177, Tyr183, Val227, and Val231 are the key amino acid residues in the binding pocket. The obtained results are expected to be valuable for the rational design of novel potent 11β-HSD1 inhibitors.

  6. Molecular modeling studies on series of Btk inhibitors using docking, structure-based 3D-QSAR and molecular dynamics simulation: a combined approach.

    PubMed

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

    2016-03-01

    Bruton tyrosine kinase (Btk) is a non-receptor tyrosine kinase. It is a crucial component in BCR pathway and expressed only in hematopoietic cells except T cells and Natural killer cells. BTK is a promising target because of its involvement in signaling pathways and B cell diseases such as autoimmune disorders and lymphoma. In this work, a combined molecular modeling study of molecular docking, 3D-QSAR and molecular dynamic (MD) simulation were performed on a series of 2,5-diaminopyrimidine compounds as inhibitors targeting Btk kinase to understand the interaction and key residues involved in the inhibition. A structure based CoMFA (q (2) = 0.675, NOC = 5, r (2) = 0.961) and COMSIA (q (2) = 0.704, NOC = 6, r (2) = 0.962) models were developed from the conformation obtained by docking. The developed models were subjected to various validation techniques such as leave-five-out, external test set, bootstrapping, progressive sampling and rm (2) metrics and found to have a good predictive ability in both internal and external validation. Our docking results showed the important residues that interacts in the active site residues in inhibition of Btk kinase. Furthermore, molecular dynamics simulation was employed to study the stability of the docked conformation and to investigate the binding interactions in detail. The MD simulation analyses identified several important hydrogen bonds with Btk, including the gatekeeper residue Thr474 and Met477 at the hinge region. Hydrogen bond with active site residues Leu408 and Arg525 were also recognized. A good correlation between the MD results, docking studies and the contour map analysis are observed. This indicates that the developed models are reliable. Our results from this study can provide insights in the designing and development of more potent Btk kinase inhibitors.

  7. 3D molecular modeling and evolutionary study of the Trypanosoma brucei DNA Topoisomerase IB, as a new emerging pharmacological target.

    PubMed

    Vlachakis, Dimitrios; Pavlopoulou, Athanasia; Roubelakis, Maria G; Feidakis, Christos; Anagnou, Nikolaos P; Kossida, Sophia

    2014-01-01

    In the present study, an outline is proposed that may lead to specific drug design targeting of the Trypanosoma brucei DNA Topoisomerase IB. In this direction, an unequivocally specific platform was designed for the development of selective modulators. The designed platform is focused on the unique structural and catalytic features of the enzyme. Extensive phylogenetic analysis based on all available published genomes indicated a broad distribution of DNA topoisomerases across eukaryotic species and revealed structurally important amino acids which could be assigned as potentially strong contributors to the regulation of the mechanism of the T. brucei DNA Topoisomerase IB. Based on the above, we propose a comprehensive in silico 3D model for the structure of the T. brucei DNA Topoisomerase IB. Our approach provides an efficient intergraded platform with both evolutionary and structural insights for the rational design of pharmacophore models as well as novel modulators as the anti-T. brucei DNA Topoisomerase IB agents with therapeutic potential.

  8. 3D Molecular Modelling Study of the H7N9 RNA-Dependent RNA Polymerase as an Emerging Pharmacological Target

    PubMed Central

    Vlachakis, Dimitrios

    2013-01-01

    Currently not much is known about the H7N9 strain, and this is the major drawback for a scientific strategy to tackle this virus. Herein, the 3D complex structure of the H7N9 RNA-dependent RNA polymerase has been established using a repertoire of molecular modelling techniques including homology modelling, molecular docking, and molecular dynamics simulations. Strikingly, it was found that the oligonucleotide cleft and tunnel in the H7N9 RNA-dependent RNA polymerase are structurally very similar to the corresponding region on the hepatitis C virus RNA-dependent RNA polymerase crystal structure. A direct comparison and a 3D postdynamics analysis of the 3D complex of the H7N9 RNA-dependent RNA polymerase provide invaluable clues and insight regarding the role and mode of action of a series of interacting residues on the latter enzyme. Our study provides a novel and efficiently intergraded platform with structural insights for the H7N9 RNA-dependent RNA Polymerase. We propose that future use and exploitation of these insights may prove invaluable in the fight against this lethal, ongoing epidemic. PMID:24187616

  9. 3D Microperfusion Model of ADPKD

    DTIC Science & Technology

    2015-10-01

    Stratasys 3D printer . PDMS was cast in the negative molds in order to create permanent biocompatible plastic masters (SmoothCast 310). All goals of task...1 AWARD NUMBER: W81XWH-14-1-0304 TITLE: 3D Microperfusion Model of ADPKD PRINCIPAL INVESTIGATOR: David L. Kaplan CONTRACTING ORGANIZATION...ADDRESS. 1. REPORT DATE October 2015 2. REPORT TYPE Annual Report 3. DATES COVERED 15 Sep 2014 - 14 Sep 2015 4. TITLE AND SUBTITLE 3D

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

    PubMed

    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.

  11. Molecular Cloning and 3D Structure Modeling of APEX1, DNA Base Excision Repair Enzyme from the Camel, Camelus dromedarius

    PubMed Central

    Ataya, Farid Shokry; Fouad, Dalia; Malik, Ajamaluddin; Saeed, Hesham Mahmoud

    2012-01-01

    The domesticated one-humped camel, Camelus dromedarius, is one of the most important animals in the Arabian Desert. It is exposed most of its life to both intrinsic and extrinsic genotoxic factors that are known to cause gross DNA alterations in many organisms. Ionic radiation and sunlight are known producers of Reactive Oxygen Species (ROS), one of the causes for DNA lesions. The damaged DNA is repaired by many enzymes, among of them Base Excision Repair enzymes, producing the highly mutagenic apurinic/apyrimidinicsites (AP sites). Therefore, recognition of AP sites is fundamental to cell/organism survival. In the present work, the full coding sequence of a putative cAPEX1 gene was amplified for the first time from C. dromedarius by RT-PCR and cloned (NCBI accession number are HM209828 and ADJ96599 for nucleotides and amino acids, respectively). cDNA sequencing was deduced to be 1041 nucleotides, of which 954 nucleotides encode a protein of 318 amino acids, similar to the coding region of the APEX1 gene and the protein from many other species. The calculated molecular weight and isoelectric point of cAPEX1 using Bioinformatics tools was 35.5 kDa and 8.11, respectively. The relative expressions of cAPEX1 in camel kidney, spleen, lung and testis were examined using qPCR and compared with that of the liver using a 18S ribosomal subunit as endogenous control. The highest level of cAPEX1 transcript was found in the testis; 325% higher than the liver, followed by spleen (87%), kidney (20%) and lung (5%), respectively. The cAPEX1 is 94%–97% similar to their mammalian counterparts. Phylogenetic analysis revealed that cAPEX1 is grouped together with that of S. scrofa. The predicted 3D structure of cAPEX1 has similar folds and topology with the human (hAPEX1). The root-mean-square deviation (rmsd) between cAPEX1 and hAPEX1 was 0.582 and the Q-score was 0.939. PMID:22942721

  12. BEAMS3D Neutral Beam Injection Model

    SciTech Connect

    Lazerson, Samuel

    2014-04-14

    With the advent of applied 3D fi elds in Tokamaks and modern high performance stellarators, a need has arisen to address non-axisymmetric effects on neutral beam heating and fueling. We report on the development of a fully 3D neutral beam injection (NBI) model, BEAMS3D, which addresses this need by coupling 3D equilibria to a guiding center code capable of modeling neutral and charged particle trajectories across the separatrix and into the plasma core. Ionization, neutralization, charge-exchange, viscous velocity reduction, and pitch angle scattering are modeled with the ADAS atomic physics database [1]. Benchmark calculations are presented to validate the collisionless particle orbits, neutral beam injection model, frictional drag, and pitch angle scattering effects. A calculation of neutral beam heating in the NCSX device is performed, highlighting the capability of the code to handle 3D magnetic fields.

  13. Development of 3D-QSAR Model for Acetylcholinesterase Inhibitors Using a Combination of Fingerprint, Molecular Docking, and Structure-Based Pharmacophore Approaches.

    PubMed

    Lee, Sehan; Barron, Mace G

    2015-11-01

    Acetylcholinesterase (AChE), a serine hydrolase vital for regulating the neurotransmitter acetylcholine in animals, has been used as a target for drugs and pesticides. With the increasing availability of AChE crystal structures, with or without ligands bound, structure-based approaches have been successfully applied to AChE inhibitors (AChEIs). The major limitation of these approaches has been the small applicability domain due to the lack of structural diversity in the training set. In this study, we developed a 3 dimensional quantitative structure-activity relationship (3D-QSAR) for inhibitory activity of 89 reversible and irreversible AChEIs including drugs and insecticides. A 3D-fingerprint descriptor encoding protein-ligand interactions was developed using molecular docking and structure-based pharmacophore to rationalize the structural requirements responsible for the activity of these compounds. The obtained 3D-QSAR model exhibited high correlation value (R(2) = 0.93) and low mean absolute error (MAE = 0.32 log units) for the training set (n = 63). The model was predictive across a range of structures as shown by the leave-one-out cross-validated correlation coefficient (Q(2) = 0.89) and external validation results (n = 26, R(2) = 0.89, and MAE = 0.38 log units). The model revealed that the compounds with high inhibition potency had proper conformation in the active site gorge and interacted with key amino acid residues, in particular Trp84 and Phe330 at the catalytic anionic site, Trp279 at the peripheral anionic site, and Gly118, Gly119, and Ala201 at the oxyanion hole. The resulting universal 3D-QSAR model provides insight into the multiple molecular interactions determining AChEI potency that may guide future chemical design and regulation of toxic AChEIs.

  14. 3D-QSAR, homology modeling, and molecular docking studies on spiropiperidines analogues as agonists of nociceptin/orphanin FQ receptor.

    PubMed

    Liu, Ming; He, Lin; Hu, Xiaopeng; Liu, Peiqing; Luo, Hai-Bin

    2010-12-01

    The nociceptin/orphanin FQ receptor (NOP) has been implicated in a wide range of biological functions, including pain, anxiety, depression and drug abuse. Especially, its agonists have a great potential to be developed into anxiolytics. However, the crystal structure of NOP is still not available. In the present work, both structure-based and ligand-based modeling methods have been used to achieve a comprehensive understanding on 67N-substituted spiropiperidine analogues as NOP agonists. The comparative molecular-field analysis method was performed to formulate a reasonable 3D-QSAR model (cross-validated coefficient q(2)=0.819 and conventional r(2)=0.950), whose robustness and predictability were further verified by leave-eight-out, Y-randomization, and external test-set validations. The excellent performance of CoMFA to the affinity differences among these compounds was attributed to the contributions of electrostatic/hydrogen-bonding and steric/hydrophobic interactions, which was supported by the Surflex-Dock and CDOCKER molecular-docking simulations based on the 3D model of NOP built by the homology modeling method. The CoMFA contour maps and the molecular docking simulations were integrated to propose a binding mode for the spiropiperidine analogues at the binding site of NOP.

  15. Molecular cartography of the human skin surface in 3D.

    PubMed

    Bouslimani, Amina; Porto, Carla; Rath, Christopher M; Wang, Mingxun; Guo, Yurong; Gonzalez, Antonio; Berg-Lyon, Donna; Ackermann, Gail; Moeller Christensen, Gitte Julie; Nakatsuji, Teruaki; Zhang, Lingjuan; Borkowski, Andrew W; Meehan, Michael J; Dorrestein, Kathleen; Gallo, Richard L; Bandeira, Nuno; Knight, Rob; Alexandrov, Theodore; Dorrestein, Pieter C

    2015-04-28

    The human skin is an organ with a surface area of 1.5-2 m(2) that provides our interface with the environment. The molecular composition of this organ is derived from host cells, microbiota, and external molecules. The chemical makeup of the skin surface is largely undefined. Here we advance the technologies needed to explore the topographical distribution of skin molecules, using 3D mapping of mass spectrometry data and microbial 16S rRNA amplicon sequences. Our 3D maps reveal that the molecular composition of skin has diverse distributions and that the composition is defined not only by skin cells and microbes but also by our daily routines, including the application of hygiene products. The technological development of these maps lays a foundation for studying the spatial relationships of human skin with hygiene, the microbiota, and environment, with potential for developing predictive models of skin phenotypes tailored to individual health.

  16. Molecular cartography of the human skin surface in 3D

    PubMed Central

    Bouslimani, Amina; Porto, Carla; Rath, Christopher M.; Wang, Mingxun; Guo, Yurong; Gonzalez, Antonio; Berg-Lyon, Donna; Ackermann, Gail; Moeller Christensen, Gitte Julie; Nakatsuji, Teruaki; Zhang, Lingjuan; Borkowski, Andrew W.; Meehan, Michael J.; Dorrestein, Kathleen; Gallo, Richard L.; Bandeira, Nuno; Knight, Rob; Alexandrov, Theodore; Dorrestein, Pieter C.

    2015-01-01

    The human skin is an organ with a surface area of 1.5–2 m2 that provides our interface with the environment. The molecular composition of this organ is derived from host cells, microbiota, and external molecules. The chemical makeup of the skin surface is largely undefined. Here we advance the technologies needed to explore the topographical distribution of skin molecules, using 3D mapping of mass spectrometry data and microbial 16S rRNA amplicon sequences. Our 3D maps reveal that the molecular composition of skin has diverse distributions and that the composition is defined not only by skin cells and microbes but also by our daily routines, including the application of hygiene products. The technological development of these maps lays a foundation for studying the spatial relationships of human skin with hygiene, the microbiota, and environment, with potential for developing predictive models of skin phenotypes tailored to individual health. PMID:25825778

  17. RHOCUBE: 3D density distributions modeling code

    NASA Astrophysics Data System (ADS)

    Nikutta, Robert; Agliozzo, Claudia

    2016-11-01

    RHOCUBE models 3D density distributions on a discrete Cartesian grid and their integrated 2D maps. It can be used for a range of applications, including modeling the electron number density in LBV shells and computing the emission measure. The RHOCUBE Python package provides several 3D density distributions, including a powerlaw shell, truncated Gaussian shell, constant-density torus, dual cones, and spiralling helical tubes, and can accept additional distributions. RHOCUBE provides convenient methods for shifts and rotations in 3D, and if necessary, an arbitrary number of density distributions can be combined into the same model cube and the integration ∫ dz performed through the joint density field.

  18. A Hybrid 3D Indoor Space Model

    NASA Astrophysics Data System (ADS)

    Jamali, Ali; Rahman, Alias Abdul; Boguslawski, Pawel

    2016-10-01

    GIS integrates spatial information and spatial analysis. An important example of such integration is for emergency response which requires route planning inside and outside of a building. Route planning requires detailed information related to indoor and outdoor environment. Indoor navigation network models including Geometric Network Model (GNM), Navigable Space Model, sub-division model and regular-grid model lack indoor data sources and abstraction methods. In this paper, a hybrid indoor space model is proposed. In the proposed method, 3D modeling of indoor navigation network is based on surveying control points and it is less dependent on the 3D geometrical building model. This research proposes a method of indoor space modeling for the buildings which do not have proper 2D/3D geometrical models or they lack semantic or topological information. The proposed hybrid model consists of topological, geometrical and semantical space.

  19. NUBEAM developments and 3d halo modeling

    NASA Astrophysics Data System (ADS)

    Gorelenkova, M. V.; Medley, S. S.; Kaye, S. M.

    2012-10-01

    Recent developments related to the 3D halo model in NUBEAM code are described. To have a reliable halo neutral source for diagnostic simulation, the TRANSP/NUBEAM code has been enhanced with full implementation of ADAS atomic physic ground state and excited state data for hydrogenic beams and mixed species plasma targets. The ADAS codes and database provide the density and temperature dependence of the atomic data, and the collective nature of the state excitation process. To be able to populate 3D halo output with sufficient statistical resolution, the capability to control the statistics of fast ion CX modeling and for thermal halo launch has been added to NUBEAM. The 3D halo neutral model is based on modification and extension of the ``beam in box'' aligned 3d Cartesian grid that includes the neutral beam itself, 3D fast neutral densities due to CX of partially slowed down fast ions in the beam halo region, 3D thermal neutral densities due to CX deposition and fast neutral recapture source. More details on the 3D halo simulation design will be presented.

  20. Combined 3D-QSAR modeling and molecular docking studies on pyrrole-indolin-2-ones as Aurora A kinase inhibitors.

    PubMed

    Ai, Yong; Wang, Shao-Teng; Sun, Ping-Hua; Song, Fa-Jun

    2011-01-01

    Aurora kinases have emerged as attractive targets for the design of anticancer drugs. 3D-QSAR (comparative molecular field analysis (CoMFA) and comparative molecular similarity indices analysis (CoMSIA)) and Surflex-docking studies were performed on a series of pyrrole-indoline-2-ones as Aurora A inhibitors. The CoMFA and CoMSIA models using 25 inhibitors in the training set gave r(2) (cv) values of 0.726 and 0.566, and r(2) values of 0.972 and 0.984, respectively. The adapted alignment method with the suitable parameters resulted in reliable models. The contour maps produced by the CoMFA and CoMSIA models were employed to rationalize the key structural requirements responsible for the activity. Surflex-docking studies revealed that the sulfo group, secondary amine group on indolin-2-one, and carbonyl of 6,7-dihydro-1H-indol-4(5H)-one groups were significant for binding to the receptor, and some essential features were also identified. Based on the 3D-QSAR and docking results, a set of new molecules with high predicted activities were designed.

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

    PubMed

    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.

  2. Synthesis, spectral characterization and 3D molecular modeling of some novel nickel(II) complexes derived from 4-aminoantipyrine

    NASA Astrophysics Data System (ADS)

    Nair, M. L. Harikumaran; Lalitha, K. P.

    2014-10-01

    Some novel Ni(II) complexes with the ligand (z)-4-((2-hydroxy-4-methoxyphenyl)diazenyl)-1,5-dimethyl-2-phenyl-1H-pyrazole-3(2H)-one, 3-methoxy phenol azoantipyrine, L having the formulae [Ni(L)2X2] and [Ni(L)2(Y)Cl] where X = 450 Cl-/NO3; Y = NCS- were synthesized and characterized by elemental analysis, molar conductance measurements, magnetic susceptibility measurements, spectral (IR, UV-Visible, EPR, FAB-mass) studies, thermo gravimetric analysis and by TEM image. Energy minimized configuration of the complex [Ni(L)2Cl2] was made with CHEM Bio 3D Ultra 11.0 and the respective parameters were computed. The ligand and the complex [Ni(L)2(Y)Cl] were screened for their antibacterial activities. An octahedral structure is tentatively proposed for the complexes.

  3. 3D Modeling Engine Representation Summary Report

    SciTech Connect

    Steven Prescott; Ramprasad Sampath; Curtis Smith; Timothy Yang

    2014-09-01

    Computers have been used for 3D modeling and simulation, but only recently have computational resources been able to give realistic results in a reasonable time frame for large complex models. This summary report addressed the methods, techniques, and resources used to develop a 3D modeling engine to represent risk analysis simulation for advanced small modular reactor structures and components. The simulations done for this evaluation were focused on external events, specifically tsunami floods, for a hypothetical nuclear power facility on a coastline.

  4. BEAMS3D Neutral Beam Injection Model

    NASA Astrophysics Data System (ADS)

    McMillan, Matthew; Lazerson, Samuel A.

    2014-09-01

    With the advent of applied 3D fields in Tokamaks and modern high performance stellarators, a need has arisen to address non-axisymmetric effects on neutral beam heating and fueling. We report on the development of a fully 3D neutral beam injection (NBI) model, BEAMS3D, which addresses this need by coupling 3D equilibria to a guiding center code capable of modeling neutral and charged particle trajectories across the separatrix and into the plasma core. Ionization, neutralization, charge-exchange, viscous slowing down, and pitch angle scattering are modeled with the ADAS atomic physics database. Elementary benchmark calculations are presented to verify the collisionless particle orbits, NBI model, frictional drag, and pitch angle scattering effects. A calculation of neutral beam heating in the NCSX device is performed, highlighting the capability of the code to handle 3D magnetic fields. Notice: this manuscript has been authored by Princeton University under Contract Number DE-AC02-09CH11466 with the US Department of Energy. The United States Government retains and the publisher, by accepting the article for publication, acknowledges that the United States Government retains a non-exclusive, paid-up, irrevocable, world-wide license to publish or reproduce the published form of this manuscript, or allow others to do so, for United States Government purposes.

  5. Design, synthesis and molecular modeling of novel pyrido[2,3-d]pyrimidine analogs as antifolates: Application of Buchwald-Hartwig aminations of heterocycles

    PubMed Central

    Gangjee, Aleem; Namjoshi, Ojas A.; Raghavan, Sudhir; Queener, Sherry F.; Kisliuk, Roy L.; Cody, Vivian

    2013-01-01

    Opportunistic infections caused by Pneumocystis jirovecii (P. jirovecii, pj), Toxoplasma gondii (T. gondii, tg) and Mycobacterium avium (M. avium, ma) are the principal causes of morbidity and mortality in patients with acquired immunodeficiency syndrome (AIDS). The absence of any animal models for human Pneumocystis jirovecii pneumonia and the lack of crystal structures of pjDHFR and tgDHFR make the design of inhibitors challenging. A novel series of pyrido[2,3-d]pyrimidines as selective and potent DHFR inhibitors against these opportunistic infections are presented. Buchwald-Hartwig coupling reaction of substituted anilines with pivaloyl protected 2,4-diamino-6-bromo-pyrido[2,3-d]pyrimidine was successfully explored to synthesize these analogs. Compound 26 was the most selective inhibitor with excellent potency against pjDHFR. Molecular modeling studies with a pjDHFR homology model explained the potency and selectivity of 26. Structural data are also reported for 26 with pcDHFR and 16 and 22 with variants of pcDHFR. PMID:23627352

  6. Molecular Predictors of 3D Morphogenesis by Breast Cancer Cell Lines in 3D Culture

    SciTech Connect

    Han, Ju; Chang, Hang; Giricz, Orsi; Lee, Genee; Baehner, Frederick; Gray, Joe; Bissell, Mina; Kenny, Paraic; Parvin, Bahram

    2010-02-01

    Correlative analysis of molecular markers with phenotypic signatures is the simplest model for hypothesis generation. In this paper, a panel of 24 breast cell lines was grown in 3D culture, their morphology was imaged through phase contrast microscopy, and computational methods were developed to segment and represent each colony at multiple dimensions. Subsequently, subpopulations from these morphological responses were identified through consensus clustering to reveal three clusters of round, grape-like, and stellate phenotypes. In some cases, cell lines with particular pathobiological phenotypes clustered together (e.g., ERBB2 amplified cell lines sharing the same morphometric properties as the grape-like phenotype). Next, associations with molecular features were realized through (i) differential analysis within each morphological cluster, and (ii) regression analysis across the entire panel of cell lines. In both cases, the dominant genes that are predictive of the morphological signatures were identified. Specifically, PPAR? has been associated with the invasive stellate morphological phenotype, which corresponds to triple-negative pathobiology. PPAR? has been validated through two supporting biological assays.

  7. An in-depth spectroscopic examination of molecular bands from 3D hydrodynamical model atmospheres. I. Formation of the G-band in metal-poor dwarf stars

    NASA Astrophysics Data System (ADS)

    Gallagher, A. J.; Caffau, E.; Bonifacio, P.; Ludwig, H.-G.; Steffen, M.; Spite, M.

    2016-09-01

    Context. Recent developments in the three-dimensional (3D) spectral synthesis code Linfor3D have meant that for the first time, large spectral wavelength regions, such as molecular bands, can be synthesised with it in a short amount of time. Aims: A detailed spectral analysis of the synthetic G-band for several dwarf turn-off-type 3D atmospheres (5850 ≲ Teff [ K ] ≲ 6550, 4.0 ≤ log g ≤ 4.5, - 3.0 ≤ [Fe/H] ≤-1.0) was conducted, under the assumption of local thermodynamic equilibrium. We also examine carbon and oxygen molecule formation at various metallicity regimes and discuss the impact it has on the G-band. Methods: Using a qualitative approach, we describe the different behaviours between the 3D atmospheres and the traditional one-dimensional (1D) atmospheres and how the different physics involved inevitably leads to abundance corrections, which differ over varying metallicities. Spectra computed in 1D were fit to every 3D spectrum to determine the 3D abundance correction. Results: Early analysis revealed that the CH molecules that make up the G-band exhibited an oxygen abundance dependency; a higher oxygen abundance leads to weaker CH features. Nitrogen abundances showed zero impact to CH formation. The 3D corrections are also stronger at lower metallicity. Analysis of the 3D corrections to the G-band allows us to assign estimations of the 3D abundance correction to most dwarf stars presented in the literature. Conclusions: The 3D corrections suggest that A(C) in carbon-enhanced metal-poor (CEMP) stars with high A(C) would remain unchanged, but would decrease in CEMP stars with lower A(C). It was found that the C/O ratio is an important parameter to the G-band in 3D. Additional testing confirmed that the C/O ratio is an equally important parameter for OH transitions under 3D. This presents a clear interrelation between the carbon and oxygen abundances in 3D atmospheres through their molecular species, which is not seen in 1D.

  8. 3-D Teaching Models for All

    ERIC Educational Resources Information Center

    Bradley, Joan; Farland-Smith, Donna

    2010-01-01

    Allowing a student to "see" through touch what other students see through a microscope can be a challenging task. Therefore, author Joan Bradley created three-dimensional (3-D) models with one student's visual impairment in mind. They are meant to benefit all students and can be used to teach common high school biology topics, including the…

  9. Constructing Arguments with 3-D Printed Models

    ERIC Educational Resources Information Center

    McConnell, William; Dickerson, Daniel

    2017-01-01

    In this article, the authors describe a fourth-grade lesson where 3-D printing technologies were not only a stimulus for engagement but also served as a modeling tool providing meaningful learning opportunities. Specifically, fourth-grade students construct an argument that animals' external structures function to support survival in a particular…

  10. Model-based 3D SAR reconstruction

    NASA Astrophysics Data System (ADS)

    Knight, Chad; Gunther, Jake; Moon, Todd

    2014-06-01

    Three dimensional scene reconstruction with synthetic aperture radar (SAR) is desirable for target recognition and improved scene interpretability. The vertical aperture, which is critical to reconstruct 3D SAR scenes, is almost always sparsely sampled due to practical limitations, which creates an underdetermined problem. This papers explores 3D scene reconstruction using a convex model-based approach. The approach developed is demonstrated on 3D scenes, but can be extended to SAR reconstruction of sparsely sampled signals in the spatial and, or, frequency domains. The model-based approach enables knowledge-aided image formation (KAIF) by incorporating spatial, aspect, and sparsity magnitude terms into the image reconstruction. The incorporation of these terms, which are based on prior scene knowledge, will demonstrate improved results compared to traditional image formation algorithms. The SAR image formation problem is formulated as a second order cone program (SOCP) and the results are demonstrated on 3D scenes using simulated data and data from the GOTCHA data collect.1 The model-based results are contrasted against traditional backprojected images.

  11. Do-It-Yourself: 3D Models of Hydrogenic Orbitals through 3D Printing

    ERIC Educational Resources Information Center

    Griffith, Kaitlyn M.; de Cataldo, Riccardo; Fogarty, Keir H.

    2016-01-01

    Introductory chemistry students often have difficulty visualizing the 3-dimensional shapes of the hydrogenic electron orbitals without the aid of physical 3D models. Unfortunately, commercially available models can be quite expensive. 3D printing offers a solution for producing models of hydrogenic orbitals. 3D printing technology is widely…

  12. 3D-QSAR and molecular modeling studies on 2,3-dideoxy hexenopyranosid-4-uloses as anti-tubercular agents targeting alpha-mannosidase.

    PubMed

    Shah, Priyanka; Saquib, Mohammad; Sharma, Smriti; Husain, Irfan; Sharma, Sandeep K; Singh, Vinayak; Srivastava, Ranjana; Shaw, Arun K; Siddiqi, Mohammad Imran

    2015-04-01

    Ligand-based and structure-based methods were applied in combination to exploit the physicochemical properties of 2,3-dideoxy hex-2-enopyranosid-4-uloses against Mycobacterium tuberculosis H37Rv. Statistically valid 3D-QSAR models with good correlation and predictive power were obtained with CoMFA steric and electrostatic fields (r(2) = 0.797, q(2) = 0.589) and CoMSIA with combined steric, electrostatic, hydrophobic and hydrogen bond acceptor fields (r(2) = 0.867, q(2) = 0.570) based on training set of 33 molecules with predictive r(2) of 0.808 and 0.890 for CoMFA and CoMSIA respectively. The results illustrate the requirement of optimal alkyl chain length at C-1 position and acceptor groups along hydroxy methyl substituent of C-6 to enhance the anti-tubercular activity of the 2,3-dideoxy hex-2-enopyranosid-4-uloses while any substitution at C-3 position exert diminishing effect on anti-tubercular activity of these enulosides. Further, homology modeling of M. tuberculosis alpha-mannosidase followed by molecular docking and molecular dynamics simulations on co-complexed models were performed to gain insight into the rationale for binding affinity of selected inhibitors with the target of interest. The comprehensive information obtained from this study will help to better understand the structural basis of biological activity of this class of molecules and guide further design of more potent analogues as anti-tubercular agents.

  13. Debris Dispersion Model Using Java 3D

    NASA Technical Reports Server (NTRS)

    Thirumalainambi, Rajkumar; Bardina, Jorge

    2004-01-01

    This paper describes web based simulation of Shuttle launch operations and debris dispersion. Java 3D graphics provides geometric and visual content with suitable mathematical model and behaviors of Shuttle launch. Because the model is so heterogeneous and interrelated with various factors, 3D graphics combined with physical models provides mechanisms to understand the complexity of launch and range operations. The main focus in the modeling and simulation covers orbital dynamics and range safety. Range safety areas include destruct limit lines, telemetry and tracking and population risk near range. If there is an explosion of Shuttle during launch, debris dispersion is explained. The shuttle launch and range operations in this paper are discussed based on the operations from Kennedy Space Center, Florida, USA.

  14. Illustrative visualization of 3D city models

    NASA Astrophysics Data System (ADS)

    Doellner, Juergen; Buchholz, Henrik; Nienhaus, Marc; Kirsch, Florian

    2005-03-01

    This paper presents an illustrative visualization technique that provides expressive representations of large-scale 3D city models, inspired by the tradition of artistic and cartographic visualizations typically found in bird"s-eye view and panoramic maps. We define a collection of city model components and a real-time multi-pass rendering algorithm that achieves comprehensible, abstract 3D city model depictions based on edge enhancement, color-based and shadow-based depth cues, and procedural facade texturing. Illustrative visualization provides an effective visual interface to urban spatial information and associated thematic information complementing visual interfaces based on the Virtual Reality paradigm, offering a huge potential for graphics design. Primary application areas include city and landscape planning, cartoon worlds in computer games, and tourist information systems.

  15. 3-D QSAutogrid/R: an alternative procedure to build 3-D QSAR models. Methodologies and applications.

    PubMed

    Ballante, Flavio; Ragno, Rino

    2012-06-25

    Since it first appeared in 1988 3-D QSAR has proved its potential in the field of drug design and activity prediction. Although thousands of citations now exist in 3-D QSAR, its development was rather slow with the majority of new 3-D QSAR applications just extensions of CoMFA. An alternative way to build 3-D QSAR models, based on an evolution of software, has been named 3-D QSAutogrid/R and has been developed to use only software freely available to academics. 3-D QSAutogrid/R covers all the main features of CoMFA and GRID/GOLPE with implementation by multiprobe/multiregion variable selection (MPGRS) that improves the simplification of interpretation of the 3-D QSAR map. The methodology is based on the integration of the molecular interaction fields as calculated by AutoGrid and the R statistical environment that can be easily coupled with many free graphical molecular interfaces such as UCSF-Chimera, AutoDock Tools, JMol, and others. The description of each R package is reported in detail, and, to assess its validity, 3-D QSAutogrid/R has been applied to three molecular data sets of which either CoMFA or GRID/GOLPE models were reported in order to compare the results. 3-D QSAutogrid/R has been used as the core engine to prepare more that 240 3-D QSAR models forming the very first 3-D QSAR server ( www.3d-qsar.com ) with its code freely available through R-Cran distribution.

  16. 3-D model-based vehicle tracking.

    PubMed

    Lou, Jianguang; Tan, Tieniu; Hu, Weiming; Yang, Hao; Maybank, Steven J

    2005-10-01

    This paper aims at tracking vehicles from monocular intensity image sequences and presents an efficient and robust approach to three-dimensional (3-D) model-based vehicle tracking. Under the weak perspective assumption and the ground-plane constraint, the movements of model projection in the two-dimensional image plane can be decomposed into two motions: translation and rotation. They are the results of the corresponding movements of 3-D translation on the ground plane (GP) and rotation around the normal of the GP, which can be determined separately. A new metric based on point-to-line segment distance is proposed to evaluate the similarity between an image region and an instantiation of a 3-D vehicle model under a given pose. Based on this, we provide an efficient pose refinement method to refine the vehicle's pose parameters. An improved EKF is also proposed to track and to predict vehicle motion with a precise kinematics model. Experimental results with both indoor and outdoor data show that the algorithm obtains desirable performance even under severe occlusion and clutter.

  17. Sensing and compressing 3-D models

    SciTech Connect

    Krumm, J.

    1998-02-01

    The goal of this research project was to create a passive and robust computer vision system for producing 3-D computer models of arbitrary scenes. Although the authors were unsuccessful in achieving the overall goal, several components of this research have shown significant potential. Of particular interest is the application of parametric eigenspace methods for planar pose measurement of partially occluded objects in gray-level images. The techniques presented provide a simple, accurate, and robust solution to the planar pose measurement problem. In addition, the representational efficiency of eigenspace methods used with gray-level features were successfully extended to binary features, which are less sensitive to illumination changes. The results of this research are presented in two papers that were written during the course of this project. The papers are included in sections 2 and 3. The first section of this report summarizes the 3-D modeling efforts.

  18. Vision models for 3D surfaces

    NASA Astrophysics Data System (ADS)

    Mitra, Sunanda

    1992-11-01

    Different approaches to computational stereo to represent human stereo vision have been developed over the past two decades. The Marr-Poggio theory of human stereo vision is probably the most widely accepted model of the human stereo vision. However, recently developed motion stereo models which use a sequence of images taken by either a moving camera or a moving object provide an alternative method of achieving multi-resolution matching without the use of Laplacian of Gaussian operators. While using image sequences, the baseline between two camera positions for a image pair is changed for the subsequent image pair so as to achieve different resolution for each image pair. Having different baselines also avoids the inherent occlusion problem in stereo vision models. The advantage of using multi-resolution images acquired by camera positioned at different baselines over those acquired by LOG operators is that one does not have to encounter spurious edges often created by zero-crossings in the LOG operated images. Therefore in designing a computer vision system, a motion stereo model is more appropriate than a stereo vision model. However, in some applications where only a stereo pair of images are available, recovery of 3D surfaces of natural scenes are possible in a computationally efficient manner by using cepstrum matching and regularization techniques. Section 2 of this paper describes a motion stereo model using multi-scale cepstrum matching for the detection of disparity between image pairs in a sequence of images and subsequent recovery of 3D surfaces from depth-map obtained by a non convergent triangulation technique. Section 3 presents a 3D surface recovery technique from a stereo pair using cepstrum matching for disparity detection and cubic B-splines for surface smoothing. Section 4 contains the results of 3D surface recovery using both of the techniques mentioned above. Section 5 discusses the merit of 2D cepstrum matching and cubic B

  19. 3D Printed Molecules and Extended Solid Models for Teaching Symmetry and Point Groups

    ERIC Educational Resources Information Center

    Scalfani, Vincent F.; Vaid, Thomas P.

    2014-01-01

    Tangible models help students and researchers visualize chemical structures in three dimensions (3D). 3D printing offers a unique and straightforward approach to fabricate plastic 3D models of molecules and extended solids. In this article, we prepared a series of digital 3D design files of molecular structures that will be useful for teaching…

  20. Robust hashing for 3D models

    NASA Astrophysics Data System (ADS)

    Berchtold, Waldemar; Schäfer, Marcel; Rettig, Michael; Steinebach, Martin

    2014-02-01

    3D models and applications are of utmost interest in both science and industry. With the increment of their usage, their number and thereby the challenge to correctly identify them increases. Content identification is commonly done by cryptographic hashes. However, they fail as a solution in application scenarios such as computer aided design (CAD), scientific visualization or video games, because even the smallest alteration of the 3D model, e.g. conversion or compression operations, massively changes the cryptographic hash as well. Therefore, this work presents a robust hashing algorithm for 3D mesh data. The algorithm applies several different bit extraction methods. They are built to resist desired alterations of the model as well as malicious attacks intending to prevent correct allocation. The different bit extraction methods are tested against each other and, as far as possible, the hashing algorithm is compared to the state of the art. The parameters tested are robustness, security and runtime performance as well as False Acceptance Rate (FAR) and False Rejection Rate (FRR), also the probability calculation of hash collision is included. The introduced hashing algorithm is kept adaptive e.g. in hash length, to serve as a proper tool for all applications in practice.

  1. Toll-like receptor 22 in Labeo rohita: molecular cloning, characterization, 3D modeling, and expression analysis following ligands stimulation and bacterial infection.

    PubMed

    Samanta, Mrinal; Swain, Banikalyan; Basu, Madhubanti; Mahapatra, Girishbala; Sahoo, Bikash R; Paichha, Mahismita; Lenka, Saswati S; Jayasankar, Pallipuram

    2014-09-01

    Toll-like receptors (TLRs) are a class of innate immune receptors that sense pathogens or their molecular signatures and activate signaling cascades to induce a quick and non-specific immune response in the host. Among various types of TLRs, TLR22 is exclusively present in teleosts and amphibians and is expected to play the distinctive role in innate immunity. This report describes molecular cloning, three-dimensional (3D) modeling, and expression analysis of TLR22 in rohu (Labeo rohita), the most commercially important freshwater fish species in the Indian subcontinent. The open reading frame (ORF) of rohu TLR22 (LrTLR22) comprised of 2,838 nucleotides (nt), encoding 946 amino acid (aa) residues with the molecular mass of ∼ 107.6 kDa. The secondary structure of deduced LrTLR22 exhibited the presence of signal peptide (1-22 aa), 18 leucine-rich repeat (LRR) regions (79-736 aa), and TIR domain (792-935 aa). The 3D model of LrTLR22-LRR regions together elucidated the horse-shoe-shaped structure having parallel β-strands at the concave surface and few α-helices at the convex surface. The TIR domain structure revealed alternate presence of five α-helices and β-sheets. Phylogenetically, LrTLR22 was closely related to common carp and exhibited significant similarity (92.2 %) and identity (86.1 %) in their amino acids. In rohu, TLR22 was constitutively expressed in all embryonic developmental stages, and tissue-specific analysis illustrated its expression in all examined tissues, highest was in liver and lowest in brain. In vivo modulation of TLR22 gene expression was analyzed by quantitative real-time PCR (qRT-PCR) assay following stimulation with lipopolysaccharide (LPS), synthetic double stranded RNA (polyinosinic-polycytidylic acid), and bacterial (Aeromonas hydrophila) RNA. Among these ligands, bacterial RNA most significantly (p < 0.05) induced TLR22 gene expression in most of the tested tissues. In A. hydrophila infection, induction of TLR22 gene expression

  2. Fallon FORGE 3D Geologic Model

    SciTech Connect

    Doug Blankenship

    2016-03-01

    An x,y,z scattered data file for the 3D geologic model of the Fallon FORGE site. Model created in Earthvision by Dynamic Graphic Inc. The model was constructed with a grid spacing of 100 m. Geologic surfaces were extrapolated from the input data using a minimum tension gridding algorithm. The data file is tabular data in a text file, with lithology data associated with X,Y,Z grid points. All the relevant information is in the file header (the spatial reference, the projection etc.) In addition all the fields in the data file are identified in the header.

  3. Inferential modeling of 3D chromatin structure.

    PubMed

    Wang, Siyu; Xu, Jinbo; Zeng, Jianyang

    2015-04-30

    For eukaryotic cells, the biological processes involving regulatory DNA elements play an important role in cell cycle. Understanding 3D spatial arrangements of chromosomes and revealing long-range chromatin interactions are critical to decipher these biological processes. In recent years, chromosome conformation capture (3C) related techniques have been developed to measure the interaction frequencies between long-range genome loci, which have provided a great opportunity to decode the 3D organization of the genome. In this paper, we develop a new Bayesian framework to derive the 3D architecture of a chromosome from 3C-based data. By modeling each chromosome as a polymer chain, we define the conformational energy based on our current knowledge on polymer physics and use it as prior information in the Bayesian framework. We also propose an expectation-maximization (EM) based algorithm to estimate the unknown parameters of the Bayesian model and infer an ensemble of chromatin structures based on interaction frequency data. We have validated our Bayesian inference approach through cross-validation and verified the computed chromatin conformations using the geometric constraints derived from fluorescence in situ hybridization (FISH) experiments. We have further confirmed the inferred chromatin structures using the known genetic interactions derived from other studies in the literature. Our test results have indicated that our Bayesian framework can compute an accurate ensemble of 3D chromatin conformations that best interpret the distance constraints derived from 3C-based data and also agree with other sources of geometric constraints derived from experimental evidence in the previous studies. The source code of our approach can be found in https://github.com/wangsy11/InfMod3DGen.

  4. 3D Printing of Biomolecular Models for Research and Pedagogy.

    PubMed

    Da Veiga Beltrame, Eduardo; Tyrwhitt-Drake, James; Roy, Ian; Shalaby, Raed; Suckale, Jakob; Pomeranz Krummel, Daniel

    2017-03-13

    The construction of physical three-dimensional (3D) models of biomolecules can uniquely contribute to the study of the structure-function relationship. 3D structures are most often perceived using the two-dimensional and exclusively visual medium of the computer screen. Converting digital 3D molecular data into real objects enables information to be perceived through an expanded range of human senses, including direct stereoscopic vision, touch, and interaction. Such tangible models facilitate new insights, enable hypothesis testing, and serve as psychological or sensory anchors for conceptual information about the functions of biomolecules. Recent advances in consumer 3D printing technology enable, for the first time, the cost-effective fabrication of high-quality and scientifically accurate models of biomolecules in a variety of molecular representations. However, the optimization of the virtual model and its printing parameters is difficult and time consuming without detailed guidance. Here, we provide a guide on the digital design and physical fabrication of biomolecule models for research and pedagogy using open source or low-cost software and low-cost 3D printers that use fused filament fabrication technology.

  5. A 3D visualization system for molecular structures

    NASA Technical Reports Server (NTRS)

    Green, Terry J.

    1989-01-01

    The properties of molecules derive in part from their structures. Because of the importance of understanding molecular structures various methodologies, ranging from first principles to empirical technique, were developed for computing the structure of molecules. For large molecules such as polymer model compounds, the structural information is difficult to comprehend by examining tabulated data. Therefore, a molecular graphics display system, called MOLDS, was developed to help interpret the data. MOLDS is a menu-driven program developed to run on the LADC SNS computer systems. This program can read a data file generated by the modeling programs or data can be entered using the keyboard. MOLDS has the following capabilities: draws the 3-D representation of a molecule using stick, ball and ball, or space filled model from Cartesian coordinates, draws different perspective views of the molecule; rotates the molecule on the X, Y, Z axis or about some arbitrary line in space, zooms in on a small area of the molecule in order to obtain a better view of a specific region; and makes hard copy representation of molecules on a graphic printer. In addition, MOLDS can be easily updated and readily adapted to run on most computer systems.

  6. 3D Model of Surfactant Replacement Therapy

    NASA Astrophysics Data System (ADS)

    Grotberg, James; Tai, Cheng-Feng; Filoche, Marcel

    2015-11-01

    Surfactant Replacement Therapy (SRT) involves instillation of a liquid-surfactant mixture directly into the lung airway tree. Though successful in neonatal applications, its use in adults had early success followed by failure. We present the first mathematical model of 3D SRT where a liquid plug propagates through the tree from forced inspiration. In two separate modeling steps, the plug first deposits a coating film on the airway wall which subtracts from its volume, a ``coating cost''. Then the plug splits unevenly at the airway bifurcation due to gravity. The steps are repeated until a plug ruptures or reaches the tree endpoint alveoli/acinus. The model generates 3D images of the resulting acinar distribution and calculates two global indexes, efficiency and homogeneity. Simulating published literature, the earlier successful adult SRT studies show comparatively good index values, while the later failed studies do not. Those unsuccessful studies used smaller dose volumes with higher concentration mixtures, apparently assuming a well mixed compartment. The model shows that adult lungs are not well mixed in SRT due to the coating cost and gravity effects. Returning to the higher dose volume protocols could save many thousands of lives annually in the US. Supported by NIH Grants HL85156, HL84370 and Agence Nationale de la Recherche, ANR no. 2010-BLAN-1119-05.

  7. MOSSFRAC: An anisotropic 3D fracture model

    SciTech Connect

    Moss, W C; Levatin, J L

    2006-08-14

    Despite the intense effort for nearly half a century to construct detailed numerical models of plastic flow and plastic damage accumulation, models for describing fracture, an equally important damage mechanism still cannot describe basic fracture phenomena. Typical fracture models set the stress tensor to zero for tensile fracture and set the deviatoric stress tensor to zero for compressive fracture. One consequence is that the simple case of the tensile fracture of a cylinder under combined compressive radial and tensile axial loads is not modeled correctly. The experimental result is a cylinder that can support compressive radial loads, but no axial load, whereas, the typical numerical result is a cylinder with all stresses equal to zero. This incorrect modeling of fracture locally also has a global effect, because material that is fracturing produces stress release waves, which propagate from the fracture and influence the surrounding material. Consequently, it would be useful to have a model that can describe the stress relief and the resulting anisotropy due to fracture. MOSSFRAC is a material model that simulates three-dimensional tensile and shear fracture in initially isotropic elastic-plastic materials, although its framework is also amenable to initially anisotropic materials. It differs from other models by accounting for the effects of cracks on the constitutive response of the material, so that the previously described experiment, as well as complicated fracture scenarios are simulated more accurately. The model is implemented currently in the LLNL hydrocodes DYNA3D, PARADYN, and ALE3D. The purpose of this technical note is to present a complete qualitative description of the model and quantitative descriptions of salient features.

  8. 3D Stratigraphic Modeling of Central Aachen

    NASA Astrophysics Data System (ADS)

    Dong, M.; Neukum, C.; Azzam, R.; Hu, H.

    2010-05-01

    Since 1980s, advanced computer hardware and software technologies, as well as multidisciplinary research have provided possibilities to develop advanced three dimensional (3D) simulation software for geosciences application. Some countries, such as USA1) and Canada2) 3), have built up regional 3D geological models based on archival geological data. Such models have played huge roles in engineering geology2), hydrogeology2) 3), geothermal industry1) and so on. In cooperating with the Municipality of Aachen, the Department of Engineering Geology of RWTH Aachen University have built up a computer-based 3D stratigraphic model of 50 meter' depth for the center of Aachen, which is a 5 km by 7 km geologically complex area. The uncorrelated data from multi-resources, discontinuous nature and unconformable connection of the units are main challenges for geological modeling in this area. The reliability of 3D geological models largely depends on the quality and quantity of data. Existing 1D and 2D geological data were collected, including 1) approximately 6970 borehole data of different depth compiled in Microsoft Access database and MapInfo database; 2) a Digital Elevation Model (DEM); 3) geological cross sections; and 4) stratigraphic maps in 1m, 2m and 5m depth. Since acquired data are of variable origins, they were managed step by step. The main processes are described below: 1) Typing errors of borehole data were identified and the corrected data were exported to Variowin2.2 to distinguish duplicate points; 2) The surface elevation of borehole data was compared to the DEM, and differences larger than 3m were eliminated. Moreover, where elevation data missed, it was read from the DEM; 3) Considerable data were collected from municipal constructions, such as residential buildings, factories, and roads. Therefore, many boreholes are spatially clustered, and only one or two representative points were picked out in such areas; After above procedures, 5839 boreholes with -x

  9. CH5M3D: an HTML5 program for creating 3D molecular structures

    PubMed Central

    2013-01-01

    Background While a number of programs and web-based applications are available for the interactive display of 3-dimensional molecular structures, few of these provide the ability to edit these structures. For this reason, we have developed a library written in JavaScript to allow for the simple creation of web-based applications that should run on any browser capable of rendering HTML5 web pages. While our primary interest in developing this application was for educational use, it may also prove useful to researchers who want a light-weight application for viewing and editing small molecular structures. Results Molecular compounds are drawn on the HTML5 Canvas element, with the JavaScript code making use of standard techniques to allow display of three-dimensional structures on a two-dimensional canvas. Information about the structure (bond lengths, bond angles, and dihedral angles) can be obtained using a mouse or other pointing device. Both atoms and bonds can be added or deleted, and rotation about bonds is allowed. Routines are provided to read structures either from the web server or from the user’s computer, and creation of galleries of structures can be accomplished with only a few lines of code. Documentation and examples are provided to demonstrate how users can access all of the molecular information for creation of web pages with more advanced features. Conclusions A light-weight (≈ 75 kb) JavaScript library has been made available that allows for the simple creation of web pages containing interactive 3-dimensional molecular structures. Although this library is designed to create web pages, a web server is not required. Installation on a web server is straightforward and does not require any server-side modules or special permissions. The ch5m3d.js library has been released under the GNU GPL version 3 open-source license and is available from http://sourceforge.net/projects/ch5m3d/. PMID:24246004

  10. SB3D User Manual, Santa Barbara 3D Radiative Transfer Model

    SciTech Connect

    O'Hirok, William

    1999-01-01

    SB3D is a three-dimensional atmospheric and oceanic radiative transfer model for the Solar spectrum. The microphysics employed in the model are the same as used in the model SBDART. It is assumed that the user of SB3D is familiar with SBDART and IDL. SB3D differs from SBDART in that computations are conducted on media in three-dimensions rather than a single column (i.e. plane-parallel), and a stochastic method (Monte Carlo) is employed instead of a numerical approach (Discrete Ordinates) for estimating a solution to the radiative transfer equation. Because of these two differences between SB3D and SBDART, the input and running of SB3D is more unwieldy and requires compromises between model performance and computational expense. Hence, there is no one correct method for running the model and the user must develop a sense to the proper input and configuration of the model.

  11. Reservoir geology using 3D modelling tools

    SciTech Connect

    Dubrule, O.; Samson, P.; Segonds, D.

    1996-12-31

    The last decade has seen tremendous developments in the area of quantitative geological modelling. These developments have a significant impact on the current practice of constructing reservoir models. A structural model can first be constructed on the basis of depth-converted structural interpretations produced on a seismic interpretation workstation. Surfaces and faults can be represented as geological objects, and interactively modified. Once the tectonic framework has been obtained, intermediate stratigraphic surfaces can be constructed between the main structural surfaces. Within each layer, reservoir attributes can be represented using various techniques. Examples show how the distribution of different facies (i.e. from fine to coarse grain) can be represented, or how various depositional units (for instance channels, crevasses and lobes in a turbidite setting) can be modelled as geological {open_quotes}objects{close_quotes} with complex geometries. Elf Aquitaine, in close co-operation with the GOCAD project in Nancy (France) is investigating how geological models can be made more realistic by developing interactive functionalities. Examples show that, contrary to standard deterministic or geostatistical modelling techniques (which tend to be difficult to control) the use of new 3D tools allows the geologist to interactively modify geological surfaces (including faults) or volumetric properties. Thus, the sensitivity of various economic parameters (oil in place, connected volumes, reserves) to major geological uncertainties can be evaluated. It is argued that future breakthroughs in geological modelling techniques are likely to happen in the development of interactive approaches rather than in the research of new mathematical algorithms.

  12. Reservoir geology using 3D modelling tools

    SciTech Connect

    Dubrule, O. ); Samson, P. ); Segonds, D. )

    1996-01-01

    The last decade has seen tremendous developments in the area of quantitative geological modelling. These developments have a significant impact on the current practice of constructing reservoir models. A structural model can first be constructed on the basis of depth-converted structural interpretations produced on a seismic interpretation workstation. Surfaces and faults can be represented as geological objects, and interactively modified. Once the tectonic framework has been obtained, intermediate stratigraphic surfaces can be constructed between the main structural surfaces. Within each layer, reservoir attributes can be represented using various techniques. Examples show how the distribution of different facies (i.e. from fine to coarse grain) can be represented, or how various depositional units (for instance channels, crevasses and lobes in a turbidite setting) can be modelled as geological [open quotes]objects[close quotes] with complex geometries. Elf Aquitaine, in close co-operation with the GOCAD project in Nancy (France) is investigating how geological models can be made more realistic by developing interactive functionalities. Examples show that, contrary to standard deterministic or geostatistical modelling techniques (which tend to be difficult to control) the use of new 3D tools allows the geologist to interactively modify geological surfaces (including faults) or volumetric properties. Thus, the sensitivity of various economic parameters (oil in place, connected volumes, reserves) to major geological uncertainties can be evaluated. It is argued that future breakthroughs in geological modelling techniques are likely to happen in the development of interactive approaches rather than in the research of new mathematical algorithms.

  13. Scalable 3D GIS environment managed by 3D-XML-based modeling

    NASA Astrophysics Data System (ADS)

    Shi, Beiqi; Rui, Jianxun; Chen, Neng

    2008-10-01

    Nowadays, the namely 3D GIS technologies become a key factor in establishing and maintaining large-scale 3D geoinformation services. However, with the rapidly increasing size and complexity of the 3D models being acquired, a pressing needed for suitable data management solutions has become apparent. This paper outlines that storage and exchange of geospatial data between databases and different front ends like 3D models, GIS or internet browsers require a standardized format which is capable to represent instances of 3D GIS models, to minimize loss of information during data transfer and to reduce interface development efforts. After a review of previous methods for spatial 3D data management, a universal lightweight XML-based format for quick and easy sharing of 3D GIS data is presented. 3D data management based on XML is a solution meeting the requirements as stated, which can provide an efficient means for opening a new standard way to create an arbitrary data structure and share it over the Internet. To manage reality-based 3D models, this paper uses 3DXML produced by Dassault Systemes. 3DXML uses opening XML schemas to communicate product geometry, structure and graphical display properties. It can be read, written and enriched by standard tools; and allows users to add extensions based on their own specific requirements. The paper concludes with the presentation of projects from application areas which will benefit from the functionality presented above.

  14. Automated modeling of RNA 3D structure.

    PubMed

    Rother, Kristian; Rother, Magdalena; Skiba, Pawel; Bujnicki, Janusz M

    2014-01-01

    This chapter gives an overview over the current methods for automated modeling of RNA structures, with emphasis on template-based methods. The currently used approaches to RNA modeling are presented with a side view on the protein world, where many similar ideas have been used. Two main programs for automated template-based modeling are presented: ModeRNA assembling structures from fragments and MacroMoleculeBuilder performing a simulation to satisfy spatial restraints. Both approaches have in common that they require an alignment of the target sequence to a known RNA structure that is used as a modeling template. As a way to find promising template structures and to align the target and template sequences, we propose a pipeline combining the ParAlign and Infernal programs on RNA family data from Rfam. We also briefly summarize template-free methods for RNA 3D structure prediction. Typically, RNA structures generated by automated modeling methods require local or global optimization. Thus, we also discuss methods that can be used for local or global refinement of RNA structures.

  15. Regional geothermal 3D modelling in Denmark

    NASA Astrophysics Data System (ADS)

    Poulsen, S. E.; Balling, N.; Bording, T. S.; Nielsen, S. B.

    2012-04-01

    In the pursuit of sustainable and low carbon emission energy sources, increased global attention has been given to the exploration and exploitation of geothermal resources within recent decades. In 2009 a national multi-disciplinary geothermal research project was established. As a significant part of this project, 3D temperature modelling is to be carried out, with special emphasis on temperatures of potential geothermal reservoirs in the Danish area. The Danish subsurface encompasses low enthalpy geothermal reservoirs of mainly Triassic and Jurassic age. Geothermal plants at Amager (Copenhagen) and Thisted (Northern Jutland) have the capacity of supplying the district heating network with up to 14 MW and 7 MW, respectively, by withdrawing warm pore water from the Gassum (Lower Jurassic/Upper Triassic) and Bunter (Lower Triassic) sandstone reservoirs, respectively. Explorative studies of the subsurface temperature regime typically are based on a combination of observations and modelling. In this study, the open-source groundwater modelling code MODFLOW is modified to simulate the subsurface temperature distribution in three dimensions by taking advantage of the mathematical similarity between saturated groundwater flow (Darcy flow) and heat conduction. A numerical model of the subsurface geology in Denmark is built and parameterized from lithological information derived from joint interpretation of seismic surveys and borehole information. Boundary conditions are constructed from knowledge about the heat flow from the Earth's interior and the shallow ground temperature. Matrix thermal conductivities have been estimated from analysis of high-resolution temperature logs measured in deep wells and porosity-depth relations are included using interpreted main lithologies. The model takes into account the dependency of temperature and pressure on thermal conductivity. Moreover, a transient model based correction of the paleoclimatic thermal disturbance caused by the

  16. 3D Modelling of Kizildag Monument

    NASA Astrophysics Data System (ADS)

    Karauguz, Güngör; Kalayci, İbrahim; Öğütcü, Sermet

    2016-10-01

    The most important cultural property that the nations possess is their historical accumulation, and bringing these to light, taking measures to preserve them or at least maintain the continuity of transferring them to next generations by means of recent technic and technology, ought to be the business of present generations. Although, nowadays, intensive documentation and archiving studies are done by means of classical techniques, besides studies towards preserving historical objects, modelling one-to-one or scaled modelling were not possible until recently. Computing devices and the on-going reflection of this, which is acknowledged as digital technology, is widely used in many areas and makes it possible to document and archive historical works. Even virtual forms in quantitative environments can be transferred to next generations in a scaled and one-to-one modelled way. Within this scope, every single artefact categorization belonging to any era or civilization present in our country can be considered in separate study areas. Furthermore, any work or likewise can be evaluated in separate categories. Also, it is possible to construct travelable virtual 3D museums that make it possible to visit these artefacts. Under the auspices of these technologies, it is quite possible to construct single virtual indoor museums or also, at the final stage, a 3D travelable open-air museum, a platform or more precisely, to establish a data system that spreads all over the country on a broad spectrum. With a long-termed, significant and extensive study and a substantial organization, such a data system can be established, which also serves as a serious infrastructure for alternative tourism possibilities. Located beside a stepped altar and right above the Kizildag IV inscription, the offering pot is destructed and rolled away a few meters to the south slope of the mould. Every time visiting these artefacts with our undergraduate students, unfortunately, we observe more

  17. 3-D physical models of amitosis (cytokinesis).

    PubMed

    Cheng, Kang; Zou, Changhua

    2005-01-01

    Based on Newton's laws, extended Coulomb's law and published biological data, we develop our 3-D physical models of natural and normal amitosis (cytokinesis), for prokaryotes (bacterial cells) in M phase. We propose following hypotheses: Chromosome rings exclusion: No normally and naturally replicated chromosome rings (RCR) can occupy the same prokaryote, a bacterial cell. The RCR produce spontaneous and strong electromagnetic fields (EMF), that can be alternated environmentally, in protoplasm and cortex. The EMF is approximately a repulsive quasi-static electric (slowly variant and mostly electric) field (EF). The EF forces between the RCR are strong enough, and orderly accumulate contractile proteins that divide the procaryotes in the cell cortex of division plane or directly split the cell compartment envelope longitudinally. The radial component of the EF forces could also make furrows or cleavages of procaryotes. The EF distribution controls the protoplasm partition and completes the amitosis (cytokinesis). After the cytokinesis, the spontaneous and strong EF disappear because the net charge accumulation becomes weak, in the protoplasm. The exclusion is because the two sets of informative objects (RCR) have identical DNA codes information and they are electro magnetically identical, therefore they repulse from each other. We also compare divisions among eukaryotes, prokaryotes, mitochondria and chloroplasts and propose our hypothesis: The principles of our models are applied to divisions of mitochondria and chloroplasts of eucaryotes too because these division mechanisms are closer than others in a view of physics. Though we develop our model using 1 division plane (i.e., 1 cell is divided into 2 cells) as an example, the principle of our model is applied to the cases with multiple division planes (i.e., 1 cell is divided into multiple cells) too.

  18. Multi-view and 3D deformable part models.

    PubMed

    Pepik, Bojan; Stark, Michael; Gehler, Peter; Schiele, Bernt

    2015-11-01

    As objects are inherently 3D, they have been modeled in 3D in the early days of computer vision. Due to the ambiguities arising from mapping 2D features to 3D models, 3D object representations have been neglected and 2D feature-based models are the predominant paradigm in object detection nowadays. While such models have achieved outstanding bounding box detection performance, they come with limited expressiveness, as they are clearly limited in their capability of reasoning about 3D shape or viewpoints. In this work, we bring the worlds of 3D and 2D object representations closer, by building an object detector which leverages the expressive power of 3D object representations while at the same time can be robustly matched to image evidence. To that end, we gradually extend the successful deformable part model [1] to include viewpoint information and part-level 3D geometry information, resulting in several different models with different level of expressiveness. We end up with a 3D object model, consisting of multiple object parts represented in 3D and a continuous appearance model. We experimentally verify that our models, while providing richer object hypotheses than the 2D object models, provide consistently better joint object localization and viewpoint estimation than the state-of-the-art multi-view and 3D object detectors on various benchmarks (KITTI [2] , 3D object classes [3] , Pascal3D+ [4] , Pascal VOC 2007 [5] , EPFL multi-view cars[6] ).

  19. Ames interactive molecular model building system - A 3-D computer modelling system applied to the study of the origin of life

    NASA Technical Reports Server (NTRS)

    Coeckelenbergh, Y.; Macelroy, R. D.; Rein, R.

    1978-01-01

    The investigation of specific interactions among biological molecules must take into consideration the stereochemistry of the structures. Thus, models of the molecules are essential for describing the spatial organization of potentially interacting groups, and estimations of conformation are required for a description of spatial organization. Both the function of visualizing molecules, and that of estimating conformation through calculations of energy, are part of the molecular modeling system described in the present paper. The potential uses of the system in investigating some aspects of the origin of life rest on the assumption that translation of conformation from genetic elements to catalytic elements would have been required for the development of the first replicating systems subject to the process of biological evolution.

  20. 3D-GNOME: an integrated web service for structural modeling of the 3D genome.

    PubMed

    Szalaj, Przemyslaw; Michalski, Paul J; Wróblewski, Przemysław; Tang, Zhonghui; Kadlof, Michal; Mazzocco, Giovanni; Ruan, Yijun; Plewczynski, Dariusz

    2016-07-08

    Recent advances in high-throughput chromosome conformation capture (3C) technology, such as Hi-C and ChIA-PET, have demonstrated the importance of 3D genome organization in development, cell differentiation and transcriptional regulation. There is now a widespread need for computational tools to generate and analyze 3D structural models from 3C data. Here we introduce our 3D GeNOme Modeling Engine (3D-GNOME), a web service which generates 3D structures from 3C data and provides tools to visually inspect and annotate the resulting structures, in addition to a variety of statistical plots and heatmaps which characterize the selected genomic region. Users submit a bedpe (paired-end BED format) file containing the locations and strengths of long range contact points, and 3D-GNOME simulates the structure and provides a convenient user interface for further analysis. Alternatively, a user may generate structures using published ChIA-PET data for the GM12878 cell line by simply specifying a genomic region of interest. 3D-GNOME is freely available at http://3dgnome.cent.uw.edu.pl/.

  1. 3D-GNOME: an integrated web service for structural modeling of the 3D genome

    PubMed Central

    Szalaj, Przemyslaw; Michalski, Paul J.; Wróblewski, Przemysław; Tang, Zhonghui; Kadlof, Michal; Mazzocco, Giovanni; Ruan, Yijun; Plewczynski, Dariusz

    2016-01-01

    Recent advances in high-throughput chromosome conformation capture (3C) technology, such as Hi-C and ChIA-PET, have demonstrated the importance of 3D genome organization in development, cell differentiation and transcriptional regulation. There is now a widespread need for computational tools to generate and analyze 3D structural models from 3C data. Here we introduce our 3D GeNOme Modeling Engine (3D-GNOME), a web service which generates 3D structures from 3C data and provides tools to visually inspect and annotate the resulting structures, in addition to a variety of statistical plots and heatmaps which characterize the selected genomic region. Users submit a bedpe (paired-end BED format) file containing the locations and strengths of long range contact points, and 3D-GNOME simulates the structure and provides a convenient user interface for further analysis. Alternatively, a user may generate structures using published ChIA-PET data for the GM12878 cell line by simply specifying a genomic region of interest. 3D-GNOME is freely available at http://3dgnome.cent.uw.edu.pl/. PMID:27185892

  2. Use of molecular modeling, docking, and 3D-QSAR studies for the determination of the binding mode of benzofuran-3-yl-(indol-3-yl)maleimides as GSK-3beta inhibitors.

    PubMed

    Kim, Ki Hwan; Gaisina, Irina; Gallier, Franck; Holzle, Denise; Blond, Sylvie Y; Mesecar, Andrew; Kozikowski, Alan P

    2009-12-01

    Molecular modeling and docking studies along with three-dimensional quantitative structure relationships (3D-QSAR) studies have been used to determine the correct binding mode of glycogen synthase kinase 3beta (GSK-3beta) inhibitors. The approaches of comparative molecular field analysis (CoMFA) and comparative molecular similarity index analysis (CoMSIA) are used for the 3D-QSAR of 51 substituted benzofuran-3-yl-(indol-3-yl)maleimides as GSK-3beta inhibitors. Two binding modes of the inhibitors to the binding site of GSK-3beta are investigated. The binding mode 1 yielded better 3D-QSAR correlations using both CoMFA and CoMSIA methodologies. The three-component CoMFA model from the steric and electrostatic fields for the experimentally determined pIC(50) values has the following statistics: R(2)(cv) = 0.386 nd SE(cv) = 0.854 for the cross-validation, and R(2) = 0.811 and SE = 0.474 for the fitted correlation. F (3,47) = 67.034, and probability of R(2) = 0 (3,47) = 0.000. The binding mode suggested by the results of this study is consistent with the preliminary results of X-ray crystal structures of inhibitor-bound GSK-3beta. The 3D-QSAR models were used for the estimation of the inhibitory potency of two additional compounds.

  3. In Silico 3D Modeling of Binding Activities.

    PubMed

    Moro, Stefano; Sturlese, Mattia; Ciancetta, Antonella; Floris, Matteo

    2016-01-01

    In silico three-dimensional (3D) molecular modeling tools based upon the receptor/enzyme-ligand docking simulation in protein crystal structures and/or homology modeling of receptors have been reliably used in pharmacological research and development for decades. Molecular docking methodologies are helpful for revealing facets of activation and inactivation, thus improving mechanistic understanding and predicting molecular ligand binding activity, and they can have a high level of accuracy, and have also been explored and applied in chemical risk assessment. This computational approach is, however, only applicable for chemical hazard identification situations where the specific target receptor for a given chemical is known and the crystal structure/homology model of the receptor is available.

  4. Generation of a 3D model for human GABA transporter hGAT-1 using molecular modeling and investigation of the binding of GABA.

    PubMed

    Wein, Thomas; Wanner, Klaus T

    2010-01-01

    A three-dimensional model of the human Na(+)/Cl(-)-dependent gamma-aminobutyric acid (GABA) transporter hGAT-1 was developed by homology modeling and refined by subsequent molecular modeling using the crystal structure of a bacterial homologue leucine transporter from Aquifex aeolicus (LeuT(Aa)) as the template. Protein structure quality checks show that the resulting structure is particularly suited for the analysis of the substrate binding pocket and virtual screening experiments. Interactions of GABA and the substrate binding pocket were investigated using docking studies. The difference of 6 out of 13 substrate interacting side chains between hGAT-1 and LeuT(Aa) lead to the different substrate preference which can be explained using our three-dimensional model of hGAT-1. In particular the replacement of serine 256 and isoleucine 359 in LeuT(Aa) with glycine and threonine in hGAT-1 seems to facilitate the selection of GABA as the main substrate by changing the hydrogen bonding pattern in the active site to the amino group of the substrate. For a set of 12 compounds flexible docking experiments were performed using LigandFit in combination with the Jain scoring function. With few exceptions the obtained rank order of potency was in line with experimental data. Thus, the method can be assumed to give at least a rough estimate of the potency of the potential of GABA uptake inhibitors.

  5. 3D fast wavelet network model-assisted 3D face recognition

    NASA Astrophysics Data System (ADS)

    Said, Salwa; Jemai, Olfa; Zaied, Mourad; Ben Amar, Chokri

    2015-12-01

    In last years, the emergence of 3D shape in face recognition is due to its robustness to pose and illumination changes. These attractive benefits are not all the challenges to achieve satisfactory recognition rate. Other challenges such as facial expressions and computing time of matching algorithms remain to be explored. In this context, we propose our 3D face recognition approach using 3D wavelet networks. Our approach contains two stages: learning stage and recognition stage. For the training we propose a novel algorithm based on 3D fast wavelet transform. From 3D coordinates of the face (x,y,z), we proceed to voxelization to get a 3D volume which will be decomposed by 3D fast wavelet transform and modeled after that with a wavelet network, then their associated weights are considered as vector features to represent each training face . For the recognition stage, an unknown identity face is projected on all the training WN to obtain a new vector features after every projection. A similarity score is computed between the old and the obtained vector features. To show the efficiency of our approach, experimental results were performed on all the FRGC v.2 benchmark.

  6. A 3-D shape model of Interamnia

    NASA Astrophysics Data System (ADS)

    Sato, Isao

    2015-08-01

    A 3-D shape model of the sixth largest of the main belt asteroids, (704) Interamnia, is presented. The model is reproduced from its two stellar occultation observations and six lightcurves between 1969 and 2011. The first stellar occultation was the occultation of TYC 234500183 on 1996 December 17 observed from 13 sites in the USA. An elliptical cross section of (344.6±9.6km)×(306.2±9.1km), for position angle P=73.4±12.5 was fitted. The lightcurve around the occultation shows that the peak-to-peak amplitude was 0.04 mag. and the occultation phase was just before the minimum. The second stellar occultation was the occultation of HIP 036189 on 2003 March 23 observed from 39 sites in Japan and Hawaii. An elliptical cross section of (349.8±0.9km)×(303.7±1.7km), for position angle P=86.0±1.1 was fitted. A companion of 8.5 mag. of the occulted star was discovered whose separation is 12±2 mas (milli-arcseconds), P=148±11 . A combined analysis of rotational lightcurves and occultation chords can return more information than can be obtained with either technique alone. From follow-up photometric observations of the asteroid between 2003 and 2011, its rotation period is determined to be 8.728967167±0.00000007 hours, which is accurate enough to fix the rotation phases at other occultation events. The derived north pole is λ2000=259±8, β2000=-50±5 (retrograde rotation); the lengths of the three principal axes are 2a=361.8±2.8km, 2b=324.4±5.0km, 2c=297.3±3.5km, and the mean diameter is D=326.8±3.0km. Supposing the mass of Interamnia as (3.5±0.9)×10-11 solar masses, the density is then ρ=3.8±1.0 g cm-3.

  7. Anatomy-based 3D skeleton extraction from femur model.

    PubMed

    Gharenazifam, Mina; Arbabi, Ehsan

    2014-11-01

    Using 3D models of bones can highly improve accuracy and reliability of orthopaedic evaluation. However, it may impose excessive computational load. This article proposes a fully automatic method for extracting a compact model of the femur from its 3D model. The proposed method works by extracting a 3D skeleton based on the clinical parameters of the femur. Therefore, in addition to summarizing a 3D model of the bone, the extracted skeleton would preserve important clinical and anatomical information. The proposed method has been applied on 3D models of 10 femurs and the results have been evaluated for different resolutions of data.

  8. 3D Modeling Techniques for Print and Digital Media

    NASA Astrophysics Data System (ADS)

    Stephens, Megan Ashley

    In developing my thesis, I looked to gain skills using ZBrush to create 3D models, 3D scanning, and 3D printing. The models created compared the hearts of several vertebrates and were intended for students attending Comparative Vertebrate Anatomy. I used several resources to create a model of the human heart and was able to work from life while creating heart models from other vertebrates. I successfully learned ZBrush and 3D scanning, and successfully printed 3D heart models. ZBrush allowed me to create several intricate models for use in both animation and print media. The 3D scanning technique did not fit my needs for the project, but may be of use for later projects. I was able to 3D print using two different techniques as well.

  9. 3D metamaterial absorber for attomole molecular detection (Conference Presentation)

    NASA Astrophysics Data System (ADS)

    Tanaka, Takuo; Ishikawa, Atsushi

    2016-09-01

    3D Metamaterial absorber was used for a background-suppressed surface-enhanced molecular detection technique. By utilizing the resonant coupling of plasmonic modes of a metamaterial absorber and infrared (IR) vibrational modes of a self-assembled monolayer (SAM), attomole level molecular sensitivity was experimentally demonstrated. IR absorption spectroscopy of molecular vibrations is of importance in chemical, material, medical science and so on, since it provides essential information of the molecular structure, composition, and orientation. In the vibrational spectroscopic techniques, in addition to the weak signals from the molecules, strong background degrades the signal-to-noise ratio, and suppression of the background is crucial for the further improvement of the sensitivity. Here, we demonstrate low-background resonant Surface enhanced IR absorption (SEIRA) by using the metamaterial IR absorber that offers significant background suppression as well as plasmonic enhancement. The fabricated metamaterial consisted of 1D array of Au micro-ribbons on a thick Au film separated by a transparent gap layer made of MgF2. The surface structures were designed to exhibit an anomalous IR absorption at 3000 cm-1, which spectrally overlapped with C-H stretching vibrational modes. 16-Mercaptohexadecanoic acid (16-MHDA) was used as a test molecule, which formed a 2-nm thick SAM with their thiol head-group chemisorbed on the Au surface. In the FTIR measurements, the symmetric and asymmetric C-H stretching modes were clearly observed as reflection peaks within a broad plasmonic absorption of the metamaterial.

  10. Elastic wave modelling in 3D heterogeneous media: 3D grid method

    NASA Astrophysics Data System (ADS)

    Jianfeng, Zhang; Tielin, Liu

    2002-09-01

    We present a new numerical technique for elastic wave modelling in 3D heterogeneous media with surface topography, which is called the 3D grid method in this paper. This work is an extension of the 2D grid method that models P-SV wave propagation in 2D heterogeneous media. Similar to the finite-element method in the discretization of a numerical mesh, the proposed scheme is flexible in incorporating surface topography and curved interfaces; moreover it satisfies the free-surface boundary conditions of 3D topography naturally. The algorithm, developed from a parsimonious staggered-grid scheme, solves the problem using integral equilibrium around each node, instead of satisfying elastodynamic differential equations at each node as in the conventional finite-difference method. The computational cost and memory requirements for the proposed scheme are approximately the same as those used by the same order finite-difference method. In this paper, a mixed tetrahedral and parallelepiped grid method is presented; and the numerical dispersion and stability criteria on the tetrahedral grid method and parallelepiped grid method are discussed in detail. The proposed scheme is successfully tested against an analytical solution for the 3D Lamb problem and a solution of the boundary method for the diffraction of a hemispherical crater. Moreover, examples of surface-wave propagation in an elastic half-space with a semi-cylindrical trench on the surface and 3D plane-layered model are presented.

  11. The 3D rocket combustor acoustics model

    NASA Technical Reports Server (NTRS)

    Priem, Richard J.; Breisacher, Kevin J.

    1992-01-01

    The theory and procedures for determining the characteristics of pressure oscillations in rocket engines with prescribed burning rate oscillations are presented. Analyses including radial and hub baffles and absorbers can be performed in one, two, and three dimensions. Pressure and velocity oscillations calculated using this procedure are presented for the SSME to show the influence of baffles and absorbers on the burning rate oscillations required to achieve neutral stability. Comparisons are made between the results obtained utilizing 1-D, 2-D, and 3-D assumptions with regards to capturing the physical phenomena of interest and computational requirements.

  12. 3D modeling based on CityEngine

    NASA Astrophysics Data System (ADS)

    Jia, Guangyin; Liao, Kaiju

    2017-03-01

    Currently, there are many 3D modeling softwares, like 3DMAX, AUTOCAD, and more populous BIM softwares represented by REVIT. CityEngine modeling software introduced in this paper can fully utilize the existing GIS data and combine other built models to make 3D modeling on internal and external part of buildings in a rapid and batch manner, so as to improve the 3D modeling efficiency.

  13. 3-d Periodic Packaging: Sodalite, a Model System

    DTIC Science & Technology

    1992-05-15

    to 05-31-92 4. TITLE AND SUBTITLE S. FUNDING NUMBERS 3-d Periodic Packaging: N00014-90-J-1159 Sodalite , A Model System 6. AUTHOR(S) G.D. Stucky, V.I...assembly of confined atomic and molecular arrays. Sodalite , one of the simplest zeolite analogue structures with a 60 atom cage can be synthesized with...structure of both the frameworks and the clusters within the cages of sodalite structural analogues can be precisely determined. In addition to new

  14. 3-D Periodic Packaging: Sodalite, a Model System

    DTIC Science & Technology

    1992-05-15

    hfww 05-15-92 Technical 06-1-91 o 05-31-92 ,mA AMU SUBSTIl SI. FUNDING NUMBUS 3-d Periodic Packaging: Sodalite , A Model System N00014-81-K-0598 AUTNO(S...considerable latitude in the assembly of confined atomic and molecular arrays. Sodalite , one of the simplest zeolite analogue structures with a 60 atom...framework electric field. The structure of both the fiameworks and the clusters within the cages of sodalite structural analogues can be precisely

  15. Single-Tooth Modeling for 3D Dental Model

    PubMed Central

    Yuan, Tianran; Liao, Wenhe; Dai, Ning; Cheng, Xiaosheng; Yu, Qing

    2010-01-01

    An integrated single-tooth modeling scheme is proposed for the 3D dental model acquired by optical digitizers. The cores of the modeling scheme are fusion regions extraction, single tooth shape restoration, and single tooth separation. According to the “valley” shape-like characters of the fusion regions between two adjoining teeth, the regions of the 3D dental model are analyzed and classified based on the minimum curvatures of the surface. The single tooth shape is restored according to the bioinformation along the hole boundary, which is generated after the fusion region being removed. By using the extracted boundary from the blending regions between the teeth and soft tissues as reference, the teeth can be separated from the 3D dental model one by one correctly. Experimental results show that the proposed method can achieve satisfying modeling results with high-degree approximation of the real tooth and meet the requirements of clinical oral medicine. PMID:20689718

  16. ProteinVista: a fast molecular visualization system using Microsoft Direct3D.

    PubMed

    Park, Chan-Yong; Park, Sung-Hee; Park, Soo-Jun; Park, Sun-Hee; Hwang, Chi-Jung

    2008-09-01

    Many tools have been developed to visualize protein and molecular structures. Most high quality protein visualization tools use the OpenGL graphics library as a 3D graphics system. Currently, the performance of recent 3D graphics hardware has rapidly improved. Recent high-performance 3D graphics hardware support Microsoft Direct3D graphics library more than OpenGL and have become very popular in personal computers (PCs). In this paper, a molecular visualization system termed ProteinVista is proposed. ProteinVista is well-designed visualization system using the Microsoft Direct3D graphics library. It provides various visualization styles such as the wireframe, stick, ball and stick, space fill, ribbon, and surface model styles, in addition to display options for 3D visualization. As ProteinVista is optimized for recent 3D graphics hardware platforms and because it uses a geometry instancing technique, its rendering speed is 2.7 times faster compared to other visualization tools.

  17. 3D tumor models: history, advances and future perspectives.

    PubMed

    Benien, Parul; Swami, Archana

    2014-05-01

    Evaluation of cancer therapeutics by utilizing 3D tumor models, before clinical studies, could be more advantageous than conventional 2D tumor models (monolayer cultures). The 3D systems mimic the tumor microenvironment more closely than 2D systems. The following review discusses the various 3D tumor models present today with the advantages and limitations of each. 3D tumor models replicate the elements of a tumor microenvironment such as hypoxia, necrosis, angiogenesis and cell adhesion. The review introduces application of techniques such as microfluidics, imaging and tissue engineering to improve the 3D tumor models. Despite their tremendous potential to better screen chemotherapeutics, 3D tumor models still have a long way to go before they are used commonly as in vitro tumor models in pharmaceutical industrial research.

  18. Investigation of surface wave amplitudes in 3-D velocity and 3-D Q models

    NASA Astrophysics Data System (ADS)

    Ruan, Y.; Zhou, Y.

    2010-12-01

    It has been long recognized that seismic amplitudes depend on both wave speed structures and anelasticity (Q) structures. However, the effects of lateral heterogeneities in wave speed and Q structures on seismic amplitudes has not been well understood. We investigate the effects of 3-D wave speed and 3-D anelasticity (Q) structures on surface-wave amplitudes based upon wave propagation simulations of twelve globally-distributed earthquakes and 801 stations in Earth models with and without lateral heterogeneities in wave speed and anelasticity using a Spectral Element Method (SEM). Our tomographic-like 3-D Q models are converted from a velocity model S20RTS using a set of reasonable mineralogical parameters, assuming lateral perturbations in both velocity and Q are due to temperature perturbations. Surface-wave amplitude variations of SEM seismograms are measured in the period range of 50--200 s using boxcar taper, cosine taper and Slepian multi-tapers. We calculate ray-theoretical predictions of surface-wave amplitude perturbations due to elastic focusing, attenuation, and anelastic focusing which respectively depend upon the second spatial derivative (''roughness'') of perturbations in phase velocity, 1/Q, and the roughness of perturbations in 1/Q. Both numerical experiments and theoretical calculations show that (1) for short-period (~ 50 s) surface waves, the effects of amplitude attenuation due to 3-D Q structures are comparable with elastic focusing effects due to 3-D wave speed structures; and (2) for long-period (> 100 s) surface waves, the effects of attenuation become much weaker than elastic focusing; and (3) elastic focusing effects are correlated with anelastic focusing at all periods due to the correlation between velocity and Q models; and (4) amplitude perturbations are depend on measurement techniques and therefore cannot be directly compared with ray-theoretical predictions because ray theory does not account for the effects of measurement

  19. 3D Face modeling using the multi-deformable method.

    PubMed

    Hwang, Jinkyu; Yu, Sunjin; Kim, Joongrock; Lee, Sangyoun

    2012-09-25

    In this paper, we focus on the problem of the accuracy performance of 3D face modeling techniques using corresponding features in multiple views, which is quite sensitive to feature extraction errors. To solve the problem, we adopt a statistical model-based 3D face modeling approach in a mirror system consisting of two mirrors and a camera. The overall procedure of our 3D facial modeling method has two primary steps: 3D facial shape estimation using a multiple 3D face deformable model and texture mapping using seamless cloning that is a type of gradient-domain blending. To evaluate our method's performance, we generate 3D faces of 30 individuals and then carry out two tests: accuracy test and robustness test. Our method shows not only highly accurate 3D face shape results when compared with the ground truth, but also robustness to feature extraction errors. Moreover, 3D face rendering results intuitively show that our method is more robust to feature extraction errors than other 3D face modeling methods. An additional contribution of our method is that a wide range of face textures can be acquired by the mirror system. By using this texture map, we generate realistic 3D face for individuals at the end of the paper.

  20. Vel-IO 3D: A tool for 3D velocity model construction, optimization and time-depth conversion in 3D geological modeling workflow

    NASA Astrophysics Data System (ADS)

    Maesano, Francesco E.; D'Ambrogi, Chiara

    2017-02-01

    We present Vel-IO 3D, a tool for 3D velocity model creation and time-depth conversion, as part of a workflow for 3D model building. The workflow addresses the management of large subsurface dataset, mainly seismic lines and well logs, and the construction of a 3D velocity model able to describe the variation of the velocity parameters related to strong facies and thickness variability and to high structural complexity. Although it is applicable in many geological contexts (e.g. foreland basins, large intermountain basins), it is particularly suitable in wide flat regions, where subsurface structures have no surface expression. The Vel-IO 3D tool is composed by three scripts, written in Python 2.7.11, that automate i) the 3D instantaneous velocity model building, ii) the velocity model optimization, iii) the time-depth conversion. They determine a 3D geological model that is consistent with the primary geological constraints (e.g. depth of the markers on wells). The proposed workflow and the Vel-IO 3D tool have been tested, during the EU funded Project GeoMol, by the construction of the 3D geological model of a flat region, 5700 km2 in area, located in the central part of the Po Plain. The final 3D model showed the efficiency of the workflow and Vel-IO 3D tool in the management of large amount of data both in time and depth domain. A 4 layer-cake velocity model has been applied to a several thousand (5000-13,000 m) thick succession, with 15 horizons from Triassic up to Pleistocene, complicated by a Mesozoic extensional tectonics and by buried thrusts related to Southern Alps and Northern Apennines.

  1. 3D Modelling of X-pinches.

    NASA Astrophysics Data System (ADS)

    Ciardi, A.; Chittenden, J. P.; Lebedev, S. V.; Bland, S. N.; Jennings, C. A.

    2003-10-01

    X-pinch produced plasmas are an intense source of soft x-rays generated by passing a large, fast rising current through two or more thin metallic wires crossed in the shape of <93>an "X". During the current pulse, the plasma is pinched at the crossing point where a dense Z-pinch plasma column develops. Further compression produces micron sized x-ray hot spots with energy densities in excess of ˜10^24 eV cm-3. We present 3D resistive magnetohydrodynamic simulations of two- and four-wire X-pinches for a variety of wire materials. The simulations naturally follow the evolution of the X-pinch: jet-like structures on axis, formation of a Z-pinch and its subsequent rapid evolution and production of x-ray hot spots. The effects of wire material and wire number are studied with particular consideration to the relationship between the magnetic confinement and radiative cooling mechanisms, which ultimately determine the complex behaviour of the X-pinch.

  2. Comparing a quasi-3D to a full 3D nearshore circulation model: SHORECIRC and ROMS

    USGS Publications Warehouse

    Haas, K.A.; Warner, J.C.

    2009-01-01

    Predictions of nearshore and surf zone processes are important for determining coastal circulation, impacts of storms, navigation, and recreational safety. Numerical modeling of these systems facilitates advancements in our understanding of coastal changes and can provide predictive capabilities for resource managers. There exists many nearshore coastal circulation models, however they are mostly limited or typically only applied as depth integrated models. SHORECIRC is an established surf zone circulation model that is quasi-3D to allow the effect of the variability in the vertical structure of the currents while maintaining the computational advantage of a 2DH model. Here we compare SHORECIRC to ROMS, a fully 3D ocean circulation model which now includes a three dimensional formulation for the wave-driven flows. We compare the models with three different test applications for: (i) spectral waves approaching a plane beach with an oblique angle of incidence; (ii) monochromatic waves driving longshore currents in a laboratory basin; and (iii) monochromatic waves on a barred beach with rip channels in a laboratory basin. Results identify that the models are very similar for the depth integrated flows and qualitatively consistent for the vertically varying components. The differences are primarily the result of the vertically varying radiation stress utilized by ROMS and the utilization of long wave theory for the radiation stress formulation in vertical varying momentum balance by SHORECIRC. The quasi-3D model is faster, however the applicability of the fully 3D model allows it to extend over a broader range of processes, temporal, and spatial scales. ?? 2008 Elsevier Ltd.

  3. a Fast Method for Measuring the Similarity Between 3d Model and 3d Point Cloud

    NASA Astrophysics Data System (ADS)

    Zhang, Zongliang; Li, Jonathan; Li, Xin; Lin, Yangbin; Zhang, Shanxin; Wang, Cheng

    2016-06-01

    This paper proposes a fast method for measuring the partial Similarity between 3D Model and 3D point Cloud (SimMC). It is crucial to measure SimMC for many point cloud-related applications such as 3D object retrieval and inverse procedural modelling. In our proposed method, the surface area of model and the Distance from Model to point Cloud (DistMC) are exploited as measurements to calculate SimMC. Here, DistMC is defined as the weighted distance of the distances between points sampled from model and point cloud. Similarly, Distance from point Cloud to Model (DistCM) is defined as the average distance of the distances between points in point cloud and model. In order to reduce huge computational burdens brought by calculation of DistCM in some traditional methods, we define SimMC as the ratio of weighted surface area of model to DistMC. Compared to those traditional SimMC measuring methods that are only able to measure global similarity, our method is capable of measuring partial similarity by employing distance-weighted strategy. Moreover, our method is able to be faster than other partial similarity assessment methods. We demonstrate the superiority of our method both on synthetic data and laser scanning data.

  4. Visualization of 3D Geological Models on Google Earth

    NASA Astrophysics Data System (ADS)

    Choi, Y.; Um, J.; Park, M.

    2013-05-01

    Google Earth combines satellite imagery, aerial photography, thematic maps and various data sets to make a three-dimensional (3D) interactive image of the world. Currently, Google Earth is a popular visualization tool in a variety of fields and plays an increasingly important role not only for private users in daily life, but also for scientists, practitioners, policymakers and stakeholders in research and application. In this study, a method to visualize 3D geological models on Google Earth is presented. COLLAborative Design Activity (COLLADA, an open standard XML schema for establishing interactive 3D applications) was used to represent different 3D geological models such as borehole, fence section, surface-based 3D volume and 3D grid by triangle meshes (a set of triangles connected by their common edges or corners). In addition, we designed Keyhole Markup Language (KML, the XML-based scripting language of Google Earth) codes to import the COLLADA files into the 3D render window of Google Earth. The method was applied to the Grosmont formation in Alberta, Canada. The application showed that the combination of COLLADA and KML enables Google Earth to effectively visualize 3D geological structures and properties.; Visualization of the (a) boreholes, (b) fence sections, (c) 3D volume model and (d) 3D grid model of Grossmont formation on Google Earth

  5. A 3D Geometry Model Search Engine to Support Learning

    ERIC Educational Resources Information Center

    Tam, Gary K. L.; Lau, Rynson W. H.; Zhao, Jianmin

    2009-01-01

    Due to the popularity of 3D graphics in animation and games, usage of 3D geometry deformable models increases dramatically. Despite their growing importance, these models are difficult and time consuming to build. A distance learning system for the construction of these models could greatly facilitate students to learn and practice at different…

  6. [Potentials of 3D-modeling in reconstructive orbital surgery].

    PubMed

    Butsan, S B; Khokhlachev, S B; Ĭigitaliev, Sh N; Zaiakin, Ia A

    2012-01-01

    A technique of bone reconstructive surgery of orbitofrontonasomalar region using 3D-modeling based on multispiral computer tomography data is presented. The efficacy of intraoperative templates created using 3D-modeling was showed for harvesting and modeling of bone calvarial autografts. The steps of reconstructive procedure are explained in details for repair of medial and inferior orbital fractures.

  7. Predicted 3D Model of the Rabies Virus Glycoprotein Trimer.

    PubMed

    Fernando, Bastida-González; Yersin, Celaya-Trejo; José, Correa-Basurto; Paola, Zárate-Segura

    2016-01-01

    The RABVG ectodomain is a homotrimer, and trimers are often called spikes. They are responsible for the attachment of the virus through the interaction with nicotinic acetylcholine receptors, neural cell adhesion molecule (NCAM), and the p75 neurotrophin receptor (p75NTR). This makes them relevant in viral pathogenesis. The antigenic structure differs significantly between the trimers and monomers. Surfaces rich in hydrophobic amino acids are important for trimer stabilization in which the C-terminal of the ectodomain plays an important role; to understand these interactions between the G proteins, a mechanistic study of their functions was performed with a molecular model of G protein in its trimeric form. This verified its 3D conformation. The molecular modeling of G protein was performed by a I-TASSER server and was evaluated via a Rachamandran plot and ERRAT program obtained 84.64% and 89.9% of the residues in the favorable regions and overall quality factor, respectively. The molecular dynamics simulations were carried out on RABVG trimer at 310 K. From these theoretical studies, we retrieved the RMSD values from Cα atoms to assess stability. Preliminary model of G protein of rabies virus stable at 12 ns with molecular dynamics was obtained.

  8. Predicted 3D Model of the Rabies Virus Glycoprotein Trimer

    PubMed Central

    Fernando, Bastida-González; Yersin, Celaya-Trejo; José, Correa-Basurto; Paola, Zárate-Segura

    2016-01-01

    The RABVG ectodomain is a homotrimer, and trimers are often called spikes. They are responsible for the attachment of the virus through the interaction with nicotinic acetylcholine receptors, neural cell adhesion molecule (NCAM), and the p75 neurotrophin receptor (p75NTR). This makes them relevant in viral pathogenesis. The antigenic structure differs significantly between the trimers and monomers. Surfaces rich in hydrophobic amino acids are important for trimer stabilization in which the C-terminal of the ectodomain plays an important role; to understand these interactions between the G proteins, a mechanistic study of their functions was performed with a molecular model of G protein in its trimeric form. This verified its 3D conformation. The molecular modeling of G protein was performed by a I-TASSER server and was evaluated via a Rachamandran plot and ERRAT program obtained 84.64% and 89.9% of the residues in the favorable regions and overall quality factor, respectively. The molecular dynamics simulations were carried out on RABVG trimer at 310 K. From these theoretical studies, we retrieved the RMSD values from Cα atoms to assess stability. Preliminary model of G protein of rabies virus stable at 12 ns with molecular dynamics was obtained. PMID:27294109

  9. Computational modeling of RNA 3D structures and interactions.

    PubMed

    Dawson, Wayne K; Bujnicki, Janusz M

    2016-04-01

    RNA molecules have key functions in cellular processes beyond being carriers of protein-coding information. These functions are often dependent on the ability to form complex three-dimensional (3D) structures. However, experimental determination of RNA 3D structures is difficult, which has prompted the development of computational methods for structure prediction from sequence. Recent progress in 3D structure modeling of RNA and emerging approaches for predicting RNA interactions with ions, ligands and proteins have been stimulated by successes in protein 3D structure modeling.

  10. San Francisco Bay test case for 3-D model verification

    USGS Publications Warehouse

    Smith, Peter E.

    1994-01-01

    This paper describes a field test case for 3-D hydrodynamic model verification using data from Carquinez Strait in San Francisco Bay, California. It will be disseminated by the ASCE Computational Hydraulics task committee on 3-D Free-Surface Hydrodynamic Model Verifications during late 1994.

  11. An Automatic Registration Algorithm for 3D Maxillofacial Model

    NASA Astrophysics Data System (ADS)

    Qiu, Luwen; Zhou, Zhongwei; Guo, Jixiang; Lv, Jiancheng

    2016-09-01

    3D image registration aims at aligning two 3D data sets in a common coordinate system, which has been widely used in computer vision, pattern recognition and computer assisted surgery. One challenging problem in 3D registration is that point-wise correspondences between two point sets are often unknown apriori. In this work, we develop an automatic algorithm for 3D maxillofacial models registration including facial surface model and skull model. Our proposed registration algorithm can achieve a good alignment result between partial and whole maxillofacial model in spite of ambiguous matching, which has a potential application in the oral and maxillofacial reparative and reconstructive surgery. The proposed algorithm includes three steps: (1) 3D-SIFT features extraction and FPFH descriptors construction; (2) feature matching using SAC-IA; (3) coarse rigid alignment and refinement by ICP. Experiments on facial surfaces and mandible skull models demonstrate the efficiency and robustness of our algorithm.

  12. Interactive mapping on 3-D terrain models

    NASA Astrophysics Data System (ADS)

    Bernardin, T.; Cowgill, E.; Gold, R.; Hamann, B.; Kreylos, O.; Schmitt, A.

    2006-10-01

    We present an interactive, real-time mapping system for use with digital elevation models and remotely sensed multispectral imagery that aids geoscientists in the creation and interpretation of geologic/neotectonic maps at length scales of 10 m to 1000 km. Our system provides a terrain visualization of the surface of the Earth or other terrestrial planets by displaying a virtual terrain model generated from a digital elevation model overlain by a color texture generated from orthophotos or satellite imagery. We use a quadtree-based, multiresolution display method to render in real time high-resolution virtual terrain models that span large spatial regions. The system allows users to measure the orientations of geologic surfaces and record their observations by drawing lines directly on the virtual terrain model. In addition, interpretive surfaces can be generated from these drawings and displayed to facilitate understanding of the three-dimensional geometry of geologic surfaces. The main strength of our system is the combination of real-time rendering and interactive mapping performed directly on the virtual terrain model with the ability to navigate the scene while changing viewpoints arbitrarily during mapping. User studies and comparisons with commercially available mapping software show that our system improves mapping accuracy and efficiency and also yields observations that cannot be made with existing systems.

  13. 3-D model-based Bayesian classification

    SciTech Connect

    Soenneland, L.; Tenneboe, P.; Gehrmann, T.; Yrke, O.

    1994-12-31

    The challenging task of the interpreter is to integrate different pieces of information and combine them into an earth model. The sophistication level of this earth model might vary from the simplest geometrical description to the most complex set of reservoir parameters related to the geometrical description. Obviously the sophistication level also depend on the completeness of the available information. The authors describe the interpreter`s task as a mapping between the observation space and the model space. The information available to the interpreter exists in observation space and the task is to infer a model in model-space. It is well-known that this inversion problem is non-unique. Therefore any attempt to find a solution depend son constraints being added in some manner. The solution will obviously depend on which constraints are introduced and it would be desirable to allow the interpreter to modify the constraints in a problem-dependent manner. They will present a probabilistic framework that gives the interpreter the tools to integrate the different types of information and produce constrained solutions. The constraints can be adapted to the problem at hand.

  14. Extending 3D city models with legal information

    NASA Astrophysics Data System (ADS)

    Frank, A. U.; Fuhrmann, T.; Navratil, G.

    2012-10-01

    3D city models represent existing physical objects and their topological and functional relations. In everyday life the rights and responsibilities connected to these objects, primarily legally defined rights and obligations but also other socially and culturally established rights, are of importance. The rights and obligations are defined in various laws and it is often difficult to identify the rules applicable for a certain case. The existing 2D cadastres show civil law rights and obligations and plans to extend them to provide information about public law restrictions for land use are in several countries under way. It is tempting to design extensions to the 3D city models to provide information about legal rights in 3D. The paper analyses the different types of information that are needed to reduce conflicts and to facilitate decisions about land use. We identify the role 3D city models augmented with planning information in 3D can play, but do not advocate a general conversion from 2D to 3D for the legal cadastre. Space is not anisotropic and the up/down dimension is practically very different from the two dimensional plane - this difference must be respected when designing spatial information systems. The conclusions are: (1) continue the current regime for ownership of apartments, which is not ownership of a 3D volume, but co-ownership of a building with exclusive use of some rooms; such exclusive use rights could be shown in a 3D city model; (2) ownership of 3D volumes for complex and unusual building situations can be reported in a 3D city model, but are not required everywhere; (3) indicate restrictions for land use and building in 3D city models, with links to the legal sources.

  15. Opportunity Landing Spot Panorama (3-D Model)

    NASA Technical Reports Server (NTRS)

    2004-01-01

    The rocky outcrop traversed by the Mars Exploration Rover Opportunity is visible in this three-dimensional model of the rover's landing site. Opportunity has acquired close-up images along the way, and scientists are using the rover's instruments to closely examine portions of interest. The white fragments that look crumpled near the center of the image are portions of the airbags. Distant scenery is displayed on a spherical backdrop or 'billboard' for context. Artifacts near the top rim of the crater are a result of the transition between the three-dimensional model and the billboard. Portions of the terrain model lacking sufficient data appear as blank spaces or gaps, colored reddish-brown for better viewing. This image was generated using special software from NASA's Ames Research Center and a mosaic of images taken by the rover's panoramic camera.

    [figure removed for brevity, see original site] Click on image for larger view

    The rocky outcrop traversed by the Mars Exploration Rover Opportunity is visible in this zoomed-in portion of a three-dimensional model of the rover's landing site. Opportunity has acquired close-up images along the way, and scientists are using the rover's instruments to closely examine portions of interest. The white fragments that look crumpled near the center of the image are portions of the airbags. Distant scenery is displayed on a spherical backdrop or 'billboard' for context. Artifacts near the top rim of the crater are a result of the transition between the three-dimensional model and the billboard. Portions of the terrain model lacking sufficient data appear as blank spaces or gaps, colored reddish-brown for better viewing. This image was generated using special software from NASA's Ames Research Center and a mosaic of images taken by the rover's panoramic camera.

  16. Venusian Applications of 3D Convection Modeling

    NASA Technical Reports Server (NTRS)

    Bonaccorso, Timary Annie

    2011-01-01

    This study models mantle convection on Venus using the 'cubed sphere' code OEDIPUS, which models one-sixth of the planet in spherical geometry. We are attempting to balance internal heating, bottom mantle viscosity, and temperature difference across Venus' mantle, in order to create a realistic model that matches with current planetary observations. We also have begun to run both lower and upper mantle simulations to determine whether layered (as opposed to whole-mantle) convection might produce more efficient heat transfer, as well as to model coronae formation in the upper mantle. Upper mantle simulations are completed using OEDIPUS' Cartesian counterpart, JOCASTA. This summer's central question has been how to define a mantle plume. Traditionally, we have defined a hot plume the region with temperature at or above 40% of the difference between the maximum and horizontally averaged temperature, and a cold plume as the region with 40% of the difference between the minimum and average temperature. For less viscous cases (1020 Pa?s), the plumes generated by that definition lacked vigor, displaying buoyancies 1/100th of those found in previous, higher viscosity simulations (1021 Pa?s). As the mantle plumes with large buoyancy flux are most likely to produce topographic uplift and volcanism, the low viscosity cases' plumes may not produce observable deformation. In an effort to eliminate the smallest plumes, we experimented with different lower bound parameters and temperature percentages.

  17. RELAP5-3D Compressor Model

    SciTech Connect

    James E. Fisher; Cliff B. Davis; Walter L. Weaver

    2005-06-01

    A compressor model has been implemented in the RELAP5-3D© code. The model is similar to that of the existing pump model, and performs the same function on a gas as the pump performs on a single-phase or two-phase fluid. The compressor component consists of an inlet junction and a control volume, and optionally, an outlet junction. This feature permits cascading compressor components in series. The equations describing the physics of the compressor are derived from first principles. These equations are used to obtain the head, the torque, and the energy dissipation. Compressor performance is specified using a map, specific to the design of the machine, in terms of the ratio of outlet-to-inlet total (or stagnation) pressure and adiabatic efficiency as functions of rotational velocity and flow rate. The input quantities are specified in terms of dimensionless variables, which are corrected to stagnation density and stagnation sound speed. A small correction was formulated for the input of efficiency to account for the error introduced by assumption of constant density when integrating the momentum equation. Comparison of the results of steady-state operation of the compressor model to those of the MIT design calculation showed excellent agreement for both pressure ratio and power.

  18. Global Magnetospheric Modeling of 3D Reconnection

    NASA Technical Reports Server (NTRS)

    Spicer, Daniel S.

    1999-01-01

    A review of approaches to the global modeling of the terrestrial magnetosphere, how these approaches are utilized to interpret satellite data, and how these approaches have been successful at predicting magnetospheric phenomena will be presented. In addition, the importance of the ionospheric boundary and its effect on the globally topology of the magnetospheric magnetic field will be reviewed. In particular, numerical results that are rapidly changing our view of magnetospheric reconnection within the magnetospheric magnetic field will be discussed.

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

    NASA Astrophysics Data System (ADS)

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

    2013-10-01

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

  20. Modeling 3D facial shape from DNA.

    PubMed

    Claes, Peter; Liberton, Denise K; Daniels, Katleen; Rosana, Kerri Matthes; Quillen, Ellen E; Pearson, Laurel N; McEvoy, Brian; Bauchet, Marc; Zaidi, Arslan A; Yao, Wei; Tang, Hua; Barsh, Gregory S; Absher, Devin M; Puts, David A; Rocha, Jorge; Beleza, Sandra; Pereira, Rinaldo W; Baynam, Gareth; Suetens, Paul; Vandermeulen, Dirk; Wagner, Jennifer K; Boster, James S; Shriver, Mark D

    2014-03-01

    Human facial diversity is substantial, complex, and largely scientifically unexplained. We used spatially dense quasi-landmarks to measure face shape in population samples with mixed West African and European ancestry from three locations (United States, Brazil, and Cape Verde). Using bootstrapped response-based imputation modeling (BRIM), we uncover the relationships between facial variation and the effects of sex, genomic ancestry, and a subset of craniofacial candidate genes. The facial effects of these variables are summarized as response-based imputed predictor (RIP) variables, which are validated using self-reported sex, genomic ancestry, and observer-based facial ratings (femininity and proportional ancestry) and judgments (sex and population group). By jointly modeling sex, genomic ancestry, and genotype, the independent effects of particular alleles on facial features can be uncovered. Results on a set of 20 genes showing significant effects on facial features provide support for this approach as a novel means to identify genes affecting normal-range facial features and for approximating the appearance of a face from genetic markers.

  1. Modeling 3D Facial Shape from DNA

    PubMed Central

    Claes, Peter; Liberton, Denise K.; Daniels, Katleen; Rosana, Kerri Matthes; Quillen, Ellen E.; Pearson, Laurel N.; McEvoy, Brian; Bauchet, Marc; Zaidi, Arslan A.; Yao, Wei; Tang, Hua; Barsh, Gregory S.; Absher, Devin M.; Puts, David A.; Rocha, Jorge; Beleza, Sandra; Pereira, Rinaldo W.; Baynam, Gareth; Suetens, Paul; Vandermeulen, Dirk; Wagner, Jennifer K.; Boster, James S.; Shriver, Mark D.

    2014-01-01

    Human facial diversity is substantial, complex, and largely scientifically unexplained. We used spatially dense quasi-landmarks to measure face shape in population samples with mixed West African and European ancestry from three locations (United States, Brazil, and Cape Verde). Using bootstrapped response-based imputation modeling (BRIM), we uncover the relationships between facial variation and the effects of sex, genomic ancestry, and a subset of craniofacial candidate genes. The facial effects of these variables are summarized as response-based imputed predictor (RIP) variables, which are validated using self-reported sex, genomic ancestry, and observer-based facial ratings (femininity and proportional ancestry) and judgments (sex and population group). By jointly modeling sex, genomic ancestry, and genotype, the independent effects of particular alleles on facial features can be uncovered. Results on a set of 20 genes showing significant effects on facial features provide support for this approach as a novel means to identify genes affecting normal-range facial features and for approximating the appearance of a face from genetic markers. PMID:24651127

  2. Modelling Polymer Deformation during 3D Printing

    NASA Astrophysics Data System (ADS)

    McIlroy, Claire; Olmsted, Peter

    Three-dimensional printing has the potential to transform manufacturing processes, yet improving the strength of printed parts, to equal that of traditionally-manufactured parts, remains an underlying issue. The fused deposition modelling technique involves melting a thermoplastic, followed by layer-by-layer extrusion to fabricate an object. The key to ensuring strength at the weld between layers is successful inter-diffusion. However, prior to welding, both the extrusion process and the cooling temperature profile can significantly deform the polymer micro-structure and, consequently, how well the polymers are able to ``re-entangle'' across the weld. In particular, polymer alignment in the flow can cause de-bonding of the layers and create defects. We have developed a simple model of the non-isothermal extrusion process to explore the effects that typical printing conditions and material rheology have on the conformation of a polymer melt. In particular, we incorporate both stretch and orientation using the Rolie-Poly constitutive equation to examine the melt structure as it flows through the nozzle, the subsequent alignment with the build plate and the resulting deformation due to the fixed nozzle height, which is typically less than the nozzle radius.

  3. Exploring 3D structure of human gonadotropin hormone receptor at antagonist state using homology modeling, molecular dynamic simulation, and cross-docking studies.

    PubMed

    Sakhteman, Amirhossein; Khoddami, Minasadat; Negahdaripour, Manica; Mehdizadeh, Arash; Tatar, Mohsen; Ghasemi, Younes

    2016-09-01

    Human gonadotropin hormone receptor, a G-protein coupled receptor, is the target of many medications used in fertility disorders. Obtaining more structural information about the receptor could be useful in many studies related to drug design. In this study, the structure of human gonadotropin receptor was subjected to homology modeling studies and molecular dynamic simulation within a DPPC lipid bilayer for 100 ns. Several frames were thereafter extracted from simulation trajectories representing the receptor at different states. In order to find a proper model of the receptor at the antagonist state, all frames were subjected to cross-docking studies of some antagonists with known experimental values (Ki). Frame 194 revealed a reasonable correlation between docking calculated energy scores and experimental activity values (|r| = 0.91). The obtained correlation was validated by means of SSLR and showed the presence of no chance correlation for the obtained model. Different structural features reported for the receptor, such as two disulfide bridges and ionic lock between GLU90 and LYS 121 were also investigated in the final model.

  4. Image based 3D city modeling : Comparative study

    NASA Astrophysics Data System (ADS)

    Singh, S. P.; Jain, K.; Mandla, V. R.

    2014-06-01

    3D city model is a digital representation of the Earth's surface and it's related objects such as building, tree, vegetation, and some manmade feature belonging to urban area. The demand of 3D city modeling is increasing rapidly for various engineering and non-engineering applications. Generally four main image based approaches were used for virtual 3D city models generation. In first approach, researchers were used Sketch based modeling, second method is Procedural grammar based modeling, third approach is Close range photogrammetry based modeling and fourth approach is mainly based on Computer Vision techniques. SketchUp, CityEngine, Photomodeler and Agisoft Photoscan are the main softwares to represent these approaches respectively. These softwares have different approaches & methods suitable for image based 3D city modeling. Literature study shows that till date, there is no complete such type of comparative study available to create complete 3D city model by using images. This paper gives a comparative assessment of these four image based 3D modeling approaches. This comparative study is mainly based on data acquisition methods, data processing techniques and output 3D model products. For this research work, study area is the campus of civil engineering department, Indian Institute of Technology, Roorkee (India). This 3D campus acts as a prototype for city. This study also explains various governing parameters, factors and work experiences. This research work also gives a brief introduction, strengths and weakness of these four image based techniques. Some personal comment is also given as what can do or what can't do from these softwares. At the last, this study shows; it concluded that, each and every software has some advantages and limitations. Choice of software depends on user requirements of 3D project. For normal visualization project, SketchUp software is a good option. For 3D documentation record, Photomodeler gives good result. For Large city

  5. NoSQL Based 3D City Model Management System

    NASA Astrophysics Data System (ADS)

    Mao, B.; Harrie, L.; Cao, J.; Wu, Z.; Shen, J.

    2014-04-01

    To manage increasingly complicated 3D city models, a framework based on NoSQL database is proposed in this paper. The framework supports import and export of 3D city model according to international standards such as CityGML, KML/COLLADA and X3D. We also suggest and implement 3D model analysis and visualization in the framework. For city model analysis, 3D geometry data and semantic information (such as name, height, area, price and so on) are stored and processed separately. We use a Map-Reduce method to deal with the 3D geometry data since it is more complex, while the semantic analysis is mainly based on database query operation. For visualization, a multiple 3D city representation structure CityTree is implemented within the framework to support dynamic LODs based on user viewpoint. Also, the proposed framework is easily extensible and supports geoindexes to speed up the querying. Our experimental results show that the proposed 3D city management system can efficiently fulfil the analysis and visualization requirements.

  6. Modeling cell migration in 3D: Status and challenges.

    PubMed

    Rangarajan, Rajagopal; Zaman, Muhammad H

    2008-01-01

    Cell migration is a multi-scale process that integrates signaling, mechanics and biochemical reaction kinetics. Various mathematical models accurately predict cell migration on 2D surfaces, but are unable to capture the complexities of 3D migration. Additionally, quantitative 3D cell migration models have been few and far between. In this review we look and characterize various mathematical models available in literature to predict cell migration in 3D matrices and analyze their strengths and possible changes to these models that could improve their predictive capabilities.

  7. 3D PIC Modeling of Microcavity Discharge

    NASA Astrophysics Data System (ADS)

    Hopkins, Matthew; Manginell, Ronald; Moore, Christopher; Yee, Benjamin; Moorman, Matthew

    2015-09-01

    We present a number of techniques and challenges in simulating the transient behavior of a microcavity discharge. Our microcavities are typically cylindrical with diameters approximately 50 - 100 μm, heights of 50 - 200 μm, pressure near atmospheric, and operate at a few hundred volts. We employ a fully kinetic simulation methodology, the Particle-in-Cell (PIC) method, with interparticle collisions handled via methods based on direct simulation Monte Carlo (DSMC). In particular, we explicitly include kinetic electrons. Some of the challenges we encounter include variations in number densities, external circuit coupling, and time step resolution constraints. By employing dynamic particle weighting (particle weights vary over time by species and location) we can mitigate some of the challenges modeling systems with 107 variations in number densities. Smoothing mechanisms have been used to attempt to mitigate external circuit response. We perform our simulations on hundreds or thousands of processing cores to accommodate the computational work inherent in using relatively small time step sizes (e.g., 50 fs for a 100 ns calculation). In addition, particle weighting issues inherent to three-dimensional low temperature plasma systems will be mentioned. Sandia National Laboratories is a multi-program laboratory managed and operated by Sandia Corporation, a wholly owned subsidiary of Lockheed Martin Corporation, for the U.S. Department of Energy's NNSA under Contract DE-AC04-94AL85000.

  8. Kongsfjorden-MIKE 3D model

    NASA Astrophysics Data System (ADS)

    Przyborska, Anna; Kosecki, Szymon; Jakacki, Jaromir

    2014-05-01

    Kongsfjorden is a West Svalbard fjord with a surface area of about 210 km2. It is obvious that the depths of the outer and central basins are influenced by the open sea, under influence of West Spitsbergen Current (WSC), which curry out warm Atlantic water and cold East Spitsbergen Current, while the shallower, inner basin has a large glacial outflow and its maximum depths do not exceed 100 m. Freshwater stored in Spitsbergen glaciers have strong influence on local hydrology and physical fjord conditions. Both, local and shelf conditions have impact on state of the fjord. External forces like tides, velocities at the boundary and atmospheric forces together with sources of cold and dens fresh water in the fjords will give reliable representation of physical conditions in Kongsfjorden. Modeling could help to solve this problem and we have hope that we find answer which one is the most important for local conditions in fjord. Calculations of balances between cold fresh water and warm and salt will provide additional information that could help to answer the main question of the GAME (Growing of the Arctic Marine Ecosystem) project - what is the reaction of physically controlled Arctic marine ecosystem to temperature rise.

  9. 3D model retrieval method based on mesh segmentation

    NASA Astrophysics Data System (ADS)

    Gan, Yuanchao; Tang, Yan; Zhang, Qingchen

    2012-04-01

    In the process of feature description and extraction, current 3D model retrieval algorithms focus on the global features of 3D models but ignore the combination of global and local features of the model. For this reason, they show less effective performance to the models with similar global shape and different local shape. This paper proposes a novel algorithm for 3D model retrieval based on mesh segmentation. The key idea is to exact the structure feature and the local shape feature of 3D models, and then to compares the similarities of the two characteristics and the total similarity between the models. A system that realizes this approach was built and tested on a database of 200 objects and achieves expected results. The results show that the proposed algorithm improves the precision and the recall rate effectively.

  10. High Resolution 3d Modeling of the Behaim Globe

    NASA Astrophysics Data System (ADS)

    Menna, F.; Rizzi, A.; Nocerino, E.; Remondino, F.; Gruen, A.

    2012-07-01

    The article describes the 3D surveying and modeling of the Behaim globe, the oldest still existing and intact globe of the earth, preserved at the German National Museum of Nuremberg, Germany. The work is primarily performed using high-resolution digital images and automatic photogrammetric techniques. Triangulation-based laser scanning is also employed to fill some gaps in the derived image-based 3D geometry and perform geometric comparisons. Major problems are encountered in texture mapping. The 3D modeling project and the creation of high-resolution map-projections is performed for scientific, conservation, visualization and education purposes.

  11. 3D-model building of the jaw impression

    NASA Astrophysics Data System (ADS)

    Ahmed, Moumen T.; Yamany, Sameh M.; Hemayed, Elsayed E.; Farag, Aly A.

    1997-03-01

    A novel approach is proposed to obtain a record of the patient's occlusion using computer vision. Data acquisition is obtained using intra-oral video cameras. The technique utilizes shape from shading to extract 3D information from 2D views of the jaw, and a novel technique for 3D data registration using genetic algorithms. The resulting 3D model can be used for diagnosis, treatment planning, and implant purposes. The overall purpose of this research is to develop a model-based vision system for orthodontics to replace traditional approaches. This system will be flexible, accurate, and will reduce the cost of orthodontic treatments.

  12. Molecular modeling studies of 4,5-dihydro-1H-pyrazolo[4,3-h] quinazoline derivatives as potent CDK2/Cyclin a inhibitors using 3D-QSAR and docking.

    PubMed

    Ai, Yong; Wang, Shao-Teng; Sun, Ping-Hua; Song, Fa-Jun

    2010-09-28

    CDK2/cyclin A has appeared as an attractive drug targets over the years with diverse therapeutic potentials. A computational strategy based on comparative molecular fields analysis (CoMFA) and comparative molecular similarity indices analysis (CoMSIA) followed by molecular docking studies were performed on a series of 4,5-dihydro-1H-pyrazolo[4,3-h]quinazoline derivatives as potent CDK2/cyclin A inhibitors. The CoMFA and CoMSIA models, using 38 molecules in the training set, gave r(2) (cv) values of 0.747 and 0.518 and r(2) values of 0.970 and 0.934, respectively. 3D contour maps generated by the CoMFA and CoMSIA models were used to identify the key structural requirements responsible for the biological activity. Molecular docking was applied to explore the binding mode between the ligands and the receptor. The information obtained from molecular modeling studies may be helpful to design novel inhibitors of CDK2/cyclin A with desired activity.

  13. Summary on several key techniques in 3D geological modeling.

    PubMed

    Mei, Gang

    2014-01-01

    Several key techniques in 3D geological modeling including planar mesh generation, spatial interpolation, and surface intersection are summarized in this paper. Note that these techniques are generic and widely used in various applications but play a key role in 3D geological modeling. There are two essential procedures in 3D geological modeling: the first is the simulation of geological interfaces using geometric surfaces and the second is the building of geological objects by means of various geometric computations such as the intersection of surfaces. Discrete geometric surfaces that represent geological interfaces can be generated by creating planar meshes first and then spatially interpolating; those surfaces intersect and then form volumes that represent three-dimensional geological objects such as rock bodies. In this paper, the most commonly used algorithms of the key techniques in 3D geological modeling are summarized.

  14. Summary on Several Key Techniques in 3D Geological Modeling

    PubMed Central

    2014-01-01

    Several key techniques in 3D geological modeling including planar mesh generation, spatial interpolation, and surface intersection are summarized in this paper. Note that these techniques are generic and widely used in various applications but play a key role in 3D geological modeling. There are two essential procedures in 3D geological modeling: the first is the simulation of geological interfaces using geometric surfaces and the second is the building of geological objects by means of various geometric computations such as the intersection of surfaces. Discrete geometric surfaces that represent geological interfaces can be generated by creating planar meshes first and then spatially interpolating; those surfaces intersect and then form volumes that represent three-dimensional geological objects such as rock bodies. In this paper, the most commonly used algorithms of the key techniques in 3D geological modeling are summarized. PMID:24772029

  15. Formal representation of 3D structural geological models

    NASA Astrophysics Data System (ADS)

    Wang, Zhangang; Qu, Honggang; Wu, Zixing; Yang, Hongjun; Du, Qunle

    2016-05-01

    The development and widespread application of geological modeling methods has increased demands for the integration and sharing services of three dimensional (3D) geological data. However, theoretical research in the field of geological information sciences is limited despite the widespread use of Geographic Information Systems (GIS) in geology. In particular, fundamental research on the formal representations and standardized spatial descriptions of 3D structural models is required. This is necessary for accurate understanding and further applications of geological data in 3D space. In this paper, we propose a formal representation method for 3D structural models using the theory of point set topology, which produces a mathematical definition for the major types of geological objects. The spatial relationships between geologic boundaries, structures, and units are explained in detail using the 9-intersection model. Reasonable conditions for describing the topological space of 3D structural models are also provided. The results from this study can be used as potential support for the standardized representation and spatial quality evaluation of 3D structural models, as well as for specific needs related to model-based management, query, and analysis.

  16. Vehicle Surveillance with a Generic, Adaptive, 3D Vehicle Model.

    PubMed

    Leotta, Matthew J; Mundy, Joseph L

    2011-07-01

    In automated surveillance, one is often interested in tracking road vehicles, measuring their shape in 3D world space, and determining vehicle classification. To address these tasks simultaneously, an effective approach is the constrained alignment of a prior model of 3D vehicle shape to images. Previous 3D vehicle models are either generic but overly simple or rigid and overly complex. Rigid models represent exactly one vehicle design, so a large collection is needed. A single generic model can deform to a wide variety of shapes, but those shapes have been far too primitive. This paper uses a generic 3D vehicle model that deforms to match a wide variety of passenger vehicles. It is adjustable in complexity between the two extremes. The model is aligned to images by predicting and matching image intensity edges. Novel algorithms are presented for fitting models to multiple still images and simultaneous tracking while estimating shape in video. Experiments compare the proposed model to simple generic models in accuracy and reliability of 3D shape recovery from images and tracking in video. Standard techniques for classification are also used to compare the models. The proposed model outperforms the existing simple models at each task.

  17. 3D Modeling from Photos Given Topological Information.

    PubMed

    Kim, Young Min; Cho, Junghyun; Ahn, Sang Chul

    2016-09-01

    Reconstructing 3D models given a single-view 2D information is inherently an ill-posed problem and requires additional information such as shape prior or user input.We introduce a method to generate multiple 3D models of a particular category given corresponding photographs when the topological information is known. While there is a wide range of shapes for an object of a particular category, the basic topology usually remains constant.In consequence, the topological prior needs to be provided only once for each category and can be easily acquired by consulting an existing database of 3D models or by user input. The input of topological description is only connectivity information between parts; this is in contrast to previous approaches that have required users to interactively mark individual parts. Given the silhouette of an object and the topology, our system automatically finds a skeleton and generates a textured 3D model by jointly fitting multiple parts. The proposed method, therefore, opens the possibility of generating a large number of 3D models by consulting a massive number of photographs. We demonstrate examples of the topological prior and reconstructed 3D models using photos.

  18. Molecular tectonics: 3-D organisation of decanuclear silver nanoclusters.

    PubMed

    Kozlova, Marina N; Ferlay, Sylvie; Kyritsakas, Nathalie; Hosseini, Mir Wais; Solovieva, Svetlana E; Antipin, Igor S; Konovalov, Alexander I

    2009-05-14

    The combination of silver nitrate with a thiacalix[4]arene derivative bearing at the lower rim four benzonitrile groups leads in the crystalline phase to the formation of a 3-D coordination network in which the organic tectons are connected by decanuclear silver nanoclusters.

  19. Performance Evaluation of 3d Modeling Software for Uav Photogrammetry

    NASA Astrophysics Data System (ADS)

    Yanagi, H.; Chikatsu, H.

    2016-06-01

    UAV (Unmanned Aerial Vehicle) photogrammetry, which combines UAV and freely available internet-based 3D modeling software, is widely used as a low-cost and user-friendly photogrammetry technique in the fields such as remote sensing and geosciences. In UAV photogrammetry, only the platform used in conventional aerial photogrammetry is changed. Consequently, 3D modeling software contributes significantly to its expansion. However, the algorithms of the 3D modelling software are black box algorithms. As a result, only a few studies have been able to evaluate their accuracy using 3D coordinate check points. With this motive, Smart3DCapture and Pix4Dmapper were downloaded from the Internet and commercial software PhotoScan was also employed; investigations were performed in this paper using check points and images obtained from UAV.

  20. Mapping molecular orientational distributions for biological sample in 3D (Conference Presentation)

    NASA Astrophysics Data System (ADS)

    HE, Wei; Ferrand, Patrick; Richter, Benjamin; Bastmeyer, Martin; Brasselet, Sophie

    2016-04-01

    Measuring molecular orientation properties is very appealing for scientists in molecular and cell biology, as well as biomedical research. Orientational organization at the molecular scale is indeed an important brick to cells and tissues morphology, mechanics, functions and pathologies. Recent work has shown that polarized fluorescence imaging, based on excitation polarization tuning in the sample plane, is able to probe molecular orientational order in biological samples; however this applies only to information in 2D, projected in the sample plane. To surpass this limitation, we extended this approach to excitation polarization tuning in 3D. The principle is based on the decomposition of any arbitrary 3D linear excitation in a polarization along the longitudinal z-axis, and a polarization in the transverse xy-sample plane. We designed an interferometer with one arm generating radial polarization light (thus producing longitudinal polarization under high numerical aperture focusing), the other arm controlling a linear polarization in the transverse plane. The amplitude ratio between the two arms can vary so as to get any linear polarized excitation in 3D at the focus of a high NA objective. This technique has been characterized by polarimetry imaging at the back focal plane of the focusing objective, and modeled theoretically. 3D polarized fluorescence microscopy is demonstrated on actin stress fibers in non-flat cells suspended on synthetic polymer structures forming supporting pillars, for which heterogeneous actin orientational order could be identified. This technique shows a great potential in structural investigations in 3D biological systems, such as cell spheroids and tissues.

  1. Automatic Texture Mapping of Architectural and Archaeological 3d Models

    NASA Astrophysics Data System (ADS)

    Kersten, T. P.; Stallmann, D.

    2012-07-01

    Today, detailed, complete and exact 3D models with photo-realistic textures are increasingly demanded for numerous applications in architecture and archaeology. Manual texture mapping of 3D models by digital photographs with software packages, such as Maxon Cinema 4D, Autodesk 3Ds Max or Maya, still requires a complex and time-consuming workflow. So, procedures for automatic texture mapping of 3D models are in demand. In this paper two automatic procedures are presented. The first procedure generates 3D surface models with textures by web services, while the second procedure textures already existing 3D models with the software tmapper. The program tmapper is based on the Multi Layer 3D image (ML3DImage) algorithm and developed in the programming language C++. The studies showing that the visibility analysis using the ML3DImage algorithm is not sufficient to obtain acceptable results of automatic texture mapping. To overcome the visibility problem the Point Cloud Painter algorithm in combination with the Z-buffer-procedure will be applied in the future.

  2. Quasi-3D Algorithm in Multi-scale Modeling Framework

    NASA Astrophysics Data System (ADS)

    Jung, J.; Arakawa, A.

    2008-12-01

    As discussed in the companion paper by Arakawa and Jung, the Quasi-3D (Q3D) Multi-scale Modeling Framework (MMF) is a 4D estimation/prediction framework that combines a GCM with a 3D anelastic vector vorticity equation model (VVM) applied to a Q3D network of horizontal grid points. This paper presents an outline of the recently revised Q3D algorithm and a highlight of the results obtained by application of the algorithm to an idealized model setting. The Q3D network of grid points consists of two sets of grid-point arrays perpendicular to each other. For a scalar variable, for example, each set consists of three parallel rows of grid points. Principal and supplementary predictions are made on the central and the two adjacent rows, respectively. The supplementary prediction is to allow the principal prediction be three-dimensional at least to the second-order accuracy. To accommodate a higher-order accuracy and to make the supplementary predictions formally three-dimensional, a few rows of ghost points are added at each side of the array. Values at these ghost points are diagnostically determined by a combination of statistical estimation and extrapolation. The basic structure of the estimation algorithm is determined in view of the global stability of Q3D advection. The algorithm is calibrated using the statistics of past data at and near the intersections of the two sets of grid- point arrays. Since the CRM in the Q3D MMF extends beyond individual GCM boxes, the CRM can be a GCM by itself. However, it is better to couple the CRM with the GCM because (1) the CRM is a Q3D CRM based on a highly anisotropic network of grid points and (2) coupling with a GCM makes it more straightforward to inherit our experience with the conventional GCMs. In the coupled system we have selected, prediction of thermdynamic variables is almost entirely done by the Q3D CRM with no direct forcing by the GCM. The coupling of the dynamics between the two components is through mutual

  3. 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.

    PubMed

    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

  4. Gis-Based Smart Cartography Using 3d Modeling

    NASA Astrophysics Data System (ADS)

    Malinverni, E. S.; Tassetti, A. N.

    2013-08-01

    3D City Models have evolved to be important tools for urban decision processes and information systems, especially in planning, simulation, analysis, documentation and heritage management. On the other hand existing and in use numerical cartography is often not suitable to be used in GIS because not geometrically and topologically correctly structured. The research aim is to 3D structure and organize a numeric cartography for GIS and turn it into CityGML standardized features. The work is framed around a first phase of methodological analysis aimed to underline which existing standard (like ISO and OGC rules) can be used to improve the quality requirement of a cartographic structure. Subsequently, from this technical specifics, it has been investigated the translation in formal contents, using an owner interchange software (SketchUp), to support some guide lines implementations to generate a GIS3D structured in GML3. It has been therefore predisposed a test three-dimensional numerical cartography (scale 1:500, generated from range data captured by 3D laser scanner), tested on its quality according to the previous standard and edited when and where necessary. Cad files and shapefiles are converted into a final 3D model (Google SketchUp model) and then exported into a 3D city model (CityGML LoD1/LoD2). The GIS3D structure has been managed in a GIS environment to run further spatial analysis and energy performance estimate, not achievable in a 2D environment. In particular geometrical building parameters (footprint, volume etc.) are computed and building envelop thermal characteristics are derived from. Lastly, a simulation is carried out to deal with asbestos and home renovating charges and show how the built 3D city model can support municipal managers with risk diagnosis of the present situation and development of strategies for a sustainable redevelop.

  5. Combined registration of 3D tibia and femur implant models in 3D magnetic resonance images

    NASA Astrophysics Data System (ADS)

    Englmeier, Karl-Hans; Siebert, Markus; von Eisenhart-Rothe, Ruediger; Graichen, Heiko

    2008-03-01

    The most frequent reasons for revision of total knee arthroplasty are loosening and abnormal axial alignment leading to an unphysiological kinematic of the knee implant. To get an idea about the postoperative kinematic of the implant, it is essential to determine the position and orientation of the tibial and femoral prosthesis. Therefore we developed a registration method for fitting 3D CAD-models of knee joint prostheses into an 3D MR image. This rigid registration is the basis for a quantitative analysis of the kinematics of knee implants. Firstly the surface data of the prostheses models are converted into a voxel representation; a recursive algorithm determines all boundary voxels of the original triangular surface data. Secondly an initial preconfiguration of the implants by the user is still necessary for the following step: The user has to perform a rough preconfiguration of both remaining prostheses models, so that the fine matching process gets a reasonable starting point. After that an automated gradient-based fine matching process determines the best absolute position and orientation: This iterative process changes all 6 parameters (3 rotational- and 3 translational parameters) of a model by a minimal amount until a maximum value of the matching function is reached. To examine the spread of the final solutions of the registration, the interobserver variability was measured in a group of testers. This variability, calculated by the relative standard deviation, improved from about 50% (pure manual registration) to 0.5% (rough manual preconfiguration and subsequent fine registration with the automatic fine matching process).

  6. Implementation of virtual models from sheet metal forming simulation into physical 3D colour models using 3D printing

    NASA Astrophysics Data System (ADS)

    Junk, S.

    2016-08-01

    Today the methods of numerical simulation of sheet metal forming offer a great diversity of possibilities for optimization in product development and in process design. However, the results from simulation are only available as virtual models. Because there are any forming tools available during the early stages of product development, physical models that could serve to represent the virtual results are therefore lacking. Physical 3D-models can be created using 3D-printing and serve as an illustration and present a better understanding of the simulation results. In this way, the results from the simulation can be made more “comprehensible” within a development team. This paper presents the possibilities of 3D-colour printing with particular consideration of the requirements regarding the implementation of sheet metal forming simulation. Using concrete examples of sheet metal forming, the manufacturing of 3D colour models will be expounded upon on the basis of simulation results.

  7. Manipulating 3D-Printed and Paper Models Enhances Student Understanding of Viral Replication

    ERIC Educational Resources Information Center

    Couper, Lisa; Johannes, Kristen; Powers, Jackie; Silberglitt, Matt; Davenport, Jodi

    2016-01-01

    Understanding key concepts in molecular biology requires reasoning about molecular processes that are not directly observable and, as such, presents a challenge to students and teachers. We ask whether novel interactive physical models and activities can help students understand key processes in viral replication. Our 3D tangible models are…

  8. Categorical prototyping: incorporating molecular mechanisms into 3D printing.

    PubMed

    Brommer, Dieter B; Giesa, Tristan; Spivak, David I; Buehler, Markus J

    2016-01-15

    We apply the mathematical framework of category theory to articulate the precise relation between the structure and mechanics of a nanoscale system in a macroscopic domain. We maintain the chosen molecular mechanical properties from the nanoscale to the continuum scale. Therein we demonstrate a procedure to 'protoype a model', as category theory enables us to maintain certain information across disparate fields of study, distinct scales, or physical realizations. This process fits naturally with prototyping, as a prototype is not a complete product but rather a reduction to test a subset of properties. To illustrate this point, we use large-scale multi-material printing to examine the scaling of the elastic modulus of 2D carbon allotropes at the macroscale and validate our printed model using experimental testing. The resulting hand-held materials can be examined more readily, and yield insights beyond those available in the original digital representations. We demonstrate this concept by twisting the material, a test beyond the scope of the original model. The method developed can be extended to other methods of additive manufacturing.

  9. 3D Bioprinting of Tissue/Organ Models.

    PubMed

    Pati, Falguni; Gantelius, Jesper; Svahn, Helene Andersson

    2016-04-04

    In vitro tissue/organ models are useful platforms that can facilitate systematic, repetitive, and quantitative investigations of drugs/chemicals. The primary objective when developing tissue/organ models is to reproduce physiologically relevant functions that typically require complex culture systems. Bioprinting offers exciting prospects for constructing 3D tissue/organ models, as it enables the reproducible, automated production of complex living tissues. Bioprinted tissues/organs may prove useful for screening novel compounds or predicting toxicity, as the spatial and chemical complexity inherent to native tissues/organs can be recreated. In this Review, we highlight the importance of developing 3D in vitro tissue/organ models by 3D bioprinting techniques, characterization of these models for evaluating their resemblance to native tissue, and their application in the prioritization of lead candidates, toxicity testing, and as disease/tumor models.

  10. 3D WHOLE-PROMINENCE FINE STRUCTURE MODELING

    SciTech Connect

    Gunár, Stanislav; Mackay, Duncan H.

    2015-04-20

    We present the first 3D whole-prominence fine structure model. The model combines a 3D magnetic field configuration of an entire prominence obtained from nonlinear force-free field simulations, with a detailed description of the prominence plasma. The plasma is located in magnetic dips in hydrostatic equilibrium and is distributed along multiple fine structures within the 3D magnetic model. Through the use of a novel radiative transfer visualization technique for the Hα line such plasma-loaded magnetic field model produces synthetic images of the modeled prominence comparable with high-resolution observations. This allows us for the first time to use a single technique to consistently study, in both emission on the limb and absorption against the solar disk, the fine structures of prominences/filaments produced by a magnetic field model.

  11. 3D web visualization of huge CityGML models

    NASA Astrophysics Data System (ADS)

    Prandi, F.; Devigili, F.; Soave, M.; Di Staso, U.; De Amicis, R.

    2015-08-01

    Nowadays, rapid technological development into acquiring geo-spatial information; joined to the capabilities to process these data in a relative short period of time, allows the generation of detailed 3D textured city models that will become an essential part of the modern city information infrastructure (Spatial Data Infrastructure) and, can be used to integrate various data from different sources for public accessible visualisation and many other applications. One of the main bottlenecks, which at the moment limit the use of these datasets to few experts, is a lack on efficient visualization systems through the web and interoperable frameworks that allow standardising the access to the city models. The work presented in this paper tries to satisfy these two requirements developing a 3D web-based visualization system based on OGC standards and effective visualization concepts. The architectural framework, based on Services Oriented Architecture (SOA) concepts, provides the 3D city data to a web client designed to support the view process in a very effective way. The first part of the work is to design a framework compliant to the 3D Portrayal Service drafted by the of the Open Geospatial Consortium (OGC) 3D standardization working group. The latter is related to the development of an effective web client able to render in an efficient way the 3D city models.

  12. 3D microstructure modeling of compressed fiber-based materials

    NASA Astrophysics Data System (ADS)

    Gaiselmann, Gerd; Tötzke, Christian; Manke, Ingo; Lehnert, Werner; Schmidt, Volker

    2014-07-01

    A novel parametrized model that describes the 3D microstructure of compressed fiber-based materials is introduced. It allows to virtually generate the microstructure of realistically compressed gas-diffusion layers (GDL). Given the input of a 3D microstructure of some fiber-based material, the model compresses the system of fibers in a uniaxial direction for arbitrary compression rates. The basic idea is to translate the fibers in the direction of compression according to a vector field which depends on the rate of compression and on the locations of fibers within the material. In order to apply the model to experimental 3D image data of fiber-based materials given for several compression states, an optimal vector field is estimated by simulated annealing. The model is applied to 3D image data of non-woven GDL in PEMFC gained by synchrotron tomography for different compression rates. The compression model is validated by comparing structural characteristics computed for experimentally compressed and virtually compressed microstructures, where two kinds of compression - using a flat stamp and a stamp with a flow-field profile - are applied. For both stamps types, a good agreement is found. Furthermore, the compression model is combined with a stochastic 3D microstructure model for uncompressed fiber-based materials. This allows to efficiently generate compressed fiber-based microstructures in arbitrary volumes.

  13. Perception-based shape retrieval for 3D building models

    NASA Astrophysics Data System (ADS)

    Zhang, Man; Zhang, Liqiang; Takis Mathiopoulos, P.; Ding, Yusi; Wang, Hao

    2013-01-01

    With the help of 3D search engines, a large number of 3D building models can be retrieved freely online. A serious disadvantage of most rotation-insensitive shape descriptors is their inability to distinguish between two 3D building models which are different at their main axes, but appear similar when one of them is rotated. To resolve this problem, we present a novel upright-based normalization method which not only correctly rotates such building models, but also greatly simplifies and accelerates the abstraction and the matching of building models' shape descriptors. Moreover, the abundance of architectural styles significantly hinders the effective shape retrieval of building models. Our research has shown that buildings with different designs are not well distinguished by the widely recognized shape descriptors for general 3D models. Motivated by this observation and to further improve the shape retrieval quality, a new building matching method is introduced and analyzed based on concepts found in the field of perception theory and the well-known Light Field descriptor. The resulting normalized building models are first classified using the qualitative shape descriptors of Shell and Unevenness which outline integral geometrical and topological information. These models are then put in on orderly fashion with the help of an improved quantitative shape descriptor which we will term as Horizontal Light Field Descriptor, since it assembles detailed shape characteristics. To accurately evaluate the proposed methodology, an enlarged building shape database which extends previous well-known shape benchmarks was implemented as well as a model retrieval system supporting inputs from 2D sketches and 3D models. Various experimental performance evaluation results have shown that, as compared to previous methods, retrievals employing the proposed matching methodology are faster and more consistent with human recognition of spatial objects. In addition these performance

  14. Shape: A 3D Modeling Tool for Astrophysics.

    PubMed

    Steffen, Wolfgang; Koning, Nicholas; Wenger, Stephan; Morisset, Christophe; Magnor, Marcus

    2011-04-01

    We present a flexible interactive 3D morpho-kinematical modeling application for astrophysics. Compared to other systems, our application reduces the restrictions on the physical assumptions, data type, and amount that is required for a reconstruction of an object's morphology. It is one of the first publicly available tools to apply interactive graphics to astrophysical modeling. The tool allows astrophysicists to provide a priori knowledge about the object by interactively defining 3D structural elements. By direct comparison of model prediction with observational data, model parameters can then be automatically optimized to fit the observation. The tool has already been successfully used in a number of astrophysical research projects.

  15. Categorical prototyping: incorporating molecular mechanisms into 3D printing

    NASA Astrophysics Data System (ADS)

    Brommer, Dieter B.; Giesa, Tristan; Spivak, David I.; Buehler, Markus J.

    2016-01-01

    We apply the mathematical framework of category theory to articulate the precise relation between the structure and mechanics of a nanoscale system in a macroscopic domain. We maintain the chosen molecular mechanical properties from the nanoscale to the continuum scale. Therein we demonstrate a procedure to ‘protoype a model’, as category theory enables us to maintain certain information across disparate fields of study, distinct scales, or physical realizations. This process fits naturally with prototyping, as a prototype is not a complete product but rather a reduction to test a subset of properties. To illustrate this point, we use large-scale multi-material printing to examine the scaling of the elastic modulus of 2D carbon allotropes at the macroscale and validate our printed model using experimental testing. The resulting hand-held materials can be examined more readily, and yield insights beyond those available in the original digital representations. We demonstrate this concept by twisting the material, a test beyond the scope of the original model. The method developed can be extended to other methods of additive manufacturing.

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

    PubMed

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

    2016-08-01

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

  17. To What Degree Does Handling Concrete Molecular Models Promote the Ability to Translate and Coordinate between 2D and 3D Molecular Structure Representations? A Case Study with Algerian Students

    ERIC Educational Resources Information Center

    Mohamed-Salah, Boukhechem; Alain, Dumon

    2016-01-01

    This study aims to assess whether the handling of concrete ball-and-stick molecular models promotes translation between diagrammatic representations and a concrete model (or vice versa) and the coordination of the different types of structural representations of a given molecular structure. Forty-one Algerian undergraduate students were requested…

  18. Potential of 3D City Models to assess flood vulnerability

    NASA Astrophysics Data System (ADS)

    Schröter, Kai; Bochow, Mathias; Schüttig, Martin; Nagel, Claus; Ross, Lutz; Kreibich, Heidi

    2016-04-01

    Vulnerability, as the product of exposure and susceptibility, is a key factor of the flood risk equation. Furthermore, the estimation of flood loss is very sensitive to the choice of the vulnerability model. Still, in contrast to elaborate hazard simulations, vulnerability is often considered in a simplified manner concerning the spatial resolution and geo-location of exposed objects as well as the susceptibility of these objects at risk. Usually, area specific potential flood loss is quantified on the level of aggregated land-use classes, and both hazard intensity and resistance characteristics of affected objects are represented in highly simplified terms. We investigate the potential of 3D City Models and spatial features derived from remote sensing data to improve the differentiation of vulnerability in flood risk assessment. 3D City Models are based on CityGML, an application scheme of the Geography Markup Language (GML), which represents the 3D geometry, 3D topology, semantics and appearance of objects on different levels of detail. As such, 3D City Models offer detailed spatial information which is useful to describe the exposure and to characterize the susceptibility of residential buildings at risk. This information is further consolidated with spatial features of the building stock derived from remote sensing data. Using this database a spatially detailed flood vulnerability model is developed by means of data-mining. Empirical flood damage data are used to derive and to validate flood susceptibility models for individual objects. We present first results from a prototype application in the city of Dresden, Germany. The vulnerability modeling based on 3D City Models and remote sensing data is compared i) to the generally accepted good engineering practice based on area specific loss potential and ii) to a highly detailed representation of flood vulnerability based on a building typology using urban structure types. Comparisons are drawn in terms of

  19. 3D head model classification using optimized EGI

    NASA Astrophysics Data System (ADS)

    Tong, Xin; Wong, Hau-san; Ma, Bo

    2006-02-01

    With the general availability of 3D digitizers and scanners, 3D graphical models have been used widely in a variety of applications. This has led to the development of search engines for 3D models. Especially, 3D head model classification and retrieval have received more and more attention in view of their many potential applications in criminal identifications, computer animation, movie industry and medical industry. This paper addresses the 3D head model classification problem using 2D subspace analysis methods such as 2D principal component analysis (2D PCA[3]) and 2D fisher discriminant analysis (2DLDA[5]). It takes advantage of the fact that the histogram is a 2D image, and we can extract the most useful information from these 2D images to get a good result accordingingly. As a result, there are two main advantages: First, we can perform less calculation to obtain the same rate of classification; second, we can reduce the dimensionality more than PCA to obtain a higher efficiency.

  20. 3D MHD Models of Active Region Loops

    NASA Technical Reports Server (NTRS)

    Ofman, Leon

    2004-01-01

    Present imaging and spectroscopic observations of active region loops allow to determine many physical parameters of the coronal loops, such as the density, temperature, velocity of flows in loops, and the magnetic field. However, due to projection effects many of these parameters remain ambiguous. Three dimensional imaging in EUV by the STEREO spacecraft will help to resolve the projection ambiguities, and the observations could be used to setup 3D MHD models of active region loops to study the dynamics and stability of active regions. Here the results of 3D MHD models of active region loops are presented, and the progress towards more realistic 3D MHD models of active regions. In particular the effects of impulsive events on the excitation of active region loop oscillations, and the generation, propagations and reflection of EIT waves are shown. It is shown how 3D MHD models together with 3D EUV observations can be used as a diagnostic tool for active region loop physical parameters, and to advance the science of the sources of solar coronal activity.

  1. 3D model of amphioxus steroid receptor complexed with estradiol

    SciTech Connect

    Baker, Michael E.; Chang, David J.

    2009-08-28

    The origins of signaling by vertebrate steroids are not fully understood. An important advance was the report that an estrogen-binding steroid receptor [SR] is present in amphioxus, a basal chordate with a similar body plan as vertebrates. To investigate the evolution of estrogen-binding to steroid receptors, we constructed a 3D model of amphioxus SR complexed with estradiol. This 3D model indicates that although the SR is activated by estradiol, some interactions between estradiol and human ER{alpha} are not conserved in the SR, which can explain the low affinity of estradiol for the SR. These differences between the SR and ER{alpha} in the steroid-binding domain are sufficient to suggest that another steroid is the physiological regulator of the SR. The 3D model predicts that mutation of Glu-346 to Gln will increase the affinity of testosterone for amphioxus SR and elucidate the evolution of steroid-binding to nuclear receptors.

  2. A 3D Model of Double-Helical DNA Showing Variable Chemical Details

    ERIC Educational Resources Information Center

    Cady, Susan G.

    2005-01-01

    Since the first DNA model was created approximately 50 years ago using molecular models, students and teachers have been building simplified DNA models from various practical materials. A 3D double-helical DNA model, made by placing beads on a wire and stringing beads through holes in plastic canvas, is described. Suggestions are given to enhance…

  3. Air Pollution Modeling Using A 3-d Hemispheric Nested Model

    NASA Astrophysics Data System (ADS)

    Frohn, L. M.; Christensen, J. H.; Brandt, J.; Hertel, O.

    A 3-D Eulerian transport-chemistry model based on modules and parameterisations from models developed over the last decade at the National Environmental Research Institute (DREAM, DEHM, ACDEP and DEOM) has been developed. The model is hemispheric with currently two nests implemented. The horizontal resolution in the mother domain is 150 km x 150 km. First nest covers the European area wit,h a 50 km x 50 km resolution, second covers the Scandinavian area with a resolution of 16.67 km x 16.67 km. The model employs a chemical scheme (originally 53 species) which has been modified to include a detailed description of the nitrogen chemistry. The concentration of air pollutants, such as sulfur and nitrogen in various forms, has been calculated with the model, applying no nesting as well as one and two nests. The calculated values have been validated by comparison to measurements from more than 200 EMEP monitoring stations. Furthermore deposition of nitrogen to marine waters has been estimated with the model. The goal is to obtain an improved description of spatial and temporal variations in the nutrient deposition to the marine environment. In the presentation the physics and chemistry of the model will be shortly described. Validations of the model calculations by comparison to EMEP measurements will be shown and discussed together with the results of the deposition calculations.

  4. Parallel Optimization of 3D Cardiac Electrophysiological Model Using GPU.

    PubMed

    Xia, Yong; Wang, Kuanquan; Zhang, Henggui

    2015-01-01

    Large-scale 3D virtual heart model simulations are highly demanding in computational resources. This imposes a big challenge to the traditional computation resources based on CPU environment, which already cannot meet the requirement of the whole computation demands or are not easily available due to expensive costs. GPU as a parallel computing environment therefore provides an alternative to solve the large-scale computational problems of whole heart modeling. In this study, using a 3D sheep atrial model as a test bed, we developed a GPU-based simulation algorithm to simulate the conduction of electrical excitation waves in the 3D atria. In the GPU algorithm, a multicellular tissue model was split into two components: one is the single cell model (ordinary differential equation) and the other is the diffusion term of the monodomain model (partial differential equation). Such a decoupling enabled realization of the GPU parallel algorithm. Furthermore, several optimization strategies were proposed based on the features of the virtual heart model, which enabled a 200-fold speedup as compared to a CPU implementation. In conclusion, an optimized GPU algorithm has been developed that provides an economic and powerful platform for 3D whole heart simulations.

  5. Parallel Optimization of 3D Cardiac Electrophysiological Model Using GPU

    PubMed Central

    Xia, Yong; Wang, Kuanquan; Zhang, Henggui

    2015-01-01

    Large-scale 3D virtual heart model simulations are highly demanding in computational resources. This imposes a big challenge to the traditional computation resources based on CPU environment, which already cannot meet the requirement of the whole computation demands or are not easily available due to expensive costs. GPU as a parallel computing environment therefore provides an alternative to solve the large-scale computational problems of whole heart modeling. In this study, using a 3D sheep atrial model as a test bed, we developed a GPU-based simulation algorithm to simulate the conduction of electrical excitation waves in the 3D atria. In the GPU algorithm, a multicellular tissue model was split into two components: one is the single cell model (ordinary differential equation) and the other is the diffusion term of the monodomain model (partial differential equation). Such a decoupling enabled realization of the GPU parallel algorithm. Furthermore, several optimization strategies were proposed based on the features of the virtual heart model, which enabled a 200-fold speedup as compared to a CPU implementation. In conclusion, an optimized GPU algorithm has been developed that provides an economic and powerful platform for 3D whole heart simulations. PMID:26581957

  6. Geospatial Modelling Approach for 3d Urban Densification Developments

    NASA Astrophysics Data System (ADS)

    Koziatek, O.; Dragićević, S.; Li, S.

    2016-06-01

    With growing populations, economic pressures, and the need for sustainable practices, many urban regions are rapidly densifying developments in the vertical built dimension with mid- and high-rise buildings. The location of these buildings can be projected based on key factors that are attractive to urban planners, developers, and potential buyers. Current research in this area includes various modelling approaches, such as cellular automata and agent-based modelling, but the results are mostly linked to raster grids as the smallest spatial units that operate in two spatial dimensions. Therefore, the objective of this research is to develop a geospatial model that operates on irregular spatial tessellations to model mid- and high-rise buildings in three spatial dimensions (3D). The proposed model is based on the integration of GIS, fuzzy multi-criteria evaluation (MCE), and 3D GIS-based procedural modelling. Part of the City of Surrey, within the Metro Vancouver Region, Canada, has been used to present the simulations of the generated 3D building objects. The proposed 3D modelling approach was developed using ESRI's CityEngine software and the Computer Generated Architecture (CGA) language.

  7. 3D Model Generation From the Engineering Drawing

    NASA Astrophysics Data System (ADS)

    Vaský, Jozef; Eliáš, Michal; Bezák, Pavol; Červeňanská, Zuzana; Izakovič, Ladislav

    2010-01-01

    The contribution deals with the transformation of engineering drawings in a paper form into a 3D computer representation. A 3D computer model can be further processed in CAD/CAM system, it can be modified, archived, and a technical drawing can be then generated from it as well. The transformation process from paper form to the data one is a complex and difficult one, particularly owing to the different types of drawings, forms of displayed objects and encountered errors and deviations from technical standards. The algorithm for 3D model generating from an orthogonal vector input representing a simplified technical drawing of the rotational part is described in this contribution. The algorithm was experimentally implemented as ObjectARX application in the AutoCAD system and the test sample as the representation of the rotational part was used for verificaton.

  8. Space Partitioning for Privacy Enabled 3D City Models

    NASA Astrophysics Data System (ADS)

    Filippovska, Y.; Wichmann, A.; Kada, M.

    2016-10-01

    Due to recent technological progress, data capturing and processing of highly detailed (3D) data has become extensive. And despite all prospects of potential uses, data that includes personal living spaces and public buildings can also be considered as a serious intrusion into people's privacy and a threat to security. It becomes especially critical if data is visible by the general public. Thus, a compromise is needed between open access to data and privacy requirements which can be very different for each application. As privacy is a complex and versatile topic, the focus of this work particularly lies on the visualization of 3D urban data sets. For the purpose of privacy enabled visualizations of 3D city models, we propose to partition the (living) spaces into privacy regions, each featuring its own level of anonymity. Within each region, the depicted 2D and 3D geometry and imagery is anonymized with cartographic generalization techniques. The underlying spatial partitioning is realized as a 2D map generated as a straight skeleton of the open space between buildings. The resulting privacy cells are then merged according to the privacy requirements associated with each building to form larger regions, their borderlines smoothed, and transition zones established between privacy regions to have a harmonious visual appearance. It is exemplarily demonstrated how the proposed method generates privacy enabled 3D city models.

  9. 3-D world modeling for an autonomous robot

    SciTech Connect

    Goldstein, M.; Pin, F.G.; Weisbin, C.R.

    1987-08-01

    This paper presents a methodology for a concise representation of the 3-D world model for a mobile robot, using range data. The process starts with the segmentation of the scene into ''objects'' that are given a unique label, based on principles of range continuity. Then the external surface of each object is partitioned into homogeneous surface patches. Contours of surface patches in 3-D space are identified by estimating the normal and curvature associated with each pixel. The resulting surface patches are then classified as planar, convex or concave. Since the world model uses a volumetric representation for the 3-D environment, planar surfaces are represented by thin volumetric polyhedra. Spherical and cylindrical surfaces are extracted and represented by appropriate volumetric primitives. All other surfaces are represented using the boolean union of spherical volumes (as described in a separate paper by the same authors). The result is a general, concise representation of the external 3-D world, which allows for efficient and robust 3-D object recognition. 20 refs., 14 figs.

  10. Modeling the 3D structure of wheat subtilisin/chymotrypsin inhibitor (WSCI). Probing the reactive site with two susceptible proteinases by time-course analysis and molecular dynamics simulations.

    PubMed

    Facchiano, Angelo M; Costantini, Susan; Di Maro, Antimo; Panichi, Daniela; Chambery, Angela; Parente, Augusto; Di Gennaro, Simone; Poerio, Elia

    2006-07-01

    Comparative modeling and time-course hydrolysis experiments have been applied to investigate two enzyme-inhibitor complexes formed between the wheat subtilisin-chymotrypsin inhibitor (WSCI) and two susceptible proteinases. WSCI represents the first case of a wheat protein inhibitor active against animal chymotrypsins and bacterial subtilisins. The model was created using as template structure that of the CI-2A inhibitor from barley (PDB code: 2CI2), which shares 87% sequence identity with WSCI. Under these conditions of high similarity, the comparative modeling approach can be successfully applied. We predicted the WSCI 3D model and used it to investigate enzyme-inhibitor complex systems. Experimental observations indicated that chymotrypsin, but not subtilisin, in addition to cleavage at the primary reactive site Met48-Glu49, is able to hydrolyze a second peptide bond between Phe58 and Val59. Here, we report on cleavage of the peptide bond at the inhibitor's reactive site (Met48-Glu49) determined using time-course hydrolysis experiments; the same event was investigated for both subtilisin/WSCI and chymotrypsin/WSCI complexes using molecular dynamics simulations. The molecular details of the initial inhibitor-enzyme interactions, as well as of the changes observed during the simulations, allow us to speculate on the different fates of the two WSCI-proteinase complexes.

  11. Coronal roots of solar wind streams: 3-D MHD modeling

    NASA Technical Reports Server (NTRS)

    Pisanko, Yu. V.

    1995-01-01

    Weak (discontinuous) solutions of the 3-D MHD equations look like a promising tool to model the transonic solar wind with structural elements: current sheets, coronal plumes etc. Using the observational information about various coronal emissions one can include these structural elements into the 3-D MHD solar wind model by embedding the discontinuities of given type. Such 3-D MHD structured solar wind is calculated self-consistently: variants are examined via numerical experiments. In particular, the behavior of coronal plumes in the transonic solar wind flow, is modeled. The input information for numerical modeling (for example, the magnetic field map at the very base of the solar corona) can be adjusted so that fast stream arises over the center of the coronal hole, over the coronal hole boundaries and, even, over the region with closed magnetic topology. 3-D MHD equations have the analytical solution which can serve as a model of supersonic trans-alfvenic solar wind in the (5-20) solar radii heliocentric distance interval. The transverse, nonradial total (gas + magnetic field) pressure balance in the flow is the corner-stone of this solution. The solution describes the filamentation (ray-like structure of the solar corona) and streaming (formation of high-speed streams with velocities up to 800 km/sec) as a consequence of the magnetic field spatial inhomogeneous structure and trans-alfvenic character of the flow. The magnetic field works in the model as a 'controller' for the solar wind streaming and filamentation.

  12. 3D modeling of dual-gate FinFET.

    PubMed

    Mil'shtein, Samson; Devarakonda, Lalitha; Zanchi, Brian; Palma, John

    2012-11-13

    The tendency to have better control of the flow of electrons in a channel of field-effect transistors (FETs) did lead to the design of two gates in junction field-effect transistors, field plates in a variety of metal semiconductor field-effect transistors and high electron mobility transistors, and finally a gate wrapping around three sides of a narrow fin-shaped channel in a FinFET. With the enhanced control, performance trends of all FETs are still challenged by carrier mobility dependence on the strengths of the electrical field along the channel. However, in cases when the ratio of FinFET volume to its surface dramatically decreases, one should carefully consider the surface boundary conditions of the device. Moreover, the inherent non-planar nature of a FinFET demands 3D modeling for accurate analysis of the device performance. Using the Silvaco modeling tool with quantization effects, we modeled a physical FinFET described in the work of Hisamoto et al. (IEEE Tran. Elec. Devices 47:12, 2000) in 3D. We compared it with a 2D model of the same device. We demonstrated that 3D modeling produces more accurate results. As 3D modeling results came close to experimental measurements, we made the next step of the study by designing a dual-gate FinFET biased at Vg1 >Vg2. It is shown that the dual-gate FinFET carries higher transconductance than the single-gate device.

  13. 3D shape decomposition and comparison for gallbladder modeling

    NASA Astrophysics Data System (ADS)

    Huang, Weimin; Zhou, Jiayin; Liu, Jiang; Zhang, Jing; Yang, Tao; Su, Yi; Law, Gim Han; Chui, Chee Kong; Chang, Stephen

    2011-03-01

    This paper presents an approach to gallbladder shape comparison by using 3D shape modeling and decomposition. The gallbladder models can be used for shape anomaly analysis and model comparison and selection in image guided robotic surgical training, especially for laparoscopic cholecystectomy simulation. The 3D shape of a gallbladder is first represented as a surface model, reconstructed from the contours segmented in CT data by a scheme of propagation based voxel learning and classification. To better extract the shape feature, the surface mesh is further down-sampled by a decimation filter and smoothed by a Taubin algorithm, followed by applying an advancing front algorithm to further enhance the regularity of the mesh. Multi-scale curvatures are then computed on the regularized mesh for the robust saliency landmark localization on the surface. The shape decomposition is proposed based on the saliency landmarks and the concavity, measured by the distance from the surface point to the convex hull. With a given tolerance the 3D shape can be decomposed and represented as 3D ellipsoids, which reveal the shape topology and anomaly of a gallbladder. The features based on the decomposed shape model are proposed for gallbladder shape comparison, which can be used for new model selection. We have collected 19 sets of abdominal CT scan data with gallbladders, some shown in normal shape and some in abnormal shapes. The experiments have shown that the decomposed shapes reveal important topology features.

  14. Enhanced visualization of angiograms using 3D models

    NASA Astrophysics Data System (ADS)

    Marovic, Branko S.; Duckwiler, Gary R.; Villablanca, Pablo; Valentino, Daniel J.

    1999-05-01

    The 3D visualization of intracranial vasculature can facilitate the planning of endovascular therapy and the evaluation of interventional result. To create 3D visualizations, volumetric datasets from x-ray computed tomography angiography (CTA) and magnetic resonance angiography (MRA) are commonly rendered using maximum intensity projection (MIP), volume rendering, or surface rendering techniques. However, small aneurysms and mild stenoses are very difficult to detect using these methods. Furthermore, the instruments used during endovascular embolization or surgical treatment produce artifacts that typically make post-intervention CTA inapplicable, and the presence of magnetic material prohibits the use of MRA. Therefore, standard digital angiography is typically used. In order to address these problems, we developed a visualization and modeling system that displays 2D and 3D angiographic images using a simple Web-based interface. Polygonal models of vasculature were generated from CT and MR data using 3D segmentation of bones and vessels and polygonal surface extraction and simplification. A web-based 3D environment was developed for interactive examination of reconstructed surface models, creation of oblique cross- sections and maximum intensity projections, and distance measurements and annotations. This environment uses a multi- tier client/server approach employing VRML and Java. The 3D surface model and angiographic images can be aligned and displayed simultaneously to permit better perception of complex vasculature and to determine optical viewing positions and angles before starting an angiographic sessions. Polygonal surface reconstruction allows interactive display of complex spatial structures on inexpensive platforms such as personal computers as well as graphic workstations. The aneurysm assessment procedure demonstrated the utility of web-based technology for clinical visualization. The resulting system facilitated the treatment of serious vascular

  15. Improving Semantic Updating Method on 3d City Models Using Hybrid Semantic-Geometric 3d Segmentation Technique

    NASA Astrophysics Data System (ADS)

    Sharkawi, K.-H.; Abdul-Rahman, A.

    2013-09-01

    Cities and urban areas entities such as building structures are becoming more complex as the modern human civilizations continue to evolve. The ability to plan and manage every territory especially the urban areas is very important to every government in the world. Planning and managing cities and urban areas based on printed maps and 2D data are getting insufficient and inefficient to cope with the complexity of the new developments in big cities. The emergence of 3D city models have boosted the efficiency in analysing and managing urban areas as the 3D data are proven to represent the real world object more accurately. It has since been adopted as the new trend in buildings and urban management and planning applications. Nowadays, many countries around the world have been generating virtual 3D representation of their major cities. The growing interest in improving the usability of 3D city models has resulted in the development of various tools for analysis based on the 3D city models. Today, 3D city models are generated for various purposes such as for tourism, location-based services, disaster management and urban planning. Meanwhile, modelling 3D objects are getting easier with the emergence of the user-friendly tools for 3D modelling available in the market. Generating 3D buildings with high accuracy also has become easier with the availability of airborne Lidar and terrestrial laser scanning equipments. The availability and accessibility to this technology makes it more sensible to analyse buildings in urban areas using 3D data as it accurately represent the real world objects. The Open Geospatial Consortium (OGC) has accepted CityGML specifications as one of the international standards for representing and exchanging spatial data, making it easier to visualize, store and manage 3D city models data efficiently. CityGML able to represents the semantics, geometry, topology and appearance of 3D city models in five well-defined Level-of-Details (LoD), namely LoD0

  16. Enhanced LOD Concepts for Virtual 3d City Models

    NASA Astrophysics Data System (ADS)

    Benner, J.; Geiger, A.; Gröger, G.; Häfele, K.-H.; Löwner, M.-O.

    2013-09-01

    Virtual 3D city models contain digital three dimensional representations of city objects like buildings, streets or technical infrastructure. Because size and complexity of these models continuously grow, a Level of Detail (LoD) concept effectively supporting the partitioning of a complete model into alternative models of different complexity and providing metadata, addressing informational content, complexity and quality of each alternative model is indispensable. After a short overview on various LoD concepts, this paper discusses the existing LoD concept of the CityGML standard for 3D city models and identifies a number of deficits. Based on this analysis, an alternative concept is developed and illustrated with several examples. It differentiates between first, a Geometric Level of Detail (GLoD) and a Semantic Level of Detail (SLoD), and second between the interior building and its exterior shell. Finally, a possible implementation of the new concept is demonstrated by means of an UML model.

  17. Teaching the geological subsurface with 3D models

    NASA Astrophysics Data System (ADS)

    Thorpe, Steve; Ward, Emma

    2014-05-01

    3D geological models have great potential as a resource when teaching geological concepts as it allows the student to visualise and interrogate UK geology. They are especially useful when dealing with the conversion of 2D field, map and GIS outputs into three dimensional geological units, which is a common problem for many students. Today's earth science students use a variety of skills and processes during their learning experience including spatial thinking, image construction, detecting patterns, making predictions and deducing the orientation of themselves. 3D geological models can reinforce spatial thinking strategies and encourage students to think about processes and properties, in turn helping the student to recognise pre-learnt geological principles in the field and to convert what they see at the surface into a picture of what is going on at depth. The British Geological Survey (BGS) has been producing digital 3D geological models for over 10 years. The models produced are revolutionising the working practices, data standards and products of the BGS. Sharing our geoscience information with academia is highlighted throughout the BGS strategy as is instilling practical skills in future geoscience professionals, such as model building and interpretation. In 2009 a project was launched to investigate the potential of the models as a teaching resource. The study included justifying if and how the models help students to learn, how models have been used historically, and how other forms of modelling are being used today. BGS now produce 3D geological models for use by anyone teaching or learning geoscience. They incorporate educational strategies that will develop geospatial skills and alleviate potential problems that some students experience. They are contained within contemporary case studies and show standard geological concepts, structures, sedimentary rocks, cross sections and field techniques. 3D geological models of the Isle of Wight and Ingleborough

  18. The application of 3D Zernike moments for the description of "model-free" molecular structure, functional motion, and structural reliability.

    PubMed

    Grandison, Scott; Roberts, Carl; Morris, Richard J

    2009-03-01

    Protein structures are not static entities consisting of equally well-determined atomic coordinates. Proteins undergo continuous motion, and as catalytic machines, these movements can be of high relevance for understanding function. In addition to this strong biological motivation for considering shape changes is the necessity to correctly capture different levels of detail and error in protein structures. Some parts of a structural model are often poorly defined, and the atomic displacement parameters provide an excellent means to characterize the confidence in an atom's spatial coordinates. A mathematical framework for studying these shape changes, and handling positional variance is therefore of high importance. We present an approach for capturing various protein structure properties in a concise mathematical framework that allows us to compare features in a highly efficient manner. We demonstrate how three-dimensional Zernike moments can be employed to describe functions, not only on the surface of a protein but throughout the entire molecule. A number of proof-of-principle examples are given which demonstrate how this approach may be used in practice for the representation of movement and uncertainty.

  19. 3D Geological Model for "LUSI" - a Deep Geothermal System

    NASA Astrophysics Data System (ADS)

    Sohrabi, Reza; Jansen, Gunnar; Mazzini, Adriano; Galvan, Boris; Miller, Stephen A.

    2016-04-01

    Geothermal applications require the correct simulation of flow and heat transport processes in porous media, and many of these media, like deep volcanic hydrothermal systems, host a certain degree of fracturing. This work aims to understand the heat and fluid transport within a new-born sedimentary hosted geothermal system, termed Lusi, that began erupting in 2006 in East Java, Indonesia. Our goal is to develop conceptual and numerical models capable of simulating multiphase flow within large-scale fractured reservoirs such as the Lusi region, with fractures of arbitrary size, orientation and shape. Additionally, these models can also address a number of other applications, including Enhanced Geothermal Systems (EGS), CO2 sequestration (Carbon Capture and Storage CCS), and nuclear waste isolation. Fractured systems are ubiquitous, with a wide-range of lengths and scales, making difficult the development of a general model that can easily handle this complexity. We are developing a flexible continuum approach with an efficient, accurate numerical simulator based on an appropriate 3D geological model representing the structure of the deep geothermal reservoir. Using previous studies, borehole information and seismic data obtained in the framework of the Lusi Lab project (ERC grant n°308126), we present here the first 3D geological model of Lusi. This model is calculated using implicit 3D potential field or multi-potential fields, depending on the geological context and complexity. This method is based on geological pile containing the geological history of the area and relationship between geological bodies allowing automatic computation of intersections and volume reconstruction. Based on the 3D geological model, we developed a new mesh algorithm to create hexahedral octree meshes to transfer the structural geological information for 3D numerical simulations to quantify Thermal-Hydraulic-Mechanical-Chemical (THMC) physical processes.

  20. Modeling the Properties of 3D Woven Composites

    NASA Technical Reports Server (NTRS)

    Cox, Brian N.

    1995-01-01

    An extensive study has been completed of the internal geometry, the mechanisms of failure, and the micromechanics of local failure events in graphite/epoxy composites with three dimensional (3D) woven reinforcement. This work has led to the development of models for predicting elastic constants, strength, notch sensitivity, and fatigue life. A summary is presented here.

  1. Performance and Cognitive Assessment in 3-D Modeling

    ERIC Educational Resources Information Center

    Fahrer, Nolan E.; Ernst, Jeremy V.; Branoff, Theodore J.; Clark, Aaron C.

    2011-01-01

    The purpose of this study was to investigate identifiable differences between performance and cognitive assessment scores in a 3-D modeling unit of an engineering drafting course curriculum. The study aimed to provide further investigation of the need of skill-based assessments in engineering/technical graphics courses to potentially increase…

  2. Coarse-grained modeling of RNA 3D structure.

    PubMed

    Dawson, Wayne K; Maciejczyk, Maciej; Jankowska, Elzbieta J; Bujnicki, Janusz M

    2016-07-01

    Functional RNA molecules depend on three-dimensional (3D) structures to carry out their tasks within the cell. Understanding how these molecules interact to carry out their biological roles requires a detailed knowledge of RNA 3D structure and dynamics as well as thermodynamics, which strongly governs the folding of RNA and RNA-RNA interactions as well as a host of other interactions within the cellular environment. Experimental determination of these properties is difficult, and various computational methods have been developed to model the folding of RNA 3D structures and their interactions with other molecules. However, computational methods also have their limitations, especially when the biological effects demand computation of the dynamics beyond a few hundred nanoseconds. For the researcher confronted with such challenges, a more amenable approach is to resort to coarse-grained modeling to reduce the number of data points and computational demand to a more tractable size, while sacrificing as little critical information as possible. This review presents an introduction to the topic of coarse-grained modeling of RNA 3D structures and dynamics, covering both high- and low-resolution strategies. We discuss how physics-based approaches compare with knowledge based methods that rely on databases of information. In the course of this review, we discuss important aspects in the reasoning process behind building different models and the goals and pitfalls that can result.

  3. Assessment of 3D Models Used in Contours Studies

    ERIC Educational Resources Information Center

    Alvarez, F. J. Ayala; Parra, E. B. Blazquez; Tubio, F. Montes

    2015-01-01

    This paper presents an experimental research focusing on the view of first year students. The aim is to check the quality of implementing 3D models integrated in the curriculum. We search to determine students' preference between the various means facilitated in order to understand the given subject. Students have been respondents to prove the…

  4. Tracking people and cars using 3D modeling and CCTV.

    PubMed

    Edelman, Gerda; Bijhold, Jurrien

    2010-10-10

    The aim of this study was to find a method for the reconstruction of movements of people and cars using CCTV footage and a 3D model of the environment. A procedure is proposed, in which video streams are synchronized and displayed in a 3D model, by using virtual cameras. People and cars are represented by cylinders and boxes, which are moved in the 3D model, according to their movements as shown in the video streams. The procedure was developed and tested in an experimental setup with test persons who logged their GPS coordinates as a recording of the ground truth. Results showed that it is possible to implement this procedure and to reconstruct movements of people and cars from video recordings. The procedure was also applied to a forensic case. In this work we experienced that more situational awareness was created by the 3D model, which made it easier to track people on multiple video streams. Based on all experiences from the experimental set up and the case, recommendations are formulated for use in practice.

  5. Robust 3D reconstruction system for human jaw modeling

    NASA Astrophysics Data System (ADS)

    Yamany, Sameh M.; Farag, Aly A.; Tazman, David; Farman, Allan G.

    1999-03-01

    This paper presents a model-based vision system for dentistry that will replace traditional approaches used in diagnosis, treatment planning and surgical simulation. Dentistry requires accurate 3D representation of the teeth and jaws for many diagnostic and treatment purposes. For example orthodontic treatment involves the application of force systems to teeth over time to correct malocclusion. In order to evaluate tooth movement progress, the orthodontists monitors this movement by means of visual inspection, intraoral measurements, fabrication of plastic models, photographs and radiographs, a process which is both costly and time consuming. In this paper an integrate system has been developed to record the patient's occlusion using computer vision. Data is acquired with an intraoral video camera. A modified shape from shading (SFS) technique, using perspective projection and camera calibration, is used to extract accurate 3D information from a sequence of 2D images of the jaw. A new technique for 3D data registration, using a Grid Closest Point transform and genetic algorithms, is used to register the SFS output. Triangulization is then performed, and a solid 3D model is obtained via a rapid prototype machine.

  6. 3D Geological modelling - towards a European level infrastructure

    NASA Astrophysics Data System (ADS)

    Lee, Kathryn A.; van der Krogt, Rob; Busschers, Freek S.

    2013-04-01

    The joint European Geological Surveys are preparing the ground for a "European Geological Data Infrastructure" (EGDI), under the framework of the FP7-project EGDI-Scope. This scoping study, started in June 2012, for a pan-European e-Infrastructure is based on the successes of earlier joint projects including 'OneGeology-Europe' and aims to provide the backbone for serving interoperable, geological data currently held by European Geological Surveys. Also data from past, ongoing and future European projects will be incorporated. The scope will include an investigation of the functional and technical requirements for serving 3D geological models and will look to research the potential for providing a framework to integrate models at different scales, and form a structure for enabling the development of new and innovative model delivery mechanisms. The EGDI-scope project encourages pan-European inter-disciplinary collaboration between all European Geological Surveys. It aims to enhance emerging web based technologies that will facilitate the delivery of geological data to user communities involved in European policy making and international industry, but also to geoscientific research communities and the general public. Therefore, stakeholder input and communication is imperative to the success, as is the collaboration with all the Geological Surveys of Europe. The most important functional and technical requirements for delivery of such information at pan-European level will be derived from exchanges with relevant European stakeholder representatives and providers of geological data. For handling and delivering 3D geological model data the project will need to address a number of strategic issues: • Which are the most important issues and queries for the relevant stakeholders, requiring 3D geological models? How can this be translated to functional requirements for development and design of an integrated European application? • How to handle the very large

  7. Quasi-3D Multi-scale Modeling Framework Development

    NASA Astrophysics Data System (ADS)

    Arakawa, A.; Jung, J.

    2008-12-01

    When models are truncated in or near an energetically active range of the spectrum, model physics must be changed as the resolution changes. The model physics of GCMs and that of CRMs are, however, quite different from each other and at present there is no unified formulation of model physics that automatically provides transition between these model physics. The Quasi-3D (Q3D) Multi-scale Modeling Framework (MMF) is an attempt to bridge this gap. Like the recently proposed Heterogeneous Multiscale Method (HMM) (E and Engquist 2003), MMF combines a macroscopic model, GCM, and a microscopic model, CRM. Unlike the traditional multiscale methods such as the multi-grid and adapted mesh refinement techniques, HMM and MMF are for solving multi-physics problems. They share the common objective "to design combined macroscopic-microscopic computational methods that are much more efficient than solving the full microscopic model and at the same time give the information we need" (E et al. 2008). The question is then how to meet this objective in practice, which can be highly problem dependent. In HHM, the efficiency is gained typically by localization of the microscale problem. Following the pioneering work by Grabowski and Smolarkiewicz (1999) and Grabowski (2001), MMF takes advantage of the fact that 2D CRMs are reasonably successful in simulating deep clouds. In this approach, the efficiency is gained by sacrificing the three-dimensionality of cloud-scale motion. It also "localizes" the algorithm through embedding a CRM in each GCM grid box using cyclic boundary condition. The Q3D MMF is an attempt to reduce the expense due to these constraints by partially including the cloud-scale 3D effects and extending the CRM beyond individual GCM grid boxes. As currently formulated, the Q3D MMF is a 4D estimation/prediction framework that combines a GCM with a 3D anelastic cloud-resolving vector vorticity equation model (VVM) applied to a network of horizontal grids. The network

  8. Grid cells in 3-D: Reconciling data and models.

    PubMed

    Horiuchi, Timothy K; Moss, Cynthia F

    2015-12-01

    It is well documented that place cells and grid cells in echolocating bats show properties similar to those described in rodents, and yet, continuous theta-frequency oscillations, proposed to play a central role in grid/place cell formation, are not present in bat recordings. These comparative neurophysiological data have raised many questions about the role of theta-frequency oscillations in spatial memory and navigation. Additionally, spatial navigation in three-dimensions poses new challenges for the representation of space in neural models. Inspired by the literature on space representation in the echolocating bat, we have developed a nonoscillatory model of 3-D grid cell creation that shares many of the features of existing oscillatory-interference models. We discuss the model in the context of current knowledge of 3-D space representation and highlight directions for future research.

  9. RNA and protein 3D structure modeling: similarities and differences.

    PubMed

    Rother, Kristian; Rother, Magdalena; Boniecki, Michał; Puton, Tomasz; Bujnicki, Janusz M

    2011-09-01

    In analogy to proteins, the function of RNA depends on its structure and dynamics, which are encoded in the linear sequence. While there are numerous methods for computational prediction of protein 3D structure from sequence, there have been very few such methods for RNA. This review discusses template-based and template-free approaches for macromolecular structure prediction, with special emphasis on comparison between the already tried-and-tested methods for protein structure modeling and the very recently developed "protein-like" modeling methods for RNA. We highlight analogies between many successful methods for modeling of these two types of biological macromolecules and argue that RNA 3D structure can be modeled using "protein-like" methodology. We also highlight the areas where the differences between RNA and proteins require the development of RNA-specific solutions.

  10. Stereoscopic display of 3D models for design visualization

    NASA Astrophysics Data System (ADS)

    Gilson, Kevin J.

    2006-02-01

    Advances in display technology and 3D design visualization applications have made real-time stereoscopic visualization of architectural and engineering projects a reality. Parsons Brinkerhoff (PB) is a transportation consulting firm that has used digital visualization tools from their inception and has helped pioneer the application of those tools to large scale infrastructure projects. PB is one of the first Architecture/Engineering/Construction (AEC) firms to implement a CAVE- an immersive presentation environment that includes stereoscopic rear-projection capability. The firm also employs a portable stereoscopic front-projection system, and shutter-glass systems for smaller groups. PB is using commercial real-time 3D applications in combination with traditional 3D modeling programs to visualize and present large AEC projects to planners, clients and decision makers in stereo. These presentations create more immersive and spatially realistic presentations of the proposed designs. This paper will present the basic display tools and applications, and the 3D modeling techniques PB is using to produce interactive stereoscopic content. The paper will discuss several architectural and engineering design visualizations we have produced.

  11. Parallel 3-D viscoelastic finite difference seismic modelling

    NASA Astrophysics Data System (ADS)

    Bohlen, Thomas

    2002-10-01

    Computational power has advanced to a state where we can begin to perform wavefield simulations for realistic (complex) 3-D earth models at frequencies of interest to both seismologists and engineers. On serial platforms, however, 3-D calculations are still limited to small grid sizes and short seismic wave traveltimes. To make use of the efficiency of network computers a parallel 3-D viscoelastic finite difference (FD) code is implemented which allows to distribute the work on several PCs or workstations connected via standard ethernet in an in-house network. By using the portable message passing interface standard (MPI) for the communication between processors, running times can be reduced and grid sizes can be increased significantly. Furthermore, the code shows good performance on massive parallel supercomputers which makes the computation of very large grids feasible. This implementation greatly expands the applicability of the 3-D elastic/viscoelastic finite-difference modelling technique by providing an efficient, portable and practical C-program.

  12. 3-D HYDRODYNAMIC MODELING IN A GEOSPATIAL FRAMEWORK

    SciTech Connect

    Bollinger, J; Alfred Garrett, A; Larry Koffman, L; David Hayes, D

    2006-08-24

    3-D hydrodynamic models are used by the Savannah River National Laboratory (SRNL) to simulate the transport of thermal and radionuclide discharges in coastal estuary systems. Development of such models requires accurate bathymetry, coastline, and boundary condition data in conjunction with the ability to rapidly discretize model domains and interpolate the required geospatial data onto the domain. To facilitate rapid and accurate hydrodynamic model development, SRNL has developed a pre- and post-processor application in a geospatial framework to automate the creation of models using existing data. This automated capability allows development of very detailed models to maximize exploitation of available surface water radionuclide sample data and thermal imagery.

  13. Modeling of 3D Woven Composites Containing Multiple Delaminations

    DTIC Science & Technology

    2012-08-20

    researchers 3D woven composites shows better damage tolerance than laminated textile composites without z-yarns such as plain woven composites even...modeling of quasi-static short beam shear test of plain woven laminated composites. Cohesive elements were used in regions where transverse cracks and...Title ABSTRACT In this paper we present FE modeling of quasi-static short beam shear test of plain woven laminated composites. Cohesive elements were

  14. Geometric and Colour Data Fusion for Outdoor 3D Models

    PubMed Central

    Merchán, Pilar; Adán, Antonio; Salamanca, Santiago; Domínguez, Vicente; Chacón, Ricardo

    2012-01-01

    This paper deals with the generation of accurate, dense and coloured 3D models of outdoor scenarios from scanners. This is a challenging research field in which several problems still remain unsolved. In particular, the process of 3D model creation in outdoor scenes may be inefficient if the scene is digitalized under unsuitable technical (specific scanner on-board camera) and environmental (rain, dampness, changing illumination) conditions. We address our research towards the integration of images and range data to produce photorealistic models. Our proposal is based on decoupling the colour integration and geometry reconstruction stages, making them independent and controlled processes. This issue is approached from two different viewpoints. On the one hand, given a complete model (geometry plus texture), we propose a method to modify the original texture provided by the scanner on-board camera with the colour information extracted from external images taken at given moments and under specific environmental conditions. On the other hand, we propose an algorithm to directly assign external images onto the complete geometric model, thus avoiding tedious on-line calibration processes. We present the work conducted on two large Roman archaeological sites dating from the first century A.D., namely, the Theatre of Segobriga and the Fori Porticus of Emerita Augusta, both in Spain. The results obtained demonstrate that our approach could be useful in the digitalization and 3D modelling fields. PMID:22969327

  15. A method for building 3D models of barchan dunes

    NASA Astrophysics Data System (ADS)

    Nai, Yang; Li-lan, Su; Lin, Wan; Jie, Yang; Shi-yi, Chen; Wei-lu, Hu

    2016-01-01

    The distributions of barchan dunes are usually represented by digital terrain models (DTMs) overlaid with digital orthophoto maps. Given that most regions with barchan dues have low relief, a 3D map obtained from a DTM may ineffectively show the stereoscopic shape of each dune. The method of building 3D models of barchan dunes using existing modeling software seldom considers the geographical environment. As a result, barchan dune models are often inconsistent with actual DTMs and incompletely express the morphological characteristics of dunes. Manual construction of barchan dune models is also costly and time consuming. Considering these problems, the morphological characteristics of barchan dunes and the mathematical relationships between the morphological parameters of the dunes, such as length, height, and width, are analyzed in this study. The methods of extracting the morphological feature points of barchan dunes, calculating their morphological parameters and building dune outlines and skeleton lines based on the medial axes, are also presented. The dune outlines, skeleton lines, and part of the medial axes of dunes are used to construct a constrained triangulated irregular network. C# and ArcEngine are employed to build 3D models of barchan dunes automatically. Experimental results of a study conducted in Tengger Desert show that the method can be used to approximate the morphological characteristics of barchan dunes and is less time consuming than manual methods.

  16. Geometric and colour data fusion for outdoor 3D models.

    PubMed

    Merchán, Pilar; Adán, Antonio; Salamanca, Santiago; Domínguez, Vicente; Chacón, Ricardo

    2012-01-01

    This paper deals with the generation of accurate, dense and coloured 3D models of outdoor scenarios from scanners. This is a challenging research field in which several problems still remain unsolved. In particular, the process of 3D model creation in outdoor scenes may be inefficient if the scene is digitalized under unsuitable technical (specific scanner on-board camera) and environmental (rain, dampness, changing illumination) conditions. We address our research towards the integration of images and range data to produce photorealistic models. Our proposal is based on decoupling the colour integration and geometry reconstruction stages, making them independent and controlled processes. This issue is approached from two different viewpoints. On the one hand, given a complete model (geometry plus texture), we propose a method to modify the original texture provided by the scanner on-board camera with the colour information extracted from external images taken at given moments and under specific environmental conditions. On the other hand, we propose an algorithm to directly assign external images onto the complete geometric model, thus avoiding tedious on-line calibration processes. We present the work conducted on two large Roman archaeological sites dating from the first century A.D., namely, the Theatre of Segobriga and the Fori Porticus of Emerita Augusta, both in Spain. The results obtained demonstrate that our approach could be useful in the digitalization and 3D modelling fields.

  17. Towards a 3d Spatial Urban Energy Modelling Approach

    NASA Astrophysics Data System (ADS)

    Bahu, J.-M.; Koch, A.; Kremers, E.; Murshed, S. M.

    2013-09-01

    Today's needs to reduce the environmental impact of energy use impose dramatic changes for energy infrastructure and existing demand patterns (e.g. buildings) corresponding to their specific context. In addition, future energy systems are expected to integrate a considerable share of fluctuating power sources and equally a high share of distributed generation of electricity. Energy system models capable of describing such future systems and allowing the simulation of the impact of these developments thus require a spatial representation in order to reflect the local context and the boundary conditions. This paper describes two recent research approaches developed at EIFER in the fields of (a) geo-localised simulation of heat energy demand in cities based on 3D morphological data and (b) spatially explicit Agent-Based Models (ABM) for the simulation of smart grids. 3D city models were used to assess solar potential and heat energy demand of residential buildings which enable cities to target the building refurbishment potentials. Distributed energy systems require innovative modelling techniques where individual components are represented and can interact. With this approach, several smart grid demonstrators were simulated, where heterogeneous models are spatially represented. Coupling 3D geodata with energy system ABMs holds different advantages for both approaches. On one hand, energy system models can be enhanced with high resolution data from 3D city models and their semantic relations. Furthermore, they allow for spatial analysis and visualisation of the results, with emphasis on spatially and structurally correlations among the different layers (e.g. infrastructure, buildings, administrative zones) to provide an integrated approach. On the other hand, 3D models can benefit from more detailed system description of energy infrastructure, representing dynamic phenomena and high resolution models for energy use at component level. The proposed modelling strategies

  18. 3-D model-based tracking for UAV indoor localization.

    PubMed

    Teulière, Céline; Marchand, Eric; Eck, Laurent

    2015-05-01

    This paper proposes a novel model-based tracking approach for 3-D localization. One main difficulty of standard model-based approach lies in the presence of low-level ambiguities between different edges. In this paper, given a 3-D model of the edges of the environment, we derive a multiple hypotheses tracker which retrieves the potential poses of the camera from the observations in the image. We also show how these candidate poses can be integrated into a particle filtering framework to guide the particle set toward the peaks of the distribution. Motivated by the UAV indoor localization problem where GPS signal is not available, we validate the algorithm on real image sequences from UAV flights.

  19. Parallel tempering and 3D spin glass models

    NASA Astrophysics Data System (ADS)

    Papakonstantinou, T.; Malakis, A.

    2014-03-01

    We review parallel tempering schemes and examine their main ingredients for accuracy and efficiency. We discuss two selection methods of temperatures and some alternatives for the exchange of replicas, including all-pair exchange methods. We measure specific heat errors and round-trip efficiency using the two-dimensional (2D) Ising model, and also test the efficiency for the ground state production in 3D spin glass models. We find that the optimization of the GS problem is highly influenced by the choice of the temperature range of the PT process. Finally, we present numerical evidence concerning the universality aspects of an anisotropic case of the 3D spin-glass model.

  20. 3D Multispectral Light Propagation Model For Subcutaneous Veins Imaging

    SciTech Connect

    Paquit, Vincent C; Price, Jeffery R; Meriaudeau, Fabrice; Tobin Jr, Kenneth William

    2008-01-01

    In this paper, we describe a new 3D light propagation model aimed at understanding the effects of various physiological properties on subcutaneous vein imaging. In particular, we build upon the well known MCML (Monte Carlo Multi Layer) code and present a tissue model that improves upon the current state-of-the-art by: incorporating physiological variation, such as melanin concentration, fat content, and layer thickness; including veins of varying depth and diameter; using curved surfaces from real arm shapes; and modeling the vessel wall interface. We describe our model, present results from the Monte Carlo modeling, and compare these results with those obtained with other Monte Carlo methods.

  1. Generation and use of human 3D-CAD models

    NASA Astrophysics Data System (ADS)

    Grotepass, Juergen; Speyer, Hartmut; Kaiser, Ralf

    2002-05-01

    Individualized Products are one of the ten mega trends of the 21st Century with human modeling as the key issue for tomorrow's design and product development. The use of human modeling software for computer based ergonomic simulations within the production process increases quality while reducing costs by 30- 50 percent and shortening production time. This presentation focuses on the use of human 3D-CAD models for both, the ergonomic design of working environments and made to measure garment production. Today, the entire production chain can be designed, individualized models generated and analyzed in 3D computer environments. Anthropometric design for ergonomics is matched to human needs, thus preserving health. Ergonomic simulation includes topics as human vision, reachability, kinematics, force and comfort analysis and international design capabilities. In German more than 17 billions of Mark are moved to other industries, because clothes do not fit. Individual clothing tailored to the customer's preference means surplus value, pleasure and perfect fit. The body scanning technology is the key to generation and use of human 3D-CAD models for both, the ergonomic design of working environments and made to measure garment production.

  2. Method for modeling post-mortem biometric 3D fingerprints

    NASA Astrophysics Data System (ADS)

    Rajeev, Srijith; Shreyas, Kamath K. M.; Agaian, Sos S.

    2016-05-01

    Despite the advancements of fingerprint recognition in 2-D and 3-D domain, authenticating deformed/post-mortem fingerprints continue to be an important challenge. Prior cleansing and reconditioning of the deceased finger is required before acquisition of the fingerprint. The victim's finger needs to be precisely and carefully operated by a medium to record the fingerprint impression. This process may damage the structure of the finger, which subsequently leads to higher false rejection rates. This paper proposes a non-invasive method to perform 3-D deformed/post-mortem finger modeling, which produces a 2-D rolled equivalent fingerprint for automated verification. The presented novel modeling method involves masking, filtering, and unrolling. Computer simulations were conducted on finger models with different depth variations obtained from Flashscan3D LLC. Results illustrate that the modeling scheme provides a viable 2-D fingerprint of deformed models for automated verification. The quality and adaptability of the obtained unrolled 2-D fingerprints were analyzed using NIST fingerprint software. Eventually, the presented method could be extended to other biometric traits such as palm, foot, tongue etc. for security and administrative applications.

  3. 3D cartographic modeling of the Alpine arc

    NASA Astrophysics Data System (ADS)

    Vouillamoz, Naomi; Sue, Christian; Champagnac, Jean-Daniel; Calcagno, Philippe

    2012-12-01

    We built a 3D cartography of the Alpine arc, a highly non-cylindrical mountain belt, using the 3D GeoModeller of the BRGM (French geological survey). The model allows to handle the large-scale 3D structure of seventeen major crustal units of the belt (from the lower crust to the sedimentary cover nappes), and two main discontinuities (the Insubric Line and the Crustal Penninic Front). It provides a unique document to better understand their structural relationships and to produce new sections. The study area comprises the western Alpine arc, from the Jura to the Northwest, up to the Bergell granite intrusion and the Lepontine Dome to the East, and is limited to the South by the Ligurian basin. The model is limited vertically 10 km above sea level at the top, and the moho interface at the bottom. We discarded the structural relationships between the Alps sensus stricto and the surrounding geodynamic systems such as the Rhine graben or the connection with the Apennines. The 3D-model is based on the global integration of various data such as the DEM of the Alps, the moho isobaths, the simplified geological and tectonic maps of the belt, the crustal cross-sections ECORS-CROP and NFP-20, and complementary cross-sections specifically built to precise local complexities. The database has first been integrated in a GIS-project to prepare their implementation in the GeoModeller, by homogenizing the different spatial referencing systems. The global model is finally interpolated from all these data, using the potential field method. The final document is a new tri-dimensional cartography that would be used as input for further alpine studies.

  4. Geometric and Textural Blending for 3D Model Stylization.

    PubMed

    Huang, YiJheng; Lin, Wen-Chieh; Yeh, I-Cheng; Lee, Tong-Yee

    2017-01-25

    Stylizing a 3D model with characteristic shapes or appearances is common in product design, particularly in the design of 3D model merchandise, such as souvenirs, toys, furniture, and stylized items. A model stylization approach is proposed in this study. The approach combines base and style models while preserving user-specified shape features of the base model and the attractive features of the style model with limited assistance from a user. The two models are first combined at the topological level. A tree-growing technique is utilized to search for all possible combinations of the two models. Second, the models are combined at textural and geometric levels by employing a morphing technique. Results show that the proposed approach generates various appealing models and allows users to control the diversity of the output models and adjust the blending degree between the base and style models. The results of this work are also experimentally compared with those of a recent work through a user study. The comparison indicates that our results are more appealing, feature-preserving, and reasonable than those of the compared previous study. The proposed system allows product designers to easily explore design possibilities and assists novice users in creating their own stylized models.

  5. CityGML - Interoperable semantic 3D city models

    NASA Astrophysics Data System (ADS)

    Gröger, Gerhard; Plümer, Lutz

    2012-07-01

    CityGML is the international standard of the Open Geospatial Consortium (OGC) for the representation and exchange of 3D city models. It defines the three-dimensional geometry, topology, semantics and appearance of the most relevant topographic objects in urban or regional contexts. These definitions are provided in different, well-defined Levels-of-Detail (multiresolution model). The focus of CityGML is on the semantical aspects of 3D city models, its structures, taxonomies and aggregations, allowing users to employ virtual 3D city models for advanced analysis and visualization tasks in a variety of application domains such as urban planning, indoor/outdoor pedestrian navigation, environmental simulations, cultural heritage, or facility management. This is in contrast to purely geometrical/graphical models such as KML, VRML, or X3D, which do not provide sufficient semantics. CityGML is based on the Geography Markup Language (GML), which provides a standardized geometry model. Due to this model and its well-defined semantics and structures, CityGML facilitates interoperable data exchange in the context of geo web services and spatial data infrastructures. Since its standardization in 2008, CityGML has become used on a worldwide scale: tools from notable companies in the geospatial field provide CityGML interfaces. Many applications and projects use this standard. CityGML is also having a strong impact on science: numerous approaches use CityGML, particularly its semantics, for disaster management, emergency responses, or energy-related applications as well as for visualizations, or they contribute to CityGML, improving its consistency and validity, or use CityGML, particularly its different Levels-of-Detail, as a source or target for generalizations. This paper gives an overview of CityGML, its underlying concepts, its Levels-of-Detail, how to extend it, its applications, its likely future development, and the role it plays in scientific research. Furthermore, its

  6. Lattice percolation approach to 3D modeling of tissue aging

    NASA Astrophysics Data System (ADS)

    Gorshkov, Vyacheslav; Privman, Vladimir; Libert, Sergiy

    2016-11-01

    We describe a 3D percolation-type approach to modeling of the processes of aging and certain other properties of tissues analyzed as systems consisting of interacting cells. Lattice sites are designated as regular (healthy) cells, senescent cells, or vacancies left by dead (apoptotic) cells. The system is then studied dynamically with the ongoing processes including regular cell dividing to fill vacant sites, healthy cells becoming senescent or dying, and senescent cells dying. Statistical-mechanics description can provide patterns of time dependence and snapshots of morphological system properties. The developed theoretical modeling approach is found not only to corroborate recent experimental findings that inhibition of senescence can lead to extended lifespan, but also to confirm that, unlike 2D, in 3D senescent cells can contribute to tissue's connectivity/mechanical stability. The latter effect occurs by senescent cells forming the second infinite cluster in the regime when the regular (healthy) cell's infinite cluster still exists.

  7. The 3D model control of image processing

    NASA Technical Reports Server (NTRS)

    Nguyen, An H.; Stark, Lawrence

    1989-01-01

    Telerobotics studies remote control of distant robots by a human operator using supervisory or direct control. Even if the robot manipulators has vision or other senses, problems arise involving control, communications, and delay. The communication delays that may be expected with telerobots working in space stations while being controlled from an Earth lab have led to a number of experiments attempting to circumvent the problem. This delay in communication is a main motivating factor in moving from well understood instantaneous hands-on manual control to less well understood supervisory control; the ultimate step would be the realization of a fully autonomous robot. The 3-D model control plays a crucial role in resolving many conflicting image processing problems that are inherent in resolving in the bottom-up approach of most current machine vision processes. The 3-D model control approach is also capable of providing the necessary visual feedback information for both the control algorithms and for the human operator.

  8. Bioengineered silk scaffolds in 3D tissue modeling with focus on mammary tissues.

    PubMed

    Maghdouri-White, Yas; Bowlin, Gary L; Lemmon, Christopher A; Dréau, Didier

    2016-02-01

    In vitro generation of three-dimensional (3D) biological tissues and organ-like structures is a promising strategy to study and closely model complex aspects of the molecular, cellular, and physiological interactions of tissue. In particular, in vitro 3D tissue modeling holds promises to further our understanding of breast development. Indeed, biologically relevant 3D structures that combine mammary cells and engineered matrices have improved our knowledge of mammary tissue growth, organization, and differentiation. Several polymeric biomaterials have been used as scaffolds to engineer 3D mammary tissues. Among those, silk fibroin-based biomaterials have many biologically relevant properties and have been successfully used in multiple medical applications. Here, we review the recent advances in engineered scaffolds with an emphasis on breast-like tissue generation and the benefits of modified silk-based scaffolds.

  9. Modeling 3D faces from samplings via compressive sensing

    NASA Astrophysics Data System (ADS)

    Sun, Qi; Tang, Yanlong; Hu, Ping

    2013-07-01

    3D data is easier to acquire for family entertainment purpose today because of the mass-production, cheapness and portability of domestic RGBD sensors, e.g., Microsoft Kinect. However, the accuracy of facial modeling is affected by the roughness and instability of the raw input data from such sensors. To overcome this problem, we introduce compressive sensing (CS) method to build a novel 3D super-resolution scheme to reconstruct high-resolution facial models from rough samples captured by Kinect. Unlike the simple frame fusion super-resolution method, this approach aims to acquire compressed samples for storage before a high-resolution image is produced. In this scheme, depth frames are firstly captured and then each of them is measured into compressed samples using sparse coding. Next, the samples are fused to produce an optimal one and finally a high-resolution image is recovered from the fused sample. This framework is able to recover 3D facial model of a given user from compressed simples and this can reducing storage space as well as measurement cost in future devices e.g., single-pixel depth cameras. Hence, this work can potentially be applied into future applications, such as access control system using face recognition, and smart phones with depth cameras, which need high resolution and little measure time.

  10. 3D modelling of the Black Sea ecosystem

    NASA Astrophysics Data System (ADS)

    Capet, A.; Gregoire, M.; Beckers, J.-M.; Joassin, P.; Naithani, J.; Soetart, K.

    2009-04-01

    A coupled physical-biogeochemical model has been developed to simulate the ecosystem of the Black Sea at the end of the 80's when eutrophication and invasion by gelatinous organisms seriously affected the stability and dynamics of the system. The biogeochemical model describes the cycle of carbon, nitrogen, silicate, oxygen and phosphorus through the foodweb from bacteria to gelatinous carnivores and explicitly represents processes in the anoxic layer down to the bottom. For calibration and analyses purposes, the coupled model has first been run in 1D at several places in the Black Sea. The biogeochemical model involves some hundred parameters which have been first calibrated by hand using published values. Then, an identifiability analysis has been performed in order to determine a subset of 15 identifiable parameters. An automatic calibration subroutine has been used to fine tune these parameters. In 1D, the model solution exhibits a complex dynamics with several years of transient adjustment. This complexity is imparted by the explicit modelling of top predators. The model has been calibrated and validated using a large set of data available in the Black Sea TU Ocean Base. The calibrated biogeochemical model is implemented in a 3D hydrodynamical model of the Black Sea. Results of these 3D simulations will be presented and compared with maps of in-situ data reconstructed from available data base using the software DIVA (Data Interpolation and Variational analysis).

  11. West Flank Coso, CA FORGE 3D geologic model

    SciTech Connect

    Doug Blankenship

    2016-03-01

    This is an x,y,z file of the West Flank FORGE 3D geologic model. Model created in Earthvision by Dynamic Graphic Inc. The model was constructed with a grid spacing of 100 m. Geologic surfaces were extrapolated from the input data using a minimum tension gridding algorithm. The data file is tabular data in a text file, with lithology data associated with X,Y,Z grid points. All the relevant information is in the file header (the spatial reference, the projection etc.) In addition all the fields in the data file are identified in the header.

  12. 3D-printer visualization of neuron models.

    PubMed

    McDougal, Robert A; Shepherd, Gordon M

    2015-01-01

    Neurons come in a wide variety of shapes and sizes. In a quest to understand this neuronal diversity, researchers have three-dimensionally traced tens of thousands of neurons; many of these tracings are freely available through online repositories like NeuroMorpho.Org and ModelDB. Tracings can be visualized on the computer screen, used for statistical analysis of the properties of different cell types, used to simulate neuronal behavior, and more. We introduce the use of 3D printing as a technique for visualizing traced morphologies. Our method for generating printable versions of a cell or group of cells is to expand dendrite and axon diameters and then to transform the tracing into a 3D object with a neuronal surface generating algorithm like Constructive Tessellated Neuronal Geometry (CTNG). We show that 3D printed cells can be readily examined, manipulated, and compared with other neurons to gain insight into both the biology and the reconstruction process. We share our printable models in a new database, 3DModelDB, and encourage others to do the same with cells that they generate using our code or other methods. To provide additional context, 3DModelDB provides a simulatable version of each cell, links to papers that use or describe it, and links to associated entries in other databases.

  13. 3D-printer visualization of neuron models

    PubMed Central

    McDougal, Robert A.; Shepherd, Gordon M.

    2015-01-01

    Neurons come in a wide variety of shapes and sizes. In a quest to understand this neuronal diversity, researchers have three-dimensionally traced tens of thousands of neurons; many of these tracings are freely available through online repositories like NeuroMorpho.Org and ModelDB. Tracings can be visualized on the computer screen, used for statistical analysis of the properties of different cell types, used to simulate neuronal behavior, and more. We introduce the use of 3D printing as a technique for visualizing traced morphologies. Our method for generating printable versions of a cell or group of cells is to expand dendrite and axon diameters and then to transform the tracing into a 3D object with a neuronal surface generating algorithm like Constructive Tessellated Neuronal Geometry (CTNG). We show that 3D printed cells can be readily examined, manipulated, and compared with other neurons to gain insight into both the biology and the reconstruction process. We share our printable models in a new database, 3DModelDB, and encourage others to do the same with cells that they generate using our code or other methods. To provide additional context, 3DModelDB provides a simulatable version of each cell, links to papers that use or describe it, and links to associated entries in other databases. PMID:26175684

  14. Northern California Seismic Attenuation: 3-D Qp and Qs models

    NASA Astrophysics Data System (ADS)

    Eberhart-Phillips, D. M.

    2015-12-01

    The northern California crust exhibits a wide range of rock types and deformation processes which produce pronounced heterogeneity in regional attenuation. Using local earthquakes, 3-D Qp and Qs crustal models have been obtained for this region which includes the San Andreas fault system, the Central Valley, the Sierra Nevada batholith, and the Mendocino subduction volcanic system. Path attenuation t* values were determined from P and S spectra of 959 spatially distributed earthquakes, magnitude 2.5-6.0 from 2005-2014, using 1254 stations from NCEDC networks and IRIS Mendocino and Sierra Nevada temporary arrays. The t* data were used in Q inversions, using existing hypocenters and 3-D velocity models, with basic 10-km node spacing. The uneven data coverage was accounted for with linking of nodes into larger areas in order to provide useful Q images across the 3-D volume. The results at shallow depth (< 2 km) show very low Q in the Sacramento Delta, the Eureka area, and parts of the Bay Area. In the brittle crust, fault zones that have high seismicity exhibit low Q. In the lower crust, low Q is observed along fault zones that have large cumulative displacement and have experienced grain size reduction. Underlying active volcanic areas, low Q features are apparent below 20-km depth. Moderately high Q is associated with igneous rocks of the Sierra Nevada and Salinian block, while the Franciscan subduction complex shows moderately low Q. The most prominent high Q feature is related to the Great Valley Ophiolite.

  15. Right approach to 3D modeling using CAD tools

    NASA Astrophysics Data System (ADS)

    Baddam, Mounica Reddy

    The thesis provides a step-by-step methodology to enable an instructor dealing with CAD tools to optimally guide his/her students through an understandable 3D modeling approach which will not only enhance their knowledge about the tool's usage but also enable them to achieve their desired result in comparatively lesser time. In the known practical field, there is particularly very little information available to apply CAD skills to formal beginners' training sessions. Additionally, advent of new software in 3D domain cumulates updating into a more difficult task. Keeping up to the industry's advanced requirements emphasizes the importance of more skilled hands in the field of CAD development, rather than just prioritizing manufacturing in terms of complex software features. The thesis analyses different 3D modeling approaches specified to the varieties of CAD tools currently available in the market. Utilizing performance-time databases, learning curves have been generated to measure their performance time, feature count etc. Based on the results, improvement parameters have also been provided for (Asperl, 2005).

  16. Effective 3-D surface modeling for geographic information systems

    NASA Astrophysics Data System (ADS)

    Yüksek, K.; Alparslan, M.; Mendi, E.

    2016-01-01

    In this work, we propose a dynamic, flexible and interactive urban digital terrain platform with spatial data and query processing capabilities of geographic information systems, multimedia database functionality and graphical modeling infrastructure. A new data element, called Geo-Node, which stores image, spatial data and 3-D CAD objects is developed using an efficient data structure. The system effectively handles data transfer of Geo-Nodes between main memory and secondary storage with an optimized directional replacement policy (DRP) based buffer management scheme. Polyhedron structures are used in digital surface modeling and smoothing process is performed by interpolation. The experimental results show that our framework achieves high performance and works effectively with urban scenes independent from the amount of spatial data and image size. The proposed platform may contribute to the development of various applications such as Web GIS systems based on 3-D graphics standards (e.g., X3-D and VRML) and services which integrate multi-dimensional spatial information and satellite/aerial imagery.

  17. Underwater 3d Modeling: Image Enhancement and Point Cloud Filtering

    NASA Astrophysics Data System (ADS)

    Sarakinou, I.; Papadimitriou, K.; Georgoula, O.; Patias, P.

    2016-06-01

    This paper examines the results of image enhancement and point cloud filtering on the visual and geometric quality of 3D models for the representation of underwater features. Specifically it evaluates the combination of effects from the manual editing of images' radiometry (captured at shallow depths) and the selection of parameters for point cloud definition and mesh building (processed in 3D modeling software). Such datasets, are usually collected by divers, handled by scientists and used for geovisualization purposes. In the presented study, have been created 3D models from three sets of images (seafloor, part of a wreck and a small boat's wreck) captured at three different depths (3.5m, 10m and 14m respectively). Four models have been created from the first dataset (seafloor) in order to evaluate the results from the application of image enhancement techniques and point cloud filtering. The main process for this preliminary study included a) the definition of parameters for the point cloud filtering and the creation of a reference model, b) the radiometric editing of images, followed by the creation of three improved models and c) the assessment of results by comparing the visual and the geometric quality of improved models versus the reference one. Finally, the selected technique is tested on two other data sets in order to examine its appropriateness for different depths (at 10m and 14m) and different objects (part of a wreck and a small boat's wreck) in the context of an ongoing research in the Laboratory of Photogrammetry and Remote Sensing.

  18. Modeling and Processing of Continuous 3D Elastic Wavefield Data

    NASA Astrophysics Data System (ADS)

    Milkereit, B.; Bohlen, T.

    2001-12-01

    Continuous seismic wavefields are excited by earthquake clustering, induced seismicity in reservoirs, and mining. In hydrocarbon reservoirs, for example, pore pressure changes and fluid flow (mass transfer) will cause incremental deviatoric stresses sufficient to trigger and sustain seismic activity. Here we address three aspects of seismic wavefields in three-dimensional heterogeneous media triggered by distributed sources in space and time: forward modeling, multichannel data processing, and source location imaging. A power law distribution of seismic sources (such as the Gutenberg-Richter law) is used for the modeling of viscoelastic/elastic wave propagation through a realistic earth model. 3D modeling provides new insight in the interaction of multi-source wavefields and the role of scale-dependend elastic model parameters on transmitted and reflected/back-scattered wavefields. There exists a strong correlation between the spatial properties of the compressional, shear wave and density perturbations and the lateral correlation length of the resulting reflected or transmitted seismic wavefields. Modeling is based on the implementation of 3D elastic/viscoelastic FD codes on massive parallel and/or distributed computing resources using MPI (message passing interface). For parallelization, large grid 3D earth models are decomposed into subvolume processing elements whereby each processing element is updating the wavefield within its portion of the grid. Processing of continuous seismic wavefields excited by multiple distributed sources is based on a combination of crosscorrelated or slowness-transformed array data and Kirchhoff or reverse time migration for source location or source volume imaging. The appearance of slowness in both migration and array data processing suggests the possibility of combining them into a single process. In order to place further constraints on the migration, the directivity properties of 3-component receiver arrays can be included in

  19. 3D Geologic Model of the San Diego Area

    NASA Astrophysics Data System (ADS)

    Danskin, W. R.; Cromwell, G.; Glockhoff, C.; Martin, D.

    2015-12-01

    Prior geologic studies of the San Diego area, including northern Baja California, Mexico, focused on site investigations, characterization of rock formations, or earthquake hazards. No comprehensive, quantitative model characterizing the three-dimensional (3D) geology of the entire area has been developed. The lack of such a model limits understanding of large-scale processes, such as development of ancient landforms, and groundwater movement and availability. To evaluate these regional processes, the United States Geological Survey (USGS) conducted a study to better understand the geologic structure of the San Diego area. A cornerstone of this study is the installation and analysis of 77 wells at 12 multiple-depth monitoring-well sites. Geologic information from these wells was combined with lithologic data from 81 oil exploration wells and municipal and private water wells, gravity and seismic interpretations, and paleontological interpretations. These data were analyzed in conjunction with geologic maps and digital elevation models to develop a 3D geologic model of the San Diego area, in particular of the San Diego embayment. Existing interpretations of regional surficial geology, faulting, and tectonic history provided the framework for this model, which was refined by independent evaluation of subsurface geology. Geologic formations were simplified into five sedimentary units (Quaternary, Plio-Pleistocene, Oligocene, Eocene and Cretaceous ages), and one basal crystalline unit (primarily Cretaceous and Jurassic). Complex fault systems are represented in the model by ten fault strands that maintain overall displacement. The 3D geologic model corroborates existing geologic concepts of the San Diego area, refines the extent of subsurface geology, and allows users to holistically evaluate subsurface structures and regional hydrogeology.

  20. 3D flare particle model for ShipIR/NTCS

    NASA Astrophysics Data System (ADS)

    Ramaswamy, Srinivasan; Vaitekunas, David A.

    2016-05-01

    A key component in any soft-kill response to an incoming guided missile is the flare /chaff decoy used to distract or seduce the seeker homing system away from the naval platform. This paper describes a new 3D flare particle model in the naval threat countermeasure simulator (NTCS) of the NATO-standard ship signature model (ShipIR), which provides independent control over the size and radial distribution of its signature. The 3D particles of each flare sub-munition are modelled stochastically and rendered using OpenGL z-buffering, 2D projection, and alpha-blending to produce a unique and time varying signature. A sensitivity analysis on each input parameter provides the data and methods needed to synthesize a model from an IR measurement of a decoy. The new model also eliminated artifacts and deficiencies in our previous model which prevented reliable tracks from the adaptive track gate algorithm already presented by Ramaswamy and Vaitekunas (2015). A sequence of scenarios are used to test and demonstrate the new flare model during a missile engagement.

  1. Delineation of the complement receptor type 2-C3d complex by site-directed mutagenesis and molecular docking.

    PubMed

    Shaw, Craig D; Storek, Michael J; Young, Kendra A; Kovacs, James M; Thurman, Joshua M; Holers, V Michael; Hannan, Jonathan P

    2010-12-10

    The interactions between the complement receptor type 2 (CR2) and the C3 complement fragments C3d, C3dg, and iC3b are essential for the initiation of a normal immune response. A crystal-derived structure of the two N-terminal short consensus repeat (SCR1-2) domains of CR2 in complex with C3d has previously been elucidated. However, a number of biochemical and biophysical studies targeting both CR2 and C3d appear to be in conflict with these structural data. Previous mutagenesis and heteronuclear NMR spectroscopy studies directed toward the C3d-binding site on CR2 have indicated that the CR2-C3d cocrystal structure may represent an encounter/intermediate or nonphysiological complex. With regard to the CR2-binding site on C3d, mutagenesis studies by Isenman and coworkers [Isenman, D. E., Leung, E., Mackay, J. D., Bagby, S. & van den Elsen, J. M. H. (2010). Mutational analyses reveal that the staphylococcal immune evasion molecule Sbi and complement receptor 2 (CR2) share overlapping contact residues on C3d: Implications for the controversy regarding the CR2/C3d cocrystal structure. J. Immunol. 184, 1946-1955] have implicated an electronegative "concave" surface on C3d in the binding process. This surface is discrete from the CR2-C3d interface identified in the crystal structure. We generated a total of 18 mutations targeting the two (X-ray crystallographic- and mutagenesis-based) proposed CR2 SCR1-2 binding sites on C3d. Using ELISA analyses, we were able to assess binding of mutant forms of C3d to CR2. Mutations directed toward the concave surface of C3d result in substantially compromised CR2 binding. By contrast, targeting the CR2-C3d interface identified in the cocrystal structure and the surrounding area results in significantly lower levels of disruption in binding. Molecular modeling approaches used to investigate disparities between the biochemical data and the X-ray structure of the CR2-C3d cocrystal result in highest-scoring solutions in which CR2 SCR1-2 is

  2. Identifying Affordances of 3D Printed Tangible Models for Understanding Core Biological Concepts

    ERIC Educational Resources Information Center

    Davenport, Jodi L.; Silberglitt, Matt; Boxerman, Jonathan; Olson, Arthur

    2014-01-01

    3D models derived from actual molecular structures have the potential to transform student learning in biology. We share findings related to our research questions: 1) what types of interactions with a protein folding kit promote specific learning objectives?, and 2) what features of the instructional environment (e.g., peer interactions, teacher…

  3. 3D Printing of Protein Models in an Undergraduate Laboratory: Leucine Zippers

    ERIC Educational Resources Information Center

    Meyer, Scott C.

    2015-01-01

    An upper-division undergraduate laboratory experiment is described that explores the structure/function relationship of protein domains, namely leucine zippers, through a molecular graphics computer program and physical models fabricated by 3D printing. By generating solvent accessible surfaces and color-coding hydrophobic, basic, and acidic amino…

  4. Modeling Extracellular Matrix Reorganization in 3D Environments

    PubMed Central

    Harjanto, Dewi; Zaman, Muhammad H.

    2013-01-01

    Extracellular matrix (ECM) remodeling is a key physiological process that occurs in a number of contexts, including cell migration, and is especially important for cellular form and function in three-dimensional (3D) matrices. However, there have been few attempts to computationally model how cells modify their environment in a manner that accounts for both cellular properties and the architecture of the surrounding ECM. To this end, we have developed and validated a novel model to simulate matrix remodeling that explicitly defines cells in a 3D collagenous matrix. In our simulation, cells can degrade, deposit, or pull on local fibers, depending on the fiber density around each cell. The cells can also move within the 3D matrix. Different cell phenotypes can be modeled by varying key cellular parameters. Using the model we have studied how two model cancer cell lines, of differing invasiveness, modify matrices with varying fiber density in their vicinity by tracking the metric of fraction of matrix occupied by fibers. Our results quantitatively demonstrate that in low density environments, cells deposit more collagen to uniformly increase fibril fraction. On the other hand, in higher density environments, the less invasive model cell line reduced the fibril fraction as compared to the highly invasive phenotype. These results show good qualitative and quantitative agreement with existing experimental literature. Our simulation is therefore able to function as a novel platform to provide new insights into the clinically relevant and physiologically critical process of matrix remodeling by helping identify critical parameters that dictate cellular behavior in complex native-like environments. PMID:23341900

  5. 3D statistical shape models incorporating 3D random forest regression voting for robust CT liver segmentation

    NASA Astrophysics Data System (ADS)

    Norajitra, Tobias; Meinzer, Hans-Peter; Maier-Hein, Klaus H.

    2015-03-01

    During image segmentation, 3D Statistical Shape Models (SSM) usually conduct a limited search for target landmarks within one-dimensional search profiles perpendicular to the model surface. In addition, landmark appearance is modeled only locally based on linear profiles and weak learners, altogether leading to segmentation errors from landmark ambiguities and limited search coverage. We present a new method for 3D SSM segmentation based on 3D Random Forest Regression Voting. For each surface landmark, a Random Regression Forest is trained that learns a 3D spatial displacement function between the according reference landmark and a set of surrounding sample points, based on an infinite set of non-local randomized 3D Haar-like features. Landmark search is then conducted omni-directionally within 3D search spaces, where voxelwise forest predictions on landmark position contribute to a common voting map which reflects the overall position estimate. Segmentation experiments were conducted on a set of 45 CT volumes of the human liver, of which 40 images were randomly chosen for training and 5 for testing. Without parameter optimization, using a simple candidate selection and a single resolution approach, excellent results were achieved, while faster convergence and better concavity segmentation were observed, altogether underlining the potential of our approach in terms of increased robustness from distinct landmark detection and from better search coverage.

  6. Digital 3D Borobudur - Integration of 3D surveying and modeling techniques

    NASA Astrophysics Data System (ADS)

    Suwardhi, D.; Menna, F.; Remondino, F.; Hanke, K.; Akmalia, R.

    2015-08-01

    The Borobudur temple (Indonesia) is one of the greatest Buddhist monuments in the world, now listed as an UNESCO World Heritage Site. The present state of the temple is the result of restorations after being exposed to natural disasters several times. Today there is still a growing rate of deterioration of the building stones whose causes need further researches. Monitoring programs, supported at institutional level, have been effectively executed to observe the problem. The paper presents the latest efforts to digitally document the Borobudur Temple and its surrounding area in 3D with photogrammetric techniques. UAV and terrestrial images were acquired to completely digitize the temple, produce DEM, orthoimages and maps at 1:100 and 1:1000 scale. The results of the project are now employed by the local government organizations to manage the heritage area and plan new policies for the conservation and preservation of the UNESCO site. In order to help data management and policy makers, a web-based information system of the heritage area was also built to visualize and easily access all the data and achieved 3D results.

  7. 3-D modelling of seamount topography from satellite altimetry

    SciTech Connect

    Baudry, N. ); Calmant, S. )

    1991-06-01

    The authors develop a complete set of algorithms to perform 3D modelling of seamount bathymetry from satellite altimetry. The first stage of the data processing consists in gridding the geoid: to account for the long wavelength errors geoid heights are first bias-adjusted at cross-overs. Then a collocation on a regular grid is performed, accounting for the altimeter errors. In a second stage, geoid heights are converted into bathymetry. No simplifying assumption on the shape and location of the bathymetry highs is necessary. Bathymetric uncertainties due to the data sampling and the parameters of the mechanical and crustal models are evaluated.

  8. 3D Numerical Simulations of the Breakout Model

    NASA Astrophysics Data System (ADS)

    Choe, G. S.; Cheng, C. Z.; Lee, J.; Lynch, B. J.; Antiochos, S. K.; DeVore, C. R.; Zurbuchen, T. H.

    2005-05-01

    We present the continuing progress of the numerical simulations of the breakout model for coronal mass ejection initiation. To validate the 3D spherical ARMS code we have run the 2.5D breakout problem and compare the eruption to the published 2D results. The ARMS 2.5D CME also forms a large magnetic island ahead of the erupting plasmoid due to the code's excellent maintenance of equatorial symmetry. Progress on the fully 3D breakout problem is also discussed. To build up enough magnetic free energy for an eruption the active region field must be strong with a steep gradient near the polarity inversion line and the shear must be highly concentrated there. This requires adaptive griding techniques. In the current simulation, the active region to background field ratio is 20-to-1 and the neutral line is long compared to the active region width. We present the evolution of this topology under Br-conserving shearing flow and discuss implications for a 3D eruption. This work is supported by NASA and ONR. BJL is supported by NASA GSRP grant NGT5-50453.

  9. Discrete Method of Images for 3D Radio Propagation Modeling

    NASA Astrophysics Data System (ADS)

    Novak, Roman

    2016-09-01

    Discretization by rasterization is introduced into the method of images (MI) in the context of 3D deterministic radio propagation modeling as a way to exploit spatial coherence of electromagnetic propagation for fine-grained parallelism. Traditional algebraic treatment of bounding regions and surfaces is replaced by computer graphics rendering of 3D reflections and double refractions while building the image tree. The visibility of reception points and surfaces is also resolved by shader programs. The proposed rasterization is shown to be of comparable run time to that of the fundamentally parallel shooting and bouncing rays. The rasterization does not affect the signal evaluation backtracking step, thus preserving its advantage over the brute force ray-tracing methods in terms of accuracy. Moreover, the rendering resolution may be scaled back for a given level of scenario detail with only marginal impact on the image tree size. This allows selection of scene optimized execution parameters for faster execution, giving the method a competitive edge. The proposed variant of MI can be run on any GPU that supports real-time 3D graphics.

  10. Modeling the GFR with RELAP5-3D

    SciTech Connect

    Cliff B. Davis; Theron D. Marshall; K. D. Weaver

    2005-09-01

    Significant improvements have been made to the RELAP5-3D computer code for analysis of the Gas Fast Reactor (GFR). These improvements consisted of adding carbon dioxide as a working fluid, improving the turbine component, developing a compressor model, and adding the Gnielinski heat transfer correlation. The code improvements were validated, generally through comparisons with independent design calculations. A model of the power conversion unit of the GFR was developed. The model of the power conversion unit was coupled to a reactor model to develop a complete model of the GFR system. The RELAP5 model of the GFR was used to simulate two transients, one initiated by a reactor trip and the other initiated by a loss of load.

  11. Neutral dioxovanadium(V) complexes of biomimetic hydrazones ONO donor ligands of bioinorganic and medicinal relevance: Synthesis via air oxidation of bis(acetylaceto-nato)oxovanadium(IV), characterization, biological activity and 3D molecular modeling

    NASA Astrophysics Data System (ADS)

    Maurya, R. C.; Rajput, S.

    2007-05-01

    The interaction of bis(acetylacetonato)oxovanadium(IV), [VO(acac) 2] with biomimetic hydrazone ONO donor ligands HL in 1:1 mole ratio [where, HL = N-(4'-benzoylidene-3'-methyl-1'-phenyl-2'-pyrazolin-5'-one)-isonicotinic acid hydrazide (bmphp-inH, I), N-(4'-butyrylidene-3'-methyl-1'-phenyl-2'-pyrazolin-5'-one)-isonicotinic acid hydrazide (bumphp-inH, II), N-(4'-acetylidene-3'-methyl-1'-phenyl-2'-pyrazolin-5'-one)-isonicotinic acid hydrazide (amphp-inH, III), N-(3'-methyl-1'-phenyl-4'-propionylidene-2'-pyrazolin-5'-one)-isonicotinic acid hydrazide (mphpp-inH, IV) and N-(4'- iso-butyrylidene-3'-methyl-1'-phenyl-2'-pyrazolin-5'-one)-isonicotinic acid hydrazide ( iso-bumphp-inH, V)] in a mixed solvent (ethanol-methanol, 1:10) via aerial oxidation for 2-3 days yield dioxovanadium(V) complexes of composition [VO 2(L)(H 2O)] · H 2O. The compounds so obtained were characterized on the basis of elemental analyses, thermogravimetry, vanadium determination, IR, Electronic, 51V NMR, 1H NMR and mass spectral studies. The 3D molecular modeling and analysis for bond lengths and bond angles have also been carried out for one of the representative compounds, [VO 2(ampph-in)(H 2O)] ( 3).

  12. Quantitative Proteomic and Phosphoproteomic Comparison of 2D and 3D Colon Cancer Cell Culture Models.

    PubMed

    Yue, Xiaoshan; Lukowski, Jessica K; Weaver, Eric M; Skube, Susan B; Hummon, Amanda B

    2016-12-02

    Cell cultures are widely used model systems. Some immortalized cell lines can be grown in either two-dimensional (2D) adherent monolayers or in three-dimensional (3D) multicellular aggregates, or spheroids. Here, the quantitative proteome and phosphoproteome of colon carcinoma HT29 cells cultures in 2D monolayers and 3D spheroids were compared with a stable isotope labeling of amino acids (SILAC) labeling strategy. Two biological replicates from each sample were examined, and notable differences in both the proteome and the phosphoproteome were determined by nanoliquid chromatography tandem mass spectrometry (LC-MS/MS) to assess how growth configuration affects molecular expression. A total of 5867 protein groups, including 2523 phosphoprotein groups and 8733 phosphopeptides were identified in the samples. The Gene Ontology analysis revealed enriched GO terms in the 3D samples for RNA binding, nucleic acid binding, enzyme binding, cytoskeletal protein binding, and histone binding for their molecular functions (MF) and in the process of cell cycle, cytoskeleton organization, and DNA metabolic process for the biological process (BP). The KEGG pathway analysis indicated that 3D cultures are enriched for oxidative phosphorylation pathways, metabolic pathways, peroxisome pathways, and biosynthesis of amino acids. In contrast, analysis of the phosphoproteomes indicated that 3D cultures have decreased phosphorylation correlating with slower growth rates and lower cell-to-extracellular matrix interactions. In sum, these results provide quantitative assessments of the effects on the proteome and phosphoproteome of culturing cells in 2D versus 3D cell culture configurations.

  13. Testing Mercury Porosimetry with 3D Printed Porosity Models

    NASA Astrophysics Data System (ADS)

    Hasiuk, F.; Ewing, R. P.; Hu, Q.

    2014-12-01

    Mercury intrusion porosimetry is one of the most widely used techniques to study the porous nature of a geological and man-made materials. In the geosciences, it is commonly used to describe petroleum reservoir and seal rocks as well as to grade aggregates for the design of asphalt and portland cement concretes. It's wide utility stems from its ability to characterize a wide range of pore throat sizes (from nanometers to around a millimeter). The fundamental physical model underlying mercury intrusion porosimetry, the Washburn Equation, is based on the assumption that rock porosity can be described as a bundle of cylindrical tubes. 3D printing technology, also known as rapid prototyping, allows the construction of intricate and accurate models, exactly what is required to build models of rock porosity. We evaluate the applicability of the Washburn Equation by comparing properties (like porosity, pore and pore throat size distribution, and surface area) computed on digital porosity models (built from CT data, CAD designs, or periodic geometries) to properties measured via mercury intrusion porosimetry on 3D printed versions of the same digital porosity models.

  14. DYNA3D Material Model 71 - Solid Element Test Problem

    SciTech Connect

    Zywicz, E

    2008-01-24

    A general phenomenological-based elasto-plastic nonlinear isotropic strain hardening material model was implemented in DYNA3D for use in solid, beam, truss, and shell elements. The constitutive model, Model 71, is based upon conventional J2 plasticity and affords optional temperature and rate dependence (visco-plasticity). The expressions for strain hardening, temperature dependence, and rate dependence allow it to represent a wide variety of material responses. Options to capture temperature changes due to adiabatic heating and thermal straining are incorporated into the constitutive framework as well. The verification problem developed for this constitutive model consists of four uni-axial right cylinders subject to constant true strain-rate boundary conditions. Three of the specimens have different constant strain rates imposed, while the fourth specimen is subjected to several strain rate jumps. The material parameters developed by Fehlmann (2005) for 21-6-9 Nitronic steel are utilized. As demonstrated below, the finite element (FE) simulations are in excellent agreement with the theoretical responses and indicated the model is functioning as desired. Consequently, this problem serves as both a verification problem and regression test problem for DYNA3D.

  15. Modeling radiative transfer in heterogeneous 3D vegetation canopies

    NASA Astrophysics Data System (ADS)

    Gastellu-Etchegorry, J. P.; Demarez, V.; Pinel, Veronique; Zagolski, Francis

    1995-01-01

    The DART (discrete anisotropic radiative transfer) model simulates radiative transfer in heterogeneous 3-D scenes; here, a forest plantation. Similarly to Kimes model, the scene is divided into a rectangular cell matrix, i.e., a building block for simulating larger scenes. Cells are parallelipipedic. The scene encompasses different landscape features (i.e., trees with leaves and trunks, grass, water, and soil) with specific optical (reflectance, transmittance) and structural (LAI, LAD) characteristics. Radiation directions are subdivided into contiguous sectors with possibly uneven spacing. Topography, hot spot, and multiple interactions (scattering, attenuation) within cells are modeled. Two major steps are distinguished: (1) Illumination of cells by direct sun radiation. Actual locations of within cell scattering are determined for optimizing scattering computation. (2) Interception and scattering of previously scattered radiation. Diffuse atmospheric radiation is input at this level. Multiple scattering is represented with a spherical harmonic decomposition, for reducing data volume. The model iterates on step 2 for all cells, and stops with the energetic equilibrium. This model predicts the bi-directional reflectance factors of 3D canopies, with each scene component contribution; it was successfully tested with homogeneous covers. It gives also the radiation regime with canopies, and consequently some information about volume distribution of photosynthesis rates and primary production.

  16. Complex tephra dispersion from 3D plume modeling using ATHAM

    NASA Astrophysics Data System (ADS)

    Nicholson, B. C.; Kobs-Nawotniak, S. E.

    2014-12-01

    Most volcanic hazard assessments are based on a classic inversion tool for tephra deposits that relies on a simple integral model to explain the eruption plume. While this tool is adequate for first-order predictions of tephra deposition under no-wind conditions, the simplifying assumptions make it unreliable for ambient winds >10 m/s. Advances in computational power now make it possible to improve the inversion tool using 3D fluid dynamics. We do this with the physics-based Active Tracer High-resolution Atmospheric Model (ATHAM) to model tephra dispersion and deposition from volcanic eruption columns. The model, when run in 3D, is able to capture the complex morphology of bent plumes. Tephra distributions produced by these morphologies differ significantly from distributions created by idealized advection solutions, reflecting the effects of counter-rotating vortex pairs, puffing modes, or plume bifurcation. The modeled tephra deposition better captures the complex effects of wind-plume interaction, allowing us to update classic inversion tools with more realistic weak plume conditions consistent with typical historical explosive eruptions.

  17. 3-D physical modeling of a complex salt canopy

    SciTech Connect

    Wiley, R.W.; Sekharan, K.K.

    1996-12-31

    Recent drilling has confirmed both significant reservoir potential and the presence of commercial hydrocarbons below salt structures in the Gulf of Mexico. Obtaining definitive seismic images with standard processing schemes beneath these salt structures is very difficult if not impossible. Because of the complicated seismic behavior of these structures, full volume 3-D prestack depth migration is required. Unfortunately, carrying out the multitude of calculations needed to create a proper image requires the largest and fastest supercomputers and rather complex numerical algorithms. Furthermore, developing and testing the imaging algorithms is quite involved and requires appropriate test data sets. To better understand the problems and issues of subsalt imaging, Marathon Oil Company and Louisiana Land and Exploration Company contracted with the University of Houston`s Allied Geophysical Laboratories (AGL) to construct a salt canopy physical model. The model is patterned after the SEG/EAEG Salt Model and is made from synthetic materials. It is a full three-dimensional model with an irregularly shaped, lateral salt structure embedded in five distinct sedimentary layers. The model was used to acquire a multi-offset 3-D marine-style survey. These data are being used to address problems of subsalt imaging. In addition to standard processing techniques, the authors investigate algorithms for multiple removal and prestack depth migration.

  18. Exploiting Textured 3D Models for Developing Serious Games

    NASA Astrophysics Data System (ADS)

    Kontogianni, G.; Georgopoulos, A.

    2015-08-01

    Digital technologies have affected significantly many fields of computer graphics such as Games and especially the field of the Serious Games. These games are usually used for educational proposes in many fields such as Health Care, Military applications, Education, Government etc. Especially Digital Cultural Heritage is a scientific area that Serious Games are applied and lately many applications appear in the related literature. Realistic 3D textured models which have been produced using different photogrammetric methods could be a useful tool for the creation of Serious Game applications in order to make the final result more realistic and close to the reality. The basic goal of this paper is how 3D textured models which are produced by photogrammetric methods can be useful for developing a more realistic environment of a Serious Game. The application of this project aims at the creation of an educational game for the Ancient Agora of Athens. The 3D models used vary not only as far as their production methods (i.e. Time of Flight laser scanner, Structure from Motion, Virtual historical reconstruction etc.) is concerned, but also as far as their era as some of them illustrated according to their existing situation and some others according to how these monuments looked like in the past. The Unity 3D® game developing environment was used for creating this application, in which all these models were inserted in the same file format. For the application two diachronic virtual tours of the Athenian Agora were produced. The first one illustrates the Agora as it is today and the second one at the 2nd century A.D. Finally the future perspective for the evolution of this game is presented which includes the addition of some questions that the user will be able to answer. Finally an evaluation is scheduled to be performed at the end of the project.

  19. 3D model tools for architecture and archaeology reconstruction

    NASA Astrophysics Data System (ADS)

    Vlad, Ioan; Herban, Ioan Sorin; Stoian, Mircea; Vilceanu, Clara-Beatrice

    2016-06-01

    The main objective of architectural and patrimonial survey is to provide a precise documentation of the status quo of the surveyed objects (monuments, buildings, archaeological object and sites) for preservation and protection, for scientific studies and restoration purposes, for the presentation to the general public. Cultural heritage documentation includes an interdisciplinary approach having as purpose an overall understanding of the object itself and an integration of the information which characterize it. The accuracy and the precision of the model are directly influenced by the quality of the measurements realized on field and by the quality of the software. The software is in the process of continuous development, which brings many improvements. On the other side, compared to aerial photogrammetry, close range photogrammetry and particularly architectural photogrammetry is not limited to vertical photographs with special cameras. The methodology of terrestrial photogrammetry has changed significantly and various photographic acquisitions are widely in use. In this context, the present paper brings forward a comparative study of TLS (Terrestrial Laser Scanner) and digital photogrammetry for 3D modeling. The authors take into account the accuracy of the 3D models obtained, the overall costs involved for each technology and method and the 4th dimension - time. The paper proves its applicability as photogrammetric technologies are nowadays used at a large scale for obtaining the 3D model of cultural heritage objects, efficacious in their assessment and monitoring, thus contributing to historic conservation. Its importance also lies in highlighting the advantages and disadvantages of each method used - very important issue for both the industrial and scientific segment when facing decisions such as in which technology to invest more research and funds.

  20. The Engelbourg's ruins: from 3D TLS point cloud acquisition to 3D virtual and historic models

    NASA Astrophysics Data System (ADS)

    Koehl, Mathieu; Berger, Solveig; Nobile, Sylvain

    2014-05-01

    The Castle of Engelbourg was built at the beginning of the 13th century, at the top of the Schlossberg. It is situated on the territory of the municipality of Thann (France), at the crossroads of Alsace and Lorraine, and dominates the outlet of the valley of Thur. Its strategic position was one of the causes of its systematic destructions during the 17th century, and Louis XIV finished his fate by ordering his demolition in 1673. Today only few vestiges remain, of which a section of the main tower from about 7m of diameter and 4m of wide laying on its slice, unique characteristic in the regional castral landscape. It is visible since the valley, was named "the Eye of the witch", and became a key attraction of the region. The site, which extends over approximately one hectare, is for several years the object of numerous archaeological studies and is at the heart of a project of valuation of the vestiges today. It was indeed a key objective, among the numerous planned works, to realize a 3D model of the site in its current state, in other words, a virtual model "such as seized", exploitable as well from a cultural and tourist point of view as by scientists and in archaeological researches. The team of the ICube/INSA lab had in responsibility the realization of this model, the acquisition of the data until the delivery of the virtual model, thanks to 3D TLS and topographic surveying methods. It was also planned to integrate into this 3D model, data of 2D archives, stemming from series of former excavations. The objectives of this project were the following ones: • Acquisition of 3D digital data of the site and 3D modelling • Digitization of the 2D archaeological data and integration in the 3D model • Implementation of a database connected to the 3D model • Virtual Visit of the site The obtained results allowed us to visualize every 3D object individually, under several forms (point clouds, 3D meshed objects and models, etc.) and at several levels of detail

  1. Modeling moving systems with RELAP5-3D

    SciTech Connect

    Mesina, G. L.; Aumiller, David L.; Buschman, Francis X.; Kyle, Matt R.

    2015-12-04

    RELAP5-3D is typically used to model stationary, land-based reactors. However, it can also model reactors in other inertial and accelerating frames of reference. By changing the magnitude of the gravitational vector through user input, RELAP5-3D can model reactors on a space station or the moon. The field equations have also been modified to model reactors in a non-inertial frame, such as occur in land-based reactors during earthquakes or onboard spacecraft. Transient body forces affect fluid flow in thermal-fluid machinery aboard accelerating crafts during rotational and translational accelerations. It is useful to express the equations of fluid motion in the accelerating frame of reference attached to the moving craft. However, careful treatment of the rotational and translational kinematics is required to accurately capture the physics of the fluid motion. Correlations for flow at angles between horizontal and vertical are generated via interpolation where no experimental studies or data exist. The equations for three-dimensional fluid motion in a non-inertial frame of reference are developed. As a result, two different systems for describing rotational motion are presented, user input is discussed, and an example is given.

  2. Modeling moving systems with RELAP5-3D

    DOE PAGES

    Mesina, G. L.; Aumiller, David L.; Buschman, Francis X.; ...

    2015-12-04

    RELAP5-3D is typically used to model stationary, land-based reactors. However, it can also model reactors in other inertial and accelerating frames of reference. By changing the magnitude of the gravitational vector through user input, RELAP5-3D can model reactors on a space station or the moon. The field equations have also been modified to model reactors in a non-inertial frame, such as occur in land-based reactors during earthquakes or onboard spacecraft. Transient body forces affect fluid flow in thermal-fluid machinery aboard accelerating crafts during rotational and translational accelerations. It is useful to express the equations of fluid motion in the acceleratingmore » frame of reference attached to the moving craft. However, careful treatment of the rotational and translational kinematics is required to accurately capture the physics of the fluid motion. Correlations for flow at angles between horizontal and vertical are generated via interpolation where no experimental studies or data exist. The equations for three-dimensional fluid motion in a non-inertial frame of reference are developed. As a result, two different systems for describing rotational motion are presented, user input is discussed, and an example is given.« less

  3. Fisheye Lenses for 3d Modeling: Evaluations and Considerations

    NASA Astrophysics Data System (ADS)

    Barazzetti, L.; Previtali, M.; Roncoroni, F.

    2017-02-01

    Fisheye lenses are becoming more popular in complete image-based modelling projects of small and narrow spaces. The growing interest in fisheye lenses is confirmed by the availability of different commercial software incorporating a fisheye camera model. Such software are now able to carry out the steps of the image processing pipeline in a fully automated way, from camera calibration and orientation to dense matching, surface generation, and orthophoto production. This paper highlights the advantages (and disadvantages) of fisheye lenses when used for 3D modelling projects through different commercial software. The goal is not only a comparison of commercial software, but also an analysis of the additional issues that arise when a fisheye lens is used for 3D modelling. Results confirm that a fisheye lens is suitable for accurate metric documentation, especially when limited space is available. On the other hand, additional issues where found during the camera calibration/image orientation step as well as the texture generation and orthophoto production phases, for which particular attention is required.

  4. From Tls Point Clouds to 3d Models of Trees: a Comparison of Existing Algorithms for 3d Tree Reconstruction

    NASA Astrophysics Data System (ADS)

    Bournez, E.; Landes, T.; Saudreau, M.; Kastendeuch, P.; Najjar, G.

    2017-02-01

    3D models of tree geometry are important for numerous studies, such as for urban planning or agricultural studies. In climatology, tree models can be necessary for simulating the cooling effect of trees by estimating their evapotranspiration. The literature shows that the more accurate the 3D structure of a tree is, the more accurate microclimate models are. This is the reason why, since 2013, we have been developing an algorithm for the reconstruction of trees from terrestrial laser scanner (TLS) data, which we call TreeArchitecture. Meanwhile, new promising algorithms dedicated to tree reconstruction have emerged in the literature. In this paper, we assess the capacity of our algorithm and of two others -PlantScan3D and SimpleTree- to reconstruct the 3D structure of trees. The aim of this reconstruction is to be able to characterize the geometric complexity of trees, with different heights, sizes and shapes of branches. Based on a specific surveying workflow with a TLS, we have acquired dense point clouds of six different urban trees, with specific architectures, before reconstructing them with each algorithm. Finally, qualitative and quantitative assessments of the models are performed using reference tree reconstructions and field measurements. Based on this assessment, the advantages and the limits of every reconstruction algorithm are highlighted. Anyway, very satisfying results can be reached for 3D reconstructions of tree topology as well as of tree volume.

  5. Computational model of mesenchymal migration in 3D under chemotaxis

    PubMed Central

    Ribeiro, F. O.; Gómez-Benito, M. J.; Folgado, J.; Fernandes, P. R.; García-Aznar, J. M.

    2017-01-01

    Abstract Cell chemotaxis is an important characteristic of cellular migration, which takes part in crucial aspects of life and development. In this work, we propose a novel in silico model of mesenchymal 3D migration with competing protrusions under a chemotactic gradient. Based on recent experimental observations, we identify three main stages that can regulate mesenchymal chemotaxis: chemosensing, dendritic protrusion dynamics and cell–matrix interactions. Therefore, each of these features is considered as a different module of the main regulatory computational algorithm. The numerical model was particularized for the case of fibroblast chemotaxis under a PDGF-bb gradient. Fibroblasts migration was simulated embedded in two different 3D matrices – collagen and fibrin – and under several PDGF-bb concentrations. Validation of the model results was provided through qualitative and quantitative comparison with in vitro studies. Our numerical predictions of cell trajectories and speeds were within the measured in vitro ranges in both collagen and fibrin matrices. Although in fibrin, the migration speed of fibroblasts is very low, because fibrin is a stiffer and more entangling matrix. Testing PDGF-bb concentrations, we noticed that an increment of this factor produces a speed increment. At 1 ng mL−1 a speed peak is reached after which the migration speed diminishes again. Moreover, we observed that fibrin exerts a dampening behavior on migration, significantly affecting the migration efficiency. PMID:27336322

  6. Computational model of mesenchymal migration in 3D under chemotaxis.

    PubMed

    Ribeiro, F O; Gómez-Benito, M J; Folgado, J; Fernandes, P R; García-Aznar, J M

    2017-01-01

    Cell chemotaxis is an important characteristic of cellular migration, which takes part in crucial aspects of life and development. In this work, we propose a novel in silico model of mesenchymal 3D migration with competing protrusions under a chemotactic gradient. Based on recent experimental observations, we identify three main stages that can regulate mesenchymal chemotaxis: chemosensing, dendritic protrusion dynamics and cell-matrix interactions. Therefore, each of these features is considered as a different module of the main regulatory computational algorithm. The numerical model was particularized for the case of fibroblast chemotaxis under a PDGF-bb gradient. Fibroblasts migration was simulated embedded in two different 3D matrices - collagen and fibrin - and under several PDGF-bb concentrations. Validation of the model results was provided through qualitative and quantitative comparison with in vitro studies. Our numerical predictions of cell trajectories and speeds were within the measured in vitro ranges in both collagen and fibrin matrices. Although in fibrin, the migration speed of fibroblasts is very low, because fibrin is a stiffer and more entangling matrix. Testing PDGF-bb concentrations, we noticed that an increment of this factor produces a speed increment. At 1 ng mL(-1) a speed peak is reached after which the migration speed diminishes again. Moreover, we observed that fibrin exerts a dampening behavior on migration, significantly affecting the migration efficiency.

  7. Simulation of 3D Global Wave Propagation Through Geodynamic Models

    NASA Astrophysics Data System (ADS)

    Schuberth, B.; Piazzoni, A.; Bunge, H.; Igel, H.; Steinle-Neumann, G.

    2005-12-01

    This project aims at a better understanding of the forward problem of global 3D wave propagation. We use the spectral element program "SPECFEM3D" (Komatitsch and Tromp, 2002a,b) with varying input models of seismic velocities derived from mantle convection simulations (Bunge et al., 2002). The purpose of this approach is to obtain seismic velocity models independently from seismological studies. In this way one can test the effects of varying parameters of the mantle convection models on the seismic wave field. In order to obtain the seismic velocities from the temperature field of the geodynamical simulations we follow a mineral physics approach. Assuming a certain mantle composition (e.g. pyrolite with CMASF composition) we compute the stable phases for each depth (i.e. pressure) and temperature by system Gibbs free energy minimization. Elastic moduli and density are calculated from the equations of state of the stable mineral phases. For this we use a mineral physics database derived from calorimetric experiments (enthalphy and entropy of formation, heat capacity) and EOS parameters.

  8. Image sequence coding using 3D scene models

    NASA Astrophysics Data System (ADS)

    Girod, Bernd

    1994-09-01

    The implicit and explicit use of 3D models for image sequence coding is discussed. For implicit use, a 3D model can be incorporated into motion compensating prediction. A scheme that estimates the displacement vector field with a rigid body motion constraint by recovering epipolar lines from an unconstrained displacement estimate and then repeating block matching along the epipolar line is proposed. Experimental results show that an improved displacement vector field can be obtained with a rigid body motion constraint. As an example for explicit use, various results with a facial animation model for videotelephony are discussed. A 13 X 16 B-spline mask can be adapted automatically to individual faces and is used to generate facial expressions based on FACS. A depth-from-defocus range camera suitable for real-time facial motion tracking is described. Finally, the real-time facial animation system `Traugott' is presented that has been used to generate several hours of broadcast video. Experiments suggest that a videophone system based on facial animation might require a transmission bitrate of 1 kbit/s or below.

  9. Pose invariant face recognition: 3D model from single photo

    NASA Astrophysics Data System (ADS)

    Napoléon, Thibault; Alfalou, Ayman

    2017-02-01

    Face recognition is widely studied in the literature for its possibilities in surveillance and security. In this paper, we report a novel algorithm for the identification task. This technique is based on an optimized 3D modeling allowing to reconstruct faces in different poses from a limited number of references (i.e. one image by class/person). Particularly, we propose to use an active shape model to detect a set of keypoints on the face necessary to deform our synthetic model with our optimized finite element method. Indeed, in order to improve our deformation, we propose a regularization by distances on graph. To perform the identification we use the VanderLugt correlator well know to effectively address this task. On the other hand we add a difference of Gaussian filtering step to highlight the edges and a description step based on the local binary patterns. The experiments are performed on the PHPID database enhanced with our 3D reconstructed faces of each person with an azimuth and an elevation ranging from -30° to +30°. The obtained results prove the robustness of our new method with 88.76% of good identification when the classic 2D approach (based on the VLC) obtains just 44.97%.

  10. Heralding a new paradigm in 3D tumor modeling.

    PubMed

    Fong, Eliza L S; Harrington, Daniel A; Farach-Carson, Mary C; Yu, Hanry

    2016-11-01

    Numerous studies to date have contributed to a paradigm shift in modeling cancer, moving from the traditional two-dimensional culture system to three-dimensional (3D) culture systems for cancer cell culture. This led to the inception of tumor engineering, which has undergone rapid advances over the years. In line with the recognition that tumors are not merely masses of proliferating cancer cells but rather, highly complex tissues consisting of a dynamic extracellular matrix together with stromal, immune and endothelial cells, significant efforts have been made to better recapitulate the tumor microenvironment in 3D. These approaches include the development of engineered matrices and co-cultures to replicate the complexity of tumor-stroma interactions in vitro. However, the tumor engineering and cancer biology fields have traditionally relied heavily on the use of cancer cell lines as a cell source in tumor modeling. While cancer cell lines have contributed to a wealth of knowledge in cancer biology, the use of this cell source is increasingly perceived as a major contributing factor to the dismal failure rate of oncology drugs in drug development. Backing this notion is the increasing evidence that tumors possess intrinsic heterogeneity, which predominantly homogeneous cancer cell lines poorly reflect. Tumor heterogeneity contributes to therapeutic resistance in patients. To overcome this limitation, cancer cell lines are beginning to be replaced by primary tumor cell sources, in the form of patient-derived xenografts and organoids cultures. Moving forward, we propose that further advances in tumor engineering would require that tumor heterogeneity (tumor variants) be taken into consideration together with tumor complexity (tumor-stroma interactions). In this review, we provide a comprehensive overview of what has been achieved in recapitulating tumor complexity, and discuss the importance of incorporating tumor heterogeneity into 3D in vitro tumor models. This

  11. Correlating 3D morphology with molecular pathology: fibrotic remodelling in human lung biopsies.

    PubMed

    Kellner, Manuela; Wehling, Judith; Warnecke, Gregor; Heidrich, Marko; Izykowski, Nicole; Vogel-Claussen, Jens; Lorbeer, Raoul-Amadeus; Antonopoulos, Georgios; Janciauskiene, Sabina; Grothausmann, Roman; Knudsen, Lars; Ripken, Tammo; Meyer, Heiko; Kreipe, Hans; Ochs, Matthias; Jonigk, Danny; Kühnel, Mark Philipp

    2015-12-01

    Assessing alterations of the parenchymal architecture is essential in understanding fibrosing interstitial lung diseases. Here, we present a novel method to visualise fibrotic remodelling in human lungs and correlate morphological three-dimensional (3D) data with gene and protein expression in the very same sample. The key to our approach is a novel embedding resin that clears samples to full optical transparency and simultaneously allows 3D laser tomography and preparation of sections for histology, immunohistochemistry and RNA isolation. Correlating 3D laser tomography with molecular diagnostic techniques enables new insights into lung diseases. This approach has great potential to become an essential tool in pulmonary research.

  12. A Prototype Digital Library for 3D Collections: Tools To Capture, Model, Analyze, and Query Complex 3D Data.

    ERIC Educational Resources Information Center

    Rowe, Jeremy; Razdan, Anshuman

    The Partnership for Research in Spatial Modeling (PRISM) project at Arizona State University (ASU) developed modeling and analytic tools to respond to the limitations of two-dimensional (2D) data representations perceived by affiliated discipline scientists, and to take advantage of the enhanced capabilities of three-dimensional (3D) data that…

  13. Canada in 3D - Toward a Sustainable 3D Model for Canadian Geology from Diverse Data Sources

    NASA Astrophysics Data System (ADS)

    Brodaric, B.; Pilkington, M.; Snyder, D. B.; St-Onge, M. R.; Russell, H.

    2015-12-01

    Many big science issues span large areas and require data from multiple heterogeneous sources, for example climate change, resource management, and hazard mitigation. Solutions to these issues can significantly benefit from access to a consistent and integrated geological model that would serve as a framework. However, such a model is absent for most large countries including Canada, due to the size of the landmass and the fragmentation of the source data into institutional and disciplinary silos. To overcome these barriers, the "Canada in 3D" (C3D) pilot project was recently launched by the Geological Survey of Canada. C3D is designed to be evergreen, multi-resolution, and inter-disciplinary: (a) it is to be updated regularly upon acquisition of new data; (b) portions vary in resolution and will initially consist of four layers (surficial, sedimentary, crystalline, and mantle) with intermediary patches of higher-resolution fill; and (c) a variety of independently managed data sources are providing inputs, such as geophysical, 3D and 2D geological models, drill logs, and others. Notably, scalability concerns dictate a decentralized and interoperable approach, such that only key control objects, denoting anchors for the modeling process, are imported into the C3D database while retaining provenance links to original sources. The resultant model is managed in the database, contains full modeling provenance as well as links to detailed information on rock units, and is to be visualized in desktop and online environments. It is anticipated that C3D will become the authoritative state of knowledge for the geology of Canada at a national scale.

  14. 3-D physical models of mitosis (with asters) and cytokinesis.

    PubMed

    Cheng, Kang; Zou, Changhua

    2004-01-01

    First, we define new concepts of Life Objects, Informative Objects and Virtual Objects, Discrete Chromosome Rings (DCR); we introduce a mathematical concept of meridian plane (MP) in a three dimensional (3-D) cylindrical coordinate system (CCS). Based on these concepts, classic mechanics, classic electromagnetism and published biological data, we develop our 3-D physical models of natural and normal mitosis (with asters) and cytokinesis, for animal cells in M phase. We propose following hypotheses: Chromosomes Exclusion: No normally and naturally replicated chromosomes can occupy the same nucleus without growing sizes of the nucleus and the cell. Spontaneous and strong electromagnetic fields (EMF) forces among chromosomes, centrosomes and microtubules split the nucleus and separate the two sets of sister chromatids when they are strong enough. Nuclei Exclusion: No normally and naturally doubled nuclei can occupy the same cell if the doubled size of nuclei is not far smaller than size of the cell. The spontaneous and strong EMF forces in protoplasm (or cortex), separate two sets of chromosomes, spindles and poles, drive contractile proteins to the equator in cell cortex, and continue to guide and to transport free charged objects until complete the cytokinesis. Centrioles Exclusion: No naturally and normally doubled centrioles can occupy the same centrosome. The spontaneous and strong repulsive EMF forces are the primary cause for the exclusions. The principles of our models are also applied to mitosis and cytokinesis for lower plant cells, to that of multiple nuclei or mutant chromosomes, and to meiosis, for both animal cells and lower plant cells.

  15. High-resolution 3D digital models of artworks

    NASA Astrophysics Data System (ADS)

    Fontana, Raffaella; Gambino, Maria Chiara; Greco, Marinella; Pampaloni, Enrico; Pezzati, Luca; Scopigno, Roberto

    2003-10-01

    The measurement of the shape of an artwork usually requires a high-resolution instrumentation, in order to catch small details such as chisel marks, sculptural relieves, surface cracks, etc. 3D scanning techniques, together with new modeling software tools, allow a high fidelity reproduction of an artwork: these can be applied either to support and document its repair or for the realization of 3D archives and virtual museums. Starting from a high-resolution digital model of an object, a further step could be its reproduction by means of fast-prototyping techniques like stereo-lithography or electro-erosion. This work is aimed at showing the performance of a high-resolution laser scanner devoted to Cultural Heritage applications. The device is portable and very versatile, in order to allow in situ applications, accurate and reliable, so to capture intricate details. This laser profilometer has been used in a few surveys, the most significant of which are the monitoring the various phases of the restoration process of an ellenistic bronze (the Minerva of Arezzo, Florence), the cataloguing of some archaeological findings (from the Grotta della Poesia, Lecce) and the documenting of wooden panels surface conditions (the "Madonna del Cardellino" by Raffaello and "La Tebaide" by Beato Angelico).

  16. Dynamic deformable models for 3D MRI heart segmentation

    NASA Astrophysics Data System (ADS)

    Zhukov, Leonid; Bao, Zhaosheng; Gusikov, Igor; Wood, John; Breen, David E.

    2002-05-01

    Automated or semiautomated segmentation of medical images decreases interstudy variation, observer bias, and postprocessing time as well as providing clincally-relevant quantitative data. In this paper we present a new dynamic deformable modeling approach to 3D segmentation. It utilizes recently developed dynamic remeshing techniques and curvature estimation methods to produce high-quality meshes. The approach has been implemented in an interactive environment that allows a user to specify an initial model and identify key features in the data. These features act as hard constraints that the model must not pass through as it deforms. We have employed the method to perform semi-automatic segmentation of heart structures from cine MRI data.

  17. Stochastic Modeling of Calcium in 3D Geometry

    PubMed Central

    Mazel, Tomáš; Raymond, Rebecca; Raymond-Stintz, Mary; Jett, Stephen; Wilson, Bridget S.

    2009-01-01

    Release of inflammatory mediators by mast cells in type 1 immediate-hypersensitivity allergic reactions relies on antigen-dependent increases in cytosolic calcium. Here, we used a series of electron microscopy images to build a 3D reconstruction representing a slice through a rat tumor mast cell, which then served as a basis for stochastic modeling of inositol-trisphosphate-mediated calcium responses. The stochastic approach was verified by reaction-diffusion modeling within the same geometry. Local proximity of the endoplasmic reticulum to either the plasma membrane or mitochondria is predicted to differentially impact local inositol trisphosphate receptor transport. The explicit consideration of organelle spatial relationships represents an important step toward building a comprehensive, realistic model of cellular calcium dynamics. PMID:19254531

  18. 3D-QSAR and molecular docking studies on HIV protease inhibitors

    NASA Astrophysics Data System (ADS)

    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.

  19. Molecular Determinants of Juvenile Hormone Action as Revealed by 3D QSAR Analysis in Drosophila

    PubMed Central

    Beňo, Milan; Farkaš, Robert

    2009-01-01

    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 Å or longer than 13.5 Å, 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. PMID:19547707

  20. Development of an aquifer management model AQMAN3D

    USGS Publications Warehouse

    Puig, Juan Carlos; Rolon-Collazo, L. I.; Pagan-Trinidad, Ishmael; Krishna, J.H.; Quinones-Aponte, Vicente; Gomez-Gomez, Fernando; Morris, G.L.

    1990-01-01

    A computer code that enables the use of the USGS Modular groundwater flow model for aquifermanagement modeling has been developed. Aquifermanagement techniques integrate groundwater flow modeling with linear quadratic optimization methods for the solution of various aquifer management problems. The model AQMAN3D, is a modified version of a previously developed two-dimensional AQMAN model. The idea of coupling the AQMAN model with the MODULAR model arose because actual groundwater flow systems behave in a three dimensional manner, therefore requiring treatment as such, and due to the widespread use of MODULAR. The use of the AQMAN3D model permits the implementation of the technique known as aquifer managementmodeling. A generalized approach to obtain an optimal solution to an aquifer management problem is proposed, and a sample test problem is presented to illustrate the use of the model. Even though the model provides the hydrologist with a new and powerful investigative tool, its applicability is limited to confined or quasiconfined systems.

  1. Geomorphological maps and 3d models in cave research

    NASA Astrophysics Data System (ADS)

    Ballesteros, Daniel; Jiménez-Sánchez, Montserrat; José Domínguez-Cuesta, María

    2013-04-01

    Cave geomorphological processes and features can be studied by geomorphological maps although topographic maps, aerial photos and GPS are not available. Methods in cave geomorphological mapping are conditioned by cave environment configuration, the need of using speleological techniques, and limitations arising from the projection of the 3D data from the cave to a 2D plan. Some of our previous works in the Cantabrian Mountains and Cantabrian Coast (NW Spain) established the approach of the design of cave geomorphological maps and its legend. Today we are improving the display of cave process combining geomorphological maps and 3d models based on the experience obtained from the research of one cave from the Cantabrian Coast and four caves in the Picos de Europa National Park (funded by GEOCAVE project, Spanish National Parks Agency). The five caves are developed in Carboniferous limestone affected by faults and thrusts. The method of work includes: 1) the elaboration of the cave survey at 1:50 to 1:500 scale; 2) the check of the cave survey of three caves by closed loops; 3) the mapping of cave features based on the performed survey; 4) the 3d modeling of the caves approximating each survey shoot by an octagonal prism; and 5) the implementation and management of the survey and geomorphological map in a Geographic Information System. Based on the survey, the cavities are small caves to deep alpine shafts with 281 to 4,438 m length and up to 738 m deep. The precision of the cave maps only could be estimated in two caves at a cavity scale, displaying both of them a 2.49 % error. The prisms of the 3d model was classified into four groups according to the morphology of the cave passage: 1) canyons, 2) phreatic and epiphreatic tubes, 3) soutirage conduits, 4) mixed forms composed by phreatic and epiphreatic tubes modified by fluvial incision, 5) pitches and 6) irregular passages enlarged strongly by gravity process. According to our previous works geomorphological

  2. Geographic Video 3d Data Model And Retrieval

    NASA Astrophysics Data System (ADS)

    Han, Z.; Cui, C.; Kong, Y.; Wu, H.

    2014-04-01

    Geographic video includes both spatial and temporal geographic features acquired through ground-based or non-ground-based cameras. With the popularity of video capture devices such as smartphones, the volume of user-generated geographic video clips has grown significantly and the trend of this growth is quickly accelerating. Such a massive and increasing volume poses a major challenge to efficient video management and query. Most of the today's video management and query techniques are based on signal level content extraction. They are not able to fully utilize the geographic information of the videos. This paper aimed to introduce a geographic video 3D data model based on spatial information. The main idea of the model is to utilize the location, trajectory and azimuth information acquired by sensors such as GPS receivers and 3D electronic compasses in conjunction with video contents. The raw spatial information is synthesized to point, line, polygon and solid according to the camcorder parameters such as focal length and angle of view. With the video segment and video frame, we defined the three categories geometry object using the geometry model of OGC Simple Features Specification for SQL. We can query video through computing the spatial relation between query objects and three categories geometry object such as VFLocation, VSTrajectory, VSFOView and VFFovCone etc. We designed the query methods using the structured query language (SQL) in detail. The experiment indicate that the model is a multiple objective, integration, loosely coupled, flexible and extensible data model for the management of geographic stereo video.

  3. Modeling tree crown dynamics with 3D partial differential equations

    PubMed Central

    Beyer, Robert; Letort, Véronique; Cournède, Paul-Henry

    2014-01-01

    We characterize a tree's spatial foliage distribution by the local leaf area density. Considering this spatially continuous variable allows to describe the spatiotemporal evolution of the tree crown by means of 3D partial differential equations. These offer a framework to rigorously take locally and adaptively acting effects into account, notably the growth toward light. Biomass production through photosynthesis and the allocation to foliage and wood are readily included in this model framework. The system of equations stands out due to its inherent dynamic property of self-organization and spontaneous adaptation, generating complex behavior from even only a few parameters. The density-based approach yields spatially structured tree crowns without relying on detailed geometry. We present the methodological fundamentals of such a modeling approach and discuss further prospects and applications. PMID:25101095

  4. Measurement of Laser Weld Temperatures for 3D Model Input

    SciTech Connect

    Dagel, Daryl; Grossetete, Grant; Maccallum, Danny O.

    2016-10-01

    Laser welding is a key joining process used extensively in the manufacture and assembly of critical components for several weapons systems. Sandia National Laboratories advances the understanding of the laser welding process through coupled experimentation and modeling. This report summarizes the experimental portion of the research program, which focused on measuring temperatures and thermal history of laser welds on steel plates. To increase confidence in measurement accuracy, researchers utilized multiple complementary techniques to acquire temperatures during laser welding. This data serves as input to and validation of 3D laser welding models aimed at predicting microstructure and the formation of defects and their impact on weld-joint reliability, a crucial step in rapid prototyping of weapons components.

  5. 3D Tissue-Engineered Model of Ewing Sarcoma

    PubMed Central

    Lamhamedi-Cherradi, Salah-Eddine; Santoro, Marco; Ramammoorthy, Vandhana; Menegaz, Brian A.; Bartholomeusz, Geoffrey; Iles, Lakesla R.; Amin, Hesham M.; Livingston, Andrew J.; Mikos, Antonios G.; Ludwig, Joseph A.

    2015-01-01

    Despite longstanding reliance upon monolayer culture for studying cancer cells, and numerous advantages from both a practical and experimental standpoint, a growing body of evidence suggests more complex three-dimensional (3D) models are necessary to properly mimic many of the critical hallmarks associated with the oncogenesis, maintenance and spread of Ewing sarcoma (ES), the second most common pediatric bone tumor. And as clinicians increasingly turn to biologically-targeted therapies that exert their effects not only on the tumor cells themselves, but also on the surrounding extracellular matrix, it is especially important that preclinical models evolve in parallel to reliably measure antineoplastic effects and possible mechanisms of de novo and acquired drug resistance. Herein, we highlight a number of innovative methods used to fabricate biomimetic ES tumors, encompassing both the surrounding cellular milieu and extracellular matrix (ECM), and suggest potential applications to advance our understanding of ES biology, preclinical drug testing, and personalized medicine. PMID:25109853

  6. 3D Model of the Eta Carinae Little Homunculus Nebula

    NASA Astrophysics Data System (ADS)

    Steffen, Wolfgang; Teodoro, Mairan; Madura, Thomas; Groh, Jose H.; Gull, Theodore R.; Corcoran, Michael F.; Damineli, Augusto; Hamaguchi, Kenji

    2015-01-01

    We extend our morpho-kinematic 3D modeling of the Homunculus nebula (Steffen et al., 2014) to the interior nested Little Homunculus. The model is based on spectroscopic observations from HST/STIS. We find that the structure of the interior Little Homunculus is rather flat in the polar regions and interacts with the main Homunculus nebula only on one side, towards the periastron direction of the binary orbit. Furthermore, the two lobes of the LH are misaligned, also towards the periastron direction. As an explanation for the misalignment we propose that, in both cases, shortly after the eruptions that created the bipolar nebulae from the primary star, the off-center wind of the secondary has pushed the ejecta towards the periastron directions, since the secondary is most of the time near the apastron. Future hydrodynamic simulations are warranted to confirm this scenario.

  7. Plasticized protein for 3D printing by fused deposition modeling

    NASA Astrophysics Data System (ADS)

    Chaunier, Laurent; Leroy, Eric; Della Valle, Guy; Lourdin, Denis

    2016-10-01

    The developments of Additive Manufacturing (AM) by Fused Deposition Modeling (FDM) now target new 3D printable materials, leading to novel properties like those given by biopolymers such as proteins: degradability, biocompatibility and edibility. Plasticized materials from zein, a storage protein issued from corn, present interesting thermomechanical and rheological properties, possibly matching with AM-FDM specifications. Thus commercial zein plasticized with 20% glycerol has a glass transition temperature (Tg) at about 42°C, after storage at intermediate relative humidity (RH=59%). Its principal mechanical relaxation at Tα ≈ 50°C leads to a drop of the elastic modulus from about 1.1 GPa, at ambient temperature, to 0.6 MPa at Tα+100°C. These values are in the same range as values obtained in the case of standard polymers for AM-FDM processing, as PLA and ABS, although relaxation mechanisms are likely different in these materials. Such results lead to the setting up of zein-based compositions printable by AM-FDM and allow processing bioresorbable printed parts, with designed 3D geometry and structure.

  8. Gene3D: modelling protein structure, function and evolution.

    PubMed

    Yeats, Corin; Maibaum, Michael; Marsden, Russell; Dibley, Mark; Lee, David; Addou, Sarah; Orengo, Christine A

    2006-01-01

    The Gene3D release 4 database and web portal (http://cathwww.biochem.ucl.ac.uk:8080/Gene3D) provide a combined structural, functional and evolutionary view of the protein world. It is focussed on providing structural annotation for protein sequences without structural representatives--including the complete proteome sets of over 240 different species. The protein sequences have also been clustered into whole-chain families so as to aid functional prediction. The structural annotation is generated using HMM models based on the CATH domain families; CATH is a repository for manually deduced protein domains. Amongst the changes from the last publication are: the addition of over 100 genomes and the UniProt sequence database, domain data from Pfam, metabolic pathway and functional data from COGs, KEGG and GO, and protein-protein interaction data from MINT and BIND. The website has been rebuilt to allow more sophisticated querying and the data returned is presented in a clearer format with greater functionality. Furthermore, all data can be downloaded in a simple XML format, allowing users to carry out complex investigations at their own computers.

  9. 3D in vitro modeling of the central nervous system

    PubMed Central

    Hopkins, Amy M.; DeSimone, Elise; Chwalek, Karolina; Kaplan, David L.

    2015-01-01

    There are currently more than 600 diseases characterized as affecting the central nervous system (CNS) which inflict neural damage. Unfortunately, few of these conditions have effective treatments available. Although significant efforts have been put into developing new therapeutics, drugs which were promising in the developmental phase have high attrition rates in late stage clinical trials. These failures could be circumvented if current 2D in vitro and in vivo models were improved. 3D, tissue-engineered in vitro systems can address this need and enhance clinical translation through two approaches: (1) bottom-up, and (2) top-down (developmental/regenerative) strategies to reproduce the structure and function of human tissues. Critical challenges remain including biomaterials capable of matching the mechanical properties and extracellular matrix (ECM) composition of neural tissues, compartmentalized scaffolds that support heterogeneous tissue architectures reflective of brain organization and structure, and robust functional assays for in vitro tissue validation. The unique design parameters defined by the complex physiology of the CNS for construction and validation of 3D in vitro neural systems are reviewed here. PMID:25461688

  10. 3D in vitro modeling of the central nervous system.

    PubMed

    Hopkins, Amy M; DeSimone, Elise; Chwalek, Karolina; Kaplan, David L

    2015-02-01

    There are currently more than 600 diseases characterized as affecting the central nervous system (CNS) which inflict neural damage. Unfortunately, few of these conditions have effective treatments available. Although significant efforts have been put into developing new therapeutics, drugs which were promising in the developmental phase have high attrition rates in late stage clinical trials. These failures could be circumvented if current 2D in vitro and in vivo models were improved. 3D, tissue-engineered in vitro systems can address this need and enhance clinical translation through two approaches: (1) bottom-up, and (2) top-down (developmental/regenerative) strategies to reproduce the structure and function of human tissues. Critical challenges remain including biomaterials capable of matching the mechanical properties and extracellular matrix (ECM) composition of neural tissues, compartmentalized scaffolds that support heterogeneous tissue architectures reflective of brain organization and structure, and robust functional assays for in vitro tissue validation. The unique design parameters defined by the complex physiology of the CNS for construction and validation of 3D in vitro neural systems are reviewed here.

  11. Modeling approaches for ligand-based 3D similarity.

    PubMed

    Tresadern, Gary; Bemporad, Daniele

    2010-10-01

    3D ligand-based similarity approaches are widely used in the early phases of drug discovery for tasks such as hit finding by virtual screening or compound design with quantitative structure-activity relationships. Here in we review widely used software for performing such tasks. Some techniques are based on relatively mature technology, shape-based similarity for instance. Typically, these methods remained in the realm of the expert user, the experienced modeler. However, advances in implementation and speed have improved usability and allow these methods to be applied to databases comprising millions of compounds. There are now many reports of such methods impacting drug-discovery projects. As such, the medicinal chemistry community has become the intended market for some of these new tools, yet they may consider the wide array and choice of approaches somewhat disconcerting. Each method has subtle differences and is better suited to certain tasks than others. In this article we review some of the widely used computational methods via application, provide straightforward background on the underlying theory and provide examples for the interested reader to pursue in more detail. In the new era of preclinical drug discovery there will be ever more pressure to move faster and more efficiently, and computational approaches based on 3D ligand similarity will play an increasing role in in this process.

  12. 3D QSAR studies, pharmacophore modeling and virtual screening on a series of steroidal aromatase inhibitors.

    PubMed

    Xie, Huiding; Qiu, Kaixiong; Xie, Xiaoguang

    2014-11-14

    Aromatase inhibitors are the most important targets in treatment of estrogen-dependent cancers. In order to search for potent steroidal aromatase inhibitors (SAIs) with lower side effects and overcome cellular resistance, comparative molecular field analysis (CoMFA) and comparative molecular similarity indices analysis (CoMSIA) were performed on a series of SAIs to build 3D QSAR models. The reliable and predictive CoMFA and CoMSIA models were obtained with statistical results (CoMFA: q² = 0.636, r²(ncv) = 0.988, r²(pred) = 0.658; CoMSIA: q² = 0.843, r²(ncv) = 0.989, r²(pred) = 0.601). This 3D QSAR approach provides significant insights that can be used to develop novel and potent SAIs. In addition, Genetic algorithm with linear assignment of hypermolecular alignment of database (GALAHAD) was used to derive 3D pharmacophore models. The selected pharmacophore model contains two acceptor atoms and four hydrophobic centers, which was used as a 3D query for virtual screening against NCI2000 database. Six hit compounds were obtained and their biological activities were further predicted by the CoMFA and CoMSIA models, which are expected to design potent and novel SAIs.

  13. Polygonal Shapes Detection in 3d Models of Complex Architectures

    NASA Astrophysics Data System (ADS)

    Benciolini, G. B.; Vitti, A.

    2015-02-01

    A sequential application of two global models defined on a variational framework is proposed for the detection of polygonal shapes in 3D models of complex architectures. As a first step, the procedure involves the use of the Mumford and Shah (1989) 1st-order variational model in dimension two (gridded height data are processed). In the Mumford-Shah model an auxiliary function detects the sharp changes, i.e., the discontinuities, of a piecewise smooth approximation of the data. The Mumford-Shah model requires the global minimization of a specific functional to simultaneously produce both the smooth approximation and its discontinuities. In the proposed procedure, the edges of the smooth approximation derived by a specific processing of the auxiliary function are then processed using the Blake and Zisserman (1987) 2nd-order variational model in dimension one (edges are processed in the plane). This second step permits to describe the edges of an object by means of piecewise almost-linear approximation of the input edges themselves and to detects sharp changes of the first-derivative of the edges so to detect corners. The Mumford-Shah variational model is used in two dimensions accepting the original data as primary input. The Blake-Zisserman variational model is used in one dimension for the refinement of the description of the edges. The selection among all the boundaries detected by the Mumford-Shah model of those that present a shape close to a polygon is performed by considering only those boundaries for which the Blake-Zisserman model identified discontinuities in their first derivative. The output of the procedure are hence shapes, coming from 3D geometric data, that can be considered as polygons. The application of the procedure is suitable for, but not limited to, the detection of objects such as foot-print of polygonal buildings, building facade boundaries or windows contours. v The procedure is applied to a height model of the building of the Engineering

  14. Advanced prior modeling for 3D bright field electron tomography

    NASA Astrophysics Data System (ADS)

    Sreehari, Suhas; Venkatakrishnan, S. V.; Drummy, Lawrence F.; Simmons, Jeffrey P.; Bouman, Charles A.

    2015-03-01

    Many important imaging problems in material science involve reconstruction of images containing repetitive non-local structures. Model-based iterative reconstruction (MBIR) could in principle exploit such redundancies through the selection of a log prior probability term. However, in practice, determining such a log prior term that accounts for the similarity between distant structures in the image is quite challenging. Much progress has been made in the development of denoising algorithms like non-local means and BM3D, and these are known to successfully capture non-local redundancies in images. But the fact that these denoising operations are not explicitly formulated as cost functions makes it unclear as to how to incorporate them in the MBIR framework. In this paper, we formulate a solution to bright field electron tomography by augmenting the existing bright field MBIR method to incorporate any non-local denoising operator as a prior model. We accomplish this using a framework we call plug-and-play priors that decouples the log likelihood and the log prior probability terms in the MBIR cost function. We specifically use 3D non-local means (NLM) as the prior model in the plug-and-play framework, and showcase high quality tomographic reconstructions of a simulated aluminum spheres dataset, and two real datasets of aluminum spheres and ferritin structures. We observe that streak and smear artifacts are visibly suppressed, and that edges are preserved. Also, we report lower RMSE values compared to the conventional MBIR reconstruction using qGGMRF as the prior model.

  15. Brandenburg 3D - a comprehensive 3D Subsurface Model, Conception of an Infrastructure Node and a Web Application

    NASA Astrophysics Data System (ADS)

    Kerschke, Dorit; Schilling, Maik; Simon, Andreas; Wächter, Joachim

    2014-05-01

    The Energiewende and the increasing scarcity of raw materials will lead to an intensified utilization of the subsurface in Germany. Within this context, geological 3D modeling is a fundamental approach for integrated decision and planning processes. Initiated by the development of the European Geospatial Infrastructure INSPIRE, the German State Geological Offices started digitizing their predominantly analog archive inventory. Until now, a comprehensive 3D subsurface model of Brandenburg did not exist. Therefore the project B3D strived to develop a new 3D model as well as a subsequent infrastructure node to integrate all geological and spatial data within the Geodaten-Infrastruktur Brandenburg (Geospatial Infrastructure, GDI-BB) and provide it to the public through an interactive 2D/3D web application. The functionality of the web application is based on a client-server architecture. Server-sided, all available spatial data is published through GeoServer. GeoServer is designed for interoperability and acts as the reference implementation of the Open Geospatial Consortium (OGC) Web Feature Service (WFS) standard that provides the interface that allows requests for geographical features. In addition, GeoServer implements, among others, the high performance certified compliant Web Map Service (WMS) that serves geo-referenced map images. For publishing 3D data, the OGC Web 3D Service (W3DS), a portrayal service for three-dimensional geo-data, is used. The W3DS displays elements representing the geometry, appearance, and behavior of geographic objects. On the client side, the web application is solely based on Free and Open Source Software and leans on the JavaScript API WebGL that allows the interactive rendering of 2D and 3D graphics by means of GPU accelerated usage of physics and image processing as part of the web page canvas without the use of plug-ins. WebGL is supported by most web browsers (e.g., Google Chrome, Mozilla Firefox, Safari, and Opera). The web

  16. Faceless identification: a model for person identification using the 3D shape and 3D motion as cues

    NASA Astrophysics Data System (ADS)

    Klasen, Lena M.; Li, Haibo

    1999-02-01

    Person identification by using biometric methods based on image sequences, or still images, often requires a controllable and cooperative environment during the image capturing stage. In the forensic case the situation is more likely to be the opposite. In this work we propose a method that makes use of the anthropometry of the human body and human actions as cues for identification. Image sequences from surveillance systems are used, which can be seen as monocular image sequences. A 3D deformable wireframe body model is used as a platform to handle the non-rigid information of the 3D shape and 3D motion of the human body from the image sequence. A recursive method for estimating global motion and local shape variations is presented, using two recursive feedback systems.

  17. The USGS 3D Seismic Velocity Model for Northern California

    NASA Astrophysics Data System (ADS)

    Brocher, T. M.; Aagaard, B.; Simpson, R. W.; Jachens, R. C.

    2006-12-01

    We present a new regional 3D seismic velocity model for Northern California for use in strong motion simulations of the 1906 San Francisco and other earthquakes. The model includes compressional-wave velocity (Vp), shear-wave velocity (Vs), density, and intrinsic attenuation (Qp, Qs). These properties were assigned for each rock type in a 3D geologic model derived from surface outcrops, boreholes, gravity and magnetic data, and seismic reflection, refraction, and tomography studies. A detailed description of the model, USGS Bay Area Velocity Model 05.1.0, is available online [http://www.sf06simulation.org/geology/velocitymodel]. For ground motion simulations Vs and Qs are more important parameters than Vp and Qp because the strongest ground motions are generated chiefly by shear and surface wave arrivals. Because Vp data are more common than Vs data, however, we first developed Vp versus depth relations for each rock type and then converted these to Vs versus depth relations. For the most important rock types in Northern California we compiled measurements of Vp versus depth using borehole logs, laboratory measurements on hand samples, seismic refraction profiles, and tomography models. These rock types include Salinian and Sierran granitic rocks, metagraywackes and greenstones of the Franciscan Complex, Tertiary and Mesozoic sedimentary and volcanic rocks, and Quaternary and Holocene deposits (Brocher, USGS OFR 05-1317, 2005). Vp versus depth curves were converted to Vs versus depth curves using new empirical nonlinear relations between Vs and Vp (Brocher, BSSA, 2005). These relations, showing that Poisson's ratio is a nonlinear function of Vp, were similarly based on compilations of diverse Vs and Vp measurements on a large suite of rock types, mainly from California and the Pacific Northwest. The model is distributed in a discretized form with routines to query the model using C++, C, and Fortran 77 programming languages. The geologic model was discretized at

  18. A 3D Bubble Merger Model for RTI Mixing

    NASA Astrophysics Data System (ADS)

    Cheng, Baolian

    2015-11-01

    In this work we present a model for the merger processes of bubbles at the edge of an unstable acceleration driven mixing layer. Steady acceleration defines a self-similar mixing process, with a time-dependent inverse cascade of structures of increasing size. The time evolution is itself a renormalization group evolution. The model predicts the growth rate of a Rayleigh-Taylor chaotic fluid-mixing layer. The 3-D model differs from the 2-D merger model in several important ways. Beyond the extension of the model to three dimensions, the model contains one phenomenological parameter, the variance of the bubble radii at fixed time. The model also predicts several experimental numbers: the bubble mixing rate, the mean bubble radius, and the bubble height separation at the time of merger. From these we also obtain the bubble height to the radius aspect ratio, which is in good agreement with experiments. Applications to recent NIF and Omega experiments will be discussed. This work was performed under the auspices of the U.S. Department of Energy by the Los Alamos National Laboratory under Contract No. W-7405-ENG-36.

  19. Quality assessment of watermarked 3D polygonal models

    NASA Astrophysics Data System (ADS)

    Funk, Wolfgang; Prasiswa, Jennifer

    2006-02-01

    In this paper, we present the design and results of subjective tests for evaluating the perceptibility of digital watermarks in 3D polygonal models. Based on the results we investigate different types of metrics with respect to their usefulness as predictors for the perceived visual quality of models that have been modified using a specific watermarking algorithm. We describe two experiments with models that have been watermarked using controlled free form deformations. The first experiment was conducted in supervised mode with still images of rendered models as stimuli and used the Two Alternative Forced Choice (2AFC) method. The second experiment was based on animated sequences and run in 2AFC mode with additional ratings of the perceived differences, but without assistance by the experimenter. We present a transparency analysis of the results and investigate the ability of image-based and geometry-based metrics to predict the perceived quality of the watermarked models. Our results show that the effectiveness of prediction depends on the type of model and in particular on the feature positions selected by the watermarking algorithm. The results of previous experiments with simplified polygonal models are confirmed, in that geometric measures are good predictors of quality ratings. We found that the symmetric Haussdorf distance is a promising candidate to evaluate the visual impact of the watermarking algorithm used in our experiments.

  20. Handheld camera 3D modeling system using multiple reference panels

    NASA Astrophysics Data System (ADS)

    Fujimura, Kouta; Oue, Yasuhiro; Terauchi, Tomoya; Emi, Tetsuichi

    2002-03-01

    A novel 3D modeling system in which a target object is easily captured and modeled by using a hand-held camera with several reference panels is presented in this paper. The reference panels are designed to be able to obtain the camera position and discriminate between each other. A conventional 3D modeling system using a reference panel has several restrictions regarding the target object, specifically the size and its location. Our system uses multiple reference panels, which are set around the target object to remove these restrictions. The main features of this system are as follows: 1) The whole shape and photo-realistic textures of the target object can be digitized based on several still images or a movie captured by using a hand-held camera; as well as each location of the camera that can be calculated using the reference panels. 2) Our system can be provided as a software product only. That means there are no special requirements for hardware; even the reference panels , because they can be printed from image files or software. 3) This system can be applied to digitize a larger object. In the experiments, we developed and used an interactive region selection tool to detect the silhouette on each image instead of using the chroma -keying method. We have tested our system with a toy object. The calculation time is about 10 minutes (except for the capturing the images and extracting the silhouette by using our tool) on a personal computer with a Pentium-III processor (600MHz) and 320MB memory. However, it depends on how complex the images are and how many images you use. Our future plan is to evaluate the system with various kind of objects, specifically, large ones in outdoor environments.

  1. 3-D numerical modeling of plume-induced subduction initiation

    NASA Astrophysics Data System (ADS)

    Baes, Marzieh; Gerya, taras; Sobolev, Stephan

    2016-04-01

    Investigation of mechanisms involved in formation of a new subduction zone can help us to better understand plate tectonics. Despite numerous previous studies, it is still unclear how and where an old oceanic plate starts to subduct beneath the other plate. One of the proposed scenarios for nucleation of subduction is plume-induced subduction initiation, which was investigated in detail, using 2-D models, by Ueda et al. (2008). Recently. Gerya et al. (2015), using 3D numerical models, proposed that plume-lithosphere interaction in the Archean led to the subduction initiation and onset of plate tectonic. In this study, we aim to pursue work of Ueda et al. (2008) by incorporation of 3-D thermo-mechanical models to investigate conditions leading to oceanic subduction initiation as a result of thermal-chemical mantle plume-lithosphere interaction in the modern earth. Results of our experiments show four different deformation regimes in response to plume-lithosphere interaction, that are a) self-sustaining subduction initiation where subduction becomes self-sustained, b) freezing subduction initiation where subduction stops at shallow depths, c) slab break-off where subducting circular slab breaks off soon after formation and d) plume underplating where plume does not pass through the lithosphere but spreads beneath it (failed subduction initiation). These different regimes depend on several parameters such as plume's size, composition and temperature, lithospheric brittle/plastic strength, age of the oceanic lithosphere and presence/absence of lithospheric heterogeneities. Results show that subduction initiates and becomes self-sustained when lithosphere is older than 10 Myr and non-dimensional ratio of the plume buoyancy force and lithospheric strength above the plume is higher than 2.

  2. 3D model generation using an airborne swarm

    NASA Astrophysics Data System (ADS)

    Clark, R. A.; Punzo, G.; Dobie, G.; MacLeod, C. N.; Summan, R.; Pierce, G.; Macdonald, M.; Bolton, G.

    2015-03-01

    Using an artificial kinematic field to provide co-ordination between multiple inspection UAVs, the authors herein demonstrate full 3D modelling capability based on a photogrammetric system. The operation of the system is demonstrated by generating a full 3D surface model of an intermediate level nuclear waste storage drum. Such drums require periodic inspection to ensure that drum distortion or corrosion is carefully monitored. Performing this inspection with multiple airborne platforms enables rapid inspection of structures that are inaccessible to on-surface remote vehicles and are in human-hazardous environments. A three-dimensional surface-meshed model of the target can then be constructed in post-processing through photogrammetry analysis of the visual inspection data. The inspection environment uses a tracking system to precisely monitor the position of each aerial vehicle within the enclosure. The vehicles used are commercially available Parrot AR. Drone quadcopters, controlled through a computer interface connected over an IEEE 802.11n (WiFi) network, implementing a distributed controller for each vehicle. This enables the autonomous and distributed elements of the control scheme to be retained, while alleviating the vehicles of the control algorithm's computational load. The control scheme relies on a kinematic field defined with the target at its centre. This field defines the trajectory for all the drones in the volume relative to the central target, enabling the drones to circle the target at a set radius while avoiding drone collisions. This function enables complete coverage along the height of the object, which is assured by transitioning to another inspection band only after completing circumferential coverage. Using a swarm of vehicles, the time until complete coverage can be significantly reduced.

  3. 3D model generation using an airborne swarm

    SciTech Connect

    Clark, R. A.; Punzo, G.; Macdonald, M.; Dobie, G.; MacLeod, C. N.; Summan, R.; Pierce, G.; Bolton, G.

    2015-03-31

    Using an artificial kinematic field to provide co-ordination between multiple inspection UAVs, the authors herein demonstrate full 3D modelling capability based on a photogrammetric system. The operation of the system is demonstrated by generating a full 3D surface model of an intermediate level nuclear waste storage drum. Such drums require periodic inspection to ensure that drum distortion or corrosion is carefully monitored. Performing this inspection with multiple airborne platforms enables rapid inspection of structures that are inaccessible to on-surface remote vehicles and are in human-hazardous environments. A three-dimensional surface-meshed model of the target can then be constructed in post-processing through photogrammetry analysis of the visual inspection data. The inspection environment uses a tracking system to precisely monitor the position of each aerial vehicle within the enclosure. The vehicles used are commercially available Parrot AR. Drone quadcopters, controlled through a computer interface connected over an IEEE 802.11n (WiFi) network, implementing a distributed controller for each vehicle. This enables the autonomous and distributed elements of the control scheme to be retained, while alleviating the vehicles of the control algorithm’s computational load. The control scheme relies on a kinematic field defined with the target at its centre. This field defines the trajectory for all the drones in the volume relative to the central target, enabling the drones to circle the target at a set radius while avoiding drone collisions. This function enables complete coverage along the height of the object, which is assured by transitioning to another inspection band only after completing circumferential coverage. Using a swarm of vehicles, the time until complete coverage can be significantly reduced.

  4. Crashworthiness analysis using advanced material models in DYNA3D

    SciTech Connect

    Logan, R.W.; Burger, M.J.; McMichael, L.D.; Parkinson, R.D.

    1993-10-22

    As part of an electric vehicle consortium, LLNL and Kaiser Aluminum are conducting experimental and numerical studies on crashworthy aluminum spaceframe designs. They have jointly explored the effect of heat treat on crush behavior and duplicated the experimental behavior with finite-element simulations. The major technical contributions to the state of the art in numerical simulation arise from the development and use of advanced material model descriptions for LLNL`s DYNA3D code. Constitutive model enhancements in both flow and failure have been employed for conventional materials such as low-carbon steels, and also for lighter weight materials such as aluminum and fiber composites being considered for future vehicles. The constitutive model enhancements are developed as extensions from LLNL`s work in anisotropic flow and multiaxial failure modeling. Analysis quality as a function of level of simplification of material behavior and mesh is explored, as well as the penalty in computation cost that must be paid for using more complex models and meshes. The lightweight material modeling technology is being used at the vehicle component level to explore the safety implications of small neighborhood electric vehicles manufactured almost exclusively from these materials.

  5. Energy flow in passive and active 3D cochlear model

    SciTech Connect

    Wang, Yanli; Steele, Charles; Puria, Sunil

    2015-12-31

    Energy flow in the cochlea is an important characteristic of the cochlear traveling wave, and many investigators, such as von Békésy and Lighthill, have discussed this phenomenon. Particularly after the discovery of the motility of the outer hair cells (OHCs), the nature of the power gain of the cochlea has been a fundamental research question. In the present work, direct three-dimensional (3D) calculations of the power on cross sections of the cochlea and on the basilar membrane are performed based on a box model of the mouse cochlea. The distributions of the fluid pressure and fluid velocity in the scala vestibuli are presented. The power output from the OHCs and the power loss due to fluid viscous damping are calculated along the length of the cochlea. This work provides a basis for theoretical calculations of the power gain of the OHCs from mechanical considerations.

  6. Energy flow in passive and active 3D cochlear model

    NASA Astrophysics Data System (ADS)

    Wang, Yanli; Puria, Sunil; Steele, Charles

    2015-12-01

    Energy flow in the cochlea is an important characteristic of the cochlear traveling wave, and many investigators, such as von Békésy and Lighthill, have discussed this phenomenon. Particularly after the discovery of the motility of the outer hair cells (OHCs), the nature of the power gain of the cochlea has been a fundamental research question. In the present work, direct three-dimensional (3D) calculations of the power on cross sections of the cochlea and on the basilar membrane are performed based on a box model of the mouse cochlea. The distributions of the fluid pressure and fluid velocity in the scala vestibuli are presented. The power output from the OHCs and the power loss due to fluid viscous damping are calculated along the length of the cochlea. This work provides a basis for theoretical calculations of the power gain of the OHCs from mechanical considerations.

  7. Appearance-based color face recognition with 3D model

    NASA Astrophysics Data System (ADS)

    Wang, Chengzhang; Bai, Xiaoming

    2013-03-01

    Appearance-based face recognition approaches explore color cues of face images, i.e. grey or color information for recognition task. They first encode color face images, and then extract facial features for classification. Similar to conventional singular value decomposition, hypercomplex matrix also exists singular value decomposition on hypercomplex field. In this paper, a novel color face recognition approach based on hypercomplex singular value decomposition is proposed. The approach employs hypercomplex to encode color face information of different channels simultaneously. Hypercomplex singular value decomposition is utilized then to compute the basis vectors of the color face subspace. To improve learning efficiency of the algorithm, 3D active deformable model is exploited to generate virtual face images. Color face samples are projected onto the subspace and projection coefficients are utilized as facial features. Experimental results on CMU PIE face database verify the effectiveness of the proposed approach.

  8. 3D Model of the San Emidio Geothermal Area

    DOE Data Explorer

    James E. Faulds

    2013-12-31

    The San Emidio geothermal system is characterized by a left-step in a west-dipping normal fault system that bounds the western side of the Lake Range. The 3D geologic model consists of 5 geologic units and 55 faults. Overlying Jurrassic-Triassic metasedimentary basement is a ~500 m-1000 m thick section of the Miocene lower Pyramid sequence, pre- syn-extensional Quaternary sedimentary rocks and post-extensional Quaternary rocks. 15-30º eastward dip of the stratigraphy is controlled by the predominant west-dipping fault set. Both geothermal production and injection are concentrated north of the step over in an area of closely spaced west dipping normal faults.

  9. 3D Model of the Neal Hot Springs Geothermal Area

    DOE Data Explorer

    Faulds, James E.

    2013-12-31

    The Neal Hot Springs geothermal system lies in a left-step in a north-striking, west-dipping normal fault system, consisting of the Neal Fault to the south and the Sugarloaf Butte Fault to the north (Edwards, 2013). The Neal Hot Springs 3D geologic model consists of 104 faults and 13 stratigraphic units. The stratigraphy is sub-horizontal to dipping <10 degrees and there is no predominant dip-direction. Geothermal production is exclusively from the Neal Fault south of, and within the step-over, while geothermal injection is into both the Neal Fault to the south of the step-over and faults within the step-over.

  10. 3D model atmospheres and the solar photospheric oxygen abundance

    NASA Astrophysics Data System (ADS)

    Caffau, E.; Ludwig, H.-G.

    2008-10-01

    In recent years the photospheric solar oxygen abundance experienced a significant downward revision. However, a low photospheric abundance is incompatible with the value in the solar interior inferred from helioseismology. For contributing to the dispute whether the solar oxygen abundance is “high” or “low”, we re-derived its photospheric abundance independently of previous analyses. We applied 3D (CO5BOLD) as well as 1D model atmospheres. We considered standard disc-centre and disc-integrated spectral atlases, as well as newly acquired solar intensity spectra at different heliocentric angles. We determined the oxygen abundances from equivalent width and/or line profile fitting of a number of atomic lines. As preliminary result, we find an oxygen abundance in the range 8.73 8.79, encompassing the value obtained by Holweger (2001), and somewhat higher than the value obtained by Asplund et al. (2005).

  11. Determination and validation of mTOR kinase-domain 3D structure by homology modeling.

    PubMed

    Lakhlili, Wiame; Chevé, Gwénaël; Yasri, Abdelaziz; Ibrahimi, Azeddine

    2015-01-01

    The AKT/mammalian target of rapamycin (mTOR) pathway is considered as one of the commonly activated and deregulated signaling pathways in human cancer. mTOR is associated with other proteins in two molecular complexes: mTOR complex 1/Raptor and the mTOR complex 2/Rictor. Using the crystal structure of the related lipid kinase PI3Kγ, we built a model of the catalytic region of mTOR. The modeling of the three-dimensional (3D) structure of the mTOR was performed by homology modeling program SWISS-MODEL. The quality and validation of the obtained model were performed using PROCHECK and PROVE softwares. The overall stereochemical property of the protein was assessed by the Ramachandran plot. The model validation was also done by docking of known inhibitors. In this paper, we describe and validate a 3D model for the mTOR catalytic site.

  12. Towards Automatic Semantic Labelling of 3D City Models

    NASA Astrophysics Data System (ADS)

    Rook, M.; Biljecki, F.; Diakité, A. A.

    2016-10-01

    The lack of semantic information in many 3D city models is a considerable limiting factor in their use, as a lot of applications rely on semantics. Such information is not always available, since it is not collected at all times, it might be lost due to data transformation, or its lack may be caused by non-interoperability in data integration from other sources. This research is a first step in creating an automatic workflow that semantically labels plain 3D city model represented by a soup of polygons, with semantic and thematic information, as defined in the CityGML standard. The first step involves the reconstruction of the topology, which is used in a region growing algorithm that clusters upward facing adjacent triangles. Heuristic rules, embedded in a decision tree, are used to compute a likeliness score for these regions that either represent the ground (terrain) or a RoofSurface. Regions with a high likeliness score, to one of the two classes, are used to create a decision space, which is used in a support vector machine (SVM). Next, topological relations are utilised to select seeds that function as a start in a region growing algorithm, to create regions of triangles of other semantic classes. The topological relationships of the regions are used in the aggregation of the thematic building features. Finally, the level of detail is detected to generate the correct output in CityGML. The results show an accuracy between 85 % and 99 % in the automatic semantic labelling on four different test datasets. The paper is concluded by indicating problems and difficulties implying the next steps in the research.

  13. 3D Model of the Tuscarora Geothermal Area

    DOE Data Explorer

    Faulds, James E.

    2013-12-31

    The Tuscarora geothermal system sits within a ~15 km wide left-step in a major west-dipping range-bounding normal fault system. The step over is defined by the Independence Mountains fault zone and the Bull Runs Mountains fault zone which overlap along strike. Strain is transferred between these major fault segments via and array of northerly striking normal faults with offsets of 10s to 100s of meters and strike lengths of less than 5 km. These faults within the step over are one to two orders of magnitude smaller than the range-bounding fault zones between which they reside. Faults within the broad step define an anticlinal accommodation zone wherein east-dipping faults mainly occupy western half of the accommodation zone and west-dipping faults lie in the eastern half of the accommodation zone. The 3D model of Tuscarora encompasses 70 small-offset normal faults that define the accommodation zone and a portion of the Independence Mountains fault zone, which dips beneath the geothermal field. The geothermal system resides in the axial part of the accommodation, straddling the two fault dip domains. The Tuscarora 3D geologic model consists of 10 stratigraphic units. Unconsolidated Quaternary alluvium has eroded down into bedrock units, the youngest and stratigraphically highest bedrock units are middle Miocene rhyolite and dacite flows regionally correlated with the Jarbidge Rhyolite and modeled with uniform cumulative thickness of ~350 m. Underlying these lava flows are Eocene volcanic rocks of the Big Cottonwood Canyon caldera. These units are modeled as intracaldera deposits, including domes, flows, and thick ash deposits that change in thickness and locally pinch out. The Paleozoic basement of consists metasedimenary and metavolcanic rocks, dominated by argillite, siltstone, limestone, quartzite, and metabasalt of the Schoonover and Snow Canyon Formations. Paleozoic formations are lumped in a single basement unit in the model. Fault blocks in the eastern

  14. A new 3D dynamical biomechanical tongue model

    NASA Astrophysics Data System (ADS)

    Gerard, Jean-Michel; Perrier, Pascal; Payan, Yohan; Wilhelms-Tricarico, Reiner

    2004-05-01

    A new dynamical biomechanical tongue model is being developed to study speech motor control. In spite of its computational complexity, a 3D representation was chosen in order to account for various contacts between tongue and external structures such as teeth, palate, and vocal tract walls. A fair representation of tongue muscle anatomy is provided, by designing the finite element mesh from the visible human data set (female subject). Model geometry was then matched to a human speaker, so that simulations can be quantitatively compared to experimental MRI data. A set of 11 muscles is modeled, whose role in speech gestures is well established. Each muscle is defined by a set of elements whose elastic properties change with muscle activation. Muscles forces are applied to the tongue model via macrofibers defined within the mesh by muscle specific sets of nodes. These forces are currently specified as step functions. Boundary conditions are set using zero-displacement nodes simulating attachments of tongue on bony structures. The nonlinear mechanical properties of tongue soft tissues are modeled using a hyperelastic material. Three-dimensional tongue deformations generated by each muscle, using FEM software ANSYS for computation, will be presented. Implications for speech motor control will be proposed.

  15. A new 3D dynamical biomechanical tongue model

    NASA Astrophysics Data System (ADS)

    Gerard, Jean-Michel; Perrier, Pascal; Payan, Yohan; Wilhelms-Tricarico, Reiner

    2001-05-01

    A new dynamical biomechanical tongue model is being developed to study speech motor control. In spite of its computational complexity, a 3D representation was chosen in order to account for various contacts between tongue and external structures such as teeth, palate, and vocal tract walls. A fair representation of tongue muscle anatomy is provided, by designing the finite element mesh from the visible human data set (female subject). Model geometry was then matched to a human speaker, so that simulations can be quantitatively compared to experimental MRI data. A set of 11 muscles is modeled, whose role in speech gestures is well established. Each muscle is defined by a set of elements whose elastic properties change with muscle activation. Muscles forces are applied to the tongue model via macrofibers defined within the mesh by muscle specific sets of nodes. These forces are currently specified as step functions. Boundary conditions are set using zero-displacement nodes simulating attachments of tongue on bony structures. The nonlinear mechanical properties of tongue soft tissues are modeled using a hyperelastic material. Three-dimensional tongue deformations generated by each muscle, using FEM software ANSYS for computation, will be presented. Implications for speech motor control will be proposed.

  16. 3D-QSAR, molecular docking and molecular dynamics studies of a series of RORγt inhibitors.

    PubMed

    Wang, Fangfang; Yang, Wei; Shi, Yonghui; Le, Guowei

    2015-09-01

    The discovery of clinically relevant inhibitors of retinoic acid receptor-related orphan receptor-gamma-t (RORγt) for autoimmune diseases therapy has proven to be a challenging task. In the present work, to find out the structural features required for the inhibitory activity, we show for the first time a three-dimensional quantitative structure-activity relationship (3D-QSAR), molecular docking and molecular dynamics (MD) simulations for a series of novel thiazole/thiophene ketone amides with inhibitory activity at the RORγt receptor. The optimum CoMFA and CoMSIA models, derived from ligand-based superimposition I, exhibit leave-one-out cross-validated correlation coefficient (R(2)cv) of .859 and .805, respectively. Furthermore, the external predictive abilities of the models were evaluated by a test set, producing the predicted correlation coefficient (R(2)pred) of .7317 and .7097, respectively. In addition, molecular docking analysis was applied to explore the binding modes between the inhibitors and the receptor. MD simulation and MM/PBSA method were also employed to study the stability and rationality of the derived conformations, and the binding free energies in detail. The QSAR models and the results of molecular docking, MD simulation, binding free energies corroborate well with each other and further provide insights regarding the development of novel RORγt inhibitors with better activity.

  17. A multipurpose 3-D grid of stellar models

    NASA Astrophysics Data System (ADS)

    Maíz Apellániz, J.

    2013-05-01

    The last two decades have produced a proliferation of stellar atmosphere grids, evolutionary tracks, and isochrones which are available to the astronomical community from different internet services. However, it is not straightforward (at least for an inexperienced user) to manipulate those models to answer questions of the type: What is the spectral energy distribution of a 9000 K giant? What about its J-band magnitude for different metallicities? What can I tell about the mass of a star if I know that its unreddened B-V color is -0.05 and its luminosity in solar units is 10^5? The answers to those questions are indeed in the models but a series of transformations and combinations involving different variables and models are required to obtain them. To make the available knowledge more user friendly, I have combined a number of state-of-the-art sources to create a 3-D (effective temperature, luminosity, and metallicity) grid of stellar models for which I provide calibrated SEDs and magnitudes as well as auxiliary variables such as mass and age. Furthermore, I have generated a grid of extinguished magnitudes using the recent Maíz Apellániz et al. (2012) extinction laws and incorporated them into the Bayesian code CHORIZOS (Maíz Apellániz 2004).

  18. 3-D Eutrophication Modeling for Lake Simcoe, Canada

    NASA Astrophysics Data System (ADS)

    Lu, Q.; Duckett, F.; Nairn, R.; Brunton, A.

    2006-12-01

    The Lake Simcoe Region Conservation Authority (LSRCA) and the Province of Ontario are undertaking a series of studies to facilitate management of the pressures of population growth in the Lake Simcoe watershed. With rapid population growth and urban development comes additional land clearing, storm water runoff and the discharge of treated sewage, all of which are sources of increased phosphorus loading to Lake Simcoe. Depressed oxygen levels were linked to phosphorous enrichment of the lake, with the resultant stimulation of algal growth in the sunlit upper waters of the lake, and its subsequent senescence and settling into the hypolimnion where bacterial decomposition consumes oxygen from the stratified waters. This poster describes a 3-D hydrodynamic, thermal and water quality model of Lake Simcoe developed using the Danish Hydraulics Institute (DHI) MIKE3 model. The hydrodynamic module includes wind-driven circulation, temperature variation, development of the thermocline and thermal stratification, and hydraulic forcing from inflowing tributaries. This is linked to the water quality module which simulates the eutrophication processes in the response of the lake to loadings of phosphorus, such as algal growth, the growth of aquatic plants and subsequent oxygen consumption. The model has been calibrated against Acoustic Doppler Current Profiler velocity data, plus measured temperature and water quality data at MOE stations in the lake and water intakes. The model is an important assessment tool for the management of the lake and its watersheds, allowing assessment of the impacts of the urban growth and land use change on the water quality in Lake Simcoe.

  19. 3-D GRACE gravity model for the 2011 Japan earthquake

    NASA Astrophysics Data System (ADS)

    Sastry, Rambhatla G.; Sonker, Mahendra K.

    2017-02-01

    The GRACE mission has contributed to the seismic characterization of major earthquakes in offshore regions of the world. Here, we isolate satellite gravity signal (μGal range) for the Japan Earthquake of 2011 using a difference method. Contrary to the existing gravity models, we propose a unit vertical pyramid based five-layer 3-D thrust fault model, which extends to the hypocenter and honors the ocean water layer and sea floor upheaval also. Our model partly uses existing seismological information (hypocenter depth of 32 km, rupture length of 300 km and vertical slip of 4 m), provides a snapshot of episodic subduction of the Pacific Plate below the Atlantic Plate and its gravity response closely matches the observed gravity (RMS error of 3.4012×10-13μGal), fully accounting for co-seismic mass redistribution including sea surface deformation. Our inferred rupture length, rupture velocity, average seismic moment magnitude and momentum, respectively, are 300 km, 4.49 km/s, 1.152×1021-1.8816×1021 N m and 2.319×106 GNs, which fairly agree with the literature. Further, our model inferred momentum at the sea floor corresponds to an area pulse that led to Tsunami generation.

  20. Automatic paper sliceform design from 3D solid models.

    PubMed

    Le-Nguyen, Tuong-Vu; Low, Kok-Lim; Ruiz, Conrado; Le, Sang N

    2013-11-01

    A paper sliceform or lattice-style pop-up is a form of papercraft that uses two sets of parallel paper patches slotted together to make a foldable structure. The structure can be folded flat, as well as fully opened (popped-up) to make the two sets of patches orthogonal to each other. Automatic design of paper sliceforms is still not supported by existing computational models and remains a challenge. We propose novel geometric formulations of valid paper sliceform designs that consider the stability, flat-foldability and physical realizability of the designs. Based on a set of sufficient construction conditions, we also present an automatic algorithm for generating valid sliceform designs that closely depict the given 3D solid models. By approximating the input models using a set of generalized cylinders, our method significantly reduces the search space for stable and flat-foldable sliceforms. To ensure the physical realizability of the designs, the algorithm automatically generates slots or slits on the patches such that no two cycles embedded in two different patches are interlocking each other. This guarantees local pairwise assembility between patches, which is empirically shown to lead to global assembility. Our method has been demonstrated on a number of example models, and the output designs have been successfully made into real paper sliceforms.

  1. 3D numerical modeling of India-Asia-like collision

    NASA Astrophysics Data System (ADS)

    -Erika Püsök, Adina; Kaus, Boris; Popov, Anton

    2013-04-01

    above a strong mantle lithosphere - the jelly sandwich model (Burov and Watts, 2006). 3D models are thus needed to investigate these hypotheses. However, fully 3D models of the dynamics of continent collision zones have only been developed very recently, and presently most research groups have relied on certain explicit assumptions for their codes. Here, we employ the parallel 3D code LaMEM (Lithosphere and Mantle Evolution Model), with a finite difference staggered grid solver, which is capable of simulating lithospheric deformation while simultaneously taking mantle flow and a free surface into account. We here report on first lithospheric and upper-mantle scale simulations in which the Indian lithosphere is indented into Asia. Acknowledgements. Funding was provided by the European Research Council under the European Community's Seventh Framework Program (FP7/2007-2013) / ERC Grant agreement #258830. Numerical computations have been performed on JUQUEEN of the Jülich high-performance computing center. • Beaumont, C., Jamieson, R.A., Nguyen, M.H., Medvedev, S.E., 2004. Crustal channel flows: 1. Numerical models with applications to the tectonics of the Himalayan-Tibetan orogeny. J. Geophys. Res. 109, B06406. • Burov, E. & Watts, W.S., 2006. The long-term strength of continental lithosphere: "jelly sandwich" or "crème brûlée"?. GSA Today, 16, doi: 10.1130/1052-5173(2006)1016<1134:TLTSOC>1132.1130.CO;1132. • England P., Houseman, G., 1986. Finite strain calculations of continental deformation. 2. Comparison with the India-Asia collision zone. J. Geophys. Res.- Solid Earth and Planets 91 (B3), 3664-3676. • Jackson, J., 2002. Strength of the continental lithosphere: time to abandon the jelly sandwich?. GSA Today, September, 4-10. • Lechmann, S.M., May, D.A., Kaus, B.J.P., Schmalholz, S.M., 2011. Comparing thin-sheet models with 3D multilayer models for continental collision. Geophy. Int. J. doi: 10.1111/j.1365-246X.2011.05164.x • Royden, L.H., Burchfiel, B

  2. 3D-Digital soil property mapping by geoadditive models

    NASA Astrophysics Data System (ADS)

    Papritz, Andreas

    2016-04-01

    In many digital soil mapping (DSM) applications, soil properties must be predicted not only for a single but for multiple soil depth intervals. In the GlobalSoilMap project, as an example, predictions are computed for the 0-5 cm, 5-15 cm, 15-30 cm, 30-60 cm, 60-100 cm, 100-200 cm depth intervals (Arrouays et al., 2014). Legacy soil data are often used for DSM. It is common for such datasets that soil properties were measured for soil horizons or for layers at varying soil depth and with non-constant thickness (support). This poses problems for DSM: One strategy is to harmonize the soil data to common depth prior to the analyses (e.g. Bishop et al., 1999) and conduct the statistical analyses for each depth interval independently. The disadvantage of this approach is that the predictions for different depths are computed independently from each other so that the predicted depth profiles may be unrealistic. Furthermore, the error induced by the harmonization to common depth is ignored in this approach (Orton et al. 2016). A better strategy is therefore to process all soil data jointly without prior harmonization by a 3D-analysis that takes soil depth and geographical position explicitly into account. Usually, the non-constant support of the data is then ignored, but Orton et al. (2016) presented recently a geostatistical approach that accounts for non-constant support of soil data and relies on restricted maximum likelihood estimation (REML) of a linear geostatistical model with a separable, heteroscedastic, zonal anisotropic auto-covariance function and area-to-point kriging (Kyriakidis, 2004.) Although this model is theoretically coherent and elegant, estimating its many parameters by REML and selecting covariates for the spatial mean function is a formidable task. A simpler approach might be to use geoadditive models (Kammann and Wand, 2003; Wand, 2003) for 3D-analyses of soil data. geoAM extend the scope of the linear model with spatially correlated errors to

  3. Alkynes as a versatile platform for construction of chemical molecular complexity and realization of molecular 3D printing

    NASA Astrophysics Data System (ADS)

    Galkin, K. I.; Ananikov, V. P.

    2016-03-01

    The current level of scientific and technological development requires the formation of general tools and techniques. One of the most versatile technologies is 3D printing, which allows fast and efficient creation of materials and biological objects of desired shape and composition. Today, methods have been developed for 3D printing of macro- and nano-sized objects and for production of films and deposited materials with molecular precision but the most promising technology is printing at the molecular level (molecular 3D printing) for the purpose of direct construction of molecular complexity. This process is currently at the initial stage concerning selection of simple molecules to be used as building blocks possessing flexibility, availability and ease of modification. In this review, we examine the possible versatile synthons suitable for preparation of the main types of organic compounds using molecular 3D printing. The surveyed data strongly indicate that alkyne molecules may be used as a building material in a molecular 3D printer working on hydrocarbons. The bibliography includes 428 references.

  4. 3D Finite Difference Modelling of Basaltic Region

    NASA Astrophysics Data System (ADS)

    Engell-Sørensen, L.

    2003-04-01

    The main purpose of the work was to generate realistic data to be applied for testing of processing and migration tools for basaltic regions. The project is based on the three - dimensional finite difference code (FD), TIGER, made by Sintef. The FD code was optimized (parallelized) by the author, to run on parallel computers. The parallel code enables us to model large-scale realistic geological models and to apply traditional seismic and micro seismic sources. The parallel code uses multiple processors in order to manipulate subsets of large amounts of data simultaneously. The general anisotropic code uses 21 elastic coefficients. Eight independent coefficients are needed as input parameters for the general TI medium. In the FD code, the elastic wave field computation is implemented by a higher order FD solution to the elastic wave equation and the wave fields are computed on a staggered grid, shifted half a node in one or two directions. The geological model is a gridded basalt model, which covers from 24 km to 37 km of a real shot line in horizontal direction and from the water surface to the depth of 3.5 km. The 2frac {1}{2}D model has been constructed using the compound modeling software from Norsk Hydro. The vertical parameter distribution is obtained from observations in two wells. At The depth of between 1100 m to 1500 m, a basalt horizon covers the whole sub surface layers. We have shown that it is possible to simulate a line survey in realistic (3D) geological models in reasonable time by using high performance computers. The author would like to thank Norsk Hydro, Statoil, GEUS, and SINTEF for very helpful discussions and Parallab for being helpful with the new IBM, p690 Regatta system.

  5. 3D finite element modeling of sliding wear

    NASA Astrophysics Data System (ADS)

    Buentello Hernandez, Rodolfo G.

    Wear is defined as "the removal of material volume through some mechanical process between two surfaces". There are many mechanical situations that can induce wear and each can involve many wear mechanisms. This research focuses on the mechanical wear due to dry sliding between two surfaces. Currently there is a need to identify and compare materials that would endure sliding wear under severe conditions such as high velocities. The high costs associated with the field experimentation of systems subject to high-speed sliding, has prevented the collection of the necessary data required to fully characterize this phenomena. Simulating wear through Finite Elements (FE) would enable its prediction under different scenarios and would reduce experimentation costs. In the aerospace, automotive and weapon industries such a model can aid in material selection, design and/or testing of systems subjected to wear in bearings, gears, brakes, gun barrels, slippers, locomotive wheels, or even rocket test tracks. The 3D wear model presented in this dissertation allows one to reasonably predict high-speed sliding mechanical wear between two materials. The model predictions are reasonable, when compared against those measured on a sled slipper traveling over the Holloman High Speed Tests Track. This slipper traveled a distance of 5,816 meters in 8.14 seconds and reached a maximum velocity of 1,530 m/s.

  6. Optimization of 3D Poisson-Nernst-Planck model for fast evaluation of diverse protein channels.

    PubMed

    Dyrka, Witold; Bartuzel, Maciej M; Kotulska, Malgorzata

    2013-10-01

    We show the accuracy and applicability of our fast algorithmic implementation of a three-dimensional Poisson-Nernst-Planck (3D-PNP) flow model for characterizing different protein channels. Due to its high computational efficiency, our model can predict the full current-voltage characteristics of a channel within minutes, based on the experimental 3D structure of the channel or its computational model structure. Compared with other methods, such as Brownian dynamics, which currently needs a few weeks of the computational time, or even much more demanding molecular dynamics modeling, 3D-PNP is the only available method for a function-based evaluation of very numerous tentative structural channel models. Flow model tests of our algorithm and its optimal parametrization are provided for five native channels whose experimental structures are available in the protein data bank (PDB) in an open conductive state, and whose experimental current-voltage characteristics have been published. The channels represent very different geometric and structural properties, which makes it the widest test to date of the accuracy of 3D-PNP on real channels. We test whether the channel conductance, rectification, and charge selectivity obtained from the flow model, could be sufficiently sensitive to single-point mutations, related to unsignificant changes in the channel structure. Our results show that the classical 3D-PNP model, under proper parametrization, is able to achieve a qualitative agreement with experimental data for a majority of the tested characteristics and channels, including channels with narrow and irregular conductivity pores. We propose that although the standard PNP model cannot provide insight into complex physical phenomena due to its intrinsic limitations, its semiquantitative agreement is achievable for rectification and selectivity at a level sufficient for the bioinformatical purpose of selecting the best structural models with a great advantage of a very short

  7. Detailed 3D representations for object recognition and modeling.

    PubMed

    Zia, M Zeeshan; Stark, Michael; Schiele, Bernt; Schindler, Konrad

    2013-11-01

    Geometric 3D reasoning at the level of objects has received renewed attention recently in the context of visual scene understanding. The level of geometric detail, however, is typically limited to qualitative representations or coarse boxes. This is linked to the fact that today's object class detectors are tuned toward robust 2D matching rather than accurate 3D geometry, encouraged by bounding-box-based benchmarks such as Pascal VOC. In this paper, we revisit ideas from the early days of computer vision, namely, detailed, 3D geometric object class representations for recognition. These representations can recover geometrically far more accurate object hypotheses than just bounding boxes, including continuous estimates of object pose and 3D wireframes with relative 3D positions of object parts. In combination with robust techniques for shape description and inference, we outperform state-of-the-art results in monocular 3D pose estimation. In a series of experiments, we analyze our approach in detail and demonstrate novel applications enabled by such an object class representation, such as fine-grained categorization of cars and bicycles, according to their 3D geometry, and ultrawide baseline matching.

  8. Pros and Cons of ID vs. 3D Modeling

    NASA Technical Reports Server (NTRS)

    Klimchuk, James A.

    2012-01-01

    Advances in computing capability have led to tremendous improvements in 3D modeling. Entire active regions are being simulated in what might be described as a first principles way, in which plasma heating is treated self consistently rather than through the specification of heating functions. There are limitations to this approach, however, as actual heating mechanisms on the Sun involve spatial scales orders of magnitude smaller than what these simulations can resolve. Other simulations begin to resolve these scales, but they only treat a tiny volume and do not include the all important coupling with larger scales or with other parts of the atmosphere, and so cannot be readily compared with observations. Finally, ID hydrodynamic models capture the field-aligned evolution of the plasma extremely well and are ideally suited for data comparison, but they treat the heating in a totally ad hoc manner. All of these approaches have important contributions to make, but we must be aware of their limitations. I will highlight some of the strengths. and weaknesses of each.

  9. A 3D world model builder with a mobile robot

    SciTech Connect

    Zhang, Z.; Faugeras, O. )

    1992-08-01

    This article describes a system to incrementally build a world model with a mobile robot in an unknown environment. The model is, for the moment, segment based. A trinocular stereo system is used to build a local map about the environment. A global map is obtained by integrating a sequence of stereo frames taken when the robot navigates in the environment. The emphasis of this article is on the representation of the uncertainty of 3D segments from stereo and on the integration of segments from multiple views. The proposed representation is simple and very convenient to characterize the uncertainty of segment. A Kalman filter is used to merge matched line segments. An important characteristic of this integration strategy is that a segment observed by the stereo system corresponds only to one part of the segment in space, so the union of the different observations gives a better estimate on the segment in space. The authors have succeeded in integrating 35 stereo frames taken in their robot room.

  10. Modelling Polymer Deformation and Welding Behaviour during 3D Printing

    NASA Astrophysics Data System (ADS)

    McIlroy, Claire; Olmsted, Peter

    2016-11-01

    3D printing has the potential to transform manufacturing processes, yet improving the strength of printed parts, to equal that of traditionally-manufactured parts, remains an underlying issue. The most common method, fused deposition modelling, involves melting a thermoplastic, followed by layer-by-layer extrusion of the material to fabricate a three-dimensional object. The key to the ensuring strength at the weld between these layers is successful inter-diffusion. However, as the printed layer cools towards the glass transition temperature, the time available for diffusion is limited. In addition, the extrusion process significantly deforms the polymer micro-structure prior to welding and consequently affects how the polymers "re-entangle" across the weld. We have developed a simple model of the non-isothermal printing process to explore the effects that typical printing conditions and amorphous polymer rheology have on the ultimate weld structure. In particular, we incorporate both the stretch and orientation of the polymer using the Rolie-Poly constitutive equation to examine how the melt flows through the nozzle and is deposited onto the build plate. We then address how this deformation relaxes and contributes to the thickness and structure of the weld. National Institute for Standards and Technology (NIST) and Georgetown University.

  11. A novel mechanotactic 3D modeling of cell morphology

    NASA Astrophysics Data System (ADS)

    Jamaleddin Mousavi, Seyed; Hamdy Doweidar, Mohamed

    2014-08-01

    Cell morphology plays a critical role in many biological processes, such as cell migration, tissue development, wound healing and tumor growth. Recent investigations demonstrate that, among other stimuli, cells adapt their shapes according to their substrate stiffness. Until now, the development of this process has not been clear. Therefore, in this work, a new three-dimensional (3D) computational model for cell morphology has been developed. This model is based on a previous cell migration model presented by the same authors. The new model considers that during cell-substrate interaction, cell shape is governed by internal cell deformation, which leads to an accurate prediction of the cell shape according to the mechanical characteristic of its surrounding micro-environment. To study this phenomenon, the model has been applied to different numerical cases. The obtained results, which are qualitatively consistent with well-known related experimental works, indicate that cell morphology not only depends on substrate stiffness but also on the substrate boundary conditions. A cell located within an unconstrained soft substrate (several kPa) with uniform stiffness is unable to adhere to its substrate or to send out pseudopodia. When the substrate stiffness increases to tens of kPa (intermediate and rigid substrates), the cell can adequately adhere to its substrate. Subsequently, as the traction forces exerted by the cell increase, the cell elongates and its shape changes. Within very stiff (hard) substrates, the cell cannot penetrate into its substrate or send out pseudopodia. On the other hand, a cell is found to be more elongated within substrates with a constrained surface. However, this elongation decreases when the cell approaches it. It can be concluded that the higher the net traction force, the greater the cell elongation, the larger the cell membrane area, and the less random the cell alignment.

  12. Numerical model of sonic boom in 3D kinematic turbulence

    NASA Astrophysics Data System (ADS)

    Coulouvrat, François; Luquet, David; Marchiano, Régis

    2015-10-01

    stratified wind superimposed to a 3D random turbulent realization. Propagation is performed either in the case of a shadow zone or of an atmospheric waveguide. To model the turbulent ABL, the mean flow and the fluctuations are handled separately. The wind fluctuations are generated using the Random Fluctuations Generation method assuming a von Kármán spectrum and a homogeneous and isotropic turbulence. The mean stratified wind is modeled based on the Monin-Obhukov Similarity Theory (MOST). To illustrate the method, the typical case of a sunny day with a strong wind has been chosen. Statistics are obtained on several parameters. It shows the importance of turbulence, which leads to an increase of the mean maximum peak pressure in the shadow zone and to its decrease in the waveguide. Moreover, the formation of random caustics that can lead to an increase of the noise perceived locally is outlined.

  13. Methods for Geometric Data Validation of 3d City Models

    NASA Astrophysics Data System (ADS)

    Wagner, D.; Alam, N.; Wewetzer, M.; Pries, M.; Coors, V.

    2015-12-01

    Geometric quality of 3D city models is crucial for data analysis and simulation tasks, which are part of modern applications of the data (e.g. potential heating energy consumption of city quarters, solar potential, etc.). Geometric quality in these contexts is however a different concept as it is for 2D maps. In the latter case, aspects such as positional or temporal accuracy and correctness represent typical quality metrics of the data. They are defined in ISO 19157 and should be mentioned as part of the metadata. 3D data has a far wider range of aspects which influence their quality, plus the idea of quality itself is application dependent. Thus, concepts for definition of quality are needed, including methods to validate these definitions. Quality on this sense means internal validation and detection of inconsistent or wrong geometry according to a predefined set of rules. A useful starting point would be to have correct geometry in accordance with ISO 19107. A valid solid should consist of planar faces which touch their neighbours exclusively in defined corner points and edges. No gaps between them are allowed, and the whole feature must be 2-manifold. In this paper, we present methods to validate common geometric requirements for building geometry. Different checks based on several algorithms have been implemented to validate a set of rules derived from the solid definition mentioned above (e.g. water tightness of the solid or planarity of its polygons), as they were developed for the software tool CityDoctor. The method of each check is specified, with a special focus on the discussion of tolerance values where they are necessary. The checks include polygon level checks to validate the correctness of each polygon, i.e. closeness of the bounding linear ring and planarity. On the solid level, which is only validated if the polygons have passed validation, correct polygon orientation is checked, after self-intersections outside of defined corner points and edges

  14. Object-oriented urban 3D spatial data model organization method

    NASA Astrophysics Data System (ADS)

    Li, Jing-wen; Li, Wen-qing; Lv, Nan; Su, Tao

    2015-12-01

    This paper combined the 3d data model with object-oriented organization method, put forward the model of 3d data based on object-oriented method, implemented the city 3d model to quickly build logical semantic expression and model, solved the city 3d spatial information representation problem of the same location with multiple property and the same property with multiple locations, designed the space object structure of point, line, polygon, body for city of 3d spatial database, and provided a new thought and method for the city 3d GIS model and organization management.

  15. 3D Loop Models and the CPn-1 Sigma Model

    NASA Astrophysics Data System (ADS)

    Nahum, Adam; Chalker, J. T.; Serna, P.; Ortuño, M.; Somoza, A. M.

    2011-09-01

    Many statistical mechanics problems can be framed in terms of random curves; we consider a class of three-dimensional loop models that are prototypes for such ensembles. The models show transitions between phases with infinite loops and short-loop phases. We map them to CPn-1 sigma models, where n is the loop fugacity. Using Monte Carlo simulations, we find continuous transitions for n=1, 2, 3, and first order transitions for n≥5. The results are relevant to line defects in random media, as well as to Anderson localization and (2+1)-dimensional quantum magnets.

  16. EM modeling for GPIR using 3D FDTD modeling codes

    SciTech Connect

    Nelson, S.D.

    1994-10-01

    An analysis of the one-, two-, and three-dimensional electrical characteristics of structural cement and concrete is presented. This work connects experimental efforts in characterizing cement and concrete in the frequency and time domains with the Finite Difference Time Domain (FDTD) modeling efforts of these substances. These efforts include Electromagnetic (EM) modeling of simple lossless homogeneous materials with aggregate and targets and the modeling dispersive and lossy materials with aggregate and complex target geometries for Ground Penetrating Imaging Radar (GPIR). Two- and three-dimensional FDTD codes (developed at LLNL) where used for the modeling efforts. Purpose of the experimental and modeling efforts is to gain knowledge about the electrical properties of concrete typically used in the construction industry for bridges and other load bearing structures. The goal is to optimize the performance of a high-sample-rate impulse radar and data acquisition system and to design an antenna system to match the characteristics of this material. Results show agreement to within 2 dB of the amplitudes of the experimental and modeled data while the frequency peaks correlate to within 10% the differences being due to the unknown exact nature of the aggregate placement.

  17. West Flank Coso, CA FORGE 3D temperature model

    SciTech Connect

    Doug Blankenship

    2016-03-01

    x,y,z data of the 3D temperature model for the West Flank Coso FORGE site. Model grid spacing is 250m. The temperature model for the Coso geothermal field used over 100 geothermal production sized wells and intermediate-depth temperature holes. At the near surface of this model, two boundary temperatures were assumed: (1) areas with surface manifestations, including fumaroles along the northeast striking normal faults and northwest striking dextral faults with the hydrothermal field, a temperature of ~104˚C was applied to datum at +1066 meters above sea level elevation, and (2) a near-surface temperature at about 10 meters depth, of 20˚C was applied below the diurnal and annual conductive temperature perturbations. These assumptions were based on heat flow studies conducted at the CVF and for the Mojave Desert. On the edges of the hydrothermal system, a 73˚C/km (4˚F/100’) temperature gradient contour was established using conductive gradient data from shallow and intermediate-depth temperature holes. This contour was continued to all elevation datums between the 20˚C surface and -1520 meters below mean sea level. Because the West Flank is outside of the geothermal field footprint, during Phase 1, the three wells inside the FORGE site were incorporated into the preexisting temperature model. To ensure a complete model was built based on all the available data sets, measured bottom-hole temperature gradients in certain wells were downward extrapolated to the next deepest elevation datum (or a maximum of about 25% of the well depth where conductive gradients are evident in the lower portions of the wells). After assuring that the margins of the geothermal field were going to be adequately modelled, the data was contoured using the Kriging method algorithm. Although the extrapolated temperatures and boundary conditions are not rigorous, the calculated temperatures are anticipated to be within ~6˚C (20˚F), or one contour interval, of the

  18. Building Proteins in a Day: Efficient 3D Molecular Structure Estimation with Electron Cryomicroscopy.

    PubMed

    Punjani, Ali; Brubaker, Marcus A; Fleet, David J

    2017-04-01

    Discovering the 3D atomic-resolution structure of molecules such as proteins and viruses is one of the foremost research problems in biology and medicine. Electron Cryomicroscopy (cryo-EM) is a promising vision-based technique for structure estimation which attempts to reconstruct 3D atomic structures from a large set of 2D transmission electron microscope images. This paper presents a new Bayesian framework for cryo-EM structure estimation that builds on modern stochastic optimization techniques to allow one to scale to very large datasets. We also introduce a novel Monte-Carlo technique that reduces the cost of evaluating the objective function during optimization by over five orders of magnitude. The net result is an approach capable of estimating 3D molecular structure from large-scale datasets in about a day on a single CPU workstation.

  19. Prediction models from CAD models of 3D objects

    NASA Astrophysics Data System (ADS)

    Camps, Octavia I.

    1992-11-01

    In this paper we present a probabilistic prediction based approach for CAD-based object recognition. Given a CAD model of an object, the PREMIO system combines techniques of analytic graphics and physical models of lights and sensors to predict how features of the object will appear in images. In nearly 4,000 experiments on analytically-generated and real images, we show that in a semi-controlled environment, predicting the detectability of features of the image can successfully guide a search procedure to make informed choices of model and image features in its search for correspondences that can be used to hypothesize the pose of the object. Furthermore, we provide a rigorous experimental protocol that can be used to determine the optimal number of correspondences to seek so that the probability of failing to find a pose and of finding an inaccurate pose are minimized.

  20. 3D Simulation Modeling of the Tooth Wear Process.

    PubMed

    Dai, Ning; Hu, Jian; Liu, Hao

    2015-01-01

    Severe tooth wear is the most common non-caries dental disease, and it can seriously affect oral health. Studying the tooth wear process is time-consuming and difficult, and technological tools are frequently lacking. This paper presents a novel method of digital simulation modeling that represents a new way to study tooth wear. First, a feature extraction algorithm is used to obtain anatomical feature points of the tooth without attrition. Second, after the alignment of non-attrition areas, the initial homogeneous surface is generated by means of the RBF (Radial Basic Function) implicit surface and then deformed to the final homogeneous by the contraction and bounding algorithm. Finally, the method of bilinear interpolation based on Laplacian coordinates between tooth with attrition and without attrition is used to inversely reconstruct the sequence of changes of the 3D tooth morphology during gradual tooth wear process. This method can also be used to generate a process simulation of nonlinear tooth wear by means of fitting an attrition curve to the statistical data of attrition index in a certain region. The effectiveness and efficiency of the attrition simulation algorithm are verified through experimental simulation.

  1. 3D Simulation Modeling of the Tooth Wear Process

    PubMed Central

    Dai, Ning; Hu, Jian; Liu, Hao

    2015-01-01

    Severe tooth wear is the most common non-caries dental disease, and it can seriously affect oral health. Studying the tooth wear process is time-consuming and difficult, and technological tools are frequently lacking. This paper presents a novel method of digital simulation modeling that represents a new way to study tooth wear. First, a feature extraction algorithm is used to obtain anatomical feature points of the tooth without attrition. Second, after the alignment of non-attrition areas, the initial homogeneous surface is generated by means of the RBF (Radial Basic Function) implicit surface and then deformed to the final homogeneous by the contraction and bounding algorithm. Finally, the method of bilinear interpolation based on Laplacian coordinates between tooth with attrition and without attrition is used to inversely reconstruct the sequence of changes of the 3D tooth morphology during gradual tooth wear process. This method can also be used to generate a process simulation of nonlinear tooth wear by means of fitting an attrition curve to the statistical data of attrition index in a certain region. The effectiveness and efficiency of the attrition simulation algorithm are verified through experimental simulation. PMID:26241942

  2. Determination of 3D molecular orientation by concurrent polarization analysis of multiple Raman modes in broadband CARS spectroscopy

    PubMed Central

    2016-01-01

    A theoretical description is presented about a new analysis method to determine three-dimensional (3D) molecular orientation by concurrently analyzing multiple Raman polarization profiles. Conventional approaches to polarization Raman spectroscopy are based on single peaks, and their 2D-projected polarization profiles are limited in providing 3D orientational information. Our new method analyzes multiple Raman profiles acquired by a single polarization scanning measurement of broadband coherent anti-Stokes Raman scattering (BCARS). Because the analysis uses only dimensionless quantities, such as intensity ratios and phase difference between multiple profiles, the results are not affected by sample concentration and the system response function. We describe how to determine the 3D molecular orientation with the dimensionless observables by using two simplified model cases. In addition, we discuss the effect of orientational broadening on the polarization profiles in the two model cases. We find that in the presence of broadening we can still determine the mean 3D orientation angles and, furthermore, the degree of orientational broadening. PMID:26561197

  3. Modeling 3-D Slope Stability of Coastal Bluffs Using 3-D Ground-Water Flow, Southwestern Seattle, Washington

    USGS Publications Warehouse

    Brien, Dianne L.; Reid, Mark E.

    2007-01-01

    Landslides are a common problem on coastal bluffs throughout the world. Along the coastal bluffs of the Puget Sound in Seattle, Washington, landslides range from small, shallow failures to large, deep-seated landslides. Landslides of all types can pose hazards to human lives and property, but deep-seated landslides are of significant concern because their large areal extent can cause extensive property damage. Although many geomorphic processes shape the coastal bluffs of Seattle, we focus on large (greater than 3,000 m3), deepseated, rotational landslides that occur on the steep bluffs along Puget Sound. Many of these larger failures occur in advance outwash deposits of the Vashon Drift (Qva); some failures extend into the underlying Lawton Clay Member of the Vashon Drift (Qvlc). The slope stability of coastal bluffs is controlled by the interplay of three-dimensional (3-D) variations in gravitational stress, strength, and pore-water pressure. We assess 3-D slope-stability using SCOOPS (Reid and others, 2000), a computer program that allows us to search a high-resolution digital-elevation model (DEM) to quantify the relative stability of all parts of the landscape by computing the stability and volume of thousands of potential spherical failures. SCOOPS incorporates topography, 3-D strength variations, and 3-D pore pressures. Initially, we use our 3-D analysis methods to examine the effects of topography and geology by using heterogeneous material properties, as defined by stratigraphy, without pore pressures. In this scenario, the least-stable areas are located on the steepest slopes, commonly in Qva or Qvlc. However, these locations do not agree well with observations of deep-seated landslides. Historically, both shallow colluvial landslides and deep-seated landslides have been observed near the contact between Qva and Qvlc, and commonly occur in Qva. The low hydraulic conductivity of Qvlc impedes ground-water flow, resulting in elevated pore pressures at the

  4. The BGY3dM model for the approximation of solvent densities.

    PubMed

    Griebel, Michael; Jager, Lukas

    2008-11-07

    We present a new approach for the approximation of solvent densities around solutes of arbitrary shape. Our model represents a three-dimensional (3d) Born-Green-Yvon (BGY) equation for an arbitrary solute immersed into a molecular (M) solvent, the BGY3dM model. It comprises the famous Kirkwood approximation as closure relation. The molecules of the solvent are modeled as rigid bodies by taking the limit of an infinite restoring force for the intramolecular interactions. Furthermore, short-range potentials as well as the long-range Coulomb interaction are taken into account. The resulting integro-differential equations are efficiently solved by a Picard iteration and a solution of the linearized equations using Fourier transformations. We compare the results obtained from the presented BGY3dM method with results obtained by extensive molecular dynamics simulations for a HCl-like model solvent. Furthermore, we apply the method to carbon disulfide as solvent. The overall performance of the method is promising.

  5. High Rayleigh Number 3d Spherical Mantle Convection Models

    NASA Astrophysics Data System (ADS)

    Davies, J. H.

    2003-04-01

    The geochemical and geophysical evidence related to the mantle can potentially be reconciled by a hypothesis of whole mantle convection where the heterogeneity stems from the continuous recycling of oceanic crust, depleted lithospheric mantle and sediments. The mantle is expected to be well but not perfectly stirred, sampled differently in different tectonic settings, and with components having wide-ranging residence times. We might for example expect very long residence times for some buoyant or dense components that can reside in either the upper (lithosphere) or lower boundary (D''). We have started testing whether such a whole mantle convection hypothesis can satisfy wide ranging first order geophysical observations, such as plate velocities, stability of upwellings, geometry of downwellings, etc. The model parameters, including the mantle's viscosity structure, are guided by extensive earlier community work. We use TERRA to model compressible convection in a 3D spherical mantle shell with a depth dependent viscosity structure, where the lower mantle is 40 times more viscous than the upper mantle. A chondritic rate of internal heating of 6 x 10^-12 W/Kg was assumed, leading to Ra(H) = 3.4x10^8. A realistic depth dependent thermal expansivity and Murnaghan equation of state was assumed, with free slip b.c.. The evolution of the system was followed for 2 Billion years. The RMS surface velocity varied from around 4 - 7cm/yr, very similar to recent plate velocities. The structures in the lower mantle are relatively stable and larger length scale in comparison to the upper mantle features. The downwellings and upwellings are linear in planform but the upwellings are dominated by stronger upflow at the columns formed at their intersection. The upwelling features embedded in the lower mantle are very stable, and it is reasonable to expect (though yet to be demonstrated) that with temperature-dependent viscosity the upwellings will be dominated by the cylindrical

  6. Verification and Validation of the k-kL Turbulence Model in FUN3D and CFL3D Codes

    NASA Technical Reports Server (NTRS)

    Abdol-Hamid, Khaled S.; Carlson, Jan-Renee; Rumsey, Christopher L.

    2015-01-01

    The implementation of the k-kL turbulence model using multiple computational uid dy- namics (CFD) codes is reported herein. The k-kL model is a two-equation turbulence model based on Abdol-Hamid's closure and Menter's modi cation to Rotta's two-equation model. Rotta shows that a reliable transport equation can be formed from the turbulent length scale L, and the turbulent kinetic energy k. Rotta's equation is well suited for term-by-term mod- eling and displays useful features compared to other two-equation models. An important di erence is that this formulation leads to the inclusion of higher-order velocity derivatives in the source terms of the scale equations. This can enhance the ability of the Reynolds- averaged Navier-Stokes (RANS) solvers to simulate unsteady ows. The present report documents the formulation of the model as implemented in the CFD codes Fun3D and CFL3D. Methodology, veri cation and validation examples are shown. Attached and sepa- rated ow cases are documented and compared with experimental data. The results show generally very good comparisons with canonical and experimental data, as well as matching results code-to-code. The results from this formulation are similar or better than results using the SST turbulence model.

  7. Explicit 3D continuum fracture modeling with smooth particle hydrodynamics

    NASA Technical Reports Server (NTRS)

    Benz, W.; Asphaug, E.

    1993-01-01

    Impact phenomena shaped our solar system. As usual for most solar system processes, the scales are far different than we can address directly in the laboratory. Impact velocities are often much higher than we can achieve, sizes are often vastly larger, and most impacts take place in an environment where the only gravitational force is the mutual pull of the impactors. The Smooth Particle Hydrodynamics (SPH) technique has been applied in the past to the simulations of giant impacts. In these simulations, the colliding objects were so massive (at least a sizeable fraction of the Earth's mass) that material strength was negligible compared to gravity. This assumption can no longer be made when the bodies are much smaller. To this end, we have developed a 3D SPH code that includes a strength model to which we have added a von Mises yielding relation for stresses beyond the Hugoniot Elastic Limit. At the lower stresses associated with brittle failure, we use a rate-dependent strength based on the nucleation of incipient flaws whose number density is given by a Weibull distribution. Following Grady and Kipp and Melosh et al., we introduce a state variable D ('damage'), 0 less than D less than 1, which expresses the local reduction in strength due to crack growth under tensile loading. Unfortunately for the hydrodynamics, Grady and Kipp's model predicts which fragments are the most probable ones and not the ones that are really formed. This means, for example, that if a given laboratory experiment is modeled, the fragment distribution obtained from the Grady-Kipp theory would be equivalent to a ensemble average over many realizations of the experiment. On the other hand, the hydrodynamics itself is explicit and evolves not an ensemble average but very specific fragments. Hence, there is a clear incompatibility with the deterministic nature of the hydrodynamics equations and the statistical approach of the Grady-Kipp dynamical fracture model. We remedy these shortcomings

  8. The 3D Structure of the Binding Pocket of the Human Oxytocin Receptor for Benzoxazine Antagonists, Determined by Molecular Docking, Scoring Functions and 3D-QSAR Methods

    NASA Astrophysics Data System (ADS)

    Jójárt, Balázs; Martinek, Tamás A.; Márki, Árpád

    2005-05-01

    Molecular docking and 3D-QSAR studies were performed to determine the binding mode for a series of benzoxazine oxytocin antagonists taken from the literature. Structural hypotheses were generated by docking the most active molecule to the rigid receptor by means of AutoDock 3.05. The cluster analysis yielded seven possible binding conformations. These structures were refined by using constrained simulated annealing, and the further ligands were aligned in the refined receptor by molecular docking. A good correlation was found between the estimated Δ G bind and the p K i values for complex F. The Connolly-surface analysis, CoMFA and CoMSIA models q CoMFA 2 = 0.653, q CoMSA 2 = 0.630 and r pred,CoMFA 2 = 0.852 , r pred,CoMSIA 2 = 0.815) confirmed the scoring function results. The structural features of the receptor-ligand complex and the CoMFA and CoMSIA fields are in closely connected. These results suggest that receptor-ligand complex F is the most likely binding hypothesis for the studied benzoxazine analogs.

  9. Numerical Results of 3-D Modeling of Moon Accumulation

    NASA Astrophysics Data System (ADS)

    Khachay, Yurie; Anfilogov, Vsevolod; Antipin, Alexandr

    2014-05-01

    For the last time for the model of the Moon usually had been used the model of mega impact in which the forming of the Earth and its sputnik had been the consequence of the Earth's collision with the body of Mercurial mass. But all dynamical models of the Earth's accumulation and the estimations after the Pb-Pb system, lead to the conclusion that the duration of the planet accumulation was about 1 milliard years. But isotopic results after the W-Hf system testify about a very early (5-10) million years, dividing of the geochemical reservoirs of the core and mantle. In [1,2] it is shown, that the account of energy dissipating by the decay of short living radioactive elements and first of all Al26,it is sufficient for heating even small bodies with dimensions about (50-100) km up to the iron melting temperature and can be realized a principal new differentiation mechanism. The inner parts of the melted preplanets can join and they are mainly of iron content, but the cold silicate fragments return to the supply zone and additionally change the content of Moon forming to silicates. Only after the increasing of the gravitational radius of the Earth, the growing area of the future Earth's core can save also the silicate envelope fragments [3]. For understanding the further system Earth-Moon evolution it is significant to trace the origin and evolution of heterogeneities, which occur on its accumulation stage.In that paper we are modeling the changing of temperature,pressure,velocity of matter flowing in a block of 3d spherical body with a growing radius. The boundary problem is solved by the finite-difference method for the system of equations, which include equations which describe the process of accumulation, the Safronov equation, the equation of impulse balance, equation Navier-Stocks, equation for above litho static pressure and heat conductivity in velocity-pressure variables using the Businesque approach.The numerical algorithm of the problem solution in velocity

  10. Induction Heating Process: 3D Modeling and Optimisation

    NASA Astrophysics Data System (ADS)

    Naar, R.; Bay, F.

    2011-05-01

    An increasing number of problems in mechanics and physics involves multiphysics coupled problems. Among these problems, we can often find electromagnetic coupled problems. Electromagnetic couplings may be involved through the use of direct or induced currents for thermal purposes—in order to generate heat inside a work piece in order to get either a prescribed temperature field or some given mechanical or metallurgical properties through an accurate control of temperature evolution with respect to time-, or for solid or fluid mechanics purposes—in order to create magnetic forces such as in fluid mechanics (electromagnetic stirring,…) or solid mechanics (magnetoforming,…). Induction heat treatment processes is therefore quite difficult to control; trying for instance to minimize distortions generated by such a process is not easy. In order to achieve these objectives, we have developed a computational tool which includes an optimsation stage. A 3D finite element modeling tool for local quenching after induction heating processes has already been developed in our laboratory. The modeling of such a multiphysics coupled process needs taking into account electromagnetic, thermal, mechanical and metallurgical phenomenon—as well as their mutual interactions during the whole process: heating and quenching. The model developed is based on Maxwell equations, heat transfer equation, mechanical equilibrium computations, Johnson-Mehl-Avrami and Koistinen-Marburger laws. All these equations and laws may be coupled but some coupling may be neglected. In our study, we will also focus on induction heating process aiming at optimising the Heat Affected Zone (HAZ). Thus problem is formalized as an optimization problem—minimizing a cost function which measures the difference between computed and optimal temperatures—along with some constraints on process parameters. The optimization algorithms may be of two kinds—either zero-order or first-order algorithms. First

  11. Orbiter/External Tank Mate 3-D Solid Modeling

    NASA Technical Reports Server (NTRS)

    Godfrey, G. S.; Brandt, B.; Rorden, D.; Kapr, F.

    2004-01-01

    This research and development project presents an overview of the work completed while attending a summer 2004 American Society of Engineering Education/National Aeronautics and Space Administration (ASEE/NASA) Faculty Fellowship. This fellowship was completed at the Kennedy Space Center, Florida. The scope of the project was to complete parts, assemblies, and drawings that could be used by Ground Support Equipment (GSE) personnel to simulate situations and scenarios commonplace to the space shuttle Orbiter/External Tank (ET) Mate (50004). This mate takes place in the Vehicle Assembly Building (VAB). These simulations could then be used by NASA engineers as decision-making tools. During the summer of 2004, parts were created that defined the Orbiter/ET structural interfaces. Emphasis was placed upon assemblies that included the Orbiter/ET forward attachment (EO-1), aft left thrust strut (EO-2), aft right tripod support structure (EO-3), and crossbeam and aft feedline/umbilical supports. These assemblies are used to attach the Orbiter to the ET. The Orbiter/ET Mate assembly was then used to compare and analyze clearance distances using different Orbiter hang angles. It was found that a 30-minute arc angle change in Orbiter hang angle affected distance at the bipod strut to Orbiter yoke fitting 8.11 inches. A 3-D solid model library was established as a result of this project. This library contains parts, assemblies, and drawings translated into several formats. This library contains a collection of the following files: sti for sterolithography, stp for neutral file work, shrinkwrap for compression. tiff for photoshop work, jpeg for Internet use, and prt and asm for Pro/Engineer use. This library was made available to NASA engineers so that they could access its contents to make angle, load, and clearance analysis studies. These decision-making tools may be used by Pro/Engineer users and non-users.

  12. Automated robust generation of compact 3D statistical shape models

    NASA Astrophysics Data System (ADS)

    Vrtovec, Tomaz; Likar, Bostjan; Tomazevic, Dejan; Pernus, Franjo

    2004-05-01

    Ascertaining the detailed shape and spatial arrangement of anatomical structures is important not only within diagnostic settings but also in the areas of planning, simulation, intraoperative navigation, and tracking of pathology. Robust, accurate and efficient automated segmentation of anatomical structures is difficult because of their complexity and inter-patient variability. Furthermore, the position of the patient during image acquisition, the imaging device and protocol, image resolution, and other factors induce additional variations in shape and appearance. Statistical shape models (SSMs) have proven quite successful in capturing structural variability. A possible approach to obtain a 3D SSM is to extract reference voxels by precisely segmenting the structure in one, reference image. The corresponding voxels in other images are determined by registering the reference image to each other image. The SSM obtained in this way describes statistically plausible shape variations over the given population as well as variations due to imperfect registration. In this paper, we present a completely automated method that significantly reduces shape variations induced by imperfect registration, thus allowing a more accurate description of variations. At each iteration, the derived SSM is used for coarse registration, which is further improved by describing finer variations of the structure. The method was tested on 64 lumbar spinal column CT scans, from which 23, 38, 45, 46 and 42 volumes of interest containing vertebra L1, L2, L3, L4 and L5, respectively, were extracted. Separate SSMs were generated for each vertebra. The results show that the method is capable of reducing the variations induced by registration errors.

  13. 3D Geological Model of Nihe ore deposit Constrained by Gravity and Magnetic Modeling

    NASA Astrophysics Data System (ADS)

    Qi, Guang; Yan, Jiayong; Lv, Qingtan; Zhao, Jinhua

    2016-04-01

    We present a case study on using integrated geologic model in mineral exploration at depth. Nihe ore deposit in Anhui Province, is deep hidden ore deposit which was discovered in recent years, this finding is the major driving force of deep mineral exploration work in Luzong. Building 3D elaborate geological model has the important significance for prospecting to deep or surround in this area, and can help us better understand the metallogenic law and ore-controlling regularity. A 3D geological model, extending a depth from +200m to -1500m in Nihe ore deposit, has been compiled from surface geological map, cross-section, borehole logs and amounts of geological inference. And then the 3D geological models have been given physical property parameter for calculating the potential field. Modelling the potential response is proposed as means of evaluating the viability of the 3D geological models, and the evidence of making small changes to the uncertain parts of the original 3D geological models. It is expected that the final models not only reproduce supplied prior geological knowledge, but also explain the observed geophysical data. The workflow used to develop the 3D geologic model in this study includes the three major steps, as follows: (1) Determine the basic information of Model: Defining the 3D limits of the model area, the basic geological and structural unit, and the tectonic contact relations and the sedimentary sequences between these units. (2) 3D model construction: Firstly, a series of 2D geological cross sections over the model area are built by using all kinds of prior information, including surface geology, borehole data, seismic sections, and local geologists' knowledge and intuition. Lastly, we put these sections into a 3D environment according to their profile locations to build a 3D model by using geostatistics method. (3) 3D gravity and magnetic modeling: we calculate the potential field responses of the 3D model, and compare the predicted and

  14. Modeling Computer Communication Networks in a Realistic 3D Environment

    DTIC Science & Technology

    2010-03-01

    visualization in OPNET . . . . . . . . . . . . 13 6. Sample NetViz visualization . . . . . . . . . . . . . . . . . . . 15 7. Realistic 3D terrains...scenario in OPNET . . . 19 10. OPNET 3DNV only displays connectivity . . . . . . . . . . . . 29 11. The digitally connected battlefield...confirmation tool 12 OPNET Optimized Network Evaluation Tool . . . . . . . . . . . . 13 NetViz Network Visualization

  15. 3D genome structure modeling by Lorentzian objective function.

    PubMed

    Trieu, Tuan; Cheng, Jianlin

    2016-11-29

    The 3D structure of the genome plays a vital role in biological processes such as gene interaction, gene regulation, DNA replication and genome methylation. Advanced chromosomal conformation capture techniques, such as Hi-C and tethered conformation capture, can generate chromosomal contact data that can be used to computationally reconstruct 3D structures of the genome. We developed a novel restraint-based method that is capable of reconstructing 3D genome structures utilizing both intra-and inter-chromosomal contact data. Our method was robust to noise and performed well in comparison with a panel of existing methods on a controlled simulated data set. On a real Hi-C data set of the human genome, our method produced chromosome and genome structures that are consistent with 3D FISH data and known knowledge about the human chromosome and genome, such as, chromosome territories and the cluster of small chromosomes in the nucleus center with the exception of the chromosome 18. The tool and experimental data are available at https://missouri.box.com/v/LorDG.

  16. Using 3D Geometric Models to Teach Spatial Geometry Concepts.

    ERIC Educational Resources Information Center

    Bertoline, Gary R.

    1991-01-01

    An explanation of 3-D Computer Aided Design (CAD) usage to teach spatial geometry concepts using nontraditional techniques is presented. The software packages CADKEY and AutoCAD are described as well as their usefulness in solving space geometry problems. (KR)

  17. Examination of 1D Solar Cell Model Limitations Using 3D SPICE Modeling: Preprint

    SciTech Connect

    McMahon, W. E.; Olson, J. M.; Geisz, J. F.; Friedman, D. J.

    2012-06-01

    To examine the limitations of one-dimensional (1D) solar cell modeling, 3D SPICE-based modeling is used to examine in detail the validity of the 1D assumptions as a function of sheet resistance for a model cell. The internal voltages and current densities produced by this modeling give additional insight into the differences between the 1D and 3D models.

  18. 3D cell culture systems modeling tumor growth determinants in cancer target discovery.

    PubMed

    Thoma, Claudio R; Zimmermann, Miriam; Agarkova, Irina; Kelm, Jens M; Krek, Wilhelm

    2014-04-01

    Phenotypic heterogeneity of cancer cells, cell biological context, heterotypic crosstalk and the microenvironment are key determinants of the multistep process of tumor development. They sign responsible, to a significant extent, for the limited response and resistance of cancer cells to molecular-targeted therapies. Better functional knowledge of the complex intra- and intercellular signaling circuits underlying communication between the different cell types populating a tumor tissue and of the systemic and local factors that shape the tumor microenvironment is therefore imperative. Sophisticated 3D multicellular tumor spheroid (MCTS) systems provide an emerging tool to model the phenotypic and cellular heterogeneity as well as microenvironmental aspects of in vivo tumor growth. In this review we discuss the cellular, chemical and physical factors contributing to zonation and cellular crosstalk within tumor masses. On this basis, we further describe 3D cell culture technologies for growth of MCTS as advanced tools for exploring molecular tumor growth determinants and facilitating drug discovery efforts. We conclude with a synopsis on technological aspects for on-line analysis and post-processing of 3D MCTS models.

  19. Quasi-Facial Communication for Online Learning Using 3D Modeling Techniques

    ERIC Educational Resources Information Center

    Wang, Yushun; Zhuang, Yueting

    2008-01-01

    Online interaction with 3D facial animation is an alternative way of face-to-face communication for distance education. 3D facial modeling is essential for virtual educational environments establishment. This article presents a novel 3D facial modeling solution that facilitates quasi-facial communication for online learning. Our algorithm builds…

  20. Numerical Results of Earth's Core Accumulation 3-D Modelling

    NASA Astrophysics Data System (ADS)

    Khachay, Yurie; Anfilogov, Vsevolod

    2013-04-01

    For a long time as a most convenient had been the model of mega impact in which the early forming of the Earth's core and mantle had been the consequence of formed protoplanet collision with the body of Mercurial mass. But all dynamical models of the Earth's accumulation and the estimations after the Pb-Pb system, lead to the conclusion that the duration of the planet accumulation was about 1 milliard years. But isotopic results after the W-Hf system testify about a very early (5-10) million years, dividing of the geochemical reservoirs of the core and mantle. In [1,3] it is shown, that the account of energy dissipating by the decay of short living radioactive elements and first of all Al,it is sufficient for heating even small bodies with dimensions about (50-100) km up to the iron melting temperature and can be realized a principal new differentiation mechanism. The inner parts of the melted preplanets can join and they are mainly of iron content, but the cold silicate fragments return to the supply zone. Only after the increasing of the gravitational radius, the growing area of the future core can save also the silicate envelope fragments. All existing dynamical accumulation models are constructed by using a spherical-symmetrical model. Hence for understanding the further planet evolution it is significant to trace the origin and evolution of heterogeneities, which occur on the planet accumulation stage. In that paper we are modeling distributions of temperature, pressure, velocity of matter flowing in a block of 3D- spherical body with a growing radius. The boundary problem is solved by the finite-difference method for the system of equations, which include equations which describe the process of accumulation, the Safronov equation, the equation of impulse balance, equation Navier-Stocks, equation for above litho static pressure and heat conductivity in velocity-pressure variables using the Businesque approach. The numerical algorithm of the problem solution in

  1. Development of a New Tool for 3D Modeling for Regenerative Medicine

    PubMed Central

    Mattoli, Filippo; Tiribuzi, Roberto; D'Angelo, Francesco; di Girolamo, Ilaria; Quattrocelli, Mattia; Montesano, Simona; Crispoltoni, Lucia; Oikonomou, Vasileios; Cusella De Angelis, Maria Gabriella; Marconi, Peggy; Orlacchio, Antonio; Sampaolesi, Maurilio; Martino, Sabata; Orlacchio, Aldo

    2011-01-01

    The effectiveness of therapeutic treatment based on regenerative medicine for degenerative diseases (i.e., neurodegenerative or cardiac diseases) requires tools allowing the visualization and analysis of the three-dimensional (3D) distribution of target drugs within the tissue. Here, we present a new computational procedure able to overcome the limitations of visual analysis emerging by the examination of a molecular signal within images of serial tissue/organ sections by using the conventional techniques. Together with the 3D anatomical reconstitution of the tissue/organ, our framework allows the detection of signals of different origins (e.g., marked generic molecules, colorimetric, or fluorimetric substrates for enzymes; microRNA; recombinant protein). Remarkably, the application does not require the employment of specific tracking reagents for the imaging analysis. We report two different representative applications: the first shows the reconstruction of a 3D model of mouse brain with the analysis of the distribution of the β-Galactosidase, the second shows the reconstruction of a 3D mouse heart with the measurement of the cardiac volume. PMID:21776249

  2. 3D Atmospheric Radiative Transfer for Cloud System-Resolving Models: Forward Modelling and Observations

    SciTech Connect

    Howard Barker; Jason Cole

    2012-05-17

    Utilization of cloud-resolving models and multi-dimensional radiative transfer models to investigate the importance of 3D radiation effects on the numerical simulation of cloud fields and their properties.

  3. Reticular synthesis of porous molecular 1D nanotubes and 3D networks

    NASA Astrophysics Data System (ADS)

    Slater, A. G.; Little, M. A.; Pulido, A.; Chong, S. Y.; Holden, D.; Chen, L.; Morgan, C.; Wu, X.; Cheng, G.; Clowes, R.; Briggs, M. E.; Hasell, T.; Jelfs, K. E.; Day, G. M.; Cooper, A. I.

    2017-01-01

    Synthetic control over pore size and pore connectivity is the crowning achievement for porous metal-organic frameworks (MOFs). The same level of control has not been achieved for molecular crystals, which are not defined by strong, directional intermolecular coordination bonds. Hence, molecular crystallization is inherently less controllable than framework crystallization, and there are fewer examples of 'reticular synthesis', in which multiple building blocks can be assembled according to a common assembly motif. Here we apply a chiral recognition strategy to a new family of tubular covalent cages to create both 1D porous nanotubes and 3D diamondoid pillared porous networks. The diamondoid networks are analogous to MOFs prepared from tetrahedral metal nodes and linear ditopic organic linkers. The crystal structures can be rationalized by computational lattice-energy searches, which provide an in silico screening method to evaluate candidate molecular building blocks. These results are a blueprint for applying the 'node and strut' principles of reticular synthesis to molecular crystals.

  4. Monte Carlo Modeling of Thin Film Deposition: Factors that Influence 3D Islands

    SciTech Connect

    Gilmer, G H; Dalla Torre, J; Baumann, F H; Diaz de la Rubia, T

    2002-01-04

    In this paper we discuss the use of atomistic Monte Carlo simulations to predict film microstructure evolution. We discuss physical vapor deposition, and are primarily concerned with films that are formed by the nucleation and coalescence of 3D islands. Multi-scale modeling is used in the sense that information obtained from molecular dynamics and first principles calculations provide atomic interaction energies, surface and grain boundary properties and diffusion rates for use in the Monte Carlo model. In this paper, we discuss some fundamental issues associated with thin film formation, together with an assessment of the sensitivity of the film morphology to the deposition conditions and materials properties.

  5. Hsp90 inhibitors, part 1: definition of 3-D QSAutogrid/R models as a tool for virtual screening.

    PubMed

    Ballante, Flavio; Caroli, Antonia; Wickersham, Richard B; Ragno, Rino

    2014-03-24

    The multichaperone heat shock protein (Hsp) 90 complex mediates the maturation and stability of a variety of oncogenic signaling proteins. For this reason, Hsp90 has emerged as a promising target for anticancer drug development. Herein, we describe a complete computational procedure for building several 3-D QSAR models used as a ligand-based (LB) component of a comprehensive ligand-based (LB) and structure-based (SB) virtual screening (VS) protocol to identify novel molecular scaffolds of Hsp90 inhibitors. By the application of the 3-D QSAutogrid/R method, eight SB PLS 3-D QSAR models were generated, leading to a final multiprobe (MP) 3-D QSAR pharmacophoric model capable of recognizing the most significant chemical features for Hsp90 inhibition. Both the monoprobe and multiprobe models were optimized, cross-validated, and tested against an external test set. The obtained statistical results confirmed the models as robust and predictive to be used in a subsequent VS.

  6. Fast, Automated, 3D Modeling of Building Interiors

    DTIC Science & Technology

    2012-10-30

    of thermographies with laser scanning point clouds [6]. Given the heterogeneous nature of the two modalities, we propose a feature-based approach...extract 2D lines from thermographies , and 3D lines are extracted through segmentation of the point cloud. Feature- matching and the relative pose between... thermographies and point cloud are obtained from an iterative procedure applied to detect and reject outliers; this includes rotation matrix and

  7. Parallel implementation of 3D FFT with volumetric decomposition schemes for efficient molecular dynamics simulations

    NASA Astrophysics Data System (ADS)

    Jung, Jaewoon; Kobayashi, Chigusa; Imamura, Toshiyuki; Sugita, Yuji

    2016-03-01

    Three-dimensional Fast Fourier Transform (3D FFT) plays an important role in a wide variety of computer simulations and data analyses, including molecular dynamics (MD) simulations. In this study, we develop hybrid (MPI+OpenMP) parallelization schemes of 3D FFT based on two new volumetric decompositions, mainly for the particle mesh Ewald (PME) calculation in MD simulations. In one scheme, (1d_Alltoall), five all-to-all communications in one dimension are carried out, and in the other, (2d_Alltoall), one two-dimensional all-to-all communication is combined with two all-to-all communications in one dimension. 2d_Alltoall is similar to the conventional volumetric decomposition scheme. We performed benchmark tests of 3D FFT for the systems with different grid sizes using a large number of processors on the K computer in RIKEN AICS. The two schemes show comparable performances, and are better than existing 3D FFTs. The performances of 1d_Alltoall and 2d_Alltoall depend on the supercomputer network system and number of processors in each dimension. There is enough leeway for users to optimize performance for their conditions. In the PME method, short-range real-space interactions as well as long-range reciprocal-space interactions are calculated. Our volumetric decomposition schemes are particularly useful when used in conjunction with the recently developed midpoint cell method for short-range interactions, due to the same decompositions of real and reciprocal spaces. The 1d_Alltoall scheme of 3D FFT takes 4.7 ms to simulate one MD cycle for a virus system containing more than 1 million atoms using 32,768 cores on the K computer.

  8. Numerical modelling of gravel unconstrained flow experiments with the DAN3D and RASH3D codes

    NASA Astrophysics Data System (ADS)

    Sauthier, Claire; Pirulli, Marina; Pisani, Gabriele; Scavia, Claudio; Labiouse, Vincent

    2015-12-01

    Landslide continuum dynamic models have improved considerably in the last years, but a consensus on the best method of calibrating the input resistance parameter values for predictive analyses has not yet emerged. In the present paper, numerical simulations of a series of laboratory experiments performed at the Laboratory for Rock Mechanics of the EPF Lausanne were undertaken with the RASH3D and DAN3D numerical codes. They aimed at analysing the possibility to use calibrated ranges of parameters (1) in a code different from that they were obtained from and (2) to simulate potential-events made of a material with the same characteristics as back-analysed past-events, but involving a different volume and propagation path. For this purpose, one of the four benchmark laboratory tests was used as past-event to calibrate the dynamic basal friction angle assuming a Coulomb-type behaviour of the sliding mass, and this back-analysed value was then used to simulate the three other experiments, assumed as potential-events. The computational findings show good correspondence with experimental results in terms of characteristics of the final deposits (i.e., runout, length and width). Furthermore, the obtained best fit values of the dynamic basal friction angle for the two codes turn out to be close to each other and within the range of values measured with pseudo-dynamic tilting tests.

  9. Virtual and Printed 3D Models for Teaching Crystal Symmetry and Point Groups

    ERIC Educational Resources Information Center

    Casas, Lluís; Estop, Euge`nia

    2015-01-01

    Both, virtual and printed 3D crystal models can help students and teachers deal with chemical education topics such as symmetry and point groups. In the present paper, two freely downloadable tools (interactive PDF files and a mobile app) are presented as examples of the application of 3D design to study point-symmetry. The use of 3D printing to…

  10. Analysis of 3D Modeling Software Usage Patterns for K-12 Students

    ERIC Educational Resources Information Center

    Wu, Yi-Chieh; Liao, Wen-Hung; Chi, Ming-Te; Li, Tsai-Yen

    2016-01-01

    In response to the recent trend in maker movement, teachers are learning 3D techniques actively and bringing 3D printing into the classroom to enhance variety and creativity in designing lectures. This study investigates the usage pattern of a 3D modeling software, Qmodel Creator, which is targeted at K-12 students. User logs containing…

  11. ODTLES : a model for 3D turbulent flow based on one-dimensional turbulence modeling concepts.

    SciTech Connect

    McDermott, Randy; Kerstein, Alan R.; Schmidt, Rodney Cannon

    2005-01-01

    This report describes an approach for extending the one-dimensional turbulence (ODT) model of Kerstein [6] to treat turbulent flow in three-dimensional (3D) domains. This model, here called ODTLES, can also be viewed as a new LES model. In ODTLES, 3D aspects of the flow are captured by embedding three, mutually orthogonal, one-dimensional ODT domain arrays within a coarser 3D mesh. The ODTLES model is obtained by developing a consistent approach for dynamically coupling the different ODT line sets to each other and to the large scale processes that are resolved on the 3D mesh. The model is implemented computationally and its performance is tested and evaluated by performing simulations of decaying isotropic turbulence, a standard turbulent flow benchmarking problem.

  12. Mass Spectrometry Based Molecular 3D-Cartography of Plant Metabolites

    PubMed Central

    Floros, Dimitrios J.; Petras, Daniel; Kapono, Clifford A.; Melnik, Alexey V.; Ling, Tie-Jun; Knight, Rob; Dorrestein, Pieter C.

    2017-01-01

    Plants play an essential part in global carbon fixing through photosynthesis and are the primary food and energy source for humans. Understanding them thoroughly is therefore of highest interest for humanity. Advances in DNA and RNA sequencing and in protein and metabolite analysis allow the systematic description of plant composition at the molecular level. With imaging mass spectrometry, we can now add a spatial level, typically in the micrometer-to-centimeter range, to their compositions, essential for a detailed molecular understanding. Here we present an LC-MS based approach for 3D plant imaging, which is scalable and allows the analysis of entire plants. We applied this approach in a case study to pepper and tomato plants. Together with MS/MS spectra library matching and spectral networking, this non-targeted workflow provides the highest sensitivity and selectivity for the molecular annotations and imaging of plants, laying the foundation for studies of plant metabolism and plant-environment interactions.

  13. Quantitative 3D molecular cutaneous absorption in human skin using label free nonlinear microscopy.

    PubMed

    Chen, Xueqin; Grégoire, Sébastien; Formanek, Florian; Galey, Jean-Baptiste; Rigneault, Hervé

    2015-02-28

    Understanding the penetration mechanisms of drugs into human skin is a key issue in pharmaceutical and cosmetics research. To date, the techniques available for percutaneous penetration of compounds fail to provide a quantitative 3D map of molecular concentration distribution in complex tissues as the detected microscopy images are an intricate combination of concentration distribution and laser beam attenuation upon deep penetration. Here we introduce and validate a novel framework for imaging and reconstructing molecular concentration within the depth of artificial and human skin samples. Our approach combines the use of deuterated molecular compounds together with coherent anti-Stokes Raman scattering spectroscopy and microscopy that permits targeted molecules to be unambiguously discriminated within skin layers. We demonstrate both intercellular and transcellular pathways for different active compounds, together with in-depth concentration profiles reflecting the detailed skin barrier architecture. This method provides an enabling platform for establishing functional activity of topically applied products.

  14. Cloud-resolving component in the quasi-3D multi-scale modeling framework

    NASA Astrophysics Data System (ADS)

    Jung, Joon-Hee; Arakawa, Akio

    2010-05-01

    A quasi-3D multi-scale modeling framework (Q3D MMF), which combines a GCM with a Q3D CRM, is an attempt to include three dimensional cloud effects in a GCM without necessarily using a global cloud-resolving model. The horizontal domain of the Q3D CRM consists of two perpendicular sets of channels crossing at the center of a GCM grid box, each of which includes two grid-point arrays. Through coupling this structure with a GCM, the whole system of the Q3D MMF can converge to a fully 3D global CRM as the GCM's resolution is refined. Consequently, the horizontal resolution of the GCM can be freely chosen depending on the objective of application. However, due to the use of very narrow channels for the cloud-resolving component, its prediction algorithm must be specially designed. As a step in developing a Q3D MMF, we have first constructed a prediction algorithm for the Q3D CRM applying a 3D anelastic vector vorticity equation model to the Q3D network of grid points. Preliminary tests of the Q3D CRM have been performed for an idealized small domain. Comparing the results with those of the straightforward application of a 3D CRM, it is concluded that the Q3D CRM can reproduce most of the important statistics of the 3D solutions and the MMF based on the Q3D CRM will be a useful framework for climate modeling. This paper presents an outline of the Q3D algorithm and highlights of the results.

  15. Inhibitory mode of indole-2-carboxamide derivatives against HLGPa: molecular docking and 3D-QSAR analyses.

    PubMed

    Liu, Guixia; Zhang, Zhenshan; Luo, Xiaomin; Shen, Jianhua; Liu, Hong; Shen, Xu; Chen, Kaixian; Jiang, Hualiang

    2004-08-01

    The interaction of a series of indole-2-carboxamide compounds with human liver glycogen phosphorylase a (HLGPa) have been studied employing molecular docking and 3D-QSAR approaches. The Lamarckian Genetic Algorithm (LGA) of AutoDock 3.0 was employed to locate the binding orientations and conformations of the inhibitors interacting with HLGPa. The binding models were demonstrated in the aspects of inhibitor's conformation, subsite interaction, and hydrogen bonding. The very similar binding conformations of these inhibitors show that they interact with HLGPa in a very similar way. Good correlations between the calculated interaction free energies and experimental inhibitory activities suggest that the binding conformations of these inhibitors are reasonable. The structural and energetic differences in inhibitory potencies of indole-2-carboxamide compounds were reasonably explored. Using the binding conformations of indole-2-carboxamides, consistent and highly predictive 3D-QSAR models were developed by CoMFA and CoMSIA analyses. The q2 values are 0.697 and 0.622 for CoMFA and CoMSIA models, respectively. The predictive ability of these models was validated by four compounds that were not included in the training set. Mapping these models back to the topology of the active site of HLGPa leads to a better understanding of the vital indole-2-carboxamide-HLGPa interactions. Structure-based investigations and the final 3D-QSAR results provide clear guidelines and accurate activity predictions for novel inhibitor design.

  16. A structure-activity relationship study of catechol- O-methyltransferase inhibitors combining molecular docking and 3D QSAR methods

    NASA Astrophysics Data System (ADS)

    Tervo, Anu J.; Nyrönen, Tommi H.; Rönkkö, Toni; Poso, Antti

    2003-12-01

    A panel of 92 catechol- O-methyltransferase (COMT) inhibitors was used to examine the molecular interactions affecting their biological activity. COMT inhibitors are used as therapeutic agents in the treatment of Parkinson's disease, but there are limitations in the currently marketed compounds due to adverse side effects. This study combined molecular docking methods with three-dimensional structure-activity relationships (3D QSAR) to analyse possible interactions between COMT and its inhibitors, and to incite the design of new inhibitors. Comparative molecular field analysis (CoMFA) and GRID/GOLPE models were made by using bioactive conformations from docking experiments, which yielded q2 values of 0.594 and 0.636, respectively. The docking results, the COMT X-ray structure, and the 3D QSAR models are in agreement with each other. The models suggest that an interaction between the inhibitor's catechol oxygens and the Mg2+ ion in the COMT active site is important. Both hydrogen bonding with Lys144, Asn170 and Glu199, and hydrophobic contacts with Trp38, Pro174 and Leu198 influence inhibitor binding. Docking suggests that a large R1 substituent of the catechol ring can form hydrophobic contacts with side chains of Val173, Leu198, Met201 and Val203 on the COMT surface. Our models propose that increasing steric volume of e.g. the diethylamine tail of entacapone is favourable for COMT inhibitory activity.

  17. TOPICAL REVIEW: Computational approaches to 3D modeling of RNA

    NASA Astrophysics Data System (ADS)

    Laing, Christian; Schlick, Tamar

    2010-07-01

    Many exciting discoveries have recently revealed the versatility of RNA and its importance in a variety of functions within the cell. Since the structural features of RNA are of major importance to their biological function, there is much interest in predicting RNA structure, either in free form or in interaction with various ligands, including proteins, metabolites and other molecules. In recent years, an increasing number of researchers have developed novel RNA algorithms for predicting RNA secondary and tertiary structures. In this review, we describe current experimental and computational advances and discuss recent ideas that are transforming the traditional view of RNA folding. To evaluate the performance of the most recent RNA 3D folding algorithms, we provide a comparative study in order to test the performance of available 3D structure prediction algorithms for an RNA data set of 43 structures of various lengths and motifs. We find that the algorithms vary widely in terms of prediction quality across different RNA lengths and topologies; most predictions have very large root mean square deviations from the experimental structure. We conclude by outlining some suggestions for future RNA folding research.

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

    SciTech Connect

    Li, Xiaolin; Ye, Li; Wang, Xiaoxiang; Wang, Xinzhou; Liu, Hongling; Zhu, Yongliang; Yu, Hongxia

    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.

  19. Foldectures: 3D Molecular Architectures from Self-Assembly of Peptide Foldamers.

    PubMed

    Yoo, Sung Hyun; Lee, Hee-Seung

    2017-02-13

    The wide range of fascinating supramolecular architectures found in nature, from DNA double helices to giant protein shells, inspires researchers to mimic the diverse shapes and functions of natural systems. Thus, a variety of artificial molecular platforms have been developed by assembling DNA-, peptide-, and protein-based building blocks for medicinal and biological applications. There has also been a significant interest in the research of non-natural oligomers (i.e., foldamers) that fold into well-defined secondary structures analogous to those found in proteins, because the assemblies of foldamers are expected not only to form biomimetic supramolecular architectures that resemble those of nature but also to display unique functions and unprecedented topologies at the same time due to their different folding propensities from those of natural building blocks. Foldamer-based supramolecular architectures have been reported in the form of nanofibers, nanochannels, nanosheets, and finite three-dimensional (3D) shapes. We have developed a new class of crystalline peptidic materials termed "foldectures" (a compound of foldamer and architecture) with unprecedented topological complexity derived from the rapid and nonequilibrium aqueous phase self-assembly of foldamers. In this Account, we discuss the morphological features, molecular packing structures, physical properties, and potential applications of foldectures. Foldectures exhibit well-defined, microscale, homogeneous, and finite structures with unique morphologies such as windmill, tooth, and trigonal bipyramid shapes. The symmetry elements of the morphologies vary with the foldamer building blocks and are retained upon surfactant-assisted shape evolution. Structural characterization by powder X-ray diffraction (PXRD) revealed the molecular packing structures, suggesting how the foldamer building blocks assembled in the 3D structure. The analysis by PXRD showed that intermolecular hydrogen bonding connects

  20. A tetraphenylethylene core-based 3D structure small molecular acceptor enabling efficient non-fullerene organic solar cells.

    PubMed

    Liu, Yuhang; Mu, Cheng; Jiang, Kui; Zhao, Jingbo; Li, Yunke; Zhang, Lu; Li, Zhengke; Lai, Joshua Yuk Lin; Hu, Huawei; Ma, Tingxuan; Hu, Rongrong; Yu, Demei; Huang, Xuhui; Tang, Ben Zhong; Yan, He

    2015-02-01

    A tetraphenylethylene core-based small molecular acceptor with a unique 3D molecular structure is developed. Bulk-heterojunction blend films with a small feature size (≈20 nm) are obtained, which lead to non-fullerene organic solar cells (OSCs) with 5.5% power conversion efficiency. The work provides a new molecular design approach to efficient non-fullerene OSCs based on 3D-structured small-molecule acceptors.

  1. Procedural 3d Modelling for Traditional Settlements. The Case Study of Central Zagori

    NASA Astrophysics Data System (ADS)

    Kitsakis, D.; Tsiliakou, E.; Labropoulos, T.; Dimopoulou, E.

    2017-02-01

    Over the last decades 3D modelling has been a fast growing field in Geographic Information Science, extensively applied in various domains including reconstruction and visualization of cultural heritage, especially monuments and traditional settlements. Technological advances in computer graphics, allow for modelling of complex 3D objects achieving high precision and accuracy. Procedural modelling is an effective tool and a relatively novel method, based on algorithmic modelling concept. It is utilized for the generation of accurate 3D models and composite facade textures from sets of rules which are called Computer Generated Architecture grammars (CGA grammars), defining the objects' detailed geometry, rather than altering or editing the model manually. In this paper, procedural modelling tools have been exploited to generate the 3D model of a traditional settlement in the region of Central Zagori in Greece. The detailed geometries of 3D models derived from the application of shape grammars on selected footprints, and the process resulted in a final 3D model, optimally describing the built environment of Central Zagori, in three levels of Detail (LoD). The final 3D scene was exported and published as 3D web-scene which can be viewed with 3D CityEngine viewer, giving a walkthrough the whole model, same as in virtual reality or game environments. This research work addresses issues regarding textures' precision, LoD for 3D objects and interactive visualization within one 3D scene, as well as the effectiveness of large scale modelling, along with the benefits and drawbacks that derive from procedural modelling techniques in the field of cultural heritage and more specifically on 3D modelling of traditional settlements.

  2. A Deformable Generic 3D Model of Haptoral Anchor of Monogenean

    PubMed Central

    Teo, Bee Guan; Dhillon, Sarinder Kaur; Lim, Lee Hong Susan

    2013-01-01

    In this paper, a digital 3D model which allows for visualisation in three dimensions and interactive manipulation is explored as a tool to help us understand the structural morphology and elucidate the functions of morphological structures of fragile microorganisms which defy live studies. We developed a deformable generic 3D model of haptoral anchor of dactylogyridean monogeneans that can subsequently be deformed into different desired anchor shapes by using direct manipulation deformation technique. We used point primitives to construct the rectangular building blocks to develop our deformable 3D model. Point primitives are manually marked on a 2D illustration of an anchor on a Cartesian graph paper and a set of Cartesian coordinates for each point primitive is manually extracted from the graph paper. A Python script is then written in Blender to construct 3D rectangular building blocks based on the Cartesian coordinates. The rectangular building blocks are stacked on top or by the side of each other following their respective Cartesian coordinates of point primitive. More point primitives are added at the sites in the 3D model where more structural variations are likely to occur, in order to generate complex anchor structures. We used Catmull-Clark subdivision surface modifier to smoothen the surface and edge of the generic 3D model to obtain a smoother and more natural 3D shape and antialiasing option to reduce the jagged edges of the 3D model. This deformable generic 3D model can be deformed into different desired 3D anchor shapes through direct manipulation deformation technique by aligning the vertices (pilot points) of the newly developed deformable generic 3D model onto the 2D illustrations of the desired shapes and moving the vertices until the desire 3D shapes are formed. In this generic 3D model all the vertices present are deployed for displacement during deformation. PMID:24204903

  3. A deformable generic 3D model of haptoral anchor of Monogenean.

    PubMed

    Teo, Bee Guan; Dhillon, Sarinder Kaur; Lim, Lee Hong Susan

    2013-01-01

    In this paper, a digital 3D model which allows for visualisation in three dimensions and interactive manipulation is explored as a tool to help us understand the structural morphology and elucidate the functions of morphological structures of fragile microorganisms which defy live studies. We developed a deformable generic 3D model of haptoral anchor of dactylogyridean monogeneans that can subsequently be deformed into different desired anchor shapes by using direct manipulation deformation technique. We used point primitives to construct the rectangular building blocks to develop our deformable 3D model. Point primitives are manually marked on a 2D illustration of an anchor on a Cartesian graph paper and a set of Cartesian coordinates for each point primitive is manually extracted from the graph paper. A Python script is then written in Blender to construct 3D rectangular building blocks based on the Cartesian coordinates. The rectangular building blocks are stacked on top or by the side of each other following their respective Cartesian coordinates of point primitive. More point primitives are added at the sites in the 3D model where more structural variations are likely to occur, in order to generate complex anchor structures. We used Catmull-Clark subdivision surface modifier to smoothen the surface and edge of the generic 3D model to obtain a smoother and more natural 3D shape and antialiasing option to reduce the jagged edges of the 3D model. This deformable generic 3D model can be deformed into different desired 3D anchor shapes through direct manipulation deformation technique by aligning the vertices (pilot points) of the newly developed deformable generic 3D model onto the 2D illustrations of the desired shapes and moving the vertices until the desire 3D shapes are formed. In this generic 3D model all the vertices present are deployed for displacement during deformation.

  4. Large scale 3-D modeling by integration of resistivity models and borehole data through inversion

    NASA Astrophysics Data System (ADS)

    Foged, N.; Marker, P. A.; Christansen, A. V.; Bauer-Gottwein, P.; Jørgensen, F.; Høyer, A.-S.; Auken, E.

    2014-02-01

    We present an automatic method for parameterization of a 3-D model of the subsurface, integrating lithological information from boreholes with resistivity models through an inverse optimization, with the objective of further detailing for geological models or as direct input to groundwater models. The parameter of interest is the clay fraction, expressed as the relative length of clay-units in a depth interval. The clay fraction is obtained from lithological logs and the clay fraction from the resistivity is obtained by establishing a simple petrophysical relationship, a translator function, between resistivity and the clay fraction. Through inversion we use the lithological data and the resistivity data to determine the optimum spatially distributed translator function. Applying the translator function we get a 3-D clay fraction model, which holds information from the resistivity dataset and the borehole dataset in one variable. Finally, we use k means clustering to generate a 3-D model of the subsurface structures. We apply the concept to the Norsminde survey in Denmark integrating approximately 700 boreholes and more than 100 000 resistivity models from an airborne survey in the parameterization of the 3-D model covering 156 km2. The final five-cluster 3-D model differentiates between clay materials and different high resistive materials from information held in resistivity model and borehole observations respectively.

  5. Large-scale 3-D modeling by integration of resistivity models and borehole data through inversion

    NASA Astrophysics Data System (ADS)

    Foged, N.; Marker, P. A.; Christansen, A. V.; Bauer-Gottwein, P.; Jørgensen, F.; Høyer, A.-S.; Auken, E.

    2014-11-01

    We present an automatic method for parameterization of a 3-D model of the subsurface, integrating lithological information from boreholes with resistivity models through an inverse optimization, with the objective of further detailing of geological models, or as direct input into groundwater models. The parameter of interest is the clay fraction, expressed as the relative length of clay units in a depth interval. The clay fraction is obtained from lithological logs and the clay fraction from the resistivity is obtained by establishing a simple petrophysical relationship, a translator function, between resistivity and the clay fraction. Through inversion we use the lithological data and the resistivity data to determine the optimum spatially distributed translator function. Applying the translator function we get a 3-D clay fraction model, which holds information from the resistivity data set and the borehole data set in one variable. Finally, we use k-means clustering to generate a 3-D model of the subsurface structures. We apply the procedure to the Norsminde survey in Denmark, integrating approximately 700 boreholes and more than 100 000 resistivity models from an airborne survey in the parameterization of the 3-D model covering 156 km2. The final five-cluster 3-D model differentiates between clay materials and different high-resistivity materials from information held in the resistivity model and borehole observations, respectively.

  6. Molecular docking and 3D-QSAR studies on gag peptide analogue inhibitors interacting with human cyclophilin A.

    PubMed

    Cui, Meng; Huang, Xiaoqin; Luo, Xiaomin; Briggs, James M; Ji, Ruyun; Chen, Kaixian; Shen, Jianhua; Jiang, Hualiang

    2002-11-21

    The interaction of a series gag peptide analogues with human cyclophilin A (hCypA) have been studied employing molecular docking and 3D-QSAR approaches. The Lamarckian Genetic Algorithm (LGA) and divide-and-conquer methods were applied to locate the binding orientations and conformations of the inhibitors interacting with hCypA. Good correlations between the calculated interaction free energies and experimental inhibitory activities suggest that the binding conformations of these inhibitors are reasonable. A novel interaction model was identified for inhibitors 11, 15, and 17 whose N-termini were modified by addition of the deaminovaline (Dav) group and the C-termini of 15 and 17 were modified by addition of a benzyl group. Accordingly, two new binding sites (sites A and D in Figure 1) were revealed, which show a strong correlation with inhibitor potency and thus can be used as a starting point for new inhibitor design. In addition, two predictive 3D-QSAR models were obtained by CoMFA and CoMSIA analyses based on the binding conformations derived from the molecular docking calculations. The reasonable r(cross)(2) (cross-validated) values 0.738 and 0.762 were obtained for CoMFA and CoMSIA models, respectively. The predictive ability of these models was validated by four peptide analogues test set. The CoMFA and CoMSIA field distributions are in general agreement with the structural characteristics of the binding groove of hCypA. This indicates the reasonableness of the binding model of the inhibitors with hCypA. Considering all these results together with the valuable clues of binding from references published recently, reasonable pharmacophore elements have been suggested, demonstrating that the 3D-QSAR models about peptide analogue inhibitors are expected to be further employed in predicting activities of the novel compounds for inhibiting hCypA.

  7. A Quantification of the 3D Modeling Capabilities of the Kinectfusion Algorithm

    DTIC Science & Technology

    2014-03-27

    A QUANTIFICATION OF THE 3D MODELING CAPABILITIES OF THE KINECTFUSTION ALGORITHM THESIS Jeremy M. Higbee, Captain, USAF AFIT-ENG-14-M-40 DEPARTMENT OF...subject to copyright protection in the United States. AFIT-ENG-14-M-40 A QUANTIFICATION OF THE 3D MODELING CAPABILITIES OF THE KINECTFUSTION ALGORITHM...M-40 A QUANTIFICATION OF THE 3D MODELING CAPABILITIES OF THE KINECTFUSTION ALGORITHM Jeremy M. Higbee, BS Captain, USAF Approved: /signed/ Maj Brian

  8. Implementation of algebraic stress models in a general 3-D Navier-Stokes method (PAB3D)

    NASA Technical Reports Server (NTRS)

    Abdol-Hamid, Khaled S.

    1995-01-01

    A three-dimensional multiblock Navier-Stokes code, PAB3D, which was developed for propulsion integration and general aerodynamic analysis, has been used extensively by NASA Langley and other organizations to perform both internal (exhaust) and external flow analysis of complex aircraft configurations. This code was designed to solve the simplified Reynolds Averaged Navier-Stokes equations. A two-equation k-epsilon turbulence model has been used with considerable success, especially for attached flows. Accurate predicting of transonic shock wave location and pressure recovery in separated flow regions has been more difficult. Two algebraic Reynolds stress models (ASM) have been recently implemented in the code that greatly improved the code's ability to predict these difficult flow conditions. Good agreement with Direct Numerical Simulation (DNS) for a subsonic flat plate was achieved with ASM's developed by Shih, Zhu, and Lumley and Gatski and Speziale. Good predictions were also achieved at subsonic and transonic Mach numbers for shock location and trailing edge boattail pressure recovery on a single-engine afterbody/nozzle model.

  9. Cryptic Species in Tropic Sands - Interactive 3D Anatomy, Molecular Phylogeny and Evolution of Meiofaunal Pseudunelidae (Gastropoda, Acochlidia)

    PubMed Central

    Neusser, Timea P.; Jörger, Katharina M.; Schrödl, Michael

    2011-01-01

    Background Towards realistic estimations of the diversity of marine animals, tiny meiofaunal species usually are underrepresented. Since the biological species concept is hardly applicable on exotic and elusive animals, it is even more important to apply a morphospecies concept on the best level of information possible, using accurate and efficient methodology such as 3D modelling from histological sections. Molecular approaches such as sequence analyses may reveal further, cryptic species. This is the first case study on meiofaunal gastropods to test diversity estimations from traditional taxonomy against results from modern microanatomical methodology and molecular systematics. Results The examined meiofaunal Pseudunela specimens from several Indo-Pacific islands cannot be distinguished by external features. Their 3D microanatomy shows differences in the organ systems and allows for taxonomic separation in some cases. Additional molecular analyses based on partial mitochondrial cytochrome c oxidase subunit I (COI) and 16S rRNA markers revealed considerable genetic structure that is largely congruent with anatomical or geographical patterns. Two new species (Pseudunela viatoris and P. marteli spp. nov.) are formally described integrating morphological and genetic analyses. Phylogenetic analysis using partial 16S rRNA, COI and the nuclear 18S rRNA markers shows a clade of Pseudunelidae species as the sister group to limnic Acochlidiidae. Within Pseudunela, two subtypes of complex excretory systems occur. A complex kidney already evolved in the ancestor of Hedylopsacea. Several habitat shifts occurred during hedylopsacean evolution. Conclusions Cryptic species occur in tropical meiofaunal Pseudunela gastropods, and likely in other meiofaunal groups with poor dispersal abilities, boosting current diversity estimations. Only a combined 3D microanatomical and molecular approach revealed actual species diversity within Pseudunela reliably. Such integrative methods are

  10. Developing and Testing a 3d Cadastral Data Model a Case Study in Australia

    NASA Astrophysics Data System (ADS)

    Aien, A.; Kalantari, M.; Rajabifard, A.; Williamson, I. P.; Shojaei, D.

    2012-07-01

    Population growth, urbanization and industrialization place more pressure on land use with the need for increased space. To extend the use and functionality of the land, complex infrastructures are being built, both vertically and horizontally, layered and stacked. These three-dimensional (3D) developments affect the interests (Rights, Restrictions, and Responsibilities (RRRs)) attached to the underlying land. A 3D cadastre will assist in managing the effects of 3D development on a particular extent of land. There are many elements that contribute to developing a 3D cadastre, such as existing of 3D property legislations, 3D DBMS, 3D visualization. However, data modelling is one of the most important elements of a successful 3D cadastre. As architectural models of houses and high rise buildings help their users visualize the final product, 3D cadastre data model supports 3D cadastre users to understand the structure or behavior of the system and has a template that guides them to construct and implement the 3D cadastre. Many jurisdictions, organizations and software developers have built their own cadastral data model. Land Administration Domain Model (DIS-ISO 19152, The Netherlands) and ePlan (Intergovernmental Committee on Surveying and Mapping, Australia) are examples of existing data models. The variation between these data models is the result of different attitudes towards cadastres. However, there is a basic common thread among them all. Current cadastral data models use a 2D land-parcel concept and extend it to support 3D requirements. These data models cannot adequately manage and represent the spatial extent of 3D RRRs. Most of the current cadastral data models have been influenced by a very broad understanding of 3D cadastral concepts because better clarity in what needs to be represented and analysed in the cadastre needs to be established. This paper presents the first version of a 3D Cadastral Data Model (3DCDM_Version 1.0). 3DCDM models both the legal

  11. Detection of Disease Symptoms on Hyperspectral 3d Plant Models

    NASA Astrophysics Data System (ADS)

    Roscher, Ribana; Behmann, Jan; Mahlein, Anne-Katrin; Dupuis, Jan; Kuhlmann, Heiner; Plümer, Lutz

    2016-06-01

    We analyze the benefit of combining hyperspectral images information with 3D geometry information for the detection of Cercospora leaf spot disease symptoms on sugar beet plants. Besides commonly used one-class Support Vector Machines, we utilize an unsupervised sparse representation-based approach with group sparsity prior. Geometry information is incorporated by representing each sample of interest with an inclination-sorted dictionary, which can be seen as an 1D topographic dictionary. We compare this approach with a sparse representation based approach without geometry information and One-Class Support Vector Machines. One-Class Support Vector Machines are applied to hyperspectral data without geometry information as well as to hyperspectral images with additional pixelwise inclination information. Our results show a gain in accuracy when using geometry information beside spectral information regardless of the used approach. However, both methods have different demands on the data when applied to new test data sets. One-Class Support Vector Machines require full inclination information on test and training data whereas the topographic dictionary approach only need spectral information for reconstruction of test data once the dictionary is build by spectra with inclination.

  12. A new approach towards image based virtual 3D city modeling by using close range photogrammetry

    NASA Astrophysics Data System (ADS)

    Singh, S. P.; Jain, K.; Mandla, V. R.

    2014-05-01

    3D city model is a digital representation of the Earth's surface and it's related objects such as building, tree, vegetation, and some manmade feature belonging to urban area. The demand of 3D city modeling is increasing day to day for various engineering and non-engineering applications. Generally three main image based approaches are using for virtual 3D city models generation. In first approach, researchers used Sketch based modeling, second method is Procedural grammar based modeling and third approach is Close range photogrammetry based modeling. Literature study shows that till date, there is no complete solution available to create complete 3D city model by using images. These image based methods also have limitations This paper gives a new approach towards image based virtual 3D city modeling by using close range photogrammetry. This approach is divided into three sections. First, data acquisition process, second is 3D data processing, and third is data combination process. In data acquisition process, a multi-camera setup developed and used for video recording of an area. Image frames created from video data. Minimum required and suitable video image frame selected for 3D processing. In second section, based on close range photogrammetric principles and computer vision techniques, 3D model of area created. In third section, this 3D model exported to adding and merging of other pieces of large area. Scaling and alignment of 3D model was done. After applying the texturing and rendering on this model, a final photo-realistic textured 3D model created. This 3D model transferred into walk-through model or in movie form. Most of the processing steps are automatic. So this method is cost effective and less laborious. Accuracy of this model is good. For this research work, study area is the campus of department of civil engineering, Indian Institute of Technology, Roorkee. This campus acts as a prototype for city. Aerial photography is restricted in many country

  13. Pharmacophore modeling, comprehensive 3D-QSAR, and binding mode analysis of TGR5 agonists.

    PubMed

    Sindhu, Thangaraj; Srinivasan, Pappu

    2017-04-01

    Takeda G-protein-coupled receptor 5 (TGR5) is emerging as an important and promising target for the development of anti-diabetic drugs. Pharmacophore modeling and atom-based 3D-QSAR studies were carried out on a new series of 5-phenoxy-1,3-dimethyl-1H-pyrazole-4-carboxamides as highly potent agonists of TGR5. The generated best six featured pharmacophore model AAHHRR consists of two hydrogen bond acceptors (A): two hydrophobic groups (H) and two aromatic rings (R). The constructed 3D-QSAR model acquired excellent correlation coefficient value (R(2 )=( )0.9018), exhibited good predictive power (Q(2 )=( )0.8494) and high Fisher ratio (F = 61.2). The pharmacophore model was validated through Guner-Henry (GH) scoring method. The GH value of 0.5743 indicated that the AAHHRR model was statistically valuable and reliable in the identification of TGR5 agonists. Furthermore, the combined approach of molecular docking and binding free energy calculations were carried out for the 5-phenoxy-1,3-dimethyl-1H-pyrazole-4-carboxamides to explore the binding mode and interaction pattern. The generated contour maps revealed the important structural insights for the activity of the compounds. The results obtained from this study could be helpful in the development of novel and more potent agonists of TGR5.

  14. Time slicing in 3D momentum imaging of the hydrogen molecular ion photo-fragmentation

    NASA Astrophysics Data System (ADS)

    Kaya, N.; Kaya, G.; Pham, F. V.; Strohaber, J.; Kolomenskii, A. A.; Schuessler, H. A.

    2017-02-01

    Photo-fragmentation of the hydrogen molecular ion was investigated with 800 nm, 50 fs laser pulses by employing a time slicing 3D imaging technique that enables the simultaneous measurement of all three momentum components which are linearly related with the pixel position and slicing time. This is done for each individual product particle arriving at the detector. This mode of detection allows us to directly measure the three-dimensional fragment momentum vector distribution without having to rely on mathematical reconstruction methods, which additionally require the investigated system to be cylindrically symmetric. We experimentally reconstruct the laser-induced photo-fragmentation of the hydrogen molecular ion. In previous experiments, neutral molecules were used as a target, but in this work, performed with molecular ions, the initial vibrational level populations are well-defined after electron bombardment, which facilitates the interpretation. We show that the employed time-slicing technique allows us to register the fragment momentum distribution that reflects the initial molecular states with greater detail, revealing features that were concealed in the full time-integrated distribution on the detector.

  15. Development and characterization of a 3D multicell microtissue culture model of airway smooth muscle

    PubMed Central

    Zaman, Nishat; Cole, Darren J.; Walker, Matthew J.; Legant, Wesley R.; Boudou, Thomas; Chen, Christopher S.; Favreau, John T.; Gaudette, Glenn R.; Cowley, Elizabeth A.; Maksym, Geoffrey N.

    2013-01-01

    Airway smooth muscle (ASM) cellular and molecular biology is typically studied with single-cell cultures grown on flat 2D substrates. However, cells in vivo exist as part of complex 3D structures, and it is well established in other cell types that altering substrate geometry exerts potent effects on phenotype and function. These factors may be especially relevant to asthma, a disease characterized by structural remodeling of the airway wall, and highlights a need for more physiologically relevant models of ASM function. We utilized a tissue engineering platform known as microfabricated tissue gauges to develop a 3D culture model of ASM featuring arrays of ∼0.4 mm long, ∼350 cell “microtissues” capable of simultaneous contractile force measurement and cell-level microscopy. ASM-only microtissues generated baseline tension, exhibited strong cellular organization, and developed actin stress fibers, but lost structural integrity and dissociated from the cantilevers within 3 days. Addition of 3T3-fibroblasts dramatically improved survival times without affecting tension development or morphology. ASM-3T3 microtissues contracted similarly to ex vivo ASM, exhibiting reproducible responses to a range of contractile and relaxant agents. Compared with 2D cultures, microtissues demonstrated identical responses to acetylcholine and KCl, but not histamine, forskolin, or cytochalasin D, suggesting that contractility is regulated by substrate geometry. Microtissues represent a novel model for studying ASM, incorporating a physiological 3D structure, realistic mechanical environment, coculture of multiple cells types, and comparable contractile properties to existing models. This new model allows for rapid screening of biochemical and mechanical factors to provide insight into ASM dysfunction in asthma. PMID:23125251

  16. 3D Building Models Segmentation Based on K-Means++ Cluster Analysis

    NASA Astrophysics Data System (ADS)

    Zhang, C.; Mao, B.

    2016-10-01

    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.

  17. Combination of Virtual Tours, 3d Model and Digital Data in a 3d Archaeological Knowledge and Information System

    NASA Astrophysics Data System (ADS)

    Koehl, M.; Brigand, N.

    2012-08-01

    The site of the Engelbourg ruined castle in Thann, Alsace, France, has been for some years the object of all the attention of the city, which is the owner, and also of partners like historians and archaeologists who are in charge of its study. The valuation of the site is one of the main objective, as well as its conservation and its knowledge. The aim of this project is to use the environment of the virtual tour viewer as new base for an Archaeological Knowledge and Information System (AKIS). With available development tools we add functionalities in particular through diverse scripts that convert the viewer into a real 3D interface. By beginning with a first virtual tour that contains about fifteen panoramic images, the site of about 150 times 150 meters can be completely documented by offering the user a real interactivity and that makes visualization very concrete, almost lively. After the choice of pertinent points of view, panoramic images were realized. For the documentation, other sets of images were acquired at various seasons and climate conditions, which allow documenting the site in different environments and states of vegetation. The final virtual tour was deducted from them. The initial 3D model of the castle, which is virtual too, was also joined in the form of panoramic images for completing the understanding of the site. A variety of types of hotspots were used to connect the whole digital documentation to the site, including videos (as reports during the acquisition phases, during the restoration works, during the excavations, etc.), digital georeferenced documents (archaeological reports on the various constituent elements of the castle, interpretation of the excavations and the searches, description of the sets of collected objects, etc.). The completely personalized interface of the system allows either to switch from a panoramic image to another one, which is the classic case of the virtual tours, or to go from a panoramic photographic image

  18. Molecular weight specific impact of soluble and immobilized hyaluronan on CD44 expressing melanoma cells in 3D collagen matrices.

    PubMed

    Sapudom, Jiranuwat; Ullm, Franziska; Martin, Steve; Kalbitzer, Liv; Naab, Johanna; Möller, Stephanie; Schnabelrauch, Matthias; Anderegg, Ulf; Schmidt, Stephan; Pompe, Tilo

    2017-03-01

    Hyaluronan (HA) and its principal receptor CD44 are known to be involved in regulating tumor cell dissemination and metastasis. The direct correlation of CD44-HA interaction on proliferation and invasion of tumor cells in dependence on the molecular weight and the presentation form of HA is not fully understood because of lack of appropriate matrix models. To address this issue, we reconstituted 3D collagen (Coll I) matrices and functionalized them with HA of molecular weight of 30-50kDa (low molecular weight; LMW-HA) and 500-750kDa (high molecular weight; HMW-HA). A post-modification strategy was applied to covalently immobilize HA to reconstituted fibrillar Coll I matrices, resulting in a non-altered Coll I network microstructure and stable immobilization over days. Functionalized Coll I matrices were characterized regarding topological and mechanical characteristics as well as HA amount using confocal laser scanning microscopy, colloidal probe force spectroscopy and quantitative Alcian blue assay, respectively. To elucidate HA dependent tumor cell behavior, BRO melanoma cell lines with and without CD44 receptor expression were used for in vitro cell experiments. We demonstrated that only soluble LMW-HA promoted cell proliferation in a CD44 dependent manner, while HMW-HA and immobilized LMW-HA did not. Furthermore, an enhanced cell invasion was found only for immobilized LMW-HA. Both findings correlated with a very strong and specific adhesive interaction of LMW-HA and CD44+ cells quantified in single cell adhesion measurements using soft colloidal force spectroscopy. Overall, our results introduce an in vitro biomaterials model allowing to test presentation mode and molecular weight specificity of HA in a 3D fibrillar matrix thus mimicking important in vivo features of tumor microenvironments.

  19. Comparing thin-sheet models with 3-D multilayer models for continental collision

    NASA Astrophysics Data System (ADS)

    Lechmann, S. M.; May, D. A.; Kaus, B. J. P.; Schmalholz, S. M.

    2011-10-01

    Various models have been proposed to explain tectonic deformations during continent collision. A frequently applied model is the thin viscous sheet model which is however not fully 3-D and assumes a priori diffuse thickening as the dominant deformation style. We compare a fully 3-D multilayer numerical model with a corresponding thin viscous sheet numerical model for the scenario of continent indentation. In our comparison we focus on the three basic viscous deformation styles thickening, buckling (folding) and lateral crustal flow. Both numerical models are based on the finite element method (FEM) and employ either a linear or power-law viscous rheology. The 3-D model consists of four layers representing a simplified continental lithosphere: strong upper crust, weak lower crust, strong upper mantle and weak lower mantle. The effective viscosity depth-profile in the 3-D model is used to calculate the depth-averaged effective viscosity used in the thin-sheet model allowing a direct comparison of both models. We quantify the differences in the strain rate and velocity fields, and investigate the evolution of crustal thickening, buckling and crustal flow resulting from the two models for two different phases of deformation: (1) indentation with a constant velocity and (2) gravitational collapse after a decrease of the indenting velocity by a factor of 5. The results indicate that thin-sheet models approximate well the overall large-scale lithospheric deformation, especially during indentation and for a linear viscous rheology. However, in the 3-D model, additional processes such as multilayer buckling and lower crustal flow emerge, which are ignored in the thin-sheet model but dominate the deformation style in the 3-D model within a range of a few hundreds of kilometres around the collision zone and indenter corner. Differences between the 3-D and thin-sheet model are considerably larger for a power-law viscous than for a linear viscous rheology. Buckling and lower

  20. Integration of 3D photogrammetric outcrop models in the reservoir modelling workflow

    NASA Astrophysics Data System (ADS)

    Deschamps, Remy; Joseph, Philippe; Lerat, Olivier; Schmitz, Julien; Doligez, Brigitte; Jardin, Anne

    2014-05-01

    3D technologies are now widely used in geosciences to reconstruct outcrops in 3D. The technology used for the 3D reconstruction is usually based on Lidar, which provides very precise models. Such datasets offer the possibility to build well-constrained outcrop analogue models for reservoir study purposes. The photogrammetry is an alternate methodology which principles are based in determining the geometric properties of an object from photographic pictures taken from different angles. Outcrop data acquisition is easy, and this methodology allows constructing 3D outcrop models with many advantages such as: - light and fast acquisition, - moderate processing time (depending on the size of the area of interest), - integration of field data and 3D outcrops into the reservoir modelling tools. Whatever the method, the advantages of digital outcrop model are numerous as already highlighted by Hodgetts (2013), McCaffrey et al. (2005) and Pringle et al. (2006): collection of data from otherwise inaccessible areas, access to different angles of view, increase of the possible measurements, attributes analysis, fast rate of data collection, and of course training and communication. This paper proposes a workflow where 3D geocellular models are built by integrating all sources of information from outcrops (surface picking, sedimentological sections, structural and sedimentary dips…). The 3D geomodels that are reconstructed can be used at the reservoir scale, in order to compare the outcrop information with subsurface models: the detailed facies models of the outcrops are transferred into petrophysical and acoustic models, which are used to test different scenarios of seismic and fluid flow modelling. The detailed 3D models are also used to test new techniques of static reservoir modelling, based either on geostatistical approaches or on deterministic (process-based) simulation techniques. A modelling workflow has been designed to model reservoir geometries and properties from

  1. Initial Comparison Between a 3D MHD Model and the HAFv2 Kinematic 3D Model: The October/November 2003 Events from the Sun to 6 AU

    SciTech Connect

    Intriligator, Devrie S.; Detman, Thomas; Fry, Craig D.; Sun Wei; Deehr, Charles; Intriligator, James

    2005-08-01

    A first-generation 3D kinematic, space weather forecasting solar wind model (HAFv2) has been used to show the importance of solar generated disturbances in Voyager 1 and Voyager 2 observations in the outer heliosphere. We extend this work by using a 3D MHD model (HHMS) that, like HAFv2, incorporates a global, pre-event, inhomogeneous, background solar wind plasma and interplanetary magnetic field. Initial comparisons are made between the two models of the solar wind out to 6 AU and with in-situ observations at the ACE spacecraft before and after the October/November 2003 solar events.

  2. [3-D endocardial surface modelling based on the convex hull algorithm].

    PubMed

    Lu, Ying; Xi, Ri-hui; Shen, Hai-dong; Ye, You-li; Zhang, Yong

    2006-11-01

    In this paper, a method based on the convex hull algorithm is presented for extracting modelling data from the locations of catheter electrodes within a cardiac chamber, so as to create a 3-D model of the heart chamber during diastole and to obtain a good result in the 3-D reconstruction of the chamber based on VTK.

  3. Rethinking Design Process: Using 3D Digital Models as an Interface in Collaborative Session

    ERIC Educational Resources Information Center

    Ding, Suining

    2008-01-01

    This paper describes a pilot study for an alternative design process by integrating a designer-user collaborative session with digital models. The collaborative session took place in a 3D AutoCAD class for a real world project. The 3D models served as an interface for designer-user collaboration during the design process. Students not only learned…

  4. 3D Modeling from Multi-views Images for Cultural Heritage in Wat-Pho, Thailand

    NASA Astrophysics Data System (ADS)

    Soontranon, N.; Srestasathiern, P.; Lawawirojwong, S.

    2015-08-01

    In Thailand, there are several types of (tangible) cultural heritages. This work focuses on 3D modeling of the heritage objects from multi-views images. The images are acquired by using a DSLR camera which costs around 1,500 (camera and lens). Comparing with a 3D laser scanner, the camera is cheaper and lighter than the 3D scanner. Hence, the camera is available for public users and convenient for accessing narrow areas. The acquired images consist of various sculptures and architectures in Wat-Pho which is a Buddhist temple located behind the Grand Palace (Bangkok, Thailand). Wat-Pho is known as temple of the reclining Buddha and the birthplace of traditional Thai massage. To compute the 3D models, a diagram is separated into following steps; Data acquisition, Image matching, Image calibration and orientation, Dense matching and Point cloud processing. For the initial work, small heritages less than 3 meters height are considered for the experimental results. A set of multi-views images of an interested object is used as input data for 3D modeling. In our experiments, 3D models are obtained from MICMAC (open source) software developed by IGN, France. The output of 3D models will be represented by using standard formats of 3D point clouds and triangulated surfaces such as .ply, .off, .obj, etc. To compute for the efficient 3D models, post-processing techniques are required for the final results e.g. noise reduction, surface simplification and reconstruction. The reconstructed 3D models can be provided for public access such as website, DVD, printed materials. The high accurate 3D models can also be used as reference data of the heritage objects that must be restored due to deterioration of a lifetime, natural disasters, etc.

  5. 3-D Geometric Modeling for the 21st Century.

    ERIC Educational Resources Information Center

    Ault, Holly K.

    1999-01-01

    Describes new geometric computer models used in contemporary computer-aided design (CAD) software including wire frame, surface, solid, and parametric models. Reviews their use in engineering design and discusses the impact of these new technologies on the engineering design graphics curriculum. (Author/CCM)

  6. Computational 3-D Model of the Human Respiratory System

    EPA Science Inventory

    We are developing a comprehensive, morphologically-realistic computational model of the human respiratory system that can be used to study the inhalation, deposition, and clearance of contaminants, while being adaptable for age, race, gender, and health/disease status. The model ...

  7. A topological framework for interactive queries on 3D models in the Web.

    PubMed

    Figueiredo, Mauro; Rodrigues, José I; Silvestre, Ivo; Veiga-Pires, Cristina

    2014-01-01

    Several technologies exist to create 3D content for the web. With X3D, WebGL, and X3DOM, it is possible to visualize and interact with 3D models in a web browser. Frequently, three-dimensional objects are stored using the X3D file format for the web. However, there is no explicit topological information, which makes it difficult to design fast algorithms for applications that require adjacency and incidence data. This paper presents a new open source toolkit TopTri (Topological model for Triangle meshes) for Web3D servers that builds the topological model for triangular meshes of manifold or nonmanifold models. Web3D client applications using this toolkit make queries to the web server to get adjacent and incidence information of vertices, edges, and faces. This paper shows the application of the topological information to get minimal local points and iso-lines in a 3D mesh in a web browser. As an application, we present also the interactive identification of stalactites in a cave chamber in a 3D web browser. Several tests show that even for large triangular meshes with millions of triangles, the adjacency and incidence information is returned in real time making the presented toolkit appropriate for interactive Web3D applications.

  8. Use of 3D Printed Models in Medical Education: A Randomized Control Trial Comparing 3D Prints versus Cadaveric Materials for Learning External Cardiac Anatomy

    ERIC Educational Resources Information Center

    Lim, Kah Heng Alexander; Loo, Zhou Yaw; Goldie, Stephen J.; Adams, Justin W.; McMenamin, Paul G.

    2016-01-01

    Three-dimensional (3D) printing is an emerging technology capable of readily producing accurate anatomical models, however, evidence for the use of 3D prints in medical education remains limited. A study was performed to assess their effectiveness against cadaveric materials for learning external cardiac anatomy. A double blind randomized…

  9. Local indices for similarity analysis (LISA)-a 3D-QSAR formalism based on local molecular similarity.

    PubMed

    Verma, Jitender; Malde, Alpeshkumar; Khedkar, Santosh; Iyer, Radhakrishnan; Coutinho, Evans

    2009-12-01

    A simple quantitative structure activity relationship (QSAR) approach termed local indices for similarity analysis (LISA) has been developed. In this technique, the global molecular similarity is broken up as local similarity at each grid point surrounding the molecules and is used as a QSAR descriptor. In this way, a view of the molecular sites permitting favorable and rational changes to enhance activity is obtained. The local similarity index, calculated on the basis of Petke's formula, segregates the regions into "equivalent", "favored similar", and "disfavored similar" (alternatively "favored dissimilar") potentials with respect to a reference molecule in the data set. The method has been tested on three large and diverse data sets-thrombin, glycogen phosphorylase b, and thermolysin inhibitors. The QSAR models derived using genetic algorithm incorporated partial least square analysis statistics are found to be comparable to the ones obtained by the standard three-dimensional (3D)-QSAR methods, such as comparative molecular field analysis and comparative molecular similarity indices analysis. The graphical interpretation of the LISA models is straightforward, and the outcome of the models corroborates well with literature data. The LISA models give insight into the binding mechanisms of the ligand with the enzyme and allow fine-tuning of the molecules at the local level to improve their activity.

  10. Molecular Phylogeny and Predicted 3D Structure of Plant beta-D-N-Acetylhexosaminidase

    PubMed Central

    Hossain, Md. Anowar

    2014-01-01

    beta-D-N-Acetylhexosaminidase, a family 20 glycosyl hydrolase, catalyzes the removal of β-1,4-linked N-acetylhexosamine residues from oligosaccharides and their conjugates. We constructed phylogenetic tree of β-hexosaminidases to analyze the evolutionary history and predicted functions of plant hexosaminidases. Phylogenetic analysis reveals the complex history of evolution of plant β-hexosaminidase that can be described by gene duplication events. The 3D structure of tomato β-hexosaminidase (β-Hex-Sl) was predicted by homology modeling using 1now as a template. Structural conformity studies of the best fit model showed that more than 98% of the residues lie inside the favoured and allowed regions where only 0.9% lie in the unfavourable region. Predicted 3D structure contains 531 amino acids residues with glycosyl hydrolase20b domain-I and glycosyl hydrolase20 superfamily domain-II including the (β/α)8 barrel in the central part. The α and β contents of the modeled structure were found to be 33.3% and 12.2%, respectively. Eleven amino acids were found to be involved in ligand-binding site; Asp(330) and Glu(331) could play important roles in enzyme-catalyzed reactions. The predicted model provides a structural framework that can act as a guide to develop a hypothesis for β-Hex-Sl mutagenesis experiments for exploring the functions of this class of enzymes in plant kingdom. PMID:25165734

  11. Molecular phylogeny and predicted 3D structure of plant beta-D-N-acetylhexosaminidase.

    PubMed

    Hossain, Md Anowar; Roslan, Hairul Azman

    2014-01-01

    beta-D-N-Acetylhexosaminidase, a family 20 glycosyl hydrolase, catalyzes the removal of β-1,4-linked N-acetylhexosamine residues from oligosaccharides and their conjugates. We constructed phylogenetic tree of β-hexosaminidases to analyze the evolutionary history and predicted functions of plant hexosaminidases. Phylogenetic analysis reveals the complex history of evolution of plant β-hexosaminidase that can be described by gene duplication events. The 3D structure of tomato β-hexosaminidase (β-Hex-Sl) was predicted by homology modeling using 1now as a template. Structural conformity studies of the best fit model showed that more than 98% of the residues lie inside the favoured and allowed regions where only 0.9% lie in the unfavourable region. Predicted 3D structure contains 531 amino acids residues with glycosyl hydrolase20b domain-I and glycosyl hydrolase20 superfamily domain-II including the (β/α)8 barrel in the central part. The α and β contents of the modeled structure were found to be 33.3% and 12.2%, respectively. Eleven amino acids were found to be involved in ligand-binding site; Asp(330) and Glu(331) could play important roles in enzyme-catalyzed reactions. The predicted model provides a structural framework that can act as a guide to develop a hypothesis for β-Hex-Sl mutagenesis experiments for exploring the functions of this class of enzymes in plant kingdom.

  12. Inspection, 3D modelling, and rapid prototyping of cultural heritage by means of a 3D optical digitiser

    NASA Astrophysics Data System (ADS)

    Docchio, F.; Sansoni, G.; Trebeschi, M.

    2005-06-01

    This paper presents the activity carried out to perform the three-dimensional acquisition of the "Vittoria Alata", a 2m-high, bronze statue, symbol of our City, located at the Civici Musei di Arte e Storia (S. Giulia) of Brescia. The acquisition of the statue has been performed by using a three-dimensional vision system based on active triangulation and on the projection of non-coherent light. This system, called OPL-3D, represents one of the research products of our Laboratory, which has been active for years in the development of techniques and systems for the contactless acquisition of free-form, complex shapes. The study, originally motivated by the need to explore a new hypothesis on the origin of the "Vittoria Alata", led to its complete digitization and description in terms of both polygonal and NURBS-based models. A suite of copies of the whole statue has been obtained in the framework of the collaboration between the City Museum and the EOS Electro Optical Systems GmbH, located in Munich, Germany. As a first step, one 30 cm-high replica of the whole statue has been produced using a low-resolution triangle model of the statue (3.5 millions of triangles). As a second step, two 1:1 scale copies of the statue have been produced. For them, the Laboratory has provided the high resolution STL file (16 millions of triangles). The paper discusses in detail the hardware and the software facilities used to implement the whole process, and gives a comprehensive description of the results.

  13. Observing molecular dynamics with time-resolved 3D momentum imaging

    NASA Astrophysics Data System (ADS)

    Sturm, F. P.; Wright, T.; Bocharova, I.; Ray, D.; Shivaram, N.; Cryan, J.; Belkacem, A.; Weber, T.; Dörner, R.

    2014-05-01

    Photo-excitation and ionization trigger rich dynamics in molecular systems which play a key role in many important processes in nature such as vision, photosynthesis or photoprotection. Observing those reactions in real-time without significantly disturbing the molecules by a strong electric field has been a great challenge. Recent experiments using Time-of-Flight and Velocity Map Imaging techniques have revealed important information on the dynamics of small molecular systems upon photo-excitation. We have developed an apparatus for time-resolved momentum imaging of electrons and ions in all three spatial dimensions that employs two-color femtosecond laser pulses in the vacuum and extreme ultraviolet (VUV, XUV) for probing molecular dynamics. Our COLTRIMS style reaction microscope can measure electrons and ions in coincidence and reconstruct the momenta of the reaction fragments in 3D. We use a high power 800 nm laser in a loose focusing geometry gas cell to efficinetly drive High Harmonic Generation. The resulting photon flux is sufficient to perform 2-photon pump-probe experiments using VUV and XUV pulses for both pump and probe. With this setup we investigate non-Born-Oppenheimer dynamics in small molecules such as C2H4 and CO2 on a femtosecond time scale. Supported by Chemical Sciences, Geosciences and Biosciences division of BES/DOE.

  14. Assessing a 3D smoothed seismicity model of induced earthquakes

    NASA Astrophysics Data System (ADS)

    Zechar, Jeremy; Király, Eszter; Gischig, Valentin; Wiemer, Stefan

    2016-04-01

    As more energy exploration and extraction efforts cause earthquakes, it becomes increasingly important to control induced seismicity. Risk management schemes must be improved and should ultimately be based on near-real-time forecasting systems. With this goal in mind, we propose a test bench to evaluate models of induced seismicity based on metrics developed by the CSEP community. To illustrate the test bench, we consider a model based on the so-called seismogenic index and a rate decay; to produce three-dimensional forecasts, we smooth past earthquakes in space and time. We explore four variants of this model using the Basel 2006 and Soultz-sous-Forêts 2004 datasets to make short-term forecasts, test their consistency, and rank the model variants. Our results suggest that such a smoothed seismicity model is useful for forecasting induced seismicity within three days, and giving more weight to recent events improves forecast performance. Moreover, the location of the largest induced earthquake is forecast well by this model. Despite the good spatial performance, the model does not estimate the seismicity rate well: it frequently overestimates during stimulation and during the early post-stimulation period, and it systematically underestimates around shut-in. In this presentation, we also describe a robust estimate of information gain, a modification that can also benefit forecast experiments involving tectonic earthquakes.

  15. Constructing stable 3D hydrodynamical models of giant stars

    NASA Astrophysics Data System (ADS)

    Ohlmann, Sebastian T.; Röpke, Friedrich K.; Pakmor, Rüdiger; Springel, Volker

    2017-02-01

    Hydrodynamical simulations of stellar interactions require stable models of stars as initial conditions. Such initial models, however, are difficult to construct for giant stars because of the wide range in spatial scales of the hydrostatic equilibrium and in dynamical timescales between the core and the envelope of the giant. They are needed for, e.g., modeling the common envelope phase where a giant envelope encompasses both the giant core and a companion star. Here, we present a new method of approximating and reconstructing giant profiles from a stellar evolution code to produce stable models for multi-dimensional hydrodynamical simulations. We determine typical stellar stratification profiles with the one-dimensional stellar evolution code mesa. After an appropriate mapping, hydrodynamical simulations are conducted using the moving-mesh code arepo. The giant profiles are approximated by replacing the core of the giant with a point mass and by constructing a suitable continuation of the profile to the center. Different reconstruction methods are tested that can specifically control the convective behaviour of the model. After mapping to a grid, a relaxation procedure that includes damping of spurious velocities yields stable models in three-dimensional hydrodynamical simulations. Initially convectively stable configurations lead to stable hydrodynamical models while for stratifications that are convectively unstable in the stellar evolution code, simulations recover the convective behaviour of the initial model and show large convective plumes with Mach numbers up to 0.8. Examples are shown for a 2 M⊙ red giant and a 0.67 M⊙ asymptotic giant branch star. A detailed analysis shows that the improved method reliably provides stable models of giant envelopes that can be used as initial conditions for subsequent hydrodynamical simulations of stellar interactions involving giant stars.

  16. Nonlinear Multiscale Modeling of 3D Woven Fiber Composites under Ballistic Loading

    DTIC Science & Technology

    2013-07-11

    advanced composites like 3D -OWC. On the other hand, a microscale simulation with resolution of individual fiber filament is impractical due to enormous...REPORT Nonlinear Multiscale Modeling of 3D Woven Fiber Composites under Ballistic Loading 14. ABSTRACT 16. SECURITY CLASSIFICATION OF: The objective of...analysis of 3D woven fiber composites under ballistic loading. Since material behavior is determined by its microstructure, it is essential to

  17. An in vitro 3D model using collagen coated gelatin nanofibers for studying breast cancer metastasis.

    PubMed

    Janani, G; Pillai, Mamatha M; Selvakumar, R; Bhattacharyya, Amitava; Sabarinath, C

    2017-02-07

    The study of breast cancer metastasis is limited due to poor knowledge of molecular progression of breast tumor and varied heterogeneity. For a better understanding of tumor metastasis, a reliable 3D in vitro model bridging the gap between 2D cultures and in vivo animal model studies is essential. Our study is focused on two key points: (i) designing a 3D microenvironment for studying metastasis and (ii) simulating the metastasis milieu by inducing epithelial to mesenchymal transition (EMT) and mesenchymal to epithelial transition (MET). An electrospun gelatin nanofiber matrix (EGNF) was fabricated using electrospinning and further dip coated with different concentrations of collagen to obtain surface complexity and mechanical properties, similar to connective tissues. Nanofiber matrices were physically characterized by Fourier transform infrared spectroscopy (FTIR), atomic force microscopy (AFM), and field-emission scanning electron microscopy (FESEM). The FTIR, AFM, and FESEM results indicated the crosslinking and confirmed the presence of pores in the nanofiber matrices. Comparative studies on biocompatibility, cell attachment, and the proliferation of MCF-7 cells on EGNF and collagen coated gelatin nanofibrous matrix (CCGM) revealed higher cellular attachment and proliferation in CCGM. CCGM with human metastatic breast cancer cell line (MCF-7) was taken to study breast cancer metastasis using estrogen (induces EMT) and progesterone (induces MET) hormones for 24 h. Quantitative real-time PCR was used for quantifying the expression of metastasis related genes, and fluorescence microscopy for verifying the invasion of cells to the matrices. The expression of E-cadherin and matrix metalloproteinase 2 (MMP 2) confirmed the occurrence of EMT and MET. Live cell imaging and cellular attachment showed significant increase of cellular invasion in crosslinked 0.15% CCGM that serves as a suitable non-toxic, biocompatible, and affordable scaffold for studying breast cancer

  18. Services Oriented Smart City Platform Based On 3d City Model Visualization

    NASA Astrophysics Data System (ADS)

    Prandi, F.; Soave, M.; Devigili, F.; Andreolli, M.; De Amicis, R.

    2014-04-01

    The rapid technological evolution, which is characterizing all the disciplines involved within the wide concept of smart cities, is becoming a key factor to trigger true user-driven innovation. However to fully develop the Smart City concept to a wide geographical target, it is required an infrastructure that allows the integration of heterogeneous geographical information and sensor networks into a common technological ground. In this context 3D city models will play an increasingly important role in our daily lives and become an essential part of the modern city information infrastructure (Spatial Data Infrastructure). The work presented in this paper describes an innovative Services Oriented Architecture software platform aimed at providing smartcities services on top of 3D urban models. 3D city models are the basis of many applications and can became the platform for integrating city information within the Smart-Cites context. In particular the paper will investigate how the efficient visualisation of 3D city models using different levels of detail (LODs) is one of the pivotal technological challenge to support Smart-Cities applications. The goal is to provide to the final user realistic and abstract 3D representations of the urban environment and the possibility to interact with a massive amounts of semantic information contained into the geospatial 3D city model. The proposed solution, using OCG standards and a custom service to provide 3D city models, lets the users to consume the services and interact with the 3D model via Web in a more effective way.

  19. Synthesis of image sequences for Korean sign language using 3D shape model

    NASA Astrophysics Data System (ADS)

    Hong, Mun-Ho; Choi, Chang-Seok; Kim, Chang-Seok; Jeon, Joon-Hyeon

    1995-05-01

    This paper proposes a method for offering information and realizing communication to the deaf-mute. The deaf-mute communicates with another person by means of sign language, but most people are unfamiliar with it. This method enables to convert text data into the corresponding image sequences for Korean sign language (KSL). Using a general 3D shape model of the upper body leads to generating the 3D motions of KSL. It is necessary to construct the general 3D shape model considering the anatomical structure of the human body. To obtain a personal 3D shape model, this general model is to adjust to the personal base images. Image synthesis for KSL consists of deforming a personal 3D shape model and texture-mapping the personal images onto the deformed model. The 3D motions for KSL have the facial expressions and the 3D movements of the head, trunk, arms and hands and are parameterized for easily deforming the model. These motion parameters of the upper body are extracted from a skilled signer's motion for each KSL and are stored to the database. Editing the parameters according to the inputs of text data yields to generate the image sequences of 3D motions.

  20. 3-D Constraint-Based Modeling: Finding Common Themes.

    ERIC Educational Resources Information Center

    Wiebe, Eric N.

    1999-01-01

    Uses Shneiderman's Object-Action Interface model along with the engineering design process as a framework for understanding software interface elements. Provides an educational framework from which instructional materials can be developed. (Author/CCM)

  1. Automated mask creation from a 3D model using Faethm.

    SciTech Connect

    Schiek, Richard Louis; Schmidt, Rodney Cannon

    2007-11-01

    We have developed and implemented a method which given a three-dimensional object can infer from topology the two-dimensional masks needed to produce that object with surface micro-machining. The masks produced by this design tool can be generic, process independent masks, or if given process constraints, specific for a target process. This design tool calculates the two-dimensional mask set required to produce a given three-dimensional model by investigating the vertical topology of the model.

  2. Pluto: Modeling of 3-D Atmosphere-Surface Interactions

    NASA Astrophysics Data System (ADS)

    Michaels, Timothy I.

    2015-11-01

    Atmosphere-surface interactions on Pluto are of great importance to creating and maintaining the atmospheric variations and heterogeneous surface that have been observed by New Horizons and two decades' prior work. Publicly released images/data from New Horizons contain numerous fascinating surface features and constrasts. Insights into their origin, maintenance, and/or evolution may be gleaned through multidisciplinary climate modeling. Some results from such modeling will be presented, with an emphasis on shorter-timescale interactions.

  3. Computational ocean acoustics: Advances in 3D ocean acoustic modeling

    NASA Astrophysics Data System (ADS)

    Schmidt, Henrik; Jensen, Finn B.

    2012-11-01

    The numerical model of ocean acoustic propagation developed in the 1980's are still in widespread use today, and the field of computational ocean acoustics is often considered a mature field. However, the explosive increase in computational power available to the community has created opportunities for modeling phenomena that earlier were beyond reach. Most notably, three-dimensional propagation and scattering problems have been prohibitive computationally, but are now addressed routinely using brute force numerical approaches such as the Finite Element Method, in particular for target scattering problems, where they are being combined with the traditional wave theory propagation models in hybrid modeling frameworks. Also, recent years has seen the development of hybrid approaches coupling oceanographic circulation models with acoustic propagation models, enabling the forecasting of sonar performance uncertainty in dynamic ocean environments. These and other advances made over the last couple of decades support the notion that the field of computational ocean acoustics is far from being mature. [Work supported by the Office of Naval Research, Code 321OA].

  4. 3D shape modeling by integration visual and tactile cues

    NASA Astrophysics Data System (ADS)

    Xiong, Hanwei; Xu, Jun; Xu, Chenxi; Pan, Ming

    2015-10-01

    With the progress in CAD (Computer Aided Design) systems, many mechanical components can be designed efficiently with high precision. But, such a system is unfit for some organic shapes, for example, a toy. In this paper, an easy way to dealing with such shapes is presented, combing visual perception with tangible interaction. The method is divided into three phases: two tangible interaction phases and one visual reconstruction. In the first tangible phase, a clay model is used to represent the raw shape, and the designer can change the shape intuitively with his hands. Then the raw shape is scanned into a digital volume model through a low cost vision system. In the last tangible phase, a desktop haptic device from SensAble is used to refine the scanned volume model and convert it into a surface model. A physical clay model and a virtual clay mode are all used in this method to deal with the main shape and the details respectively, and the vision system is used to bridge the two tangible phases. The vision reconstruction system is only made of a camera to acquire raw shape through shape from silhouettes method. All of the systems are installed on a single desktop, make it convenient for designers. The vision system details and a design example are presented in the papers.

  5. Ozone Measurements and a 3D Chemical Transport Model

    NASA Technical Reports Server (NTRS)

    Stolarski, Richard S.; Douglass, Anne R.; Frith, Stacey; Steenrod, Steven; Polansky, Brian

    2004-01-01

    We have used our three-dimensional chemical transport model (CTM) to calculate the expected reponse of stratospheric composition over the past 30 years to forcing by chlorine and bromine compounds, solar ultraviolet, and volcanic aerosols. The CTM uses off-line winds and temperatures fiom a 50-year run of the finite volume general circulation model (FVGCM). We compare the total column ozone and the ozone profile fiom the CTM output to a variety of data sources. These include a merged total ozone data set from TOMS and SBUV using the new version 8 algorithm. Total ozone fiom the CTM are compared to ground-station measurements of total ozone at specific locations. Ozone profiles are compared to satellite meausrements fiom SBUV, SAGE, and HALOE. Profiles are also compared to ozonesondes over several locations. The results of the comparisons are quantified by using a time-series statistical analysis to determine trends, solar cycle, and volcanic reponse in both the model and in the data. Initial results indicate that the model responds to forcings in a way that is similar to the observed atmospheric response. The model does seem to be more sensitive to the chlorine and bromine perturbation ihan is the data. Further details and comparisons wiii be discussed.

  6. A Cartesian scheme for compressible multimaterial models in 3D

    NASA Astrophysics Data System (ADS)

    de Brauer, Alexia; Iollo, Angelo; Milcent, Thomas

    2016-05-01

    We model the three-dimensional interaction of compressible materials separated by sharp interfaces. We simulate fluid and hyperelastic solid flows in a fully Eulerian framework. The scheme is the same for all materials and can handle large deformations and frictionless contacts. Necessary conditions for hyperbolicity of the hyperelastic neohookean model in three dimensions are proved thanks to an explicit computation of the characteristic speeds. We present stiff multimaterial interactions including air-helium and water-air shock interactions, projectile-shield impacts in air and rebounds.

  7. 3D modelling of stellar auroral radio emission

    NASA Astrophysics Data System (ADS)

    Leto, P.; Trigilio, C.; Buemi, C. S.; Umana, G.; Ingallinera, A.; Cerrigone, L.

    2016-06-01

    The electron cyclotron maser is the coherent emission process that gives rise to the radio lighthouse effect observed in the hot magnetic chemically peculiar star CU Virginis. It has also been proposed to explain the highly circularly polarized radio pulses observed in some ultracool dwarfs with spectral type earlier than M7. Coherent events of this kind resemble auroral radio emission from the magnetized planets of the Solar system. In this article, we present a three-dimensional model able to simulate the timing and profile of the pulses emitted by those stars characterized by a dipolar magnetic field by following the hypothesis of the laminar source model, used to explain the beaming of terrestrial auroral kilometric radiation. This model proves to be a powerful tool with which to understand the auroral radio emission phenomenon, allowing us to derive some general conclusions about the effects of the model's free parameters on the features of coherent pulses and to learn more about the detectability of such pulsed radio emission.

  8. 3-D modelling of glacier calving processes (Invited)

    NASA Astrophysics Data System (ADS)

    Navarro, F. J.

    2010-12-01

    Calving from tidewater glacier tongues and ice shelves is an important mass loss mechanism for many mid- and high-latitude tidewater glaciers, ice caps and ice sheets, yet an adequate representation of calving is still missing from prognostic models of ice dynamics. Benn and others (2007) proposed a calving criterion appropriate for both grounded and floating glacier tongues or ice shelves. This criterion assumes that the calving is triggered by the downward propagation of transverse surface crevasses, near the calving front, as a result of the extensional stress regime. The crevasse depth is calculated following Nye (1957), assuming that the base of a field of closely spaced crevasses lies at a depth where the longitudinal tensile strain rate tending to open the crevasse equals the creep closure resulting from the ice overburden pressure. Crevasses partially or totally filled with water will penetrate deeper, because of the contribution of water pressure to the opening of the crevasse. This criterion is readily incorporated into glacier and ice sheet models, but has not been fully validated with observations. We apply a three-dimensional extension of Benn and others’ (2007) criterion, incorporated into a full-Stokes model of glacier dynamics, to estimate the current position of the calving front of Johnsons Glacier, Antarctica. The record of the front positions of Johnsons Glacier spans only a few years during the last decade, and during this observation period the front has remained at a nearly constant position, so a full modelling exercise of time evolution to follow the front-position changes of the glacier has not been possible. Instead, our modelling experiment is a diagnostic one, aimed at establishing whether the model adequately reproduces the current front position of Johnsons Glacier (Otero et al., 2010). We develop four experiments: (i) an straightforward three-dimensional extension of Benn and other’s (2007) model; (ii) an improvement to the

  9. Construction of 3-D Terrain Models from BIG Data Sets

    DTIC Science & Technology

    2014-05-14

    support for dynamically updating the model using the submitted corrections, and using periodic re- computations though an automated system for managing the...NUMBER Pankaj Agarwal Pankaj K. Agarwal, Thomas Moelhave 665502 c. THIS PAGE The public reporting burden for this collection of information is estimated...needed, and completing and reviewing the collection of information . Send comments regarding this burden estimate or any other aspect of this collection

  10. Multiple-Relaxation-Time Lattice Boltzmann Models in 3D

    NASA Technical Reports Server (NTRS)

    dHumieres, Dominique; Ginzburg, Irina; Krafczyk, Manfred; Lallemand, Pierre; Luo, Li-Shi; Bushnell, Dennis M. (Technical Monitor)

    2002-01-01

    This article provides a concise exposition of the multiple-relaxation-time lattice Boltzmann equation, with examples of fifteen-velocity and nineteen-velocity models in three dimensions. Simulation of a diagonally lid-driven cavity flow in three dimensions at Re=500 and 2000 is performed. The results clearly demonstrate the superior numerical stability of the multiple-relaxation-time lattice Boltzmann equation over the popular lattice Bhatnagar-Gross-Krook equation.

  11. Some results on hyperscaling in the 3D Ising model

    SciTech Connect

    Baker, G.A. Jr.; Kawashima, Naoki

    1995-09-01

    The authors review exact studies on finite-sized 2 dimensional Ising models and show that the point for an infinite-sized model at the critical temperature is a point of nonuniform approach in the temperature-size plane. They also illuminate some strong effects of finite-size on quantities which do not diverge at the critical point. They then review Monte Carlo studies for 3 dimensional Ising models of various sizes (L = 2--100) at various temperatures. From these results they find that the data for the renormalized coupling constant collapses nicely when plotted against the correlation length, determined in a system of edge length L, divided by L. They also find that {zeta}{sub L}/L {ge} 0.26 is definitely too large for reliable studies of the critical value, g*, of the renormalized coupling constant. They have reasonable evidence that {zeta}{sub L}/L {approx} 0.1 is adequate for results that are within one percent of those for the infinite system size. On this basis, they have conducted a series of Monte Carlo calculations with this condition imposed. These calculations were made practical by the development of improved estimators for use in the Swendsen-Wang cluster method. The authors found from these results, coupled with a reversed limit computation (size increases with the temperature fixed at the critical temperature), that g* > 0, although there may well be a sharp downward drop in g as the critical temperature is approached in accord with the predictions of series analysis. The results support the validity of hyperscaling in the 3 dimensional Ising model.

  12. Kinetic modeling of 3D equilibria in a tokamak

    NASA Astrophysics Data System (ADS)

    Albert, C. G.; Heyn, M. F.; Kasilov, S. V.; Kernbichler, W.; Martitsch, A. F.; Runov, A. M.

    2016-11-01

    External resonant magnetic perturbations (RMPs) can modify the magnetic topology in a tokamak. In this case the magnetic field cannot generally be described by ideal MHD equilibrium equations in the vicinity of resonant magnetic surfaces where parallel and perpendicular relaxation timescales are comparable. Usually, resistive MHD models are used to describe these regions. In the present work, a kinetic model is used for this purpose. Within this model, plasma response, current and charge density are computed with help of a Monte Carlo method, where guiding center orbit equations are solved using a semianalytical geometrical integrator. Besides its higher efficiency in comparison to usual integrators this method is not sensitive to noise in field quantities. The computed charges and currents are used to calculate the electromagnetic field with help of a finite element solver. A preconditioned iterative scheme is applied to search for a self-consistent solution. The discussed method is aimed at the nonlinear kinetic description of RMPs in experiments on Edge Localized Mode (ELM) mitigation by external perturbation coil systems without simplification of the device geometry.

  13. 3-D model of ICME in the interplanetary medium

    NASA Astrophysics Data System (ADS)

    Borgazzi, A.; Lara, A.; Niembro, T.

    2011-12-01

    We developed a method that describes with simply geometry the coordinates of intersection between the leading edge of an ICME and the position of an arbitrary satellite. When a fast CME is ejected from the Sun to the interplanetary space in most of the cases drives a shock. As the CME moves in the corona and later in the interplanetary space more material is stacking in the front and edges of the ejecta. In a first approximation, it is possible to assume the shape of these structures, the CME and the stacked material as a cone of revolution, (the ice-cream model [Schwenn et al., (2005)]). The interface may change due to the interaction of the structure and the non-shocked material in front of the ICME but the original shape of a cone of revolution is preserved. We assume, in a three dimensional geometry, an ice-cream cone shape for the ICME and apply an analytical model for its transport in the interplanetary medium. The goal of the present method is to give the time and the intersection coordinates between the leading edge of the ICME and any satellite that may be in the path of the ICME. With this information we can modelate the travel of the ICME in the interplanetary space using STEREO data.

  14. Introducing a New 3D Dynamical Model for Barred Galaxies

    NASA Astrophysics Data System (ADS)

    Jung, Christof; Zotos, Euaggelos E.

    2015-11-01

    The regular or chaotic dynamics of an analytical realistic three dimensional model composed of a spherically symmetric central nucleus, a bar and a flat disk is investigated. For describing the properties of the bar, we introduce a new simple dynamical model and we explore the influence on the character of orbits of all the involved parameters of it, such as the mass and the scale length of the bar, the major semi-axis and the angular velocity of the bar, as well as the energy. Regions of phase space with ordered and chaotic motion are identified in dependence on these parameters and for breaking the rotational symmetry. First, we study in detail the dynamics in the invariant plane z = pz = 0 using the Poincaré map as a basic tool and then study the full three-dimensional case using the Smaller Alignment index method as principal tool for distinguishing between order and chaos. We also present strong evidence obtained through the numerical simulations that our new bar model can realistically describe the formation and the evolution of the observed twin spiral structure in barred galaxies.

  15. The Martian Water Cycle Based on 3-D Modeling

    NASA Technical Reports Server (NTRS)

    Houben, H.; Haberle, R. M.; Joshi, M. M.

    1999-01-01

    Understanding the distribution of Martian water is a major goal of the Mars Surveyor program. However, until the bulk of the data from the nominal missions of TES, PMIRR, GRS, MVACS, and the DS2 probes are available, we are bound to be in a state where much of our knowledge of the seasonal behavior of water is based on theoretical modeling. We therefore summarize the results of this modeling at the present time. The most complete calculations come from a somewhat simplified treatment of the Martian climate system which is capable of simulating many decades of weather. More elaborate meteorological models are now being applied to study of the problem. The results show a high degree of consistency with observations of aspects of the Martian water cycle made by Viking MAWD, a large number of ground-based measurements of atmospheric column water vapor, studies of Martian frosts, and the widespread occurrence of water ice clouds. Additional information is contained in the original extended abstract.

  16. 3D modeling of geological anomalies based on segmentation of multiattribute fusion

    NASA Astrophysics Data System (ADS)

    Liu, Zhi-Ning; Song, Cheng-Yun; Li, Zhi-Yong; Cai, Han-Peng; Yao, Xing-Miao; Hu, Guang-Min

    2016-09-01

    3D modeling of geological bodies based on 3D seismic data is used to define the shape and volume of the bodies, which then can be directly applied to reservoir prediction, reserve estimation, and exploration. However, multiattributes are not effectively used in 3D modeling. To solve this problem, we propose a novel method for building of 3D model of geological anomalies based on the segmentation of multiattribute fusion. First, we divide the seismic attributes into edge- and region-based seismic attributes. Then, the segmentation model incorporating the edge- and region-based models is constructed within the levelset-based framework. Finally, the marching cubes algorithm is adopted to extract the zero level set based on the segmentation results and build the 3D model of the geological anomaly. Combining the edge-and region-based attributes to build the segmentation model, we satisfy the independence requirement and avoid the problem of insufficient data of single seismic attribute in capturing the boundaries of geological anomalies. We apply the proposed method to seismic data from the Sichuan Basin in southwestern China and obtain 3D models of caves and channels. Compared with 3D models obtained based on single seismic attributes, the results are better agreement with reality.

  17. 3D Monte Carlo radiation transfer modelling of photodynamic therapy

    NASA Astrophysics Data System (ADS)

    Campbell, C. Louise; Christison, Craig; Brown, C. Tom A.; Wood, Kenneth; Valentine, Ronan M.; Moseley, Harry

    2015-06-01

    The effects of ageing and skin type on Photodynamic Therapy (PDT) for different treatment methods have been theoretically investigated. A multilayered Monte Carlo Radiation Transfer model is presented where both daylight activated PDT and conventional PDT are compared. It was found that light penetrates deeper through older skin with a lighter complexion, which translates into a deeper effective treatment depth. The effect of ageing was found to be larger for darker skin types. The investigation further strengthens the usage of daylight as a potential light source for PDT where effective treatment depths of about 2 mm can be achieved.

  18. A 3D Orthotropic Elastic Continuum Damage Material Model

    SciTech Connect

    English, Shawn Allen; Brown, Arthur A.

    2013-08-01

    A three dimensional orthotropic elastic constitutive model with continuum damage is implemented for polymer matrix composite lamina. Damage evolves based on a quadratic homogeneous function of thermodynamic forces in the orthotropic planes. A small strain formulation is used to assess damage. In order to account for large deformations, a Kirchhoff material formulation is implemented and coded for numerical simulation in Sandia’s Sierra Finite Element code suite. The theoretical formulation is described in detail. An example of material parameter determination is given and an example is presented.

  19. Modeling of 3-D Woven Ceramic Matrix Composites

    NASA Technical Reports Server (NTRS)

    Murthy, Pappu L. N.; Sullivan, Roy M.; Mital, Subodh K.

    2003-01-01

    Three different approaches are being pursued at the NASA Glenn Research Center to predict the nanostructural behavior of three-dimensional woven ceramic matrix composites. These are: a micromechanics-based approach using W-CEMCAN (Woven Ceramic Matrix Composite Analyzer), a laminate analogy method and a structural frame approach (based on the finite element method). All three techniques are applied to predict the thermomechanical properties of a three-dimensional woven angle interlock C/SiC composite. The properties are predicted for room temperature and 1100 C and the predicted properties are compared to measurements. General observations regarding the three approaches for three-dimensional composite modeling are discussed.

  20. 3D Weight Matrices in Modeling Real Estate Prices

    NASA Astrophysics Data System (ADS)

    Mimis, A.

    2016-10-01

    Central role in spatial econometric models of real estate data has the definition of the weight matrix by which we capture the spatial dependence between the observations. The weight matrices presented in literature so far, treats space in a two dimensional manner leaving out the effect of the third dimension or in our case the difference in height where the property resides. To overcome this, we propose a new definition of the weight matrix including the third dimensional effect by using the Hadamard product. The results illustrated that the level effect can be absorbed into the new weight matrix.

  1. A 3D Hydrodynamic Model for Cytokinesis of Eukaryotic Cells

    DTIC Science & Technology

    2014-08-01

    remark that more features can be added to the model by augmenting the corresponding free energy . 2.2 Transport equations for biomass Given the...density for component i, i = 1, 2, 3. For incompress- ible materials, we enforce ϕ1 + ϕ2 + ϕ3 = 1. (2) 2.1 Thermodynamic free energy We denote the domain...in which the cell resides together with the buffer fluid as Ω. The free energy of this mixture system is proposed as follows, F = ∫ Ω fdx, (3) where f

  2. Modeling the diffusion of phosphorus in silicon in 3-D

    SciTech Connect

    Baker, K.R.

    1994-12-31

    The use of matrix preconditioning in semiconductor process simulation is examined. The simplified nonlinear single-species model for the diffusion of phosphorus into silicon is considered. The experimental three-dimensional simulator, PEPPER3, which uses finite differences and the numerical method of lines to implement the reaction-diffusion equation is modified to allow NSPCG to be called to solve the linear system in the inner Newton loop. Use of NSPCG allowed various accelerators such as Generalized Minimal Residual (GMRES) and Conjugate Gradient (CG) to be used in conjunction with preconditioners such as Richardson, Jacobi, and Incomplete Cholesky.

  3. Evaluation of field development plans using 3-D reservoir modelling

    SciTech Connect

    Seifert, D.; Lewis, J.J.M.; Newbery, J.D.H.

    1997-08-01

    Three-dimensional reservoir modelling has become an accepted tool in reservoir description and is used for various purposes, such as reservoir performance prediction or integration and visualisation of data. In this case study, a small Northern North Sea turbiditic reservoir was to be developed with a line drive strategy utilising a series of horizontal producer and injector pairs, oriented north-south. This development plan was to be evaluated and the expected outcome of the wells was to be assessed and risked. Detailed analyses of core, well log and analogue data has led to the development of two geological {open_quotes}end member{close_quotes} scenarios. Both scenarios have been stochastically modelled using the Sequential Indicator Simulation method. The resulting equiprobable realisations have been subjected to detailed statistical well placement optimisation techniques. Based upon bivariate statistical evaluation of more than 1000 numerical well trajectories for each of the two scenarios, it was found that the wells inclinations and lengths had a great impact on the wells success, whereas the azimuth was found to have only a minor impact. After integration of the above results, the actual well paths were redesigned to meet external drilling constraints, resulting in substantial reductions in drilling time and costs.

  4. Lightning Modelling: From 3D to Circuit Approach

    NASA Astrophysics Data System (ADS)

    Moussa, H.; Abdi, M.; Issac, F.; Prost, D.

    2012-05-01

    The topic of this study is electromagnetic environment and electromagnetic interferences (EMI) effects, specifically the modelling of lightning indirect effects [1] on aircraft electrical systems present on deported and highly exposed equipments, such as nose landing gear (NLG) and nacelle, through a circuit approach. The main goal of the presented work, funded by a French national project: PREFACE, is to propose a simple equivalent electrical circuit to represent a geometrical structure, taking into account mutual, self inductances, and resistances, which play a fundamental role in the lightning current distribution. Then this model is intended to be coupled to a functional one, describing a power train chain composed of: a converter, a shielded power harness and a motor or a set of resistors used as a load for the converter. The novelty here, is to provide a pre-sizing qualitative approach allowing playing on integration in pre-design phases. This tool intends to offer a user-friendly way for replying rapidly to calls for tender, taking into account the lightning constraints. Two cases are analysed: first, a NLG that is composed of tubular pieces that can be easily approximated by equivalent cylindrical straight conductors. Therefore, passive R, L, M elements of the structure can be extracted through analytical engineer formulas such as those implemented in the partial element equivalent circuit (PEEC) [2] technique. Second, the same approach is intended to be applied on an electrical de-icing nacelle sub-system.

  5. A 3D Current Loop Model of Magnetic Clouds

    NASA Astrophysics Data System (ADS)

    Chen, James

    1992-05-01

    A magnetohydrodynamic (MHD) model is developed to study magnetic clouds (Burlaga et al. 1981). In this model, magnetic clouds observed near 1 AU are treated as a consequence of eruptive solar current loops. It is shown that current loops intially in MHD equilibrium can be triggered to rise rapidly, propelling material of up to 10(16) g at up to ~ 1000 km s(-1) and dissipating ~ 10(32) erg of magnetic energy in tens of minutes. The initial rise profile is consistent with observed height-time profiles of erupting filaments (Kahler et al. 1988). Two triggering mechanisms for eruption are suggested: (1)subphotospheric energy storage and trigger and (2) in situ (coronal) energy storage and trigger. In the former, eruption occurs as a result of changes in the subphotospheric magnetic topology and subsequent relaxation to a new equilibrium. In the latter, the current loop can evolve to exceed a local maximum in the magnetic potential associated with the ambient magnetic fields. The former scenario leads to more energetic and longer-lasting eruption than the latter. Burlaga, L. F., Sittler, E., Mariani, F., and Schwenn, R. 1981, J. Geophys. Res., 86, 6673. Kahler, S. W., Moore, R. L., Kane, S. R., and Zirin, H. 1988, Ap. J., 328, 824.

  6. 3D modeling and optimization of the ITER ICRH antenna

    NASA Astrophysics Data System (ADS)

    Louche, F.; Dumortier, P.; Durodié, F.; Messiaen, A.; Maggiora, R.; Milanesio, D.

    2011-12-01

    The prediction of the coupling properties of the ITER ICRH antenna necessitates the accurate evaluation of the resistance and reactance matrices. The latter are mostly dependent on the geometry of the array and therefore a model as accurate as possible is needed to precisely compute these matrices. Furthermore simulations have so far neglected the poloidal and toroidal profile of the plasma, and it is expected that the loading by individual straps will vary significantly due to varying strap-plasma distance. To take this curvature into account, some modifications of the alignment of the straps with respect to the toroidal direction are proposed. It is shown with CST Microwave Studio® [1] that considering two segments in the toroidal direction, i.e. a "V-shaped" toroidal antenna, is sufficient. A new CATIA model including this segmentation has been drawn and imported into both MWS and TOPICA [2] codes. Simulations show a good agreement of the impedance matrices in vacuum. Various modifications of the geometry are proposed in order to further optimize the coupling. In particular we study the effect of the strap box parameters and the recess of the vertical septa.

  7. Synthetic benchmark for modeling flow in 3D fractured media

    NASA Astrophysics Data System (ADS)

    de Dreuzy, Jean-Raynald; Pichot, Géraldine; Poirriez, Baptiste; Erhel, Jocelyne

    2013-01-01

    Intensity and localization of flows in fractured media have promoted the development of a large range of different modeling approaches including Discrete Fracture Networks, pipe networks and equivalent continuous media. While benchmarked usually within site studies, we propose an alternative numerical benchmark based on highly-resolved Discrete Fracture Networks (DFNs) and on a stochastic approach. Test cases are built on fractures of different lengths, orientations, aspect ratios and hydraulic apertures, issuing the broad ranges of topological structures and hydraulic properties classically observed. We present 18 DFN cases, with 10 random simulations by case. These 180 DFN structures are provided and fully documented. They display a representative variety of the configurations that challenge the numerical methods at the different stages of discretization, mesh generation and system solving. Using a previously assessed mixed hybrid finite element method (Erhel et al., 2009a), we systematically provide reference flow and head solutions. Because CPU and memory requirements stem mainly from system solving, we study direct and iterative sparse linear solvers. We show that the most cpu-time efficient method is a direct multifrontal method for small systems, while conjugate gradient preconditioned by algebraic multrigrid is more relevant at larger sizes. Available results can be used further as references for building up alternative numerical and physical models in both directions of improving accuracy and efficiency.

  8. Possibility of reconstruction of dental plaster cast from 3D digital study models

    PubMed Central

    2013-01-01

    Objectives To compare traditional plaster casts, digital models and 3D printed copies of dental plaster casts based on various criteria. To determine whether 3D printed copies obtained using open source system RepRap can replace traditional plaster casts in dental practice. To compare and contrast the qualities of two possible 3D printing options – open source system RepRap and commercially available 3D printing. Design and settings A method comparison study on 10 dental plaster casts from the Orthodontic department, Department of Stomatology, 2nd medical Faulty, Charles University Prague, Czech Republic. Material and methods Each of 10 plaster casts were scanned by inEos Blue scanner and the printed on 3D printer RepRap [10 models] and ProJet HD3000 3D printer [1 model]. Linear measurements between selected points on the dental arches of upper and lower jaws on plaster casts and its 3D copy were recorded and statistically analyzed. Results 3D printed copies have many advantages over traditional plaster casts. The precision and accuracy of the RepRap 3D printed copies of plaster casts were confirmed based on the statistical analysis. Although the commercially available 3D printing enables to print more details than the RepRap system, it is expensive and for the purpose of clinical use can be replaced by the cheaper prints obtained from RepRap printed copies. Conclusions Scanning of the traditional plaster casts to obtain a digital model offers a pragmatic approach. The scans can subsequently be used as a template to print the plaster casts as required. Using 3D printers can replace traditional plaster casts primarily due to their accuracy and price. PMID:23721330

  9. Impact of the 3-D model strategy on science learning of the solar system

    NASA Astrophysics Data System (ADS)

    Alharbi, Mohammed

    The purpose of this mixed method study, quantitative and descriptive, was to determine whether the first-middle grade (seventh grade) students at Saudi schools are able to learn and use the Autodesk Maya software to interact and create their own 3-D models and animations and whether their use of the software influences their study habits and their understanding of the school subject matter. The study revealed that there is value to the science students regarding the use of 3-D software to create 3-D models to complete science assignments. Also, this study aimed to address the middle-school students' ability to learn 3-D software in art class, and then ultimately use it in their science class. The success of this study may open the way to consider the impact of 3-D modeling on other school subjects, such as mathematics, art, and geography. When the students start using graphic design, including 3-D software, at a young age, they tend to develop personal creativity and skills. The success of this study, if applied in schools, will provide the community with skillful young designers and increase awareness of graphic design and the new 3-D technology. Experimental method was used to answer the quantitative research question, are there significant differences applying the learning method using 3-D models (no 3-D, premade 3-D, and create 3-D) in a science class being taught about the solar system and its impact on the students' science achievement scores? Descriptive method was used to answer the qualitative research questions that are about the difficulty of learning and using Autodesk Maya software, time that students take to use the basic levels of Polygon and Animation parts of the Autodesk Maya software, and level of students' work quality.

  10. Evolution of 3-D geologic framework modeling and its application to groundwater flow studies

    USGS Publications Warehouse

    Blome, Charles D.; Smith, David V.

    2012-01-01

    In this Fact Sheet, the authors discuss the evolution of project 3-D subsurface framework modeling, research in hydrostratigraphy and airborne geophysics, and methodologies used to link geologic and groundwater flow models.

  11. Extracting Feature Points of the Human Body Using the Model of a 3D Human Body

    NASA Astrophysics Data System (ADS)

    Shin, Jeongeun; Ozawa, Shinji

    The purpose of this research is to recognize 3D shape features of a human body automatically using a 3D laser-scanning machine. In order to recognize the 3D shape features, we selected the 23 feature points of a body and modeled its 3D features. The set of 23 feature points consists of the motion axis of a joint, the main point for the bone structure of a human body. For extracting feature points of object model, we made 2.5D templates neighbor for each feature points were extracted according to the feature points of the standard model of human body. And the feature points were extracted by the template matching. The extracted feature points can be applied as body measurement, the 3D virtual fitting system for apparel etc.

  12. Modeling electromagnetic rail launchers at speed using 3D finite elements

    SciTech Connect

    Rodger, D.; Leonard, P.J.; Eastham, J.F. )

    1991-01-01

    In this paper a new finite element technique for modelling 3D transient eddy currents in moving conductors is described. This has been implemented in the MEGA software package for 2 and 3D electromagnetic field analysis. The application of the technique to railgun launchers is illustrated.

  13. RETRAN-3D MOD003 Peach Bottom Turbine Trip 2 Multidimensional Kinetics Analysis Models and Results

    SciTech Connect

    Mori, Michitsugu; Ogura, Katsunori; Gose, Garry C.; Wu, J.-Y

    2003-04-15

    An analysis of the Peach Bottom Unit 2 Turbine Trip Test 2 (PB2/TT2) has been performed using RETRAN-3D MOD003. The purpose of the analysis was to investigate the PB2/TT2 overpressurization transient using the RETRAN-3D multidimensional kinetics model.

  14. Modeling and analysis of 3-D elongated shapes with applications to long bone morphometry

    SciTech Connect

    Burdin, V.; Roux, C.; Lefevre, C.; Stindel, E.

    1996-02-01

    This paper presents a geometric model to be used as a framework for the description and analysis of three-dimensional (3-D) elongated shapes. Elongated shapes can be decomposed into two different parts: a 3-D curve (the central axis) and a 3-D surface (the straight surface). The central axis is described in terms of curvature and torsion. A novel concept of torsion image is introduced which allows the user to study the torsion of some relevant 3-D structures such as the medulla of long bones, without computing the third derivative. The description of the straight surface is based on an ordered set of Fourier Descriptors (FD`s), each set representing a 2-D slice of the structure. These descriptors possess completeness, continuity, and stability properties, and some geometrical invariancies. A polar diagram is built which contains the anatomical information of the straight surface and can be used as a tool for the analysis and discrimination of 3-D structures. A technique for the reconstruction of the 3-D surface from the model`s two components is presented. Various applications to the analysis of long bone structures, such as the ulna and radius, are derived from the model, namely, data compression, comparison of 3-D shapes, segmentation into 3-D primitives, and torsion and curvature analysis. The relevance of the method to morphometry and to clinical applications is discussed.

  15. 3D QSAR models built on structure-based alignments of Abl tyrosine kinase inhibitors.

    PubMed

    Falchi, Federico; Manetti, Fabrizio; Carraro, Fabio; Naldini, Antonella; Maga, Giovanni; Crespan, Emmanuele; Schenone, Silvia; Bruno, Olga; Brullo, Chiara; Botta, Maurizio

    2009-06-01

    Quality QSAR: A combination of docking calculations and a statistical approach toward Abl inhibitors resulted in a 3D QSAR model, the analysis of which led to the identification of ligand portions important for affinity. New compounds designed on the basis of the model were found to have very good affinity for the target, providing further validation of the model itself.The X-ray crystallographic coordinates of the Abl tyrosine kinase domain in its active, inactive, and Src-like inactive conformations were used as targets to simulate the binding mode of a large series of pyrazolo[3,4-d]pyrimidines (known Abl inhibitors) by means of GOLD software. Receptor-based alignments provided by molecular docking calculations were submitted to a GRID-GOLPE protocol to generate 3D QSAR models. Analysis of the results showed that the models based on the inactive and Src-like inactive conformations had very poor statistical parameters, whereas the sole model based on the active conformation of Abl was characterized by significant internal and external predictive ability. Subsequent analysis of GOLPE PLS pseudo-coefficient contour plots of this model gave us a better understanding of the relationships between structure and affinity, providing suggestions for the next optimization process. On the basis of these results, new compounds were designed according to the hydrophobic and hydrogen bond donor and acceptor contours, and were found to have improved enzymatic and cellular activity with respect to parent compounds. Additional biological assays confirmed the important role of the selected compounds as inhibitors of cell proliferation in leukemia cells.

  16. Optically directed molecular transport and 3D isoelectric positioning of amphoteric biomolecules

    PubMed Central

    Hafeman, Dean G.; Harkins, James B.; Witkowski, Charles E.; Lewis, Nathan S.; Warmack, Robert J.; Brown, Gilbert M.; Thundat, Thomas

    2006-01-01

    We demonstrate the formation of charged molecular packets and their transport within optically created electrical force-field traps in a pH-buffered electrolyte. We call this process photoelectrophoretic localization and transport (PELT). The electrolyte is in contact with a photoconductive semiconductor electrode and a counterelectrode that are connected through an external circuit. A light beam directed to coordinates on the photoconductive electrode surface produces a photocurrent within the circuit and electrolyte. Within the electrolyte, the photocurrent creates localized force-field traps centered at the illuminated coordinates. Charged molecules, including polypeptides and proteins, electrophoretically accumulate into the traps and subsequently can be transported in the electrolyte by moving the traps over the photoconductive electrode in response to movement of the light beam. The molecules in a single trap can be divided into aliquots, and the aliquots can be directed along multiple routes simultaneously by using multiple light beams. This photoelectrophoretic transport of charged molecules by PELT resembles the electrostatic transport of electrons within force-field wells of solid-state charge-coupled devices. The molecules, however, travel in a liquid electrolyte rather than a solid. Furthermore, we have used PELT to position amphoteric biomolecules in three dimensions. A 3D pH gradient was created in an electrolyte medium by controlling the illumination position on a photoconductive anode where protons were generated electrolytically. Photoelectrophoretic transport of amphoteric molecules through the pH gradient resulted in accumulation of the molecules at their apparent 3D isoelectric coordinates in the medium. PMID:16618926

  17. Development of 3D electromagnetic modeling tools for airborne vehicles

    NASA Technical Reports Server (NTRS)

    Volakis, John L.

    1992-01-01

    The main goal of this project is to develop methodologies for scattering by airborne composite vehicles. Although our primary focus continues to be the development of a general purpose code for analyzing the entire structure as a single unit, a number of other tasks are also pursued in parallel with this effort. These tasks are important in testing the overall approach and in developing suitable models for materials coatings, junctions and, more generally, in assessing the effectiveness of the various parts comprising the final code. Here, we briefly discuss our progress on the five different tasks which were pursued during this period. Our progress on each of these tasks is described in the detailed reports (listed at the end of this report) and the memoranda included. The first task described below is, of course, the core of this project and deals with the development of the overall code. Undoubtedly, it is the outcome of the research which was funded by NASA-Ames and the Navy over the past three years. During this year we developed the first finite element code for scattering by structures of arbitrary shape and composition. The code employs a new absorbing boundary condition which allows termination of the finite element mesh only 0.3 lambda from the outer surface of the target. This leads to a remarkable reduction of the mesh size and is a unique feature of the code. Other unique features of this code include capabilities to model resistive sheets, impedance sheets and anisotropic materials. This last capability is the latest feature of the code and is still under development. The code has been extensively validated for a number of composite geometries and some examples are given. The validation of the code is still in progress for anisotropic and larger non-metallic geometries and cavities. The developed finite element code is based on a Galerkin's formulation and employs edge-based tetrahedral elements for discretizing the dielectric sections and the region

  18. Virtual 3D Modeling of Airways in Congenital Heart Defects.

    PubMed

    Speggiorin, Simone; Durairaj, Saravanan; Mimic, Branko; Corno, Antonio F

    2016-01-01

    The involvement of the airway is not uncommon in the presence of complex cardiovascular malformations. In these cases, a careful inspection of the relationship between the airway and the vasculature is paramount to plan the surgical procedure. Three-dimensional printing enhanced the visualization of the cardiovascular structure. Unfortunately, IT does not allow to remove selected anatomy to improve the visualization of the surrounding ones. Computerized modeling has the potential to fill this gap by allowing a dynamic handling of different anatomies, increasing the exposure of vessels or bronchi to show their relationship. We started to use this technique to plan the surgical repair in these complex cases where the airway is affected. This technique is routinely used in our Institution as an additional tool in the presurgical assessment. We report four cases in which the airways were compressed by vascular structures - ascending aorta in one, left pulmonary artery sling in one, patent ductus arteriosus in one, and major aorto-pulmonary collateral artery in one. We believe this technique can enhance the understanding of the causes of airway involvement and facilitate the creation of an appropriate surgical plan.

  19. Virtual 3D Modeling of Airways in Congenital Heart Defects

    PubMed Central

    Speggiorin, Simone; Durairaj, Saravanan; Mimic, Branko; Corno, Antonio F.

    2016-01-01

    The involvement of the airway is not uncommon in the presence of complex cardiovascular malformations. In these cases, a careful inspection of the relationship between the airway and the vasculature is paramount to plan the surgical procedure. Three-dimensional printing enhanced the visualization of the cardiovascular structure. Unfortunately, IT does not allow to remove selected anatomy to improve the visualization of the surrounding ones. Computerized modeling has the potential to fill this gap by allowing a dynamic handling of different anatomies, increasing the exposure of vessels or bronchi to show their relationship. We started to use this technique to plan the surgical repair in these complex cases where the airway is affected. This technique is routinely used in our Institution as an additional tool in the presurgical assessment. We report four cases in which the airways were compressed by vascular structures – ascending aorta in one, left pulmonary artery sling in one, patent ductus arteriosus in one, and major aorto-pulmonary collateral artery in one. We believe this technique can enhance the understanding of the causes of airway involvement and facilitate the creation of an appropriate surgical plan. PMID:27833903

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

    PubMed

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

    2016-01-01

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

  1. Modeling of Localized Neutral Particle Sources in 3D Edge Plasmas

    SciTech Connect

    Umansky, M V; Rognlien, T D; Fenstermacher, M E; Borchardt, M; Mutzke, A; Riemann, J; Schneider, R; Owen, L W

    2002-05-23

    A new edge plasma code BoRiS [1] has a fully 3D fluid plasma model. We supplement BoRiS with a 3D fluid neutral model including equations for parallel momentum and collisional perpendicular diffusion. This makes BoRiS an integrated plasma-neutral model suitable for a variety of applications. We present modeling results for a localized gas source in the geometry of the NCSX stellarator.

  2. Combination of molecular dynamics method and 3D-RISM theory for conformational sampling of large flexible molecules in solution.

    PubMed

    Miyata, Tatsuhiko; Hirata, Fumio

    2008-04-30

    We have developed an algorithm for sampling the conformational space of large flexible molecules in solution, which combines the molecular dynamics (MD) method and the three-dimensional reference interaction site model (3D-RISM) theory. The solvent-induced force acting on solute atoms was evaluated as the gradient of the solvation free energy with respect to the solute-atom coordinates. To enhance the computation speed, we have applied a multiple timestep algorithm based on the RESPA (Reversible System Propagator Algorithm) to the combined MD/3D-RISM method. By virtue of the algorithm, one can choose a longer timestep for renewing the solvent-induced force compared with that of the conformational update. To illustrate the present MD/3D-RISM simulation, we applied the method to a model of acetylacetone in aqueous solution. The multiple timestep algorithm succeeded in enhancing the computation speed by 3.4 times for this model case. Acetylacetone possesses an intramolecular hydrogen-bonding capability between the hydroxyl group and the carbonyl oxygen atom, and the molecule is significantly stabilized due to this hydrogen bond, especially in gas phase. The intramolecular hydrogen bond was kept intact during almost entire course of the MD simulation in gas phase, while in the aqueous solutions the bond is disrupted in a significant number of conformations. This result qualitatively agrees with the behavior on a free energy barrier lying upon the process for rotating a torsional degree of freedom of the hydroxyl group, where it is significantly reduced in aqueous solution by a cancellation between the electrostatic interaction and the solvation free energy.

  3. On Fundamental Evaluation Using Uav Imagery and 3d Modeling Software

    NASA Astrophysics Data System (ADS)

    Nakano, K.; Suzuki, H.; Tamino, T.; Chikatsu, H.

    2016-06-01

    Unmanned aerial vehicles (UAVs), which have been widely used in recent years, can acquire high-resolution images with resolutions in millimeters; such images cannot be acquired with manned aircrafts. Moreover, it has become possible to obtain a surface reconstruction of a realistic 3D model using high-overlap images and 3D modeling software such as Context capture, Pix4Dmapper, Photoscan based on computer vision technology such as structure from motion and multi-view stereo. 3D modeling software has many applications. However, most of them seem to not have obtained appropriate accuracy control in accordance with the knowledge of photogrammetry and/or computer vision. Therefore, we performed flight tests in a test field using an UAV equipped with a gimbal stabilizer and consumer grade digital camera. Our UAV is a hexacopter and can fly according to the waypoints for autonomous flight and can record flight logs. We acquired images from different altitudes such as 10 m, 20 m, and 30 m. We obtained 3D reconstruction results of orthoimages, point clouds, and textured TIN models for accuracy evaluation in some cases with different image scale conditions using 3D modeling software. Moreover, the accuracy aspect was evaluated for different units of input image—course unit and flight unit. This paper describes the fundamental accuracy evaluation for 3D modeling using UAV imagery and 3D modeling software from the viewpoint of close-range photogrammetry.

  4. [MOLECULAR EVOLUTION OF ION CHANNELS: AMINO ACID SEQUENCES AND 3D STRUCTURES].

    PubMed

    Korkosh, V S; Zhorov, B S; Tikhonov, D B

    2016-01-01

    An integral part of modern evolutionary biology is comparative analysis of structure and function of macromolecules such as proteins. The first and critical step to understand evolution of homologous proteins is their amino acid sequence alignment. However, standard algorithms fop not provide unambiguous sequence alignments for proteins of poor homology. More reliable results can be obtained by comparing experimental 3D structures obtained at atomic resolution, for instance, with the aid of X-ray structural analysis. If such structures are lacking, homology modeling is used, which may take into account indirect experimental data on functional roles of individual amino-acid residues. An important problem is that the sequence alignment, which reflects genetic modifications, does not necessarily correspond to the functional homology. The latter depends on three-dimensional structures which are critical for natural selection. Since alignment techniques relying only on the analysis of primary structures carry no information on the functional properties of proteins, including 3D structures into consideration is very important. Here we consider several examples involving ion channels and demonstrate that alignment of their three-dimensional structures can significantly improve sequence alignments obtained by traditional methods.

  5. Investigating the Paleoproterozoic glaciations with 3-D climate modeling

    NASA Astrophysics Data System (ADS)

    Teitler, Yoram; Le Hir, Guillaume; Fluteau, Frédéric; Philippot, Pascal; Donnadieu, Yannick

    2014-06-01

    It is generally assumed that the Earth's surface was warm during most of its early history but that significant cooling occurred between 2.45 and 2.22 Ga leading to the first global and cyclical glacial epoch. This onset of snowball Earth conditions was coeval with a large pulse of oxygenation that permanently oxygenated the atmosphere and shallow oceans (Great Oxygenation Event, GOE), though it is not known whether one influenced the other or if they were independent events. Hereafter we used a General Circulation climate Model (GCM) to estimate the partial pressures of atmospheric CO2 (pCO2) and CH4 (pCH4) required to account for the onset of snowball Earth conditions during the Paleoproterozoic. We show that Earth's surface can be maintained in an ice-free state under atmospheric CO2 concentrations lower than 2.6×10-2 bar without invoking the need of high CH4 concentrations. Assuming that the cooling of the Earth's surface is related to the collapse of atmospheric greenhouse gases, we tested the relevance of different scenarios including (i) the collapse of pCH4 in response to the GOE and (ii) the drawdown of pCO2 due to both a decrease in volcanic outgassing rate and an increase in global weathering efficiency. We show that the cyclical character of Paleoproterozoic glaciations is best explained by a long-lasted decrease of pCO2. To support this scenario, we examine how the long-term carbon cycle and the equilibrium pCO2 respond to the emplacement of large subaerial basaltic provinces (LIPs) and to a temporary shutdown of volcanism as supported by geologic data. We show that the sink of pCO2 through silicate weathering is limited by the absence of terrestrial higher plants. In such conditions, the equilibrium pCO2 remains high enough to preclude the onset of snowball conditions regardless the intensity of the pCH4 collapse. The combination of an increase in weathering efficiency and a decrease in volcanic outgassing rate can significantly reduce the

  6. 3D MODEL ATMOSPHERES FOR EXTREMELY LOW-MASS WHITE DWARFS

    SciTech Connect

    Tremblay, P.-E.; Gianninas, A.; Kilic, M.; Ludwig, H.-G.; Steffen, M.; Freytag, B.; Hermes, J. J.

    2015-08-20

    We present an extended grid of mean three-dimensional (3D) spectra for low-mass, pure-hydrogen atmosphere DA white dwarfs (WDs). We use CO5BOLD radiation-hydrodynamics 3D simulations covering T{sub eff} = 6000–11,500 K and log g = 5–6.5 (g in cm s{sup −2}) to derive analytical functions to convert spectroscopically determined 1D temperatures and surface gravities to 3D atmospheric parameters. Along with the previously published 3D models, the 1D to 3D corrections are now available for essentially all known convective DA WDs (i.e., log g = 5–9). For low-mass WDs, the correction in temperature is relatively small (a few percent at the most), but the surface gravities measured from the 3D models are lower by as much as 0.35 dex. We revisit the spectroscopic analysis of the extremely low-mass (ELM) WDs, and demonstrate that the 3D models largely resolve the discrepancies seen in the radius and mass measurements for relatively cool ELM WDs in eclipsing double WD and WD + millisecond pulsar binary systems. We also use the 3D corrections to revise the boundaries of the ZZ Ceti instability strip, including the recently found ELM pulsators.

  7. Development of a unique 3D interaction model of endogenous and synthetic peripheral benzodiazepine receptor ligands

    NASA Astrophysics Data System (ADS)

    Cinone, Nunzia; Höltje, Hans-Dieter; Carotti, Angelo

    2000-11-01

    Different classes of Peripheral-type Benzodiazepine Receptor (PBR) ligands were examined and common structural elements were detected and used to develop a rational binding model based on energetically allowed ligand conformations. Two lipophilic regions and one electrostatic interaction site are essential features for high affinity ligand binding, while a further lipophilic region plays an important modulator role. A comparative molecular field analysis, performed over 130 PBR ligands by means of the GRID/GOLPE methodology, led to a PLS model with both high fitting and predictive values (r2 = 0.898, Q2 = 0.761). The outcome from the 3D QSAR model and the GRID interaction fields computed on the putative endogenous PBR ligands DBI (Diazepam Binding Inhibitor) and TTN (Tetracontatetraneuropeptide) was used to identify the amino acids most probably involved in PBR binding. Three amino acids, bearing lipophilic side chains, were detected in DBI (Phe49, Leu47 and Met46) and in TTN (Phe33, Leu31 and Met30) as likely residues underlying receptor binding. Moreover, a qualitative comparison of the molecular electrostatic potentials of DBI, TTN and selected synthetic ligands indicated also similar electronic properties. Convergent results from the modeling studies of synthetic and endogenous ligands suggest a common binding mode to PBRs. This may help the rational design of new high affinity PBR ligands.

  8. The integration of 3-D cell printing and mesoscopic fluorescence molecular tomography of vascular constructs within thick hydrogel scaffolds.

    PubMed

    Zhao, Lingling; Lee, Vivian K; Yoo, Seung-Schik; Dai, Guohao; Intes, Xavier

    2012-07-01

    Developing methods that provide adequate vascular perfusion is an important step toward engineering large functional tissues. Meanwhile, an imaging modality to assess the three-dimensional (3-D) structures and functions of the vascular channels is lacking for thick matrices (>2 ≈ 3 mm). Herein, we report on an original approach to construct and image 3-D dynamically perfused vascular structures in thick hydrogel scaffolds. In this work, we integrated a robotic 3-D cell printing technology with a mesoscopic fluorescence molecular tomography imaging system, and demonstrated the capability of the platform to construct perfused collagen scaffolds with endothelial lining and to image both the fluid flow and fluorescent-labeled living endothelial cells at high-frame rates, with high sensitivity and accuracy. These results establish the potential of integrating both 3-D cell printing and fluorescence mesoscopic imaging for functional and molecular studies in complex tissue-engineered tissues.

  9. Molecular tectonics: self-complementary supramolecular Se...N synthons directing assembly of 1D silver chains into 3D porous molecular architectures.

    PubMed

    Zhou, Ai-Ju; Zheng, Shao-Liang; Fang, Yue; Tong, Ming-Liang

    2005-06-27

    Reaction of 2,1,3-benzoselenadiazole (bsd) with AgNO3 results in the formation of a novel model example of a Se...N synthon directed molecular network of different polymorphs at different temperatures. Alpha-[Ag(bsd)2(NO3)] x 0.5bsd formed at ambient temperature, has a 3D porous molecular network constructed with monomeric [Ag(bsd)2(NO3)] motif, and has 1D channels that are encapsulated with 1D arrays of two-fold-disordered dimeric (bsd)2 guests aggregated by the self-complementary nonbonded Se...N interactions. This is the first molecular net directed by supramolecular Se...N synthons. The second polymorph, beta-[Ag(bsd)2(NO3)] x 0.5bsd, formed from an analogous reaction at 50 degrees C, contains a similar 3D molecular network constructed with tetrameric [Ag4(bsd)8(NO3)4] motif and 1D arrays of well-ordered dimeric (bsd)2 guests are encapsulated in the channels. Such ordered (bsd)2 dimers provide an excellent simplified dimeric model for MO calculations of intermolecular nonbonded Se...N interactions.

  10. Extraction of the 3D Free Space from Building Models for Indoor Navigation

    NASA Astrophysics Data System (ADS)

    Diakité, A. A.; Zlatanova, S.

    2016-10-01

    For several decades, indoor navigation has been exclusively investigated in a 2D perspective, based on floor plans, projection and other 2D representations of buildings. Nevertheless, 3D representations are closer to our reality and offer a more intuitive description of the space configuration. Thanks to recent advances in 3D modelling, 3D navigation is timidly but increasingly gaining in interest through the indoor applications. But, because the structure of indoor environment is often more complex than outdoor, very simplified models are used and obstacles are not considered for indoor navigation leading to limited possibilities in complex buildings. In this paper we consider the entire configuration of the indoor environment in 3D and introduce a method to extract from it the actual navigable space as a network of connected 3D spaces (volumes). We describe how to construct such 3D free spaces from semantically rich and furnished IFC models. The approach combines the geometric, the topological and the semantic information available in a 3D model to isolate the free space from the rest of the components. Furthermore, the extraction of such navigable spaces in building models lacking of semantic information is also considered. A data structure named combinatorial maps is used to support the operations required by the process while preserving the topological and semantic information of the input models.

  11. A Shell/3D Modeling Technique for the Analysis of Delaminated Composite Laminates

    NASA Technical Reports Server (NTRS)

    Krueger, Ronald; OBrien, T. Kevin

    2000-01-01

    A shell/3D modeling technique was developed for which a local solid finite element model is used only in the immediate vicinity of the delamination front. The goal was to combine the accuracy of the full three-dimensional solution with the computational efficiency of a shell finite element model. Multi-point constraints provided a kinematically compatible interface between the local 3D model and the global structural model which has been meshed with shell finite elements. Double Cantilever Beam, End Notched Flexure, and Single Leg Bending specimens were analyzed first using full 3D finite element models to obtain reference solutions. Mixed mode strain energy release rate distributions were computed using the virtual crack closure technique. The analyses were repeated using the shell/3D technique to study the feasibility for pure mode I, mode II and mixed mode I/II cases. Specimens with a unidirectional layup and with a multidirectional layup were simulated. For a local 3D model, extending to a minimum of about three specimen thicknesses on either side of the delamination front, the results were in good agreement with mixed mode strain energy release rates obtained from computations where the entire specimen had been modeled with solid elements. For large built-up composite structures the shell/3D modeling technique offers a great potential for reducing the model size, since only a relatively small section in the vicinity of the delamination front needs to be modeled with solid elements.

  12. The radiological feature of anterior occiput-to-axis screw fixation as it guides the screw trajectory on 3D printed models: a feasibility study on 3D images and 3D printed models.

    PubMed

    Wu, Ai-Min; Wang, Sheng; Weng, Wan-Qing; Shao, Zhen-Xuan; Yang, Xin-Dong; Wang, Jian-Shun; Xu, Hua-Zi; Chi, Yong-Long

    2014-12-01

    Anterior occiput-to-axis screw fixation is more suitable than a posterior approach for some patients with a history of posterior surgery. The complex osseous anatomy between the occiput and the axis causes a high risk of injury to neurological and vascular structures, and it is important to have an accurate screw trajectory to guide anterior occiput-to-axis screw fixation. Thirty computed tomography (CT) scans of upper cervical spines were obtained for three-dimensional (3D) reconstruction. Cylinders (1.75 mm radius) were drawn to simulate the trajectory of an anterior occiput-to-axis screw. The imitation screw was adjusted to 4 different angles and measured, as were the values of the maximized anteroposterior width and the left-right width of the occiput (C0) to the C1 and C1 to C2 joints. Then, the 3D models were printed, and an angle guide device was used to introduce the screws into the 3D models referring to the angles calculated from the 3D images. We found the screw angle ranged from α1 (left: 4.99±4.59°; right: 4.28±5.45°) to α2 (left: 20.22±3.61°; right: 19.63±4.94°); on the lateral view, the screw angle ranged from β1 (left: 13.13±4.93°; right: 11.82±5.64°) to β2 (left: 34.86±6.00°; right: 35.01±5.77°). No statistically significant difference was found between the data of the left and right sides. On the 3D printed models, all of the anterior occiput-to-axis screws were successfully introduced, and none of them penetrated outside of the cortex; the mean α4 was 12.00±4.11 (left) and 12.25±4.05 (right), and the mean β4 was 23.44±4.21 (left) and 22.75±4.41 (right). No significant difference was found between α4 and β4 on the 3D printed models and α3 and β3 calculated from the 3D digital images of the left and right sides. Aided with the angle guide device, we could achieve an optimal screw trajectory for anterior occiput-to-axis screw fixation on 3D printed C0 to C2 models.

  13. KENO3D Visualization Tool for KENO V.a and KENO-VI Geometry Models

    SciTech Connect

    Horwedel, J.E.; Bowman, S.M.

    2000-06-01

    Criticality safety analyses often require detailed modeling of complex geometries. Effective visualization tools can enhance checking the accuracy of these models. This report describes the KENO3D visualization tool developed at the Oak Ridge National Laboratory (ORNL) to provide visualization of KENO V.a and KENO-VI criticality safety models. The development of KENO3D is part of the current efforts to enhance the SCALE (Standardized Computer Analyses for Licensing Evaluations) computer software system.

  14. Obtaining valid geologic models from 3-D resistivity inversion of magnetotelluric data at Pahute Mesa, Nevada

    USGS Publications Warehouse

    Rodriguez, Brian D.; Sweetkind, Donald S.

    2015-01-01

    The 3-D inversion was generally able to reproduce the gross resistivity structure of the “known” model, but the simulated conductive volcanic composite unit horizons were often too shallow when compared to the “known” model. Additionally, the chosen computation parameters such as station spacing appear to have resulted in computational artifacts that are difficult to interpret but could potentially be removed with further refinements of the 3-D resistivity inversion modeling technique.

  15. Considerations on the Use of 3-D Geophysical Models to Predict Test Ban Monitoring Observables

    SciTech Connect

    Harris, D B; Zucca, J J; McCallen, D B; Pasyanos, M E; Flanagan, M P; Myers, S C; Walter, W R; Rodgers, A J; Harben, P E

    2007-07-09

    The use of 3-D geophysical models to predict nuclear test ban monitoring observables (phase travel times, amplitudes, dispersion, etc.) is widely anticipated to provide improvements in the basic seismic monitoring functions of detection, association, location, discrimination and yield estimation. A number of questions arise when contemplating a transition from 1-D, 2-D and 2.5-D models to constructing and using 3-D models, among them: (1) Can a 3-D geophysical model or a collection of 3-D models provide measurably improved predictions of seismic monitoring observables over existing 1-D models, or 2-D and 2 1/2-D models currently under development? (2) Is a single model that can predict all observables achievable, or must separate models be devised for each observable? How should joint inversion of disparate observable data be performed, if required? (3) What are the options for model representation? Are multi-resolution models essential? How does representation affect the accuracy and speed of observable predictions? (4) How should model uncertainty be estimated, represented and how should it be used? Are stochastic models desirable? (5) What data types should be used to construct the models? What quality control regime should be established? (6) How will 3-D models be used in operations? Will significant improvements in the basic monitoring functions result from the use of 3-D models? Will the calculation of observables through 3-D models be fast enough for real-time use or must a strategy of pre-computation be employed? (7) What are the theoretical limits to 3-D model development (resolution, uncertainty) and performance in predicting monitoring observables? How closely can those limits be approached with projected data availability, station distribution and inverse methods? (8) What priorities should be placed on the acquisition of event ground truth information, deployment of new stations, development of new inverse techniques, exploitation of large

  16. A computational framework for 3D mechanical modeling of plant morphogenesis with cellular resolution.

    PubMed

    Boudon, Frédéric; Chopard, Jérôme; Ali, Olivier; Gilles, Benjamin; Hamant, Olivier; Boudaoud, Arezki; Traas, Jan; Godin, Christophe

    2015-01-01

    The link between genetic regulation and the definition of form and size during morphogenesis remains largely an open question in both plant and animal biology. This is partially due to the complexity of the process, involving extensive molecular networks, multiple feedbacks between different scales of organization and physical forces operating at multiple levels. Here we present a conceptual and modeling framework aimed at generating an integrated understanding of morp