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Sample records for 3d molecular descriptors

  1. Molecular Descriptors

    NASA Astrophysics Data System (ADS)

    Consonni, Viviana; Todeschini, Roberto

    In the last decades, several scientific researches have been focused on studying how to encompass and convert - by a theoretical pathway - the information encoded in the molecular structure into one or more numbers used to establish quantitative relationships between structures and properties, biological activities, or other experimental properties. Molecular descriptors are formally mathematical representations of a molecule obtained by a well-specified algorithm applied to a defined molecular representation or a well-specified experimental procedure. They play a fundamental role in chemistry, pharmaceutical sciences, environmental protection policy, toxicology, ecotoxicology, health research, and quality control. Evidence of the interest of the scientific community in the molecular descriptors is provided by the huge number of descriptors proposed up today: more than 5000 descriptors derived from different theories and approaches are defined in the literature and most of them can be calculated by means of dedicated software applications. Molecular descriptors are of outstanding importance in the research fields of quantitative structure-activity relationships (QSARs) and quantitative structure-property relationships (QSPRs), where they are the independent chemical information used to predict the properties of interest. Along with the definition of appropriate molecular descriptors, the molecular structure representation and the mathematical tools for deriving and assessing models are other fundamental components of the QSAR/QSPR approach. The remarkable progress during the last few years in chemometrics and chemoinformatics has led to new strategies for finding mathematical meaningful relationships between the molecular structure and biological activities, physico-chemical, toxicological, and environmental properties of chemicals. Different approaches for deriving molecular descriptors here reviewed and some of the most relevant descriptors are presented in

  2. Benchmarking of HPCC: A novel 3D molecular representation combining shape and pharmacophoric descriptors for efficient molecular similarity assessments.

    PubMed

    Karaboga, Arnaud S; Petronin, Florent; Marchetti, Gino; Souchet, Michel; Maigret, Bernard

    2013-04-01

    Since 3D molecular shape is an important determinant of biological activity, designing accurate 3D molecular representations is still of high interest. Several chemoinformatic approaches have been developed to try to describe accurate molecular shapes. Here, we present a novel 3D molecular description, namely harmonic pharma chemistry coefficient (HPCC), combining a ligand-centric pharmacophoric description projected onto a spherical harmonic based shape of a ligand. The performance of HPCC was evaluated by comparison to the standard ROCS software in a ligand-based virtual screening (VS) approach using the publicly available directory of useful decoys (DUD) data set comprising over 100,000 compounds distributed across 40 protein targets. Our results were analyzed using commonly reported statistics such as the area under the curve (AUC) and normalized sum of logarithms of ranks (NSLR) metrics. Overall, our HPCC 3D method is globally as efficient as the state-of-the-art ROCS software in terms of enrichment and slightly better for more than half of the DUD targets. Since it is largely admitted that VS results depend strongly on the nature of the protein families, we believe that the present HPCC solution is of interest over the current ligand-based VS methods. PMID:23467019

  3. Derivatives in discrete mathematics: a novel graph-theoretical invariant for generating new 2/3D molecular descriptors. I. Theory and QSPR application.

    PubMed

    Marrero-Ponce, Yovani; Santiago, Oscar Martínez; López, Yoan Martínez; Barigye, Stephen J; Torrens, Francisco

    2012-11-01

    In this report, we present a new mathematical approach for describing chemical structures of organic molecules at atomic-molecular level, proposing for the first time the use of the concept of the derivative ([Formula: see text]) of a molecular graph (MG) with respect to a given event (E), to obtain a new family of molecular descriptors (MDs). With this purpose, a new matrix representation of the MG, which generalizes graph's theory's traditional incidence matrix, is introduced. This matrix, denominated the generalized incidence matrix, Q, arises from the Boolean representation of molecular sub-graphs that participate in the formation of the graph molecular skeleton MG and could be complete (representing all possible connected sub-graphs) or constitute sub-graphs of determined orders or types as well as a combination of these. The Q matrix is a non-quadratic and unsymmetrical in nature, its columns (n) and rows (m) are conditions (letters) and collection of conditions (words) with which the event occurs. This non-quadratic and unsymmetrical matrix is transformed, by algebraic manipulation, to a quadratic and symmetric matrix known as relations frequency matrix, F, which characterizes the participation intensity of the conditions (letters) in the events (words). With F, we calculate the derivative over a pair of atomic nuclei. The local index for the atomic nuclei i, Δ(i), can therefore be obtained as a linear combination of all the pair derivatives of the atomic nuclei i with all the rest of the j's atomic nuclei. Here, we also define new strategies that generalize the present form of obtaining global or local (group or atom-type) invariants from atomic contributions (local vertex invariants, LOVIs). In respect to this, metric (norms), means and statistical invariants are introduced. These invariants are applied to a vector whose components are the values Δ(i) for the atomic nuclei of the molecule or its fragments. Moreover, with the purpose of differentiating

  4. 3D Face Recognition Based on Multiple Keypoint Descriptors and Sparse Representation

    PubMed Central

    Zhang, Lin; Ding, Zhixuan; Li, Hongyu; Shen, Ying; Lu, Jianwei

    2014-01-01

    Recent years have witnessed a growing interest in developing methods for 3D face recognition. However, 3D scans often suffer from the problems of missing parts, large facial expressions, and occlusions. To be useful in real-world applications, a 3D face recognition approach should be able to handle these challenges. In this paper, we propose a novel general approach to deal with the 3D face recognition problem by making use of multiple keypoint descriptors (MKD) and the sparse representation-based classification (SRC). We call the proposed method 3DMKDSRC for short. Specifically, with 3DMKDSRC, each 3D face scan is represented as a set of descriptor vectors extracted from keypoints by meshSIFT. Descriptor vectors of gallery samples form the gallery dictionary. Given a probe 3D face scan, its descriptors are extracted at first and then its identity can be determined by using a multitask SRC. The proposed 3DMKDSRC approach does not require the pre-alignment between two face scans and is quite robust to the problems of missing data, occlusions and expressions. Its superiority over the other leading 3D face recognition schemes has been corroborated by extensive experiments conducted on three benchmark databases, Bosphorus, GavabDB, and FRGC2.0. The Matlab source code for 3DMKDSRC and the related evaluation results are publicly available at http://sse.tongji.edu.cn/linzhang/3dmkdsrcface/3dmkdsrc.htm. PMID:24940876

  5. 3D face recognition based on multiple keypoint descriptors and sparse representation.

    PubMed

    Zhang, Lin; Ding, Zhixuan; Li, Hongyu; Shen, Ying; Lu, Jianwei

    2014-01-01

    Recent years have witnessed a growing interest in developing methods for 3D face recognition. However, 3D scans often suffer from the problems of missing parts, large facial expressions, and occlusions. To be useful in real-world applications, a 3D face recognition approach should be able to handle these challenges. In this paper, we propose a novel general approach to deal with the 3D face recognition problem by making use of multiple keypoint descriptors (MKD) and the sparse representation-based classification (SRC). We call the proposed method 3DMKDSRC for short. Specifically, with 3DMKDSRC, each 3D face scan is represented as a set of descriptor vectors extracted from keypoints by meshSIFT. Descriptor vectors of gallery samples form the gallery dictionary. Given a probe 3D face scan, its descriptors are extracted at first and then its identity can be determined by using a multitask SRC. The proposed 3DMKDSRC approach does not require the pre-alignment between two face scans and is quite robust to the problems of missing data, occlusions and expressions. Its superiority over the other leading 3D face recognition schemes has been corroborated by extensive experiments conducted on three benchmark databases, Bosphorus, GavabDB, and FRGC2.0. The Matlab source code for 3DMKDSRC and the related evaluation results are publicly available at http://sse.tongji.edu.cn/linzhang/3dmkdsrcface/3dmkdsrc.htm. PMID:24940876

  6. Protein-protein docking using region-based 3D Zernike descriptors

    PubMed Central

    2009-01-01

    Background Protein-protein interactions are a pivotal component of many biological processes and mediate a variety of functions. Knowing the tertiary structure of a protein complex is therefore essential for understanding the interaction mechanism. However, experimental techniques to solve the structure of the complex are often found to be difficult. To this end, computational protein-protein docking approaches can provide a useful alternative to address this issue. Prediction of docking conformations relies on methods that effectively capture shape features of the participating proteins while giving due consideration to conformational changes that may occur. Results We present a novel protein docking algorithm based on the use of 3D Zernike descriptors as regional features of molecular shape. The key motivation of using these descriptors is their invariance to transformation, in addition to a compact representation of local surface shape characteristics. Docking decoys are generated using geometric hashing, which are then ranked by a scoring function that incorporates a buried surface area and a novel geometric complementarity term based on normals associated with the 3D Zernike shape description. Our docking algorithm was tested on both bound and unbound cases in the ZDOCK benchmark 2.0 dataset. In 74% of the bound docking predictions, our method was able to find a near-native solution (interface C-αRMSD ≤ 2.5 Å) within the top 1000 ranks. For unbound docking, among the 60 complexes for which our algorithm returned at least one hit, 60% of the cases were ranked within the top 2000. Comparison with existing shape-based docking algorithms shows that our method has a better performance than the others in unbound docking while remaining competitive for bound docking cases. Conclusion We show for the first time that the 3D Zernike descriptors are adept in capturing shape complementarity at the protein-protein interface and useful for protein docking prediction

  7. Signature molecular descriptor : advanced applications.

    SciTech Connect

    Visco, Donald Patrick, Jr.

    2010-04-01

    In this work we report on the development of the Signature Molecular Descriptor (or Signature) for use in the solution of inverse design problems as well as in highthroughput screening applications. The ultimate goal of using Signature is to identify novel and non-intuitive chemical structures with optimal predicted properties for a given application. We demonstrate this in three studies: green solvent design, glucocorticoid receptor ligand design and the design of inhibitors for Factor XIa. In many areas of engineering, compounds are designed and/or modified in incremental ways which rely upon heuristics or institutional knowledge. Often multiple experiments are performed and the optimal compound is identified in this brute-force fashion. Perhaps a traditional chemical scaffold is identified and movement of a substituent group around a ring constitutes the whole of the design process. Also notably, a chemical being evaluated in one area might demonstrate properties very attractive in another area and serendipity was the mechanism for solution. In contrast to such approaches, computer-aided molecular design (CAMD) looks to encompass both experimental and heuristic-based knowledge into a strategy that will design a molecule on a computer to meet a given target. Depending on the algorithm employed, the molecule which is designed might be quite novel (re: no CAS registration number) and/or non-intuitive relative to what is known about the problem at hand. While CAMD is a fairly recent strategy (dating to the early 1980s), it contains a variety of bottlenecks and limitations which have prevented the technique from garnering more attention in the academic, governmental and industrial institutions. A main reason for this is how the molecules are described in the computer. This step can control how models are developed for the properties of interest on a given problem as well as how to go from an output of the algorithm to an actual chemical structure. This report

  8. Analyzing the relevance of shape descriptors in automated recognition of facial gestures in 3D images

    NASA Astrophysics Data System (ADS)

    Rodriguez A., Julian S.; Prieto, Flavio

    2013-03-01

    The present document shows and explains the results from analyzing shape descriptors (DESIRE and Spherical Spin Image) for facial recognition of 3D images. DESIRE is a descriptor made of depth images, silhouettes and rays extended from a polygonal mesh; whereas the Spherical Spin Image (SSI) associated to a polygonal mesh point, is a 2D histogram built from neighboring points by using the position information that captures features of the local shape. The database used contains images of facial expressions which in average were recognized 88.16% using a neuronal network and 91.11% with a Bayesian classifier in the case of the first descriptor; in contrast, the second descriptor only recognizes in average 32% and 23,6% using the same mentioned classifiers respectively.

  9. ANN expert system screening for illicit amphetamines using molecular descriptors

    NASA Astrophysics Data System (ADS)

    Gosav, S.; Praisler, M.; Dorohoi, D. O.

    2007-05-01

    The goal of this study was to develop and an artificial neural network (ANN) based on computed descriptors, which would be able to classify the molecular structures of potential illicit amphetamines and to derive their biological activity according to the similarity of their molecular structure with amphetamines of known toxicity. The system is necessary for testing new molecular structures for epidemiological, clinical, and forensic purposes. It was built using a database formed by 146 compounds representing drugs of abuse (mainly central stimulants, hallucinogens, sympathomimetic amines, narcotics and other potent analgesics), precursors, or derivatized counterparts. Their molecular structures were characterized by computing three types of descriptors: 38 constitutional descriptors (CDs), 69 topological descriptors (TDs) and 160 3D-MoRSE descriptors (3DDs). An ANN system was built for each category of variables. All three networks (CD-NN, TD-NN and 3DD-NN) were trained to distinguish between stimulant amphetamines, hallucinogenic amphetamines, and nonamphetamines. A selection of variables was performed when necessary. The efficiency with which each network identifies the class identity of an unknown sample was evaluated by calculating several figures of merit. The results of the comparative analysis are presented.

  10. Comparison of 3D interest point detectors and descriptors for point cloud fusion

    NASA Astrophysics Data System (ADS)

    Hänsch, R.; Weber, T.; Hellwich, O.

    2014-08-01

    The extraction and description of keypoints as salient image parts has a long tradition within processing and analysis of 2D images. Nowadays, 3D data gains more and more importance. This paper discusses the benefits and limitations of keypoints for the task of fusing multiple 3D point clouds. For this goal, several combinations of 3D keypoint detectors and descriptors are tested. The experiments are based on 3D scenes with varying properties, including 3D scanner data as well as Kinect point clouds. The obtained results indicate that the specific method to extract and describe keypoints in 3D data has to be carefully chosen. In many cases the accuracy suffers from a too strong reduction of the available points to keypoints.

  11. 3D model retrieval using probability density-based shape descriptors.

    PubMed

    Akgül, Ceyhun Burak; Sankur, Bülent; Yemez, Yücel; Schmitt, Francis

    2009-06-01

    We address content-based retrieval of complete 3D object models by a probabilistic generative description of local shape properties. The proposed shape description framework characterizes a 3D object with sampled multivariate probability density functions of its local surface features. This density-based descriptor can be efficiently computed via kernel density estimation (KDE) coupled with fast Gauss transform. The non-parametric KDE technique allows reliable characterization of a diverse set of shapes and yields descriptors which remain relatively insensitive to small shape perturbations and mesh resolution. Density-based characterization also induces a permutation property which can be used to guarantee invariance at the shape matching stage. As proven by extensive retrieval experiments on several 3D databases, our framework provides state-of-the-art discrimination over a broad and heterogeneous set of shape categories. PMID:19372614

  12. 3D shape descriptors for face segmentation and fiducial points detection: an anatomical-based analysis

    NASA Astrophysics Data System (ADS)

    Salazar, Augusto E.; Cerón, Alexander; Prieto, Flavio A.

    2011-03-01

    The behavior of nine 3D shape descriptors which were computed on the surface of 3D face models, is studied. The set of descriptors includes six curvature-based ones, SPIN images, Folded SPIN Images, and Finger prints. Instead of defining clusters of vertices based on the value of a given primitive surface feature, a face template composed by 28 anatomical regions, is used to segment the models and to extract the location of different landmarks and fiducial points. Vertices are grouped by: region, region boundaries, and subsampled versions of them. The aim of this study is to analyze the discriminant capacity of each descriptor to characterize regions and to identify key points on the facial surface. The experiment includes testing with data from neutral faces and faces showing expressions. Also, in order to see the usefulness of the bending-invariant canonical form (BICF) to handle variations due to facial expressions, the descriptors are computed directly from the surface and also from its BICF. In the results: the values, distributions, and relevance indexes of each set of vertices, were analyzed.

  13. A 3D Feature Descriptor Recovered from a Single 2D Palmprint Image.

    PubMed

    Zheng, Qian; Kumar, Ajay; Pan, Gang

    2016-06-01

    Design and development of efficient and accurate feature descriptors is critical for the success of many computer vision applications. This paper proposes a new feature descriptor, referred to as DoN, for the 2D palmprint matching. The descriptor is extracted for each point on the palmprint. It is based on the ordinal measure which partially describes the difference of the neighboring points' normal vectors. DoN has at least two advantages: 1) it describes the 3D information, which is expected to be highly stable under commonly occurring illumination variations during contactless imaging; 2) the size of DoN for each point is only one bit, which is computationally simple to extract, easy to match, and efficient to storage. We show that such 3D information can be extracted from a single 2D palmprint image. The analysis for the effectiveness of ordinal measure for palmprint matching is also provided. Four publicly available 2D palmprint databases are used to evaluate the effectiveness of DoN, both for identification and the verification. Our method on all these databases achieves the state-of-the-art performance. PMID:27164564

  14. 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…

  15. 3D Riesz-wavelet based Covariance descriptors for texture classification of lung nodule tissue in CT.

    PubMed

    Cirujeda, Pol; Muller, Henning; Rubin, Daniel; Aguilera, Todd A; Loo, Billy W; Diehn, Maximilian; Binefa, Xavier; Depeursinge, Adrien

    2015-08-01

    In this paper we present a novel technique for characterizing and classifying 3D textured volumes belonging to different lung tissue types in 3D CT images. We build a volume-based 3D descriptor, robust to changes of size, rigid spatial transformations and texture variability, thanks to the integration of Riesz-wavelet features within a Covariance-based descriptor formulation. 3D Riesz features characterize the morphology of tissue density due to their response to changes in intensity in CT images. These features are encoded in a Covariance-based descriptor formulation: this provides a compact and flexible representation thanks to the use of feature variations rather than dense features themselves and adds robustness to spatial changes. Furthermore, the particular symmetric definite positive matrix form of these descriptors causes them to lay in a Riemannian manifold. Thus, descriptors can be compared with analytical measures, and accurate techniques from machine learning and clustering can be adapted to their spatial domain. Additionally we present a classification model following a "Bag of Covariance Descriptors" paradigm in order to distinguish three different nodule tissue types in CT: solid, ground-glass opacity, and healthy lung. The method is evaluated on top of an acquired dataset of 95 patients with manually delineated ground truth by radiation oncology specialists in 3D, and quantitative sensitivity and specificity values are presented. PMID:26738126

  16. Local intersection volume: a new 3D descriptor applied to develop a 3D-QSAR pharmacophore model for benzodiazepine receptor ligands.

    PubMed

    Verli, Hugo; Albuquerque, Magaly Girão; Bicca de Alencastro, Ricardo; Barreiro, Eliezer J

    2002-03-01

    In this work, we have developed a new descriptor, named local intersection volume (LIV), in order to compose a 3D-QSAR pharmacophore model for benzodiazepine receptor ligands. The LIV can be classified as a 3D local shape descriptor in contraposition to the global shape descriptors. We have selected from the literature 49 non-benzodiazepine compounds as a training data set and the model was obtained and evaluated by genetic algorithms (GA) and partial least-squares (PLS) methods using LIVs as descriptors. The LIV 3D-QSAR model has a good predictive capacity according the cross-validation test by "leave-one-out" procedure (Q(2)=0.72). The developed model was compared to a comprehensive and extensive SAR pharmacophore model, recently proposed by Cook and co-workers, for benzodiazepine receptor ligands [J. Med. Chem. 43 (2000) 71]. It showed a relevant correlation with the pharmacophore groups pointed out in that work. Our LIV 3D-QSAR model was also able to predict affinity values for a series of nine compounds (test data set) that was not included into the training data set. PMID:11900866

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

    PubMed

    Mitra, Indrani; Saha, Achintya; Roy, Kunal

    2013-03-01

    The inability of the systemic antioxidants to alleviate the exacerbation of free radical formation from metabolic outputs and environmental pollutants claims an urgent demand for the identification and design of new chemical entities with potent antioxidant activity. In the present work, different QSAR approaches have been utilized for identifying the essential structural attributes imparting a potential antioxidant activity profile of the coumarin derivatives. The descriptor-based QSAR model provides a quantitative outline regarding the structural prerequisites of the molecules, while 3D pharmacophore and HQSAR models emphasize the favourable spatial arrangement of the various chemical features and the crucial molecular fragments, respectively. All the models infer that the fused benzene ring and the oxygen atom of the pyran ring constituting the parent coumarin nucleus capture the prime pharmacophoric features, imparting superior antioxidant activity to the molecules. The developed models may serve as indispensable query tools for screening untested molecules belonging to the class of coumarin derivatives. PMID:23641329

  18. Reverse engineering chemical structures from molecular descriptors : how many solutions?

    SciTech Connect

    Brown, William Michael; Martin, Shawn Bryan; Faulon, Jean-Loup Michel

    2005-06-01

    Physical, chemical and biological properties are the ultimate information of interest for chemical compounds. Molecular descriptors that map structural information to activities and properties are obvious candidates for information sharing. In this paper, we consider the feasibility of using molecular descriptors to safely exchange chemical information in such a way that the original chemical structures cannot be reverse engineered. To investigate the safety of sharing such descriptors, we compute the degeneracy (the number of structure matching a descriptor value) of several 2D descriptors, and use various methods to search for and reverse engineer structures. We examine degeneracy in the entire chemical space taking descriptors values from the alkane isomer series and the PubChem database. We further use a stochastic search to retrieve structures matching specific topological index values. Finally, we investigate the safety of exchanging of fragmental descriptors using deterministic enumeration.

  19. Novel 3D bio-macromolecular bilinear descriptors for protein science: Predicting protein structural classes.

    PubMed

    Marrero-Ponce, Yovani; Contreras-Torres, Ernesto; García-Jacas, César R; Barigye, Stephen J; Cubillán, Néstor; Alvarado, Ysaías J

    2015-06-01

    In the present study, we introduce novel 3D protein descriptors based on the bilinear algebraic form in the ℝ(n) space on the coulombic matrix. For the calculation of these descriptors, macromolecular vectors belonging to ℝ(n) space, whose components represent certain amino acid side-chain properties, were used as weighting schemes. Generalization approaches for the calculation of inter-amino acidic residue spatial distances based on Minkowski metrics are proposed. The simple- and double-stochastic schemes were defined as approaches to normalize the coulombic matrix. The local-fragment indices for both amino acid-types and amino acid-groups are presented in order to permit characterizing fragments of interest in proteins. On the other hand, with the objective of taking into account specific interactions among amino acids in global or local indices, geometric and topological cut-offs are defined. To assess the utility of global and local indices a classification model for the prediction of the major four protein structural classes, was built with the Linear Discriminant Analysis (LDA) technique. The developed LDA-model correctly classifies the 92.6% and 92.7% of the proteins on the training and test sets, respectively. The obtained model showed high values of the generalized square correlation coefficient (GC(2)) on both the training and test series. The statistical parameters derived from the internal and external validation procedures demonstrate the robustness, stability and the high predictive power of the proposed model. The performance of the LDA-model demonstrates the capability of the proposed indices not only to codify relevant biochemical information related to the structural classes of proteins, but also to yield suitable interpretability. It is anticipated that the current method will benefit the prediction of other protein attributes or functions. PMID:25843214

  20. Systems Biological Approach of Molecular Descriptors Connectivity: Optimal Descriptors for Oral Bioavailability Prediction

    PubMed Central

    Ahmed, Shiek S. S. J.; Ramakrishnan, V.

    2012-01-01

    bioavailability, with a predictive accuracy of more than 71%. Overall, the method captures the fundamental molecular descriptors, that can be used as an entity to facilitate prediction of oral bioavailability. PMID:22815781

  1. QSPR study on refractive indices of solvents commonly used in polymer chemistry using flexible molecular descriptors.

    PubMed

    Fioressi, S E; Bacelo, D E; Cui, W P; Saavedra, L M; Duchowicz, P R

    2015-06-01

    A predictive Quantitative Structure-Property Relationship (QSPR) for the refractive indices of 370 solvents commonly used in the processing and analysis of polymers is presented, using as chemical information descriptors the simplified molecular input line entry system (SMILES). The model employs a flexible molecular descriptor and a conformation-independent approach. Various well-known techniques, such as the use of an external test set of compounds, the cross-validation method, and Y-randomization were used to test and validate the established equations. The predicted values were finally compared with published results from the literature. The simple model proposed correlates the refractive index values with good accuracy, and it is not dependent on 3D-molecular geometries. PMID:26223885

  2. Segmentation of Brain MRI Using SOM-FCM-Based Method and 3D Statistical Descriptors

    PubMed Central

    Ortiz, Andrés; Palacio, Antonio A.; Górriz, Juan M.; Ramírez, Javier; Salas-González, Diego

    2013-01-01

    Current medical imaging systems provide excellent spatial resolution, high tissue contrast, and up to 65535 intensity levels. Thus, image processing techniques which aim to exploit the information contained in the images are necessary for using these images in computer-aided diagnosis (CAD) systems. Image segmentation may be defined as the process of parcelling the image to delimit different neuroanatomical tissues present on the brain. In this paper we propose a segmentation technique using 3D statistical features extracted from the volume image. In addition, the presented method is based on unsupervised vector quantization and fuzzy clustering techniques and does not use any a priori information. The resulting fuzzy segmentation method addresses the problem of partial volume effect (PVE) and has been assessed using real brain images from the Internet Brain Image Repository (IBSR). PMID:23762192

  3. Molecular surface point environments for virtual screening and the elucidation of binding patterns (MOLPRINT 3D).

    PubMed

    Bender, Andreas; Mussa, Hamse Y; Gill, Gurprem S; Glen, Robert C

    2004-12-16

    A novel method (MOLPRINT 3D) for virtual screening and the elucidation of ligand-receptor binding patterns is introduced that is based on environments of molecular surface points. The descriptor uses points relative to the molecular coordinates, thus it is translationally and rotationally invariant. Due to its local nature, conformational variations cause only minor changes in the descriptor. If surface point environments are combined with the Tanimoto coefficient and applied to virtual screening, they achieve retrieval rates comparable to that of two-dimensional (2D) fingerprints. The identification of active structures with minimal 2D similarity ("scaffold hopping") is facilitated. In combination with information-gain-based feature selection and a naive Bayesian classifier, information from multiple molecules can be combined and classification performance can be improved. Selected features are consistent with experimentally determined binding patterns. Examples are given for angiotensin-converting enzyme inhibitors, 3-hydroxy-3-methylglutaryl-coenzyme A reductase inhibitors, and thromboxane A2 antagonists. PMID:15588092

  4. Scaffold hopping through virtual screening using 2D and 3D similarity descriptors: ranking, voting, and consensus scoring.

    PubMed

    Zhang, Qiang; Muegge, Ingo

    2006-03-01

    The ability to find novel bioactive scaffolds in compound similarity-based virtual screening experiments has been studied comparing Tanimoto-based, ranking-based, voting, and consensus scoring protocols. Ligand sets for seven well-known drug targets (CDK2, COX2, estrogen receptor, neuraminidase, HIV-1 protease, p38 MAP kinase, thrombin) have been assembled such that each ligand represents its own unique chemotype, thus ensuring that each similarity recognition event between ligands constitutes a scaffold hopping event. In a series of virtual screening studies involving 9969 MDDR compounds as negative controls it has been found that atom pair descriptors and 3D pharmacophore fingerprints combined with ranking, voting, and consensus scoring strategies perform well in finding novel bioactive scaffolds. In addition, often superior performance has been observed for similarity-based virtual screening compared to structure-based methods. This finding suggests that information about a target obtained from known bioactive ligands is as valuable as knowledge of the target structures for identifying novel bioactive scaffolds through virtual screening. PMID:16509572

  5. Lattice enumeration for inverse molecular design using the signature descriptor.

    PubMed

    Martin, Shawn

    2012-07-23

    We describe an inverse quantitative structure-activity relationship (QSAR) framework developed for the design of molecular structures with desired properties. This framework uses chemical fragments encoded with a molecular descriptor known as a signature. It solves a system of linear constrained Diophantine equations to reorganize the fragments into novel molecular structures. The method has been previously applied to problems in drug and materials design but has inherent computational limitations due to the necessity of solving the Diophantine constraints. We propose a new approach to overcome these limitations using the Fincke-Pohst algorithm for lattice enumeration. We benchmark the new approach against previous results on LFA-1/ICAM-1 inhibitory peptides, linear homopolymers, and hydrofluoroether foam blowing agents. Software implementing the new approach is available at www.cs.otago.ac.nz/homepages/smartin. PMID:22657105

  6. Improving B3LYP heats of formation with three-dimensional molecular descriptors.

    PubMed

    Zhou, Yuwei; Wu, Jianming; Xu, Xin

    2016-05-15

    In the present work, we propose the X3D method that extends the B3LYP method by correcting its errors on heats of formation of hydrocarbons (HCs) with three-dimensional (3D) molecular descriptors. Inspired by the widely used Wiener index, these 3D descriptors are developed to improve over the original B3LYP method for a better description of atom-atom, atom-bond and bond-bond interactions. On top of a training set of only 45 species, the X3D method is validated against various sets of different chemistry, displaying an overall near chemical accuracy. In particular, X3D improves over B3LYP, reducing its mean absolute errors from 28.4 to 0.3 kcal/mol for (Set 1) 21 n-alkanes up to n-C32 H66 , from 19.3 to 0.6 kcal/mol for (Set 2) n-C7 H16 and its branched isomers, from 29.5 to 1.6 kcal/mol for (Set 3) 36 polycyclic saturated HCs, from 8.6 to 1.1 kcal/mol for (Set 4) 41 C6 H8 isomers of rings, alkenes, alkynes, and cumulenes, from 20.3 to 0.6 kcal/mol for (Set 5) 41 benzene-based compounds, and 8.1 to 1.3 kcal/mol for (Set 6) 66 radicals, etc. Comparisons with the G4 results are also presented. © 2016 Wiley Periodicals, Inc. PMID:26887921

  7. Heuman indices of hydrophobicity of bile acids and their comparison with a newly developed and conventional molecular descriptors.

    PubMed

    Poša, Mihalj

    2014-02-01

    Bile salts (BSs), in addition to their physiological role in the digestion of lipids in vertebrates, are also of significant importance in biomedical investigations. For predicting biological-pharmacological activity and physico-chemical properties of BSs it is important to develop such molecular descriptors that adequately describe the structural characteristics of the steroid skeleton. The present study encompassed the following bile acids (BAs): cholic, chenodeoxycholic, deoxycholic, hyodeoxycholic, ursodeoxycholic, hyocholic, and ursocholic acid, as well as oxo derivatives of certain BAs. For all of them, Heuman hydrophobicity indices (HI(BA)) (RP-HPLC parameters) were determined, and a detailed conformational analysis of the steroid skeleton showed that HI(BA) has the discrimination power for BAs based on the size of the hydrophobic surface on the β side and the lateral L7 and L12 sides of the steroid skeleton. Also, HI(BA) discerns the regiochemical characteristics of OH and oxo groups. Based on a survey of the structural factors of the steroid skeleton that influence the HI(BA) values of the tested BAs, we constructed a new molecular descriptor, CHIBA, with the characteristics of 2D and 3D topological descriptors. In respect of the structure of the steroid skeleton, the descriptor CHIBA behaves as a reversed-phase chromatographic descriptor of BAs. PMID:24076126

  8. Gesture Interaction Browser-Based 3D Molecular Viewer.

    PubMed

    Virag, Ioan; Stoicu-Tivadar, Lăcrămioara; Crişan-Vida, Mihaela

    2016-01-01

    The paper presents an open source system that allows the user to interact with a 3D molecular viewer using associated hand gestures for rotating, scaling and panning the rendered model. The novelty of this approach is that the entire application is browser-based and doesn't require installation of third party plug-ins or additional software components in order to visualize the supported chemical file formats. This kind of solution is suitable for instruction of users in less IT oriented environments, like medicine or chemistry. For rendering various molecular geometries our team used GLmol (a molecular viewer written in JavaScript). The interaction with the 3D models is made with Leap Motion controller that allows real-time tracking of the user's hand gestures. The first results confirmed that the resulting application leads to a better way of understanding various types of translational bioinformatics related problems in both biomedical research and education. PMID:27350455

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

    PubMed

    Baskin, Igor I; Zhokhova, Nelly I

    2013-05-01

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

  10. 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

  11. 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. PMID:25825778

  12. 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.

  13. A rotation-translation invariant molecular descriptor of partial charges and its use in ligand-based virtual screening

    PubMed Central

    2014-01-01

    Background Measures of similarity for chemical molecules have been developed since the dawn of chemoinformatics. Molecular similarity has been measured by a variety of methods including molecular descriptor based similarity, common molecular fragments, graph matching and 3D methods such as shape matching. Similarity measures are widespread in practice and have proven to be useful in drug discovery. Because of our interest in electrostatics and high throughput ligand-based virtual screening, we sought to exploit the information contained in atomic coordinates and partial charges of a molecule. Results A new molecular descriptor based on partial charges is proposed. It uses the autocorrelation function and linear binning to encode all atoms of a molecule into two rotation-translation invariant vectors. Combined with a scoring function, the descriptor allows to rank-order a database of compounds versus a query molecule. The proposed implementation is called ACPC (AutoCorrelation of Partial Charges) and released in open source. Extensive retrospective ligand-based virtual screening experiments were performed and other methods were compared with in order to validate the method and associated protocol. Conclusions While it is a simple method, it performed remarkably well in experiments. At an average speed of 1649 molecules per second, it reached an average median area under the curve of 0.81 on 40 different targets; hence validating the proposed protocol and implementation. PMID:24887178

  14. Collision cross section prediction of deprotonated phenolics in a travelling-wave ion mobility spectrometer using molecular descriptors and chemometrics.

    PubMed

    Gonzales, Gerard Bryan; Smagghe, Guy; Coelus, Sofie; Adriaenssens, Dieter; De Winter, Karel; Desmet, Tom; Raes, Katleen; Van Camp, John

    2016-06-14

    The combination of ion mobility and mass spectrometry (MS) affords significant improvements over conventional MS/MS, especially in the characterization of isomeric metabolites due to the differences in their collision cross sections (CCS). Experimentally obtained CCS values are typically matched with theoretical CCS values from Trajectory Method (TM) and/or Projection Approximation (PA) calculations. In this paper, predictive models for CCS of deprotonated phenolics were developed using molecular descriptors and chemometric tools, stepwise multiple linear regression (SMLR), principal components regression (PCR), and partial least squares regression (PLS). A total of 102 molecular descriptors were generated and reduced to 28 after employing a feature selection tool, composed of mass, topological descriptors, Jurs descriptors and shadow indices. Therefore, the generated models considered the effects of mass, 3D conformation and partial charge distribution on CCS, which are the main parameters for either TM or PA (only 3D conformation) calculations. All three techniques yielded highly predictive models for both the training (R(2)SMLR = 0.9911; R(2)PCR = 0.9917; R(2)PLS = 0.9918) and validation datasets (R(2)SMLR = 0.9489; R(2)PCR = 0.9761; R(2)PLS = 0.9760). Also, the high cross validated R(2) values indicate that the generated models are robust and highly predictive (Q(2)SMLR = 0.9859; Q(2)PCR = 0.9748; Q(2)PLS = 0.9760). The predictions were also very comparable to the results from TM calculations using modified mobcal (N2). Most importantly, this method offered a rapid (<10 min) alternative to TM calculations without compromising predictive ability. These methods could therefore be used in routine analysis and could be easily integrated to metabolite identification platforms. PMID:27181646

  15. Local plate/rod descriptors of 3D trabecular bone micro-CT images from medial axis topologic analysis

    SciTech Connect

    Peyrin, Francoise; Attali, Dominique; Chappard, Christine; Benhamou, Claude Laurent

    2010-08-15

    Purpose: Trabecular bone microarchitecture is made of a complex network of plate and rod structures evolving with age and disease. The purpose of this article is to propose a new 3D local analysis method for the quantitative assessment of parameters related to the geometry of trabecular bone microarchitecture. Methods: The method is based on the topologic classification of the medial axis of the 3D image into branches, rods, and plates. Thanks to the reversibility of the medial axis, the classification is next extended to the whole 3D image. Finally, the percentages of rods and plates as well as their mean thicknesses are calculated. The method was applied both to simulated test images and 3D micro-CT images of human trabecular bone. Results: The classification of simulated phantoms made of plates and rods shows that the maximum error in the quantitative percentages of plate and rods is less than 6% and smaller than with the structure model index (SMI). Micro-CT images of human femoral bone taken in osteoporosis and early or advanced osteoarthritis were analyzed. Despite the large physiological variability, the present method avoids the underestimation of rods observed with other local methods. The relative percentages of rods and plates were not significantly different between osteoarthritis and osteoporotic groups, whereas their absolute percentages were in relation to an increase of rod and plate thicknesses in advanced osteoarthritis with also higher relative and absolute number of nodes. Conclusions: The proposed method is model-independent, robust to surface irregularities, and enables geometrical characterization of not only skeletal structures but entire 3D images. Its application provided more accurate results than the standard SMI on simple simulated phantoms, but the discrepancy observed on the advanced osteoarthritis group raises questions that will require further investigations. The systematic use of such a local method in the characterization of

  16. How diverse are diversity assessment methods? A comparative analysis and benchmarking of molecular descriptor space.

    PubMed

    Koutsoukas, Alexios; Paricharak, Shardul; Galloway, Warren R J D; Spring, David R; Ijzerman, Adriaan P; Glen, Robert C; Marcus, David; Bender, Andreas

    2014-01-27

    Chemical diversity is a widely applied approach to select structurally diverse subsets of molecules, often with the objective of maximizing the number of hits in biological screening. While many methods exist in the area, few systematic comparisons using current descriptors in particular with the objective of assessing diversity in bioactivity space have been published, and this shortage is what the current study is aiming to address. In this work, 13 widely used molecular descriptors were compared, including fingerprint-based descriptors (ECFP4, FCFP4, MACCS keys), pharmacophore-based descriptors (TAT, TAD, TGT, TGD, GpiDAPH3), shape-based descriptors (rapid overlay of chemical structures (ROCS) and principal moments of inertia (PMI)), a connectivity-matrix-based descriptor (BCUT), physicochemical-property-based descriptors (prop2D), and a more recently introduced molecular descriptor type (namely, "Bayes Affinity Fingerprints"). We assessed both the similar behavior of the descriptors in assessing the diversity of chemical libraries, and their ability to select compounds from libraries that are diverse in bioactivity space, which is a property of much practical relevance in screening library design. This is particularly evident, given that many future targets to be screened are not known in advance, but that the library should still maximize the likelihood of containing bioactive matter also for future screening campaigns. Overall, our results showed that descriptors based on atom topology (i.e., fingerprint-based descriptors and pharmacophore-based descriptors) correlate well in rank-ordering compounds, both within and between descriptor types. On the other hand, shape-based descriptors such as ROCS and PMI showed weak correlation with the other descriptors utilized in this study, demonstrating significantly different behavior. We then applied eight of the molecular descriptors compared in this study to sample a diverse subset of sample compounds (4%) from an

  17. 'Quasi-Mixture' Descriptors for QSPR Analysis of Molecular Macroscopic Properties. The Critical Properties of Organic Compounds.

    PubMed

    Mokshyna, E; Nedostup, V I; Polishchuk, P G; Kuzmin, V E

    2014-10-01

    Rational approach towards the QSAR/QSPR modeling requires the descriptors to be computationally efficient, yet physically and chemically meaningful. On the basis of existing simplex representation of molecular structure (SiRMS) the novel 'quasi-mixture' descriptors were developed in order to accomplish the goal of characterization molecules on 2D level (i.e. without explicit generation of 3D structure and exhaustive conformational search) with account for potential intermolecular interactions. The critical properties of organic compounds were chosen as target properties for the estimation of descriptors' efficacy because of their well-known physical nature, rigorously estimated experimental errors and large quantity of experimental data. Among described properties are critical temperature, pressure and volume. Obtained models have high statistical characteristics, therefore showing the efficacy of suggested 'quasi-mixture' approach. Moreover, 'quasi-mixture' approach, as a branch of the SiRMS, allows to interpret results in terms of simple basic molecular properties. The obtained picture of influences corresponds to the accepted theoretical views. PMID:27485300

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

    PubMed Central

    Shiri, Fereshteh; Pirhadi, Somayeh; Ghasemi, Jahan B.

    2015-01-01

    Mer receptor tyrosine kinase is a promising novel cancer therapeutic target in many human cancers, because abnormal activation of Mer has been implicated in survival signaling and chemoresistance. 3D-QSAR analyses based on alignment independent descriptors were performed on a series of 81 Mer specific tyrosine kinase inhibitors. The fractional factorial design (FFD) and the enhanced replacement method (ERM) were applied and tested as variable selection algorithms for the selection of optimal subsets of molecular descriptors from a much greater pool of such regression variables. The data set was split into 65 molecules as the training set and 16 compounds as the test set. All descriptors were generated by using the GRid INdependent descriptors (GRIND) approach. After variable selection, GRIND were correlated with activity values (pIC50) by PLS regression. Of the two applied variable selection methods, ERM had a noticeable improvement on the statistical parameters of PLS model, and yielded a q2 value of 0.77, an rpred2 of 0.94, and a low RMSEP value of 0.25. The GRIND information contents influencing the affinity on Mer specific tyrosine kinase were also confirmed by docking studies. In a quantum calculation study, the energy difference between HOMO and LUMO (gap) implied the high interaction of the most active molecule in the active site of the protein. In addition, the molecular electrostatic potential energy at DFT level confirmed results obtained from the molecular docking. The identified key features obtained from the molecular modeling, enabled us to design novel kinase inhibitors. PMID:27013913

  19. 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.

  20. Understanding the comparative molecular field analysis (CoMFA) in terms of molecular quantum similarity and DFT-based reactivity descriptors.

    PubMed

    Morales-Bayuelo, Alejandro; Matute, Ricardo A; Caballero, Julio

    2015-06-01

    The three-dimensional quantitative structure-activity relationship (3D QSAR) models have many applications, although the inherent complexity to understand the results coming from 3D-QSAR arises the necessity of new insights in the interpretation of them. Hence, the quantum similarity field as well as reactivity descriptors based on the density functional theory were used in this work as a consistent approach to better understand the 3D-QSAR studies in drug design. For this purpose, the quantification of steric and electrostatic effects on a series of bicycle [4.1.0] heptane derivatives as melanin-concentrating hormone receptor 1 antagonists were performed on the basis of molecular quantum similarity measures. The maximum similarity superposition and the topo-geometrical superposition algorithms were used as molecular alignment methods to deal with the problem of relative molecular orientation in quantum similarity. In addition, a chemical reactivity analysis using global and local descriptors such as chemical hardness, softness, electrophilicity, and Fukui functions, was developed. Overall, our results suggest that the application of this methodology in drug design can be useful when the receptor is known or even unknown. PMID:26016942

  1. An invariant descriptor for conjugate forced convection-conduction cooling of 3D protruding heaters in channel flow

    NASA Astrophysics Data System (ADS)

    Antonini Alves, Thiago; Santos, Paulo H. D.; Barbur, Murilo A.

    2015-09-01

    In this research, the temperatures of threedimensional (3D) protruding heaters mounted on a conductive substrate in a horizontal rectangular channel with laminar airflow are related to the independent power dissipation in each heater by using a matrix G + with invariant coefficients, which are dimensionless. These coefficients are defined in this study as the conjugate influence coefficients ( g +) caused by the forced convection- conduction nature of the heaters' cooling process. The temperature increase of each heater in the channel is quantified to clearly identify the contributions attributed to the self-heating and power dissipation in the other heaters (both upstream and downstream). The conjugate coefficients are invariant with the heat generation rate in the array of heaters when assuming a defined geometry, invariable fluid and flow rate, and constant substrate and heater conductivities. The results are numerically obtained by considering three 3D protruding heaters on a twodimensional (2D) array by ANSYS/Fluent™ 15.0 software. The conservation equations are solved by a coupled procedure within a single calculation domain comprising of solid and fluid regions and by considering a steady state laminar airflow with constant properties. Some examples are shown, indicating the effects of substrate thermal conductivity and Reynolds number on conjugate influence coefficients.

  2. Molecular descriptors that influence the amount of drugs transfer into human breast milk.

    PubMed

    Agatonovic-Kustrin, S; Ling, L H; Tham, S Y; Alany, R G

    2002-06-20

    Most drugs are excreted into breast milk to some extent and are bioavailable to the infant. The ability to predict the approximate amount of drug that might be present in milk from the drug structure would be very useful in the clinical setting. The aim of this research was to simplify and upgrade the previously developed model for prediction of the milk to plasma (M/P) concentration ratio, given only the molecular structure of the drug. The set of 123 drug compounds, with experimentally derived M/P values taken from the literature, was used to develop, test and validate a predictive model. Each compound was encoded with 71 calculated molecular structure descriptors, including constitutional descriptors, topological descriptors, molecular connectivity, geometrical descriptors, quantum chemical descriptors, physicochemical descriptors and liquid properties. Genetic algorithm was used to select a subset of the descriptors that best describe the drug transfer into breast milk and artificial neural network (ANN) to correlate selected descriptors with the M/P ratio and develop a QSAR. The averaged literature M/P values were used as the ANN's output and calculated molecular descriptors as the inputs. A nine-descriptor nonlinear computational neural network model has been developed for the estimation of M/P ratio values for a data set of 123 drugs. The model included the percent of oxygen, parachor, density, highest occupied molecular orbital energy (HOMO), topological indices (chiV2, chi2 and chi1) and shape indices (kappa3, kappa2), as the inputs had four hidden neurons and one output neuron. The QSPR that was developed indicates that molecular size (parachor, density) shape (topological shape indices, molecular connectivity indices) and electronic properties (HOMO) are the most important for drug transfer into breast milk. Unlike previously reported models, the QSPR model described here does not require experimentally derived parameters and could potentially provide a

  3. A new graph-based molecular descriptor using the canonical representation of the molecule.

    PubMed

    Hentabli, Hamza; Saeed, Faisal; Abdo, Ammar; Salim, Naomie

    2014-01-01

    Molecular similarity is a pervasive concept in drug design. The basic idea underlying molecular similarity is the similar property principle, which states that structurally similar molecules will exhibit similar physicochemical and biological properties. In this paper, a new graph-based molecular descriptor (GBMD) is introduced. The GBMD is a new method of obtaining a rough description of 2D molecular structure in textual form based on the canonical representations of the molecule outline shape and it allows rigorous structure specification using small and natural grammars. Simulated virtual screening experiments with the MDDR database show clearly the superiority of the graph-based descriptor compared to many standard descriptors (ALOGP, MACCS, EPFP4, CDKFP, PCFP, and SMILE) using the Tanimoto coefficient (TAN) and the basic local alignment search tool (BLAST) when searches were carried. PMID:25140330

  4. 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…

  5. Multi-Server Approach for High-Throughput Molecular Descriptors Calculation based on Multi-Linear Algebraic Maps.

    PubMed

    García-Jacas, César R; Aguilera-Mendoza, Longendri; González-Pérez, Reisel; Marrero-Ponce, Yovani; Acevedo-Martínez, Liesner; Barigye, Stephen J; Avdeenko, Tatiana

    2015-01-01

    The present report introduces a novel module of the QuBiLS-MIDAS software for the distributed computation of the 3D Multi-Linear algebraic molecular indices. The main motivation for developing this module is to deal with the computational complexity experienced during the calculation of the descriptors over large datasets. To accomplish this task, a multi-server computing platform named T-arenal was developed, which is suited for institutions with many workstations interconnected through a local network and without resources particularly destined for computation tasks. This new system was deployed in 337 workstations and it was perfectly integrated with the QuBiLS-MIDAS software. To illustrate the usability of the T-arenal platform, performance tests over a dataset comprised of 15 000 compounds are carried out, yielding a 52 and 60 fold reduction in the sequential processing time for the 2-Linear and 3-Linear indices, respectively. Therefore, it can be stated that the T-arenal based distribution of computation tasks constitutes a suitable strategy for performing high-throughput calculations of 3D Multi-Linear descriptors over thousands of chemical structures for posterior QSAR and/or ADME-Tox studies. PMID:27490863

  6. An Infrastructure to Mine Molecular Descriptors for Ligand Selection on Virtual Screening

    PubMed Central

    Seus, Vinicius Rosa; Perazzo, Giovanni Xavier; Winck, Ana T.; Werhli, Adriano V.; Machado, Karina S.

    2014-01-01

    The receptor-ligand interaction evaluation is one important step in rational drug design. The databases that provide the structures of the ligands are growing on a daily basis. This makes it impossible to test all the ligands for a target receptor. Hence, a ligand selection before testing the ligands is needed. One possible approach is to evaluate a set of molecular descriptors. With the aim of describing the characteristics of promising compounds for a specific receptor we introduce a data warehouse-based infrastructure to mine molecular descriptors for virtual screening (VS). We performed experiments that consider as target the receptor HIV-1 protease and different compounds for this protein. A set of 9 molecular descriptors are taken as the predictive attributes and the free energy of binding is taken as a target attribute. By applying the J48 algorithm over the data we obtain decision tree models that achieved up to 84% of accuracy. The models indicate which molecular descriptors and their respective values are relevant to influence good FEB results. Using their rules we performed ligand selection on ZINC database. Our results show important reduction in ligands selection to be applied in VS experiments; for instance, the best selection model picked only 0.21% of the total amount of drug-like ligands. PMID:24812613

  7. Relationship between molecular descriptors and the enthalpies of sublimation of natural amino acids

    NASA Astrophysics Data System (ADS)

    Badelin, V. G.; Tyunina, V. V.; Girichev, G. V.; Tyunina, E. Yu.

    2016-07-01

    A multiparameter correlation between the enthalpies of sublimation and molecular descriptors of natural amino acids is proposed, based on generalized experimental and literature data on the heat effects of sublimation. The contributions from Van der Waals interactions, hydrogen bond formation, and electrostatic effects into enthalpy of sublimation has been evaluated using regression coefficients.

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

    PubMed

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

    2016-05-15

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

  9. Prediction of enantiomeric selectivity in chromatography. Application of conformation-dependent and conformation-independent descriptors of molecular chirality.

    PubMed

    Aires-de-Sousa, João; Gasteiger, Johann

    2002-03-01

    In order to process molecular chirality by computational methods and to obtain predictions for properties that are influenced by chirality, a fixed-length conformation-dependent chirality code is introduced. The code consists of a set of molecular descriptors representing the chirality of a 3D molecular structure. It includes information about molecular geometry and atomic properties, and can distinguish between enantiomers, even if chirality does not result from chiral centers. The new molecular transform was applied to two datasets of chiral compounds, each of them containing pairs of enantiomers that had been separated by chiral chromatography. The elution order within each pair of isomers was predicted by means of Kohonen neural networks (NN) using the chirality codes as input. A previously described conformation-independent chirality code was also applied and the results were compared. In both applications clustering of the two classes of enantiomers (first eluted and last eluted enantiomers) could be successfully achieved by NN and accurate predictions could be obtained for independent test sets. The chirality code described here has a potential for a broad range of applications from stereoselective reactions to analytical chemistry and to the study of biological activity of chiral compounds. PMID:11885960

  10. 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. PMID:26618369

  11. 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.

  12. Alpha shapes applied to molecular shape characterization exhibit novel properties compared to established shape descriptors

    PubMed Central

    Wilson, J. Anthony; Bender, Andreas; Kaya, Taner; Clemons, Paul A.

    2011-01-01

    Despite considerable efforts, description of molecular shape is still largely an unresolved problem. Given the importance of molecular shape in the description of spatial interactions in crystals or ligand-target complexes, this is not a satisfying state. In the current work, we propose a novel application of alpha shapes to the description of the shapes of small molecules. Alpha shapes are parameterized generalizations of the convex hull. For a specific value of α, the alpha shape is the geometric dual of the space-filling model of a molecule, with the parameter α allowing description of shape in varying degrees of detail. To date, alpha shapes have been used to find macromolecular cavities and to estimate molecular surface areas and volumes. We developed a novel methodology for computing molecular shape characteristics from the alpha shape. In this work, we show that alpha-shape descriptors reveal aspects of molecular shape that are complementary to other shape descriptors, and that accord well with chemists’ intuition about shape. While our implementation of alpha-shape descriptors is not computationally trivial, we suggest that the additional shape characteristics they provide can be used to improve and complement shape-analysis methods in domains such as crystallography and ligand-target interactions. In this communication, we present a unique methodology for computing molecular shape characteristics from the alpha shape. We first describe details of the alpha-shape calculation, an outline of validation experiments performed, and a discussion of the advantages and challenges we found while implementing this approach. The results show that, relative to known shape calculations, this method provides a high degree of shape resolution with even small changes in atomic coordinates. PMID:19775113

  13. Aquifer vulnerability to pesticide pollution - Combining soil, land-use and aquifer properties with molecular descriptors

    USGS Publications Warehouse

    Worrall, F.; Kolpin, D.W.

    2004-01-01

    This study uses an extensive survey of herbicides in groundwater across the midwest United States to predict occurrences of a range of compounds across the region from a combination of their molecular properties and the properties of the catchment of a borehole. The study covers 100 boreholes and eight pesticides. For each of the boreholes its catchment the soil, land-use and aquifer properties were characterized. Discriminating boreholes where pollution occurred from those where no pollution occurred gave a model that was 74% correct with organic carbon content, percentage sand content and depth to the water table being significant properties of the borehole catchment. Molecular topological descriptors as well as Koc, solubility and half-life were used to characterize each compound included in the study. Inclusion of molecular properties makes it possible to discriminate between occurrence and non-occurrence of each compound in each well. The best-fit model combines: organic carbon content, percentage sand content and depth to the water table with molecular descriptors representing molecular size, molecular branching and functional group composition of the herbicides.

  14. Dissecting molecular descriptors into atomic contributions in density functional reactivity theory

    SciTech Connect

    Rong, Chunying; Lu, Tian; Liu, Shubin

    2014-01-14

    Density functional reactivity theory (DFRT) employs the electron density of a molecule and its related quantities such as gradient and Laplacian to describe its structure and reactivity properties. Proper descriptions at both molecular (global) and atomic (local) levels are equally important and illuminating. In this work, we make use of Bader's zero-flux partition scheme and consider atomic contributions for a few global reactivity descriptors in DFRT, including the density-based quantification of steric effect and related indices. Earlier, we proved that these quantities are intrinsically correlated for atomic and molecular systems [S. B. Liu, J. Chem. Phys. 126, 191107 (2007); ibid. 126, 244103 (2007)]. In this work, a new basin-based integration algorithm has been implemented, whose reliability and effectiveness have been extensively examined. We also investigated a list of simple hydrocarbon systems and different scenarios of bonding processes, including stretching, bending, and rotating. Interesting changing patterns for the atomic and molecular values of these quantities have been revealed for different systems. This work not only confirms the strong correlation between these global reactivity descriptors for molecular systems, as theoretically proven earlier by us, it also provides new and unexpected changing patterns for their atomic values, which can be employed to understand the origin and nature of chemical phenomena.

  15. 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. PMID:26108569

  16. DYNAMIC 3D QSAR TECHNIQUES: APPLICATIONS IN TOXICOLOGY

    EPA Science Inventory

    Two dynamic techniques recently developed to account for conformational flexibility of chemicals in 3D QSARs are presented. In addition to the impact of conformational flexibility of chemicals in 3D QSAR models, the applicability of various molecular descriptors is discussed. The...

  17. 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.

  18. Chemical and Molecular Descriptors for the Reactivity of Amines with CO{sub 2}

    SciTech Connect

    Lee, Anita S.; Kitchin, John R.

    2012-10-24

    Amine-based solvents are likely to play an important role in CO{sub 2} capture applications in the future, and the identification of amines with superior performance will facilitate their use in CO{sub 2} capture. While some improvements in performance will be achieved through process modifications, modifying the CO{sub 2} capture performance of an amine also implies in part an ability to modify the reactions between the amine and CO{sub 2} through development of new functionalized amines. We present a computational study of trends in the reactions between CO{sub 2} and functionalized amines with a focus on identifying molecular descriptors that determine trends in reactivity. We examine the formation of bicarbonate and carbamate species on three classes of functionalized amines: alkylamines, alkanolamines, and fluorinated alkylamines including primary, secondary and tertiary amines in each class. These functional groups span electron-withdrawing to donating behavior, hydrogen-bonding, extent of functionalization, and proximity effects of the functional groups. Electron withdrawing groups tend to destabilize CO{sub 2} reaction products, whereas electron-donating groups tend to stabilize CO{sub 2} reaction products. Hydrogen bonding stabilizes CO{sub 2} reaction products. Electronic structure descriptors based on electronegativity were found to describe trends in the bicarbonate formation energy. A chemical correlation was observed between the carbamate formation energy and the carbamic acid formation energy. The local softness on the reacting N in the amine was found to partially explain trends carbamic acid formation energy.

  19. A 3D universal structure based on molecular-QCA and CNT technologies

    NASA Astrophysics Data System (ADS)

    khosroshahy, Milad Bagherian; Daliri, Mahya Sam; Abdoli, Alireza; Navi, Keivan; Bagherzadeh, Nader

    2016-09-01

    This paper presents a novel method for design and implementation of three dimensional (3D) two-layer devices with 1/0 logic values. This method uses carbon nanotube (CNT) technology as well as the molecular quantum cellular automata (MQCA) technology on a graphene substrate. The most significant characteristic of the proposed design, which makes the design unique, is the capability of generating functions in 3D; the proposed method would allow implementation of the designs in a single layer which significantly impacts on reducing the chip area and also greatly facilitates the overall synthesis of the design including placement, routing and reducing the critical path length.

  20. Molecular field extrema as descriptors of biological activity: definition and validation.

    PubMed

    Cheeseright, Tim; Mackey, Mark; Rose, Sally; Vinter, Andy

    2006-01-01

    The paper describes the generation of four types of three-dimensional molecular field descriptors or 'field points' as extrema of electrostatic, steric, and hydrophobic fields. These field points are used to define the properties necessary for a molecule to bind in a characteristic way into a specified active site. The hypothesis is that compounds showing a similar field point pattern are likely to bind at the same target site regardless of structure. The methodology to test this idea is illustrated using HIV NNRTI and thrombin ligands and validated across seven other targets. From the in silico comparisons of field point overlays, the experimentally observed binding poses of these ligands in their respective sites can be reproduced from pairwise comparisons. PMID:16562997

  1. Prioritization of in silico models and molecular descriptors for the assessment of ready biodegradability.

    PubMed

    Fernández, Alberto; Rallo, Robert; Giralt, Francesc

    2015-10-01

    Ready biodegradability is a key property for evaluating the long-term effects of chemicals on the environment and human health. As such, it is used as a screening test for the assessment of persistent, bioaccumulative and toxic substances. Regulators encourage the use of non-testing methods, such as in silico models, to save money and time. A dataset of 757 chemicals was collected to assess the performance of four freely available in silico models that predict ready biodegradability. They were applied to develop a new consensus method that prioritizes the use of each individual model according to its performance on chemical subsets driven by the presence or absence of different molecular descriptors. This consensus method was capable of almost eliminating unpredictable chemicals, while the performance of combined models was substantially improved with respect to that of the individual models. PMID:26160046

  2. Prediction of substrate-enzyme-product interaction based on molecular descriptors and physicochemical properties.

    PubMed

    Niu, Bing; Huang, Guohua; Zheng, Linfeng; Wang, Xueyuan; Chen, Fuxue; Zhang, Yuhui; Huang, Tao

    2013-01-01

    It is important to correctly and efficiently predict the interaction of substrate-enzyme and to predict their product in metabolic pathway. In this work, a novel approach was introduced to encode substrate/product and enzyme molecules with molecular descriptors and physicochemical properties, respectively. Based on this encoding method, KNN was adopted to build the substrate-enzyme-product interaction network. After selecting the optimal features that are able to represent the main factors of substrate-enzyme-product interaction in our prediction, totally 160 features out of 290 features were attained which can be clustered into ten categories: elemental analysis, geometry, chemistry, amino acid composition, predicted secondary structure, hydrophobicity, polarizability, solvent accessibility, normalized van der Waals volume, and polarity. As a result, our predicting model achieved an MCC of 0.423 and an overall prediction accuracy of 89.1% for 10-fold cross-validation test. PMID:24455714

  3. 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.

  4. Informatics calibration of a molecular descriptors database to predict solid dispersion potential of small molecule organic solids.

    PubMed

    Moore, Michael D; Wildfong, Peter L D

    2011-10-14

    The use of a novel, in silico method for making an intelligent polymer selection to physically stabilize small molecule organic (SMO) solid compounds formulated as amorphous molecular solid dispersions is reported. 12 compounds (75%, w/w) were individually co-solidified with polyvinyl pyrrolidone:vinyl acetate (PVPva) copolymer by melt-quenching. Co-solidified products were analyzed intact using differential scanning calorimetry (DSC) and the pair distribution function (PDF) transform of powder X-ray diffraction (PXRD) data to assess miscibility. Molecular descriptor indices were calculated for all twelve compounds using their reported crystallographic structures. Logistic regression was used to assess correlation between molecular descriptors and amorphous molecular solid dispersion potential. The final model was challenged with three compounds. Of the 12 compounds, 6 were miscible with PVPva (i.e. successful formation) and 6 were phase separated (i.e. unsuccessful formation). 2 of the 6 unsuccessful compounds exhibited detectable phase-separation using the PDF method, where DSC indicated miscibility. Logistic regression identified 7 molecular descriptors correlated to solid dispersion potential (α=0.001). The atomic mass-weighted third-order R autocorrelation index (R3m) was the only significant descriptor to provide completely accurate predictions of dispersion potential. The three compounds used to challenge the R3m model were also successfully predicted. PMID:21756988

  5. A molecular image-directed, 3D ultrasound-guided biopsy system for the prostate

    NASA Astrophysics Data System (ADS)

    Fei, Baowei; Schuster, David M.; Master, Viraj; Akbari, Hamed; Fenster, Aaron; Nieh, Peter

    2012-02-01

    Systematic transrectal ultrasound (TRUS)-guided biopsy is the standard method for a definitive diagnosis of prostate cancer. However, this biopsy approach uses two-dimensional (2D) ultrasound images to guide biopsy and can miss up to 30% of prostate cancers. We are developing a molecular image-directed, three-dimensional (3D) ultrasound imageguided biopsy system for improved detection of prostate cancer. The system consists of a 3D mechanical localization system and software workstation for image segmentation, registration, and biopsy planning. In order to plan biopsy in a 3D prostate, we developed an automatic segmentation method based wavelet transform. In order to incorporate PET/CT images into ultrasound-guided biopsy, we developed image registration methods to fuse TRUS and PET/CT images. The segmentation method was tested in ten patients with a DICE overlap ratio of 92.4% +/- 1.1 %. The registration method has been tested in phantoms. The biopsy system was tested in prostate phantoms and 3D ultrasound images were acquired from two human patients. We are integrating the system for PET/CT directed, 3D ultrasound-guided, targeted biopsy in human patients.

  6. Morphological and Molecular Descriptors of the Developmental Cycle of Babesia divergens Parasites in Human Erythrocytes

    PubMed Central

    Rossouw, Ingrid; Maritz-Olivier, Christine; Niemand, Jandeli; van Biljon, Riette; Smit, Annel; Olivier, Nicholas A.; Birkholtz, Lyn-Marie

    2015-01-01

    Human babesiosis, especially caused by the cattle derived Babesia divergens parasite, is on the increase, resulting in renewed attentiveness to this potentially life threatening emerging zoonotic disease. The molecular mechanisms underlying the pathophysiology and intra-erythrocytic development of these parasites are poorly understood. This impedes concerted efforts aimed at the discovery of novel anti-babesiacidal agents. By applying sensitive cell biological and molecular functional genomics tools, we describe the intra-erythrocytic development cycle of B. divergens parasites from immature, mono-nucleated ring forms to bi-nucleated paired piriforms and ultimately multi-nucleated tetrads that characterizes zoonotic Babesia spp. This is further correlated for the first time to nuclear content increases during intra-erythrocytic development progression, providing insight into the part of the life cycle that occurs during human infection. High-content temporal evaluation elucidated the contribution of the different stages to life cycle progression. Moreover, molecular descriptors indicate that B. divergens parasites employ physiological adaptation to in vitro cultivation. Additionally, differential expression is observed as the parasite equilibrates its developmental stages during its life cycle. Together, this information provides the first temporal evaluation of the functional transcriptome of B. divergens parasites, information that could be useful in identifying biological processes essential to parasite survival for future anti-babesiacidal discoveries. PMID:25955414

  7. Morphological and Molecular Descriptors of the Developmental Cycle of Babesia divergens Parasites in Human Erythrocytes.

    PubMed

    Rossouw, Ingrid; Maritz-Olivier, Christine; Niemand, Jandeli; van Biljon, Riette; Smit, Annel; Olivier, Nicholas A; Birkholtz, Lyn-Marie

    2015-05-01

    Human babesiosis, especially caused by the cattle derived Babesia divergens parasite, is on the increase, resulting in renewed attentiveness to this potentially life threatening emerging zoonotic disease. The molecular mechanisms underlying the pathophysiology and intra-erythrocytic development of these parasites are poorly understood. This impedes concerted efforts aimed at the discovery of novel anti-babesiacidal agents. By applying sensitive cell biological and molecular functional genomics tools, we describe the intra-erythrocytic development cycle of B. divergens parasites from immature, mono-nucleated ring forms to bi-nucleated paired piriforms and ultimately multi-nucleated tetrads that characterizes zoonotic Babesia spp. This is further correlated for the first time to nuclear content increases during intra-erythrocytic development progression, providing insight into the part of the life cycle that occurs during human infection. High-content temporal evaluation elucidated the contribution of the different stages to life cycle progression. Moreover, molecular descriptors indicate that B. divergens parasites employ physiological adaptation to in vitro cultivation. Additionally, differential expression is observed as the parasite equilibrates its developmental stages during its life cycle. Together, this information provides the first temporal evaluation of the functional transcriptome of B. divergens parasites, information that could be useful in identifying biological processes essential to parasite survival for future anti-babesiacidal discoveries. PMID:25955414

  8. Molecular descriptor subset selection in theoretical peptide quantitative structure-retention relationship model development using nature-inspired optimization algorithms.

    PubMed

    Žuvela, Petar; Liu, J Jay; Macur, Katarzyna; Bączek, Tomasz

    2015-10-01

    In this work, performance of five nature-inspired optimization algorithms, genetic algorithm (GA), particle swarm optimization (PSO), artificial bee colony (ABC), firefly algorithm (FA), and flower pollination algorithm (FPA), was compared in molecular descriptor selection for development of quantitative structure-retention relationship (QSRR) models for 83 peptides that originate from eight model proteins. The matrix with 423 descriptors was used as input, and QSRR models based on selected descriptors were built using partial least squares (PLS), whereas root mean square error of prediction (RMSEP) was used as a fitness function for their selection. Three performance criteria, prediction accuracy, computational cost, and the number of selected descriptors, were used to evaluate the developed QSRR models. The results show that all five variable selection methods outperform interval PLS (iPLS), sparse PLS (sPLS), and the full PLS model, whereas GA is superior because of its lowest computational cost and higher accuracy (RMSEP of 5.534%) with a smaller number of variables (nine descriptors). The GA-QSRR model was validated initially through Y-randomization. In addition, it was successfully validated with an external testing set out of 102 peptides originating from Bacillus subtilis proteomes (RMSEP of 22.030%). Its applicability domain was defined, from which it was evident that the developed GA-QSRR exhibited strong robustness. All the sources of the model's error were identified, thus allowing for further application of the developed methodology in proteomics. PMID:26346190

  9. 3D-QSAR and molecular fragment replacement study on diaminopyrimidine and pyrrolotriazine ALK inhibitors

    NASA Astrophysics Data System (ADS)

    Ke, Zhipeng; Lu, Tao; Liu, Haichun; Yuan, Haoliang; Ran, Ting; Zhang, Yanmin; Yao, Sihui; Xiong, Xiao; Xu, Jinxing; Xu, Anyang; Chen, Yadong

    2014-06-01

    Over expression of anaplastic lymphoma kinase (ALK) has been found in many types of cancer, and ALK is a promising therapeutic target for the treatment of cancer. To obtain new potent inhibitors of ALK, we conducted lead optimization using 3D-QSAR modeling and molecular docking investigation of 2,4-diaminopyrimidines and 2,7-disubstituted-pyrrolo[2,1-f][1,2,4]triazine-based compounds. Three favorable 3D-QSAR models (CoMFA with q2, 0.555; r2, 0.939; CoMSIA with q2, 0.625; r2, 0.974; Topomer CoMFA with q2, 0.557; r2 0.756) have been developed to predict the biological activity of novel compounds. Topomer Search was utilized for virtual screening to obtain suitable fragments. The novel compounds generated by molecular fragment replacement (MFR) were evaluated by Topomer CoMFA prediction, Glide (docking) and further evaluated with CoMFA and CoMSIA prediction. 25 novel 2,7-disubstituted-pyrrolo[2,1-f][1,2,4]triazine derivatives as potential ALK inhibitors were finally obtained. In this paper, a combination of CoMFA, CoMSIA and Topomer CoMFA could obtain favorable 3D-QSAR models and suitable fragments for ALK inhibitors optimization. The work flow which comprised 3D-QSAR modeling, Topomer Search, MFR, molecular docking and evaluating criteria could be applied to de novo drug design and the resulted compounds initiate us to further optimize and design new potential ALK inhibitors.

  10. Classification of signaling proteins based on molecular star graph descriptors using Machine Learning models.

    PubMed

    Fernandez-Lozano, Carlos; Cuiñas, Rubén F; Seoane, José A; Fernández-Blanco, Enrique; Dorado, Julian; Munteanu, Cristian R

    2015-11-01

    Signaling proteins are an important topic in drug development due to the increased importance of finding fast, accurate and cheap methods to evaluate new molecular targets involved in specific diseases. The complexity of the protein structure hinders the direct association of the signaling activity with the molecular structure. Therefore, the proposed solution involves the use of protein star graphs for the peptide sequence information encoding into specific topological indices calculated with S2SNet tool. The Quantitative Structure-Activity Relationship classification model obtained with Machine Learning techniques is able to predict new signaling peptides. The best classification model is the first signaling prediction model, which is based on eleven descriptors and it was obtained using the Support Vector Machines-Recursive Feature Elimination (SVM-RFE) technique with the Laplacian kernel (RFE-LAP) and an AUROC of 0.961. Testing a set of 3114 proteins of unknown function from the PDB database assessed the prediction performance of the model. Important signaling pathways are presented for three UniprotIDs (34 PDBs) with a signaling prediction greater than 98.0%. PMID:26297890

  11. QSPR models based on molecular mechanics and quantum chemical calculations. 1. Construction of Boltzmann-averaged descriptors for alkanes, alcohols, diols, ethers and cyclic compounds.

    PubMed

    Dyekjaer, Jane; Rasmussen, Kjeld; Jónsdóttir, Svava

    2002-09-01

    Values for nine descriptors for QSPR (quantitative structure-property relationships) modeling of physical properties of 96 alkanes, alcohols, ethers, diols, triols and cyclic alkanes and alcohols in conjunction with the program Codessa are presented. The descriptors are Boltzmann-averaged by selection of the most relevant conformers out of a set of possible molecular conformers generated by a systematic scheme presented in this paper. Six of these descriptors are calculated with molecular mechanics and three with quantum chemical methods. Especially interesting descriptors are the relative van der Waals energies and the molecular polarizabilities, which correlate very well with boiling points. Five more simple descriptors that only depend on the molecular constitutional formula are also discussed briefly. PMID:12415333

  12. 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.

  13. Establishment of an in silico phospholipidosis prediction method using descriptors related to molecular interactions causing phospholipid-compound complex formation.

    PubMed

    Haranosono, Yu; Nemoto, Shingo; Kurata, Masaaki; Sakaki, Hideyuki

    2016-01-01

    Although phospholipidosis (PLD) often affects drug development, there is no convenient in vitro or in vivo test system for PLD detection. In this study, we developed an in silico PLD prediction method based on the PLD-inducing mechanism. We focused on phospholipid (PL)-compound complex formation, which inhibits PL degradation by phospholipase. Thus, we used some molecular interactions, such as electrostatic interactions, hydrophobic interactions, and intermolecular forces, between PL and compounds as descriptors. First, we performed descriptor screening for intermolecular force and then developed a new in silico PLD prediction using descriptors related to molecular interactions. Based on the screening, we identified molecular refraction (MR) as a descriptor of intermolecular force. It is known that ClogP and most-basic pKa can be used for PLD prediction. Thereby, we developed an in silico prediction method using ClogP, most-basic pKa, and MR, which were related to hydrophobic interactions, electrostatic interactions, and intermolecular forces. In addition, a resampling method was used to determine the cut-off values for each descriptor. We obtained good results for 77 compounds as follows: sensitivity = 95.8%, specificity = 75.9%, and concordance = 88.3%. Although there is a concern regarding false-negative compounds for pKa calculations, this predictive ability will be adequate for PLD screening. In conclusion, the mechanism-based in silico PLD prediction method provided good prediction ability, and this method will be useful for evaluating the potential of drugs to cause PLD, particularly in the early stage of drug development, because this method only requires knowledge of the chemical structure. PMID:26961617

  14. 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. PMID:25550155

  15. On phase/current components of entropy/information descriptors of molecular states

    NASA Astrophysics Data System (ADS)

    Nalewajski, Roman F.

    2014-10-01

    Quantum-generalised descriptors of the information content of electronic states in molecules are proposed, in which non-classical (current) terms complement classical (probability) functionals of the ordinary information theory. The relation between densities of the familiar classical Fisher and Shannon information/entropy measures is applied to determine their non-classical complements. The quantum supplement of the classical Shannon entropy describes the average magnitude of the phase distribution, while the current term in the Fisher measure accounts for the gradient content of the state phase function. Illustrative applications of these quantum information concepts are presented and thermodynamical analogies are commented upon. The particle-density-constrained (vertical) and -unconstrained (horizontal) equilibria in molecules and their fragments are explored and the corresponding equilibrium 'thermodynamic' phases are determined. A separation of the density (modulus) and current (phase) factors of general many-electron states is effected using the Harriman-Zumbach-Maschke construction of antisymmetric states yielding the specified electron density. The phenomenological framework in spirit of the non-equilibrium thermodynamical description is proposed. It accounts for both the density and current degrees of freedom of molecular states. The associated entropy source in the information continuity equation is derived.

  16. Molecular determinants of thyroid hormone receptor selectivity in a series of phosphonic acid derivatives: 3D-QSAR analysis and molecular docking.

    PubMed

    Wang, Fang-Fang; Yang, Wei; Shi, Yong-Hui; Le, Guo-Wei

    2015-10-01

    A mathematical study was performed on a set of phosphonic acid derivatives that are substrates for thyroid hormone receptor β (TRβ) and thyroid hormone receptor α (TRα), three-dimensional quantitative structure-activity relationship (3D-QSAR) models using comparative molecular field analysis (CoMFA) and comparative molecular similarity indices analysis (CoMSIA) methods were employed to investigate the structural requirements for this series of compounds with improved activity. Some descriptors were also employed to significantly improve the performance of the derived models. The CoMFA model for TRβ exhibited Rcv(2) of 0.612, Rpred(2) of 0.7218, whereas CoMSIA model showed Rcv(2) of 0.621, R(2)pred of 0.7358; the CoMFA model for TRα displayed Rcv(2) of 0.678, Rpred(2) of 0.6424, and the CoMSIA model had Rcv(2) of 0.671, Rpred(2) of 0.6932, which indicate that the constructed models are statistically significant. The derived contour maps further pointed out the regions where interactive fields may influence the activity. In order to validate the QSAR models and explore the origin of the selectivity at the amino acid level, molecular docking was developed, and the results indicate that Arg282, Arg320, Asn331, Gly332, Thr329 and His435 for TRβ, but Ala225, Arg228, Met259, Arg262 and His381 for TRα, respectively are important residues. The information obtained from the QSAR models can be used in the design of more potent TR agonists. PMID:26363198

  17. 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. PMID:26202430

  18. Polyribosomes Are Molecular 3D Nanoprinters That Orchestrate the Assembly of Vault Particles

    PubMed Central

    2014-01-01

    Ribosomes are molecular machines that function in polyribosome complexes to translate genetic information, guide the synthesis of polypeptides, and modulate the folding of nascent proteins. Here, we report a surprising function for polyribosomes as a result of a systematic examination of the assembly of a large ribonucleoprotein complex, the vault particle. Structural and functional evidence points to a model of vault assembly whereby the polyribosome acts like a 3D nanoprinter to direct the ordered translation and assembly of the multi-subunit vault homopolymer, a process which we refer to as polyribosome templating. Structure-based mutagenesis and cell-free in vitro expression studies further demonstrated the critical importance of the polyribosome in vault assembly. Polyribosome templating prevents chaos by ensuring efficiency and order in the production of large homopolymeric protein structures in the crowded cellular environment and might explain the origin of many polyribosome-associated molecular assemblies inside the cell. PMID:25354757

  19. 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.

  20. Molecular docking using the molecular lipophilicity potential as hydrophobic descriptor: impact on GOLD docking performance.

    PubMed

    Nurisso, Alessandra; Bravo, Juan; Carrupt, Pierre-Alain; Daina, Antoine

    2012-05-25

    GOLD is a molecular docking software widely used in drug design. In the initial steps of docking, it creates a list of hydrophobic fitting points inside protein cavities that steer the positioning of ligand hydrophobic moieties. These points are generated based on the Lennard-Jones potential between a carbon probe and each atom of the residues delimitating the binding site. To thoroughly describe hydrophobic regions in protein pockets and properly guide ligand hydrophobic moieties toward favorable areas, an in-house tool, the MLP filter, was developed and herein applied. This strategy only retains GOLD hydrophobic fitting points that match the rigorous definition of hydrophobicity given by the molecular lipophilicity potential (MLP), a molecular interaction field that relies on an atomic fragmental system based on 1-octanol/water experimental partition coefficients (log P(oct)). MLP computations in the binding sites of crystallographic protein structures revealed that a significant number of points considered hydrophobic by GOLD were actually polar according to the MLP definition of hydrophobicity. To examine the impact of this new tool, ligand-protein complexes from the Astex Diverse Set and the PDB bind core database were redocked with and without the use of the MLP filter. Reliable docking results were obtained by using the MLP filter that increased the quality of docking in nonpolar cavities and outperformed the standard GOLD docking approach. PMID:22462609

  1. Hydration Free Energy as a Molecular Descriptor in Drug Design: A Feasibility Study.

    PubMed

    Zafar, Ayesha; Reynisson, Jóhannes

    2016-05-01

    In this work the idea was investigated whether calculated hydration energy (ΔGhyd ) can be used as a molecular descriptor in defining promising regions of chemical space for drug design. Calculating ΔGhyd using the Density Solvation Model (SMD) in conjunction with the density functional theory (DFT) gave an excellent correlation with experimental values. Furthermore, calculated ΔGhyd correlates reasonably well with experimental water solubility (r(2) =0.545) and also log P (r(2) =0.530). Three compound collections were used: Known drugs (n=150), drug-like compounds (n=100) and simple organic compounds (n=140). As an approximation only molecules, which do not de/protonate at physiological pH were considered. A relatively broad distribution was seen for the known drugs with an average at -15.3 kcal/mol and a standard deviation of 7.5 kcal/mol. Interestingly, much lower averages were found for the drug-like compounds (-7.5 kcal/mol) and the simple organic compounds (-3.1 kcal/mol) with tighter distributions; 4.3 and 3.2 kcal/mol, respectively. This trend was not observed for these collections when calculated log P and log S values were used. The considerable greater exothermic ΔGhyd average for the known drugs clearly indicates in order to develop a successful drug candidate value of ΔGhyd <-5 kcal/mol or less is preferable. PMID:27492087

  2. 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

  3. Surface 3D nanostructuring by tightly focused laser pulse: simulations by Lagrangian code and molecular dynamics

    NASA Astrophysics Data System (ADS)

    Inogamov, Nail A.; Zhakhovsky, Vasily V.

    2016-02-01

    There are many important applications in which the ultrashort diffraction-limited and therefore tightly focused laser pulses irradiates metal films mounted on dielectric substrate. Here we present the detailed picture of laser peeling and 3D structure formation of the thin (relative to a depth of a heat affected zone in the bulk targets) gold films on glass substrate. The underlying physics of such diffraction-limited laser peeling was not well understood previously. Our approach is based on a physical model which takes into consideration the new calculations of the two-temperature (2T) equation of state (2T EoS) and the two-temperature transport coefficients together with the coupling parameter between electron and ion subsystems. The usage of the 2T EoS and the kinetic coefficients is required because absorption of an ultrashort pulse with duration of 10-1000 fs excites electron subsystem of metal and transfers substance into the 2T state with hot electrons (typical electron temperatures 1-3 eV) and much colder ions. It is shown that formation of submicrometer-sized 3D structures is a result of the electron-ion energy transfer, melting, and delamination of film from substrate under combined action of electron and ion pressures, capillary deceleration of the delaminated liquid metal or semiconductor, and ultrafast freezing of molten material. We found that the freezing is going in non-equilibrium regime with strongly overcooled liquid phase. In this case the Stefan approximation is non-applicable because the solidification front speed is limited by the diffusion rate of atoms in the molten material. To solve the problem we have developed the 2T Lagrangian code including all this reach physics in. We also used the high-performance combined Monte- Carlo and molecular dynamics code for simulation of surface 3D nanostructuring at later times after completion of electron-ion relaxation.

  4. Relationships between structure and binding affinity of humic substances for polycyclic aromatic hydrocarbons: Relevance of molecular descriptors

    SciTech Connect

    Perminova, I.V.; Grechishcheva, N.Y.; Petrosyan, V.S.

    1999-11-01

    Partition coefficients for the binding affinities of pyrene, fluoranthene, and anthracene to 26 different humic materials were determined by fluorescence quenching. Sources included isolated humic acids, fulvic acids, and combined humic and fulvic fractions from soil, peat, and freshwater as well as Aldrich humic acid. Each of the humic materials was characterized by elemental composition, ultraviolet absorbance at 280 nm, molecular weight, and for 19 samples, composition of main structural fragments determined by {sup 13}C solution-state NMR. The magnitude of the K{sub oc} values correlated strongly with the independent descriptors of aromaticity of humic materials, including atomic H/C ratio, absorptivity at 280 nm, and three interdependent {sup 13}C NMR descriptors (C{sub Ar{minus}H,R}, {summation}C{sub Ar}, {summation}C{sub Ar}/{summation}C{sub Alk}). Statistical comparison of humic sources grouped by the origin revealed that binding affinities were best predicted by the {sup 13}C NMR descriptors. with a slight prevalence of {summation}C{sub Ar}/{summation}C{sub Alk} ration, while molecular weight was the poorest predictor. The latter produced either direct or inverse significant correlation with the K{sub oc} values depending upon the origin and/or fractional composition of the grouped humic materials.

  5. Optically directed molecular transport and 3D isoelectric positioning of amphoteric biomolecules

    SciTech Connect

    Hafeman, Dean G.; Harkins, James B.; WitkowskiII, Charles E.; Lewis, Nathan S.; Brown, Gilbert M; Warmack, Robert J Bruce; Thundat, Thomas George

    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.

  6. 3D molecular models of whole HIV-1 virions generated with cellPACK

    PubMed Central

    Goodsell, David S.; Autin, Ludovic; Forli, Stefano; Sanner, Michel F.; Olson, Arthur J.

    2014-01-01

    As knowledge of individual biological processes grows, it becomes increasingly useful to frame new findings within their larger biological contexts in order to generate new systems-scale hypotheses. This report highlights two major iterations of a whole virus model of HIV-1, generated with the cellPACK software. cellPACK integrates structural and systems biology data with packing algorithms to assemble comprehensive 3D models of cell-scale structures in molecular detail. This report describes the biological data, modeling parameters and cellPACK methods used to specify and construct editable models for HIV-1. Anticipating that cellPACK interfaces under development will enable researchers from diverse backgrounds to critique and improve the biological models, we discuss how cellPACK can be used as a framework to unify different types of data across all scales of biology. PMID:25253262

  7. 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.

  8. Clusters, molecular layers, and 3D crystals of water on Ni(111)

    SciTech Connect

    Thürmer, Konrad; Nie, Shu; Bartelt, Norman C.; Feibelman, Peter J.

    2014-11-14

    We examined the growth and stability of ice layers on Ni(111) up to ∼7 molecular layers (ML) thick using scanning tunneling microscopy. At low coverage, films were comprised of ∼1 nm wide two-dimensional (2D) clusters. Only above ∼0.5 ML did patches of continuous 2D layers emerge, coexisting with the clusters until the first ML was complete. The structure of the continuous layer is clearly different from that of the 2D clusters. Subsequently, a second molecular layer grew on top of the first. 3D crystallites started to form only after this 2nd ML was complete. 2D clusters re-appeared when thicker films were partially evaporated, implying that these clusters represent the equilibrium configuration at low coverage. Binding energies and image simulations computed with density functional theory suggest that the 2D clusters are partially dissociated and surrounded by H adatoms. The complete 2D layer contains only intact water molecules because of the lack of favorable binding sites for H atoms. We propose molecular structures for the 2D layer that are composed of the same pentagon-heptagon binding motif and water density observed on Pt(111). The similarity of the water structures on Pt and Ni suggests a general prescription for generating low-energy configurations on close-packed metal substrates.

  9. A 3D view of the outflow in the Orion Molecular Cloud 1 (OMC-1)

    NASA Astrophysics Data System (ADS)

    Nissen, H. D.; Cunningham, N. J.; Gustafsson, M.; Bally, J.; Lemaire, J.-L.; Favre, C.; Field, D.

    2012-04-01

    Context. Stars whose mass is an order of magnitude greater than the Sun play a prominent role in the evolution of galaxies, exploding as supernovae, triggering bursts of star formation and spreading heavy elements about their host galaxies. A fundamental aspect of star formation is the creation of an outflow. The fast outflow emerging from a region associated with massive star formation in the Orion Molecular Cloud 1 (OMC-1), located behind the Orion Nebula, appears to have been set in motion by an explosive event. Aims: We study the structure and dynamics of outflows in OMC-1. We combine radial velocity and proper motion data for near-IR emission of molecular hydrogen to obtain the first 3-dimensional (3D) structure of the OMC-1 outflow. Our work illustrates a new diagnostic tool for studies of star formation that will be exploited in the near future with the advent of high spatial resolution spectro-imaging in particular with data from the Atacama Large Millimeter Array (ALMA). Methods: We used published radial and proper motion velocities obtained from the shock-excited vibrational emission in the H2 v = 1-0 S(1) line at 2.122 μm obtained with the GriF instrument on the Canada-France-Hawaii Telescope, the Apache Point Observatory, the Anglo-Australian Observatory, and the Subaru Telescope. Results: These data give the 3D velocity of ejecta yielding a 3D reconstruction of the outflows. This allows one to view the material from different vantage points in space giving considerable insight into the geometry. Our analysis indicates that the ejection occurred ≲720 years ago from a distorted ring-like structure of ~15″ (6000 AU) in diameter centered on the proposed point of close encounter of the stars BN, source I and maybe also source n. We propose a simple model involving curvature of shock trajectories in magnetic fields through which the origin of the explosion and the center defined by extrapolated proper motions of BN, I and n may be brought into spatial

  10. A generalized operational formula based on total electronic densities to obtain 3D pictures of the dual descriptor to reveal nucleophilic and electrophilic sites accurately on closed-shell molecules.

    PubMed

    Martínez-Araya, Jorge I

    2016-09-30

    By means of the conceptual density functional theory, the so-called dual descriptor (DD) has been adapted to be used in any closed-shell molecule that presents degeneracy in its frontier molecular orbitals. The latter is of paramount importance because a correct description of local reactivity will allow to predict the most favorable sites on a molecule to undergo nucleophilic or electrophilic attacks; on the contrary, an incomplete description of local reactivity might have serio us consequences, particularly for those experimental chemists that have the need of getting an insight about reactivity of chemical reagents before using them in synthesis to obtain a new compound. In the present work, the old approach based only on electronic densities of frontier molecular orbitals is replaced by the most accurate procedure that implies the use of total electronic densities thus keeping consistency with the essential principle of the DFT in which the electronic density is the fundamental variable and not the molecular orbitals. As a result of the present work, the DD will be able to properly describe local reactivities only in terms of total electronic densities. To test the proposed operational formula, 12 very common molecules were selected as the original definition of the DD was not able to describe their local reactivities properly. The ethylene molecule was additionally used to test the capability of the proposed operational formula to reveal a correct local reactivity even in absence of degeneracy in frontier molecular orbitals. © 2016 Wiley Periodicals, Inc. PMID:27443264

  11. Predictability of physicochemical properties of polychlorinated dibenzo-p-dioxins (PCDDs) based on single-molecular descriptor models.

    PubMed

    Kim, Minhee; Li, Loretta Y; Grace, John R

    2016-06-01

    Polychlorinated dibenzo-p-dioxins (PCDDs) are of global concern due to their persistence, bioaccumulation and toxicity. Although the fate of PCDDs in the environment is determined by their physical-chemical properties, such as aqueous solubility, vapor pressure, octanol/water-, air/water-, and octanol/water-partition coefficients, experimental property data on the entire set of 75 PCDD congeners are limited. The quantitative structure-property relationship (QSPR) approach is applied to predict the properties of all PCDD congeners. Experimental property data available from the literature are correlated against 16 molecular descriptors of five types. Reported and newly developed QSPR models for PCDDs are presented and reviewed. The values calculated by the best QSPRs are further adjusted to satisfy fundamental thermodynamic relationships. Although the single-descriptor models with chlorine number, molar volume, solvent accessible surface area and polarizability are based on good statistical results, these models cannot distinguish among PCDDs having the same chlorine number. The QSPR model based on the hyper-Wiener index of quantum-chemical descriptor gives useful statistical results and is able to distinguish among congeners with the same chlorine number, as well as satisfying thermodynamic relationships. The resulting consistent properties of the 75 PCDD congeners can be used for environmental modeling. PMID:26878604

  12. 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

  13. The Integration of 3-D Cell-Printing and Mesoscopic Fluorescence Molecular Tomography of Vascular Constructs within Thick Hydrogel Scaffolds

    PubMed Central

    Zhao, Lingling; Lee, Vivian K.; Yoo, Seung-Schik; Dai, Guohao; Intes, Xavier

    2012-01-01

    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 (>2~3mm). 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. PMID:22531221

  14. In silico modelling of permeation enhancement potency in Caco-2 monolayers based on molecular descriptors and random forest.

    PubMed

    Welling, Søren H; Clemmensen, Line K H; Buckley, Stephen T; Hovgaard, Lars; Brockhoff, Per B; Refsgaard, Hanne H F

    2015-08-01

    Structural traits of permeation enhancers are important determinants of their capacity to promote enhanced drug absorption. Therefore, in order to obtain a better understanding of structure-activity relationships for permeation enhancers, a Quantitative Structural Activity Relationship (QSAR) model has been developed. The random forest-QSAR model was based upon Caco-2 data for 41 surfactant-like permeation enhancers from Whitehead et al. (2008) and molecular descriptors calculated from their structure. The QSAR model was validated by two test-sets: (i) an eleven compound experimental set with Caco-2 data and (ii) nine compounds with Caco-2 data from literature. Feature contributions, a recent developed diagnostic tool, was applied to elucidate the contribution of individual molecular descriptors to the predicted potency. Feature contributions provided easy interpretable suggestions of important structural properties for potent permeation enhancers such as segregation of hydrophilic and lipophilic domains. Focusing on surfactant-like properties, it is possible to model the potency of the complex pharmaceutical excipients, permeation enhancers. For the first time, a QSAR model has been developed for permeation enhancement. The model is a valuable in silico approach for both screening of new permeation enhancers and physicochemical optimisation of surfactant enhancer systems. PMID:26004819

  15. Controlling the Adsorption of Aromatic Compounds on Pt(111) with Oxygenate Substituents: From DFT to Simple Molecular Descriptors.

    PubMed

    Réocreux, Romain; Huynh, Minh; Michel, Carine; Sautet, Philippe

    2016-06-01

    Aromatic chemistry on metallic surfaces is involved in many processes within the contexts of biomass valorization, pollutant degradation, or corrosion protection. Albeit theoretically and experimentally challenging, knowing the structure and the stability of aromatic compounds on such surfaces is essential to understand their properties. To gain insights on this topic, we performed periodic ab initio calculations on Pt(111) to determine a set of simple molecular descriptors that predict both the stability and the structure of aromatic adsorbates substituted with alkyl and alkoxy (or hydroxy) groups. While the van der Waals (vdW) interaction is controlled by the molecular weight and the deformation energy by both the nature and the relative position of the substituents to the surface, the chemical bonding can be correlated to the Hard and Soft Acids and Bases (HSAB) interaction energy. This work gives general insights on the interaction of aromatic compounds with the Pt(111) surface. PMID:27206155

  16. QuBiLS-MIDAS: a parallel free-software for molecular descriptors computation based on multilinear algebraic maps.

    PubMed

    García-Jacas, César R; Marrero-Ponce, Yovani; Acevedo-Martínez, Liesner; Barigye, Stephen J; Valdés-Martiní, José R; Contreras-Torres, Ernesto

    2014-07-01

    The present report introduces the QuBiLS-MIDAS software belonging to the ToMoCoMD-CARDD suite for the calculation of three-dimensional molecular descriptors (MDs) based on the two-linear (bilinear), three-linear, and four-linear (multilinear or N-linear) algebraic forms. Thus, it is unique software that computes these tensor-based indices. These descriptors, establish relations for two, three, and four atoms by using several (dis-)similarity metrics or multimetrics, matrix transformations, cutoffs, local calculations and aggregation operators. The theoretical background of these N-linear indices is also presented. The QuBiLS-MIDAS software was developed in the Java programming language and employs the Chemical Development Kit library for the manipulation of the chemical structures and the calculation of the atomic properties. This software is composed by a desktop user-friendly interface and an Abstract Programming Interface library. The former was created to simplify the configuration of the different options of the MDs, whereas the library was designed to allow its easy integration to other software for chemoinformatics applications. This program provides functionalities for data cleaning tasks and for batch processing of the molecular indices. In addition, it offers parallel calculation of the MDs through the use of all available processors in current computers. The studies of complexity of the main algorithms demonstrate that these were efficiently implemented with respect to their trivial implementation. Lastly, the performance tests reveal that this software has a suitable behavior when the amount of processors is increased. Therefore, the QuBiLS-MIDAS software constitutes a useful application for the computation of the molecular indices based on N-linear algebraic maps and it can be used freely to perform chemoinformatics studies. PMID:24889018

  17. GIANT: pattern analysis of molecular interactions in 3D structures of protein–small ligand complexes

    PubMed Central

    2014-01-01

    Background Interpretation of binding modes of protein–small ligand complexes from 3D structure data is essential for understanding selective ligand recognition by proteins. It is often performed by visual inspection and sometimes largely depends on a priori knowledge about typical interactions such as hydrogen bonds and π-π stacking. Because it can introduce some biases due to scientists’ subjective perspectives, more objective viewpoints considering a wide range of interactions are required. Description In this paper, we present a web server for analyzing protein–small ligand interactions on the basis of patterns of atomic contacts, or “interaction patterns” obtained from the statistical analyses of 3D structures of protein–ligand complexes in our previous study. This server can guide visual inspection by providing information about interaction patterns for each atomic contact in 3D structures. Users can visually investigate what atomic contacts in user-specified 3D structures of protein–small ligand complexes are statistically overrepresented. This server consists of two main components: “Complex Analyzer”, and “Pattern Viewer”. The former provides a 3D structure viewer with annotations of interacting amino acid residues, ligand atoms, and interacting pairs of these. In the annotations of interacting pairs, assignment to an interaction pattern of each contact and statistical preferences of the patterns are presented. The “Pattern Viewer” provides details of each interaction pattern. Users can see visual representations of probability density functions of interactions, and a list of protein–ligand complexes showing similar interactions. Conclusions Users can interactively analyze protein–small ligand binding modes with statistically determined interaction patterns rather than relying on a priori knowledge of the users, by using our new web server named GIANT that is freely available at http://giant.hgc.jp/. PMID:24423161

  18. Convergent study of Ru-ligand interactions through QTAIM, ELF, NBO molecular descriptors and TDDFT analysis of organometallic dyes

    NASA Astrophysics Data System (ADS)

    Sánchez-Coronilla, Antonio; Sánchez-Márquez, Jesús; Zorrilla, David; Martín, Elisa I.; de los Santos, Desireé M.; Navas, Javier; Fernández-Lorenzo, Concha; Alcántara, Rodrigo; Martín-Calleja, Joaquín

    2014-08-01

    We report a theoretical study of a series of Ru complexes of interest in dye-sensitised solar cells, in organic light-emitting diodes, and in the war against cancer. Other metal centres, such as Cr, Co, Ni, Rh, Pd, and Pt, have been included for comparison purposes. The metal-ligand trends in organometallic chemistry for those compounds are shown synergistically by using three molecular descriptors: quantum theory of atoms in molecules (QTAIM), electron localisation function (ELF) and second-order perturbation theory analysis of the natural bond orbital (NBO). The metal-ligand bond order is addressed through both delocalisation index (DI) of QTAIM and fluctuation index (λ) of ELF. Correlation between DI and λ for Ru-N bond in those complexes is introduced for the first time. Electron transfer and stability was also assessed by the second-order perturbation theory analysis of the NBO. Electron transfer from the lone pair NBO of the ligands toward the antibonding lone pair NBO of the metal plays a relevant role in stabilising the complexes, providing useful insights into understanding the effect of the 'expanded ligand' principle in supramolecular chemistry. Finally, absorption wavelengths associated to the metal-to-ligand charge transfer transitions and the highest occupied molecular orbital (HOMO)--lowest unoccupied molecular orbital (LUMO) characteristics were studied by time-dependent density functional theory.

  19. Molecular basis for cytokine biomarkers of complex 3D microtissue physiology in vitro.

    PubMed

    Asthana, Amish; Kisaalita, William S

    2016-06-01

    'Physiologically more-relevant' claims are readily made for cells cultured on any surface or in a scaffold that provides loosely defined 3D geometry. A set of tools to measure culture '3D-ness' more accurately are needed. Such tools should find applications in fields ranging from high-throughput identification of substrates for tissue engineering and regenerative medicine to cell-based screening of drug candidates. Until now, these fields have not provided a consensus for the most promising place to initiate the search. Here, we review recent advances in transcriptomic, proteomic, inflammation and oncology-related pathways, as well as functional studies that strongly point to cytokines as the most likely compounds to form the missing consensus. PMID:27021792

  20. Low-Cost 3D Printers Enable High-Quality and Automated Sample Preparation and Molecular Detection

    PubMed Central

    Chan, Kamfai; Coen, Mauricio; Hardick, Justin; Gaydos, Charlotte A.; Wong, Kah-Yat; Smith, Clayton; Wilson, Scott A.; Vayugundla, Siva Praneeth; Wong, Season

    2016-01-01

    Most molecular diagnostic assays require upfront sample preparation steps to isolate the target’s nucleic acids, followed by its amplification and detection using various nucleic acid amplification techniques. Because molecular diagnostic methods are generally rather difficult to perform manually without highly trained users, automated and integrated systems are highly desirable but too costly for use at point-of-care or low-resource settings. Here, we showcase the development of a low-cost and rapid nucleic acid isolation and amplification platform by modifying entry-level 3D printers that cost between $400 and $750. Our modifications consisted of replacing the extruder with a tip-comb attachment that houses magnets to conduct magnetic particle-based nucleic acid extraction. We then programmed the 3D printer to conduct motions that can perform high-quality extraction protocols. Up to 12 samples can be processed simultaneously in under 13 minutes and the efficiency of nucleic acid isolation matches well against gold-standard spin-column-based extraction technology. Additionally, we used the 3D printer’s heated bed to supply heat to perform water bath-based polymerase chain reactions (PCRs). Using another attachment to hold PCR tubes, the 3D printer was programmed to automate the process of shuttling PCR tubes between water baths. By eliminating the temperature ramping needed in most commercial thermal cyclers, the run time of a 35-cycle PCR protocol was shortened by 33%. This article demonstrates that for applications in resource-limited settings, expensive nucleic acid extraction devices and thermal cyclers that are used in many central laboratories can be potentially replaced by a device modified from inexpensive entry-level 3D printers. PMID:27362424

  1. Low-Cost 3D Printers Enable High-Quality and Automated Sample Preparation and Molecular Detection.

    PubMed

    Chan, Kamfai; Coen, Mauricio; Hardick, Justin; Gaydos, Charlotte A; Wong, Kah-Yat; Smith, Clayton; Wilson, Scott A; Vayugundla, Siva Praneeth; Wong, Season

    2016-01-01

    Most molecular diagnostic assays require upfront sample preparation steps to isolate the target's nucleic acids, followed by its amplification and detection using various nucleic acid amplification techniques. Because molecular diagnostic methods are generally rather difficult to perform manually without highly trained users, automated and integrated systems are highly desirable but too costly for use at point-of-care or low-resource settings. Here, we showcase the development of a low-cost and rapid nucleic acid isolation and amplification platform by modifying entry-level 3D printers that cost between $400 and $750. Our modifications consisted of replacing the extruder with a tip-comb attachment that houses magnets to conduct magnetic particle-based nucleic acid extraction. We then programmed the 3D printer to conduct motions that can perform high-quality extraction protocols. Up to 12 samples can be processed simultaneously in under 13 minutes and the efficiency of nucleic acid isolation matches well against gold-standard spin-column-based extraction technology. Additionally, we used the 3D printer's heated bed to supply heat to perform water bath-based polymerase chain reactions (PCRs). Using another attachment to hold PCR tubes, the 3D printer was programmed to automate the process of shuttling PCR tubes between water baths. By eliminating the temperature ramping needed in most commercial thermal cyclers, the run time of a 35-cycle PCR protocol was shortened by 33%. This article demonstrates that for applications in resource-limited settings, expensive nucleic acid extraction devices and thermal cyclers that are used in many central laboratories can be potentially replaced by a device modified from inexpensive entry-level 3D printers. PMID:27362424

  2. Simulation of a complete triple turbo molecular pumping stage using direct simulation Monte Carlo in 3D

    NASA Astrophysics Data System (ADS)

    Rose, Martin

    2014-12-01

    A triple stage turbo molecular pump is simulated using the DSMC method in 3D. A 90° sector of the complete pump is simulated taking the symmetry of the pump into account. Simulations were performed for various fore line pressures in order to determine the compression ratio and the maximum pumping speed. Various features of the three dimensional flow field are discussed. Also the CPU time required to obtain the flow field is discussed. The simulations presented here are a powerful tool for the design and improvement of turbo molecular pumps.

  3. 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

  4. Modulating mechanical behaviour of 3D-printed cartilage-mimetic PCL scaffolds: influence of molecular weight and pore geometry.

    PubMed

    Olubamiji, Adeola D; Izadifar, Zohreh; Si, Jennifer L; Cooper, David M L; Eames, B Frank; Chen, Daniel X B

    2016-06-01

    Three-dimensional (3D)-printed poly(ε)-caprolactone (PCL)-based scaffolds are increasingly being explored for cartilage tissue engineering (CTE) applications. However, ensuring that the mechanical properties of these PCL-based constructs are comparable to that of articular cartilage that they are meant to regenerate is an area that has been under-explored. This paper presents the effects of PCL's molecular weight (MW) and scaffold's pore geometric configurations; strand size (SZ), strand spacing (SS), and strand orientation (SO), on mechanical properties of 3D-printed PCL scaffolds. The results illustrate that MW has significant effect on compressive moduli and yield strength of 3D-printed PCL scaffolds. Specifically, PCL with MW of 45 K was a more feasible choice for fabrication of visco-elastic, flexible and load-bearing PCL scaffolds. Furthermore, pore geometric configurations; SZ, SS, and SO, all significantly affect on tensile moduli of scaffolds. However, only SZ and SS have statistically significant effects on compressive moduli and porosity of these scaffolds. That said, inverse linear relationship was observed between porosity and mechanical properties of 3D-printed PCL scaffolds in Pearson's correlation test. Altogether, this study illustrates that modulating MW of PCL and pore geometrical configurations of the scaffolds enabled design and fabrication of PCL scaffolds with mechanical and biomimetic properties that better mimic mechanical behaviour of human articular cartilage. Thus, the modulated PCL scaffold proposed in this study is a framework that offers great potentials for CTE applications. PMID:27328736

  5. The use of density functional theory-based reactivity descriptors in molecular similarity calculations

    NASA Astrophysics Data System (ADS)

    Boon, Greet; De Proft, Frank; Langenaeker, Wilfried; Geerlings, Paul

    1998-10-01

    Molecular similarity is studied via density functional theory-based similarity indices using a numerical integration method. Complementary to the existing similarity indices, we introduce a reactivity-related similarity index based on the local softness. After a study of some test systems, a series of peptide isosteres is studied in view of their importance in pharmacology. The whole of the present work illustrates the importance of the study of molecular similarity based on both shape and reactivity.

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

    PubMed

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

    2013-10-01

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

  7. 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

  8. 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.

  9. Molecular descriptor data explain market prices of a large commercial chemical compound library

    NASA Astrophysics Data System (ADS)

    Polanski, Jaroslaw; Kucia, Urszula; Duszkiewicz, Roksana; Kurczyk, Agata; Magdziarz, Tomasz; Gasteiger, Johann

    2016-06-01

    The relationship between the structure and a property of a chemical compound is an essential concept in chemistry guiding, for example, drug design. Actually, however, we need economic considerations to fully understand the fate of drugs on the market. We are performing here for the first time the exploration of quantitative structure-economy relationships (QSER) for a large dataset of a commercial building block library of over 2.2 million chemicals. This investigation provided molecular statistics that shows that on average what we are paying for is the quantity of matter. On the other side, the influence of synthetic availability scores is also revealed. Finally, we are buying substances by looking at the molecular graphs or molecular formulas. Thus, those molecules that have a higher number of atoms look more attractive and are, on average, also more expensive. Our study shows how data binning could be used as an informative method when analyzing big data in chemistry.

  10. Molecular descriptor data explain market prices of a large commercial chemical compound library

    PubMed Central

    Polanski, Jaroslaw; Kucia, Urszula; Duszkiewicz, Roksana; Kurczyk, Agata; Magdziarz, Tomasz; Gasteiger, Johann

    2016-01-01

    The relationship between the structure and a property of a chemical compound is an essential concept in chemistry guiding, for example, drug design. Actually, however, we need economic considerations to fully understand the fate of drugs on the market. We are performing here for the first time the exploration of quantitative structure-economy relationships (QSER) for a large dataset of a commercial building block library of over 2.2 million chemicals. This investigation provided molecular statistics that shows that on average what we are paying for is the quantity of matter. On the other side, the influence of synthetic availability scores is also revealed. Finally, we are buying substances by looking at the molecular graphs or molecular formulas. Thus, those molecules that have a higher number of atoms look more attractive and are, on average, also more expensive. Our study shows how data binning could be used as an informative method when analyzing big data in chemistry. PMID:27334348

  11. Molecular descriptor data explain market prices of a large commercial chemical compound library.

    PubMed

    Polanski, Jaroslaw; Kucia, Urszula; Duszkiewicz, Roksana; Kurczyk, Agata; Magdziarz, Tomasz; Gasteiger, Johann

    2016-01-01

    The relationship between the structure and a property of a chemical compound is an essential concept in chemistry guiding, for example, drug design. Actually, however, we need economic considerations to fully understand the fate of drugs on the market. We are performing here for the first time the exploration of quantitative structure-economy relationships (QSER) for a large dataset of a commercial building block library of over 2.2 million chemicals. This investigation provided molecular statistics that shows that on average what we are paying for is the quantity of matter. On the other side, the influence of synthetic availability scores is also revealed. Finally, we are buying substances by looking at the molecular graphs or molecular formulas. Thus, those molecules that have a higher number of atoms look more attractive and are, on average, also more expensive. Our study shows how data binning could be used as an informative method when analyzing big data in chemistry. PMID:27334348

  12. From 3D to 2D: A Review of the Molecular Imprinting of Proteins

    PubMed Central

    Turner, Nicholas W.; Jeans, Christopher W.; Brain, Keith R.; Allender, Christopher J.; Hlady, Vladimir; Britt, David W.

    2008-01-01

    Molecular imprinting is a generic technology that allows for the introduction of sites of specific molecular affinity into otherwise homogeneous polymeric matrices. Commonly this technique has been shown to be effective when targeting small molecules of molecular weight <1500, while extending the technique to larger molecules such as proteins has proven difficult. A number of key inherent problems in protein imprinting have been identified, including permanent entrapment, poor mass transfer, denaturation, and heterogeneity in binding pocket affinity, which have been addressed using a variety of approaches. This review focuses on protein imprinting in its various forms, ranging from conventional bulk techniques to novel thin film and monolayer surface imprinting approaches. PMID:17137293

  13. 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

  14. Binary classification of chalcone derivatives with LDA or KNN based on their antileishmanial activity and molecular descriptors selected using the Successive Projections Algorithm feature-selection technique.

    PubMed

    Goodarzi, Mohammad; Saeys, Wouter; de Araujo, Mario Cesar Ugulino; Galvão, Roberto Kawakami Harrop; Vander Heyden, Yvan

    2014-01-23

    Chalcones are naturally occurring aromatic ketones, which consist of an α-, β-unsaturated carbonyl system joining two aryl rings. These compounds are reported to exhibit several pharmacological activities, including antiparasitic, antibacterial, antifungal, anticancer, immunomodulatory, nitric oxide inhibition and anti-inflammatory effects. In the present work, a Quantitative Structure-Activity Relationship (QSAR) study is carried out to classify chalcone derivatives with respect to their antileishmanial activity (active/inactive) on the basis of molecular descriptors. For this purpose, two techniques to select descriptors are employed, the Successive Projections Algorithm (SPA) and the Genetic Algorithm (GA). The selected descriptors are initially employed to build Linear Discriminant Analysis (LDA) models. An additional investigation is then carried out to determine whether the results can be improved by using a non-parametric classification technique (One Nearest Neighbour, 1NN). In a case study involving 100 chalcone derivatives, the 1NN models were found to provide better rates of correct classification than LDA, both in the training and test sets. The best result was achieved by a SPA-1NN model with six molecular descriptors, which provided correct classification rates of 97% and 84% for the training and test sets, respectively. PMID:24090733

  15. Chemometric Methods and Theoretical Molecular Descriptors in Predictive QSAR Modeling of the Environmental Behavior of Organic Pollutants

    NASA Astrophysics Data System (ADS)

    Gramatica, Paola

    This chapter surveys the QSAR modeling approaches (developed by the author's research group) for the validated prediction of environmental properties of organic pollutants. Various chemometric methods, based on different theoretical molecular descriptors, have been applied: explorative techniques (such as PCA for ranking, SOM for similarity analysis), modeling approaches by multiple-linear regression (MLR, in particular OLS), and classification methods (mainly k-NN, CART, CP-ANN). The focus of this review is on the main topics of environmental chemistry and ecotoxicology, related to the physico-chemical properties, the reactivity, and biological activity of chemicals of high environmental concern. Thus, the review deals with atmospheric degradation reactions of VOCs by tropospheric oxidants, persistence and long-range transport of POPs, sorption behavior of pesticides (Koc and leaching), bioconcentration, toxicity (acute aquatic toxicity, mutagenicity of PAHs, estrogen binding activity for endocrine disruptors compounds (EDCs)), and finally persistent bioaccumulative and toxic (PBT) behavior for the screening and prioritization of organic pollutants. Common to all the proposed models is the attention paid to model validation for predictive ability (not only internal, but also external for chemicals not participating in the model development) and checking of the chemical domain of applicability. Adherence to such a policy, requested also by the OECD principles, ensures the production of reliable predicted data, useful also in the new European regulation of chemicals, REACH.

  16. The signature molecular descriptor. 3. Inverse-quantitative structure-activity relationship of ICAM-1 inhibitory peptides.

    PubMed

    Churchwell, Carla J; Rintoul, Mark D; Martin, Shawn; Visco, Donald P; Kotu, Archana; Larson, Richard S; Sillerud, Laurel O; Brown, David C; Faulon, Jean-Loup

    2004-03-01

    We present a methodology for solving the inverse-quantitative structure-activity relationship (QSAR) problem using the molecular descriptor called signature. This methodology is detailed in four parts. First, we create a QSAR equation that correlates the occurrence of a signature to the activity values using a stepwise multilinear regression technique. Second, we construct constraint equations, specifically the graphicality and consistency equations, which facilitate the reconstruction of the solution compounds directly from the signatures. Third, we solve the set of constraint equations, which are both linear and Diophantine in nature. Last, we reconstruct and enumerate the solution molecules and calculate their activity values from the QSAR equation. We apply this inverse-QSAR method to a small set of LFA-1/ICAM-1 peptide inhibitors to assist in the search and design of more-potent inhibitory compounds. Many novel inhibitors were predicted, a number of which are predicted to be more potent than the strongest inhibitor in the training set. Two of the more potent inhibitors were synthesized and tested in-vivo, confirming them to be the strongest inhibiting peptides to date. Some of these compounds can be recycled to train a new QSAR and develop a more focused library of lead compounds. PMID:15177078

  17. 3d-transition metal induced enhancement of molecular hydrogen adsorption on Mg(0001) surface: An Ab-initio study

    NASA Astrophysics Data System (ADS)

    Banerjee, Paramita; Das, G. P.

    2016-05-01

    In our effort to do first principles design of suitable materials for hydrogen storage, we have explored the interaction characteristics of a hydrogen molecule with pure as well as a 3d-transition metal (TM) atom doped Mg(0001) surface using density functional theory (DFT) based approach. Doping of a 3d-TM atom by creating a vacancy on the top most layer of Mg(0001) surface, enhances the molecular hydrogen adsorption efficiency of this surface by ~ 6 times. The TM atom gains some charge from the defected site of the Mg(0001) surface, becomes anionic and adsorbs the hydrogen molecule via Anti Kubas-type interaction. The interaction energy of this H2 molecule, including van der Waals dispersion correction, turns out to be ~ 0.4 eV, which falls in the right energy window between physisorption and chemisorption. On full coverage of this 3d-TM atom doped Mg(0001) surface with hydrogen molecules, the gravimetric density of hydrogen has been estimated to be ~ 5.6 wt %, thereby satisfying the criteria set by the department of energy (DOE) for efficient hydrogen storage.

  18. Toward Measuring Galactic Dense Molecular Gas Properties and 3D Distribution with Hi-GAL

    NASA Astrophysics Data System (ADS)

    Zetterlund, Erika; Glenn, Jason; Maloney, Phil

    2016-01-01

    The Herschel Space Observatory's submillimeter dust continuum survey Hi-GAL provides a powerful new dataset for characterizing the structure of the dense interstellar medium of the Milky Way. Hi-GAL observed a 2° wide strip covering the entire 360° of the Galactic plane in broad bands centered at 70, 160, 250, 350, and 500 μm, with angular resolution ranging from 10 to 40 arcseconds. We are adapting a molecular cloud clump-finding algorithm and a distance probability density function distance-determination method developed for the Bolocam Galactic Plane Survey (BGPS) to the Hi-GAL data. Using these methods we expect to generate a database of 105 cloud clumps, derive distance information for roughly half the clumps, and derive precise distances for approximately 20% of them. With five-color photometry and distances, we will measure the cloud clump properties, such as luminosities, physical sizes, and masses, and construct a three-dimensional map of the Milky Way's dense molecular gas distribution.The cloud clump properties and the dense gas distribution will provide critical ground truths for comparison to theoretical models of molecular cloud structure formation and galaxy evolution models that seek to emulate spiral galaxies. For example, such models cannot resolve star formation and use prescriptive recipes, such as converting a fixed fraction of interstellar gas to stars at a specified interstellar medium density threshold. The models should be compared to observed dense molecular gas properties and galactic distributions.As a pilot survey to refine the clump-finding and distance measurement algorithms developed for BGPS, we have identified molecular cloud clumps in six 2° × 2° patches of the Galactic plane, including one in the inner Galaxy along the line of sight through the Molecular Ring and the termination of the Galactic bar and one toward the outer Galaxy. Distances have been derived for the inner Galaxy clumps and compared to Bolocam Galactic Plane

  19. Spatial decomposition of molecular ions within 3D atom probe reconstructions.

    PubMed

    Breen, Andrew; Moody, Michael P; Gault, Baptiste; Ceguerra, Anna V; Xie, Kelvin Y; Du, Sichao; Ringer, Simon P

    2013-09-01

    Two methods for separating the constituent atoms of molecular ions within atom probe tomography reconstructions are presented. The Gaussian Separation Method efficiently deconvolutes molecular ions containing two constituent atoms and is tested on simulated data before being applied to an experimental HSLA steel dataset containing NbN. The Delaunay Separation Method extends separation to larger complex ions and is also tested on simulated data before being applied to an experimental GaAs dataset containing many large (>3 atoms) complex ions. First nearest neighbour (1NN) distributions and images of the reconstruction before and after the separations are used to show the effect of the algorithms and their validity and practicality are also discussed. PMID:23522847

  20. Modeling Star-Forming Regions using a 3D Molecular Transport Code

    NASA Astrophysics Data System (ADS)

    Loughnane, R. M.; Redman, M. P.; Keto, E. R.

    2012-07-01

    This paper presents the 3-dimensional non-LTE radiative transfer code, MOLLIE (MOLelcular LIne Explorer), for solving molecular and atomic excitation and radiation transfer in a molecular gas and predicting emergent spectra. The code implementation makes use of the Accelerated Lambda Iteration (ALI) method of Rybicki & Hummer (1991) to solve the radiative transfer equation along rays passing through a spherical model cloud. When convergence between level populations, the radiation field, and the point separation has been obtained, the grid is ray-traced to produce images that can be readily compared to observations. The optimization technique, Fast Simulated Annealing (FSA), adopted by MOLLIE to increase the probability of arriving at a satisfactory output in a timely fashion, is briefly considered.

  1. A hydrogen bonded molecular capsule versus a 3D network of tripodal organopolysilanols.

    PubMed

    Fukawa, Marina; Sato, Takayuki; Kabe, Yoshio

    2015-10-11

    1,3,5-Triethylbenzene based tripodal trisilanols were synthesized. The X-ray crystal structures of trisilanols showed capsule formation as well as non-capsular network formation using silanol hydrogen bonds. The (1)H NMR and ESI-mass spectroscopy experiments for solution state binding supported encapsulation of the halide ions in the cavity of the molecular capsule with a C3 symmetry. PMID:26295069

  2. Methanol Oxidative Dehydrogenation on Oxide Catalysts: Molecular and Dissociative Routes and Hydrogen Addition Energies as Descriptors of Reactivity

    SciTech Connect

    Deshlahra, Prashant; Iglesia, Enrique

    2014-11-13

    The oxidative dehydrogenation (ODH) of alkanols on oxide catalysts is generally described as involving H-abstraction from alkoxy species formed via O–H dissociation. Kinetic and isotopic data cannot discern between such routes and those involving kinetically-relevant H-abstraction from undissociated alkanols. Here, we combine such experiments with theoretical estimates of activation energies and entropies to show that the latter molecular routes prevail over dissociative routes for methanol reactions on polyoxometalate (POM) clusters at all practical reaction temperatures. The stability of the late transition states that mediate H-abstraction depend predominantly on the stability of the O–H bond formed, making H-addition energies (HAE) accurate and single-valued descriptors of reactivity. Density functional theory-derived activation energies depend linearly on HAE values at each O-atom location on clusters with a range of composition (H3PMo12, H4SiMo12, H3PW12, H4PV1Mo11, and H4PV1W11); both barriers and HAE values reflect the lowest unoccupied molecular orbital energy of metal centers that accept the electron and the protonation energy of O-atoms that accept the proton involved in the H-atom transfer. Bridging O-atoms form O–H bonds that are stronger than those of terminal atoms and therefore exhibit more negative HAE values and higher ODH reactivity on all POM clusters. For each cluster composition, ODH turnover rates reflect the reactivity-averaged HAE of all accessible O-atoms, which can be evaluated for each cluster composition to provide a rigorous and accurate predictor of ODH reactivity for catalysts with known structure. These relations together with oxidation reactivity measurements can then be used to estimate HAE values and to infer plausible structures for catalysts with uncertain active site structures.

  3. 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.

  4. Notes on quantitative structure-properties relationships (QSPR) part 2: the role of the number of atoms as a molecular descriptor.

    PubMed

    Carbó-Dorca, Ramon; Gallegos Saliner, Ana

    2009-10-01

    A previous analysis performed in our laboratory about the polynomial dependency of the atomic quantum self-similarity measures on the atomic number, together with recent publications on quantitative structure-properties relationships (QSPR), based on the number of molecular atoms, published by various authors, have driven us to show here that a simplified form of the fundamental quantum QSPR (QQSPR) equation, permits to theoretically demonstrate the important, but obvious, role of the number of atoms in a molecule, as a possible molecular descriptor. A discussion of the practical use of the number of atoms in QSPR is also given at the end, which also contains a discussion on the role of Ockham's razor in descriptor simplification choices. PMID:19242962

  5. Molecular structure studies by 3D imaging of fast ion beams

    SciTech Connect

    Kanter, E.P.; Vager, Z.; Both, G.; Cooney, P.J.; Faibis, A.; Koenig, W.; Zabransky, B.J.; Zajfman, D.

    1986-01-01

    The use of the Coulomb-explosion technique combined with a radically new multi-particle detector, extremely thin film targets, and low-excitation ion source has enabled, for the first time, direct measurements of the complete stereochemistry of complex polyatomic molecular ions. We outline the methods used and present results for protonated acetylene (C/sub 2/H/sub 3//sup +/) and the methane cation (CH/sub 4//sup +/) as examples. We demonstrate the techniques by which these methods can be generalized to determine directly vibrational motions in polyatomic molecules. 24 refs., 4 figs.

  6. Relationship between reaction rate constants of organic pollutants and their molecular descriptors during Fenton oxidation and in situ formed ferric-oxyhydroxides.

    PubMed

    Jia, Lijuan; Shen, Zhemin; Su, Pingru

    2016-05-01

    Fenton oxidation is a promising water treatment method to degrade organic pollutants. In this study, 30 different organic compounds were selected and their reaction rate constants (k) were determined for the Fenton oxidation process. Gaussian09 and Material Studio software sets were used to carry out calculations and obtain values of 10 different molecular descriptors for each studied compound. Ferric-oxyhydroxide coagulation experiments were conducted to determine the coagulation percentage. Based upon the adsorption capacity, all of the investigated organic compounds were divided into two groups (Group A and Group B). The percentage adsorption of organic compounds in Group A was less than 15% (wt./wt.) and that in the Group B was higher than 15% (wt./wt.). For Group A, removal of the compounds by oxidation was the dominant process while for Group B, removal by both oxidation and coagulation (as a synergistic process) took place. Results showed that the relationship between the rate constants (k values) and the molecular descriptors of Group A was more pronounced than for Group B compounds. For the oxidation-dominated process, EHOMO and Fukui indices (f(0)x, f(-)x, f(+)x) were the most significant factors. The influence of bond order was more significant for the synergistic process of oxidation and coagulation than for the oxidation-dominated process. The influences of all other molecular descriptors on the synergistic process were weaker than on the oxidation-dominated process. PMID:27155432

  7. A molecular dynamics implementation of the 3D Mercedes-Benz water model

    NASA Astrophysics Data System (ADS)

    Hynninen, T.; Dias, C. L.; Mkrtchyan, A.; Heinonen, V.; Karttunen, M.; Foster, A. S.; Ala-Nissila, T.

    2012-02-01

    The three-dimensional Mercedes-Benz model was recently introduced to account for the structural and thermodynamic properties of water. It treats water molecules as point-like particles with four dangling bonds in tetrahedral coordination, representing H-bonds of water. Its conceptual simplicity renders the model attractive in studies where complex behaviors emerge from H-bond interactions in water, e.g., the hydrophobic effect. A molecular dynamics (MD) implementation of the model is non-trivial and we outline here the mathematical framework of its force-field. Useful routines written in modern Fortran are also provided. This open source code is free and can easily be modified to account for different physical context. The provided code allows both serial and MPI-parallelized execution. Program summaryProgram title: CASHEW (Coarse Approach Simulator for Hydrogen-bonding Effects in Water) Catalogue identifier: AEKM_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEKM_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.html No. of lines in distributed program, including test data, etc.: 20 501 No. of bytes in distributed program, including test data, etc.: 551 044 Distribution format: tar.gz Programming language: Fortran 90 Computer: Program has been tested on desktop workstations and a Cray XT4/XT5 supercomputer. Operating system: Linux, Unix, OS X Has the code been vectorized or parallelized?: The code has been parallelized using MPI. RAM: Depends on size of system, about 5 MB for 1500 molecules. Classification: 7.7 External routines: A random number generator, Mersenne Twister ( http://www.math.sci.hiroshima-u.ac.jp/m-mat/MT/VERSIONS/FORTRAN/mt95.f90), is used. A copy of the code is included in the distribution. Nature of problem: Molecular dynamics simulation of a new geometric water model. Solution method: New force-field for

  8. Optoacoustic system for 3D functional and molecular imaging in nude mice

    NASA Astrophysics Data System (ADS)

    Fronheiser, Matthew P.; Stein, Alan; Herzog, Don; Thompson, Scott; Liopo, Anton; Eghtedari, Mohammad; Motamedi, Massoud; Ermilov, Sergey; Conjusteau, Andre; Gharieb, Reda; Lacewell, Ron; Miller, Tom; Mehta, Ketan; Oraevsky, Alexander A.

    2008-02-01

    A three-dimensional laser optoacoustic imaging system was developed, which combines the advantages of optical spectroscopy and high resolution ultrasonic detection, to produce high contrast maps of optical absorbance in tissues. This system was tested in a nude mouse model of breast cancer and produced tissue images of tumors and vasculature. The imaging can utilize either optical properties of hemoglobin and oxyhemoglobin, which are the main endogenous tissue chromophores in the red and near-infrared spectral ranges, or exogenous contrast agent based on gold nanorods. Visualization of tissue molecules targeted by the contrast agent provides molecular information. Visulization of blood at multiple colors of light provides functional information on blood concentration and oxygen saturation. Optoacoustic imaging, using two or more laser illumination wavelengths, permits an assessment of the angiogenesis-related microvasculature, and thereby, an evaluation of the tumor stage and its metastatic potential. The optoacoustic imaging system was also used to generate molecular images of the malignancy-related receptors induced by the xenografts of BT474 mammary adenocarcinoma cells in nude mice. The development of the latter images was facilitated by the use of an optoacoustic contrast agent that utilizes gold nanorods conjugated to monoclonal antibody raised against HER2/neu antigens. These nanorods possess a very strong optical absorption peak that can be tuned in the near-infrared by changing their aspect ratio. The effective conversion of the optical energy into heat by the gold nanorods, followed by the thermal expansion of the surrounding water, makes these nanoparticles an effective optoacoustic contrast agent. Optical scattering methods and x-ray tomography may also benefit from the application of this contrast agent. Administration of the gold nanorod bioconjugates to mice resulted in an enhanced contrast of breast tumors relative the background of normal tissues

  9. Data mining PubChem using a support vector machine with the Signature molecular descriptor: classification of factor XIa inhibitors.

    PubMed

    Weis, Derick C; Visco, Donald P; Faulon, Jean-Loup

    2008-11-01

    The amount of high-throughput screening (HTS) data readily available has significantly increased because of the PubChem project (http://pubchem.ncbi.nlm.nih.gov/). There is considerable opportunity for data mining of small molecules for a variety of biological systems using cheminformatic tools and the resources available through PubChem. In this work, we trained a support vector machine (SVM) classifier using the Signature molecular descriptor on factor XIa inhibitor HTS data. The optimal number of Signatures was selected by implementing a feature selection algorithm of highly correlated clusters. Our method included an improvement that allowed clusters to work together for accuracy improvement, where previous methods have scored clusters on an individual basis. The resulting model had a 10-fold cross-validation accuracy of 89%, and additional validation was provided by two independent test sets. We applied the SVM to rapidly predict activity for approximately 12 million compounds also deposited in PubChem. Confidence in these predictions was assessed by considering the number of Signatures within the training set range for a given compound, defined as the overlap metric. To further evaluate compounds identified as active by the SVM, docking studies were performed using AutoDock. A focused database of compounds predicted to be active was obtained with several of the compounds appreciably dissimilar to those used in training the SVM. This focused database is suitable for further study. The data mining technique presented here is not specific to factor XIa inhibitors, and could be applied to other bioassays in PubChem where one is looking to expand the search for small molecules as chemical probes. PMID:18829357

  10. 3D mouse shape reconstruction based on phase-shifting algorithm for fluorescence molecular tomography imaging system.

    PubMed

    Zhao, Yue; Zhu, Dianwen; Baikejiang, Reheman; Li, Changqing

    2015-11-10

    This work introduces a fast, low-cost, robust method based on fringe pattern and phase shifting to obtain three-dimensional (3D) mouse surface geometry for fluorescence molecular tomography (FMT) imaging. We used two pico projector/webcam pairs to project and capture fringe patterns from different views. We first calibrated the pico projectors and the webcams to obtain their system parameters. Each pico projector/webcam pair had its own coordinate system. We used a cylindrical calibration bar to calculate the transformation matrix between these two coordinate systems. After that, the pico projectors projected nine fringe patterns with a phase-shifting step of 2π/9 onto the surface of a mouse-shaped phantom. The deformed fringe patterns were captured by the corresponding webcam respectively, and then were used to construct two phase maps, which were further converted to two 3D surfaces composed of scattered points. The two 3D point clouds were further merged into one with the transformation matrix. The surface extraction process took less than 30 seconds. Finally, we applied the Digiwarp method to warp a standard Digimouse into the measured surface. The proposed method can reconstruct the surface of a mouse-sized object with an accuracy of 0.5 mm, which we believe is sufficient to obtain a finite element mesh for FMT imaging. We performed an FMT experiment using a mouse-shaped phantom with one embedded fluorescence capillary target. With the warped finite element mesh, we successfully reconstructed the target, which validated our surface extraction approach. PMID:26560789

  11. 3D QSAR and molecular docking studies of benzimidazole derivatives as hepatitis C virus NS5B polymerase inhibitors.

    PubMed

    Patel, Pallav D; Patel, Maulik R; Kaushik-Basu, Neerja; Talele, Tanaji T

    2008-01-01

    The urgent need for novel HCV antiviral agents has provided an impetus for understanding the structural requisites of NS5B polymerase inhibitors at the molecular level. Toward this objective, comparative molecular field analysis (CoMFA) and comparative molecular similarity indices analysis (CoMSIA) of 67 HCV NS5B polymerase inhibitors were performed using two methods. First, ligand-based 3D QSAR studies were performed based on the lowest energy conformations employing the atom fit alignment method. Second, receptor-based 3D QSAR models were derived from the predicted binding conformations obtained by docking all NS5B inhibitors at the allosteric binding site of NS5B (PDB ID: 2dxs). Results generated from the ligand-based model were found superior (r2cv values of 0.630 for CoMFA and 0.668 for CoMSIA) to those obtained by the receptor-based model (r2cv values of 0.536 and 0.561 for CoMFA and CoMSIA, respectively). The predictive ability of the models was validated using a structurally diversified test set of 22 compounds that had not been included in a preliminary training set of 45 compounds. The predictive r2 values for the ligand-based CoMFA and CoMSIA models were 0.734 and 0.800, respectively, while the corresponding predictive r2 values for the receptor-based CoMFA and CoMSIA models were 0.538 and 0.639, respectively. The greater potency of the tryptophan derivatives over that of the tyrosine derivatives was interpreted based on CoMFA steric and electrostatic contour maps. The CoMSIA results revealed that for a NS5B inhibitor to have appreciable inhibitory activity it requires hydrogen bond donor and acceptor groups at the 5-position of the indole ring and an R substituent at the chiral carbon, respectively. Interpretation of the CoMFA and CoMSIA contour maps in context of the topology of the allosteric binding site of NS5B provided insight into NS5B-inhibitor interactions. Taken together, the present 3D QSAR models were found to accurately predict the HCV NS5B

  12. 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

    2016-02-01

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

  13. 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

  14. Requirements for Forming Efficient 3-D Charge Transport Pathway in Diketopyrrolopyrrole-Based Copolymers: Film Morphology vs Molecular Packing.

    PubMed

    Lee, Gang-Young; Han, A-Reum; Kim, Taewan; Lee, Hae Rang; Oh, Joon Hak; Park, Taiho

    2016-05-18

    To achieve extremely high planarity and processability simultaneously, we have newly designed and synthesized copolymers composed of donor units of 2,2'-(2,5-dialkoxy-1,4-phenylene)dithieno[3,2-b]thiophene (TT-P-TT) and acceptor units of diketopyrrolopyrrole (DPP). These copolymers consist of a highly planar backbone due to intramolecular interactions. We have systematically investigated the effects of intermolecular interactions by controlling the side chain bulkiness on the polymer thin-film morphologies, packing structures, and charge transport. The thin-film microstructures of the copolymers are found to be critically dependent upon subtle changes in the intermolecular interactions, and charge transport dynamics of the copolymer based field-effect transistors (FETs) has been investigated by in-depth structure-property relationship study. Although the size of the fibrillar structures increases as the bulkiness of the side chains in the copolymer increases, the copolymer with the smallest side chain shows remarkably high charge carrier mobility. Our findings reveal the requirement for forming efficient 3-D charge transport pathway and highlight the importance of the molecular packing and interdomain connectivity, rather than the crystalline domain size. The results obtained herein demonstrate the importance of tailoring the side chain bulkiness and provide new insights into the molecular design for high-performance polymer semiconductors. PMID:27117671

  15. Construction of 3D polymer brushes by dip-pen nanodisplacement lithography: understanding the molecular displacement for ultrafine and high-speed patterning.

    PubMed

    Chen, Chaojian; Zhou, Xuechang; Xie, Zhuang; Gao, Tingting; Zheng, Zijian

    2015-02-01

    Dip-pen nanodisplacement lithography (DNL) is a versatile scanning probe-based technique that can be employed for fabricating ultrafine 3D polymer brushes under ambient conditions. Many fundamental studies and applications require the large-area fabrication of 3D structures. However, the fabrication throughput and uniformity are still far from satisfactory. In this work, the molecular displacement mechanism of DNL is elucidated by systematically investigating the synergistic effect of z extension and contact time. The in-depth understanding of molecular displacement results in the successful achievement of ultrafine control of 3D structures and high-speed patterning at the same time. Remarkably, one can prepare arbitrary 3D polymer brushes on a large area (1.3 mm × 1.3 mm), with <5% vertical and lateral size variations, and a patterning speed as much as 200-fold faster than the current state-of-the-art. PMID:25256006

  16. Phospholipophilicity of CxHyN(+) amines: chromatographic descriptors and molecular simulations for understanding partitioning into membranes.

    PubMed

    Droge, S T J; Hermens, J L M; Rabone, J; Gutsell, S; Hodges, G

    2016-08-10

    Using immobilized artificial membrane high-performance liquid chromatography (IAM-HPLC) the sorption affinity of 70 charged amine structures to phospholipids was determined. The amines contained only 1 charged moiety and no other polar groups, the rest of the molecule being aliphatic and/or aromatic hydrocarbon groups. We systematically evaluated the influence of the amine type (1°, 2°, 3° amines and quaternary ammonium), alkyl chain branching, phenyl ring positioning, charge positioning (terminal vs. central in the molecule) on the phospholipid-water partitioning coefficient (KPLIPW). These experimental results were compared with quantum-chemistry based three-dimensional (3D) molecular simulations of the partitioning of charged amines, including the most likely solute conformers, using a hydrated phospholipid bilayer in the COSMOmic module of COSMOtherm software. Both IAM-HPLC retention data and the simulations suggest that the molecular orientation of charged amines at the location in the bilayer with the lowest calculated Gibbs free energy exerts a strong influence over the partitioning within the membrane. The most favourable position of charged amines coincides with the region where the phosphate anions in the phospholipid bilayer are most abundant. Hydrocarbon units oriented in this layer are located more towards the aqueous phase and contribute less to the overall membrane affinity than hydrocarbon units extending into the more hydrophobic core of the bilayer. COSMOmic simulations explain most of the trends between the structural differences observed in IAM-HPLC based KPLIPW. For this set of cationic structures, the mean absolute difference between COSMOmic simulations and IAM-HPLC data, accounting only for amine type corrective increments, is 0.31 log units. PMID:27118065

  17. Quantitative real-time detection of carcinoembryonic antigen (CEA) from pancreatic cyst fluid using 3-D surface molecular imprinting.

    PubMed

    Yu, Yingjie; Zhang, Qi; Buscaglia, Jonathan; Chang, Chung-Chueh; Liu, Ying; Yang, Zhenhua; Guo, Yichen; Wang, Yantian; Levon, Kalle; Rafailovich, Miriam

    2016-07-21

    In this study, a sensitive, yet robust, biosensing system with real-time electrochemical readout was developed. The biosensor system was applied to the detection of carcinoembryonic antigen (CEA), which is a common marker for many cancers such as pancreatic, breast, and colon cancer. Real time detection of CEA during a medical procedure can be used to make critical decisions regarding further surgical intervention. CEA was templated on gold surface (RMS roughness ∼3-4 nm) coated with a hydrophilic self-assembled monolayer (SAM) on the working electrode of an open circuit potentiometric network. The subsequent removal of template CEA makes the biosensor capable of CEA detection based on its specific structure and conformation. The molecular imprinting (MI) biosensor was further calibrated using the potentiometric responses in solutions with known CEA concentrations and a detection limit of 0.5 ng ml(-1) was achieved. Potentiometric sensing was then applied to pancreatic cyst fluid samples obtained from 18 patients when the cyst fluid was also evaluated using ELISA in a certified pathology laboratory. Excellent agreement was obtained between the quantitation of CEA obtained by both the ELISA and MI biosensor detection for CEA. A 3-D MI model, using the natural rms roughness of PVD gold layers, is presented to explain the high degree of sensitivity and linearity observed in those experiments. PMID:27193921

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

    PubMed

    Gao, Xiaodong; Han, Liping; Ren, Yujie

    2016-01-01

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

  19. Application of the quantum mechanical IEF/PCM-MST hydrophobic descriptors to selectivity in ligand binding.

    PubMed

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

    2016-06-01

    We have recently reported the development and validation of quantum mechanical (QM)-based hydrophobic descriptors derived from the parametrized IEF/PCM-MST continuum solvation model for 3D-QSAR studies within the framework of the Hydrophobic Pharmacophore (HyPhar) method. In this study we explore the applicability of these descriptors to the analysis of selectivity fields. To this end, we have examined a series of 88 compounds with inhibitory activities against thrombin, trypsin and factor Xa, and the HyPhar results have been compared with 3D-QSAR models reported in the literature. The quantitative models obtained by combining the electrostatic and non-electrostatic components of the octanol/water partition coefficient yield results that compare well with the predictive potential of standard CoMFA and CoMSIA techniques. The results also highlight the potential of HyPhar descriptors to discriminate the selectivity of the compounds against thrombin, trypsin, and factor Xa. Moreover, the graphical representation of the hydrophobic maps provides a direct linkage with the pattern of interactions found in crystallographic structures. Overall, the results support the usefulness of the QM/MST-based hydrophobic descriptors as a complementary approach for disclosing structure-activity relationships in drug design and for gaining insight into the molecular determinants of ligand selectivity. Graphical Abstract Quantum Mechanical continuum solvation calculations performed with the IEF/PCM-MST method are used to derived atomic hydrophobic descriptors, which are then used to discriminate the selectivity of ligands against thrombin, trypsin and factor Xa. The descriptors provide complementary view to standard 3D-QSAR analysis, leading to a more comprehensive understanding of ligand recognition. PMID:27188723

  20. Prediction of novel and selective TNF-alpha converting enzyme (TACE) inhibitors and characterization of correlative molecular descriptors by machine learning approaches.

    PubMed

    Cong, Yong; Yang, Xue-Gang; Lv, Wei; Xue, Ying

    2009-10-01

    The inhibition of TNF-alpha converting enzyme (TACE) has been explored as a feasible therapy for the treatment of rheumatoid arthritis (RA) and Crohn's disease (CD). Recently, large numbers of novel and selective TACE inhibitors have been reported. It is desirable to develop machine learning (ML) models for identifying the inhibitors of TACE in the early drug design phase and test the prediction capabilities of these ML models. This work evaluated four ML methods, support vector machine (SVM), k-nearest neighbor (k-NN), back-propagation neural network (BPNN) and C4.5 decision tree (C4.5 DT), which were trained and tested by using a diverse set of 443 TACE inhibitors and 759 non-inhibitors. A well-established feature selection method, the recursive feature elimination (RFE) method, was used to select the most appropriate descriptors for classification from a large pool of descriptors, and two evaluation methods, 5-fold cross-validation and independent evaluation, were used to assess the performances of these developed models. In this study, all these ML models have already achieved promising prediction accuracies. By using the RFE method, the prediction accuracies are further improved. In k-NN, the model gives the best prediction for TACE inhibitors (98.32%), and the SVM bears the best prediction for non-inhibitors (99.51%). Both the k-NN and SVM model give the best overall prediction accuracy (98.45%). To the best of our knowledge, the SVM model developed in this work is the first one for the classification prediction of TACE inhibitors with a broad applicability domain. Our study suggests that ML methods, particularly SVM, are potentially useful for facilitating the discovery of TACE inhibitors and for exhibiting the molecular descriptors associated with TACE inhibitors. PMID:19729328

  1. Studies of New Fused Benzazepine as Selective Dopamine D3 Receptor Antagonists Using 3D-QSAR, Molecular Docking and Molecular Dynamics

    PubMed Central

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

    2011-01-01

    In recent years, great interest has been paid to the development of compounds with high selectivity for central dopamine (DA) D3 receptors, an interesting therapeutic target in the treatment of different neurological disorders. In the present work, based on a dataset of 110 collected benzazepine (BAZ) DA D3 antagonists with diverse kinds of structures, a variety of in silico modeling approaches, including comparative molecular field analysis (CoMFA), comparative similarity indices analysis (CoMSIA), homology modeling, molecular docking and molecular dynamics (MD) were carried out to reveal the requisite 3D structural features for activity. Our results show that both the receptor-based (Q2 = 0.603, R2ncv = 0.829, R2pre = 0.690, SEE = 0.316, SEP = 0.406) and ligand-based 3D-QSAR models (Q2 = 0.506, R2ncv =0.838, R2pre = 0.794, SEE = 0.316, SEP = 0.296) are reliable with proper predictive capacity. In addition, a combined analysis between the CoMFA, CoMSIA contour maps and MD results with a homology DA receptor model shows that: (1) ring-A, position-2 and R3 substituent in ring-D are crucial in the design of antagonists with higher activity; (2) more bulky R1 substituents (at position-2 of ring-A) of antagonists may well fit in the binding pocket; (3) hydrophobicity represented by MlogP is important for building satisfactory QSAR models; (4) key amino acids of the binding pocket are CYS101, ILE105, LEU106, VAL151, PHE175, PHE184, PRO254 and ALA251. To our best knowledge, this work is the first report on 3D-QSAR modeling of the new fused BAZs as DA D3 antagonists. These results might provide information for a better understanding of the mechanism of antagonism and thus be helpful in designing new potent DA D3 antagonists. PMID:21541053

  2. Molecular cloning and 3D structure modeling of APEX1, DNA base excision repair enzyme from the Camel, Camelus dromedarius.

    PubMed

    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

  3. Sparsity-based Ankylography for Recovering 3D molecular structures from single-shot 2D scattered light intensity

    PubMed Central

    Mutzafi, Maor; Shechtman, Yoav; Eldar, Yonina C.; Cohen, Oren; Segev, Mordechai

    2015-01-01

    Deciphering the three-dimensional (3D) structure of complex molecules is of major importance, typically accomplished with X-ray crystallography. Unfortunately, many important molecules cannot be crystallized, hence their 3D structure is unknown. Ankylography presents an alternative, relying on scattering an ultrashort X-ray pulse off a single molecule before it disintegrates, measuring the far-field intensity on a two-dimensional surface, followed by computation. However, significant information is absent due to lower dimensionality of the measurements and the inability to measure the phase. Recent Ankylography experiments attracted much interest, but it was counter-argued that Ankylography is valid only for objects containing a small number of volume pixels. Here, we propose a sparsity-based approach to reconstruct the 3D structure of molecules. Sparsity is natural for Ankylography, because molecules can be represented compactly in stoichiometric basis. Utilizing sparsity, we surpass current limits on recoverable information by orders of magnitude, paving the way for deciphering the 3D structure of macromolecules. PMID:26289358

  4. 3D Cell-SELEX: Development of RNA aptamers as molecular probes for PC-3 tumor cell line.

    PubMed

    Souza, Aline G; Marangoni, Karina; Fujimura, Patrícia T; Alves, Patrícia T; Silva, Márcio J; Bastos, Victor Alexandre F; Goulart, Luiz R; Goulart, Vivian A

    2016-02-15

    Human prostate cancer (PCa) is a highly heterogeneous and multifactorial disease. Current clinical biomarkers are not sufficiently accurate, thus being unable to predict the clinical outcome. Therefore, searching for new biomarkers aiming to improve diagnosis, prognosis and therapy is still required. In this study, we performed 3D Cell-SELEX against PC-3 prostate cancer cell line, a novel strategy to select specific nucleic acid ligands against spheroid cells in 3D cell culture. This original system combines Cell-SELEX, a process that exploits the cellular structure to generate specific ligands, and 3D cell culture, an approach that mimics the tissue microenvironment in vitro. In the first round of 3D Cell-SELEX, a negative selection against RWPE-1, non-tumor cell line, was performed to subtract non-tumor specific aptamers. The supernatant was used in eight additional rounds of selection, which were performed against PC-3 cell line. After nine selection cycles, eight PC-3 specific RNA aptamers were selected and sequenced. The aptamers presented sizes between 20 and 50 nucleotides-long, with low free energy (∆G<-13.6), which contributed for their spontaneous folding and high stability. Furthermore, our results showed the aptamer A4 as a specific ligand to prostate tumor cells, with dissociation constant in the nanomolar scale. Therefore, the novel 3D Cell-SELEX procedure improved the selection of PCa cell-surface ligands and the aptamer A4 has shown potential for the identification of prostate tumor cells, suggesting the application of this molecule in further screening assays for PCa. PMID:26821206

  5. Increasing 3D Supramolecular Order by Decreasing Molecular Order. A Comparative Study of Helical Assemblies of Dendronized Nonchlorinated and Tetrachlorinated Perylene Bisimides.

    PubMed

    Partridge, Benjamin E; Leowanawat, Pawaret; Aqad, Emad; Imam, Mohammad R; Sun, Hao-Jan; Peterca, Mihai; Heiney, Paul A; Graf, Robert; Spiess, Hans W; Zeng, Xiangbing; Ungar, Goran; Percec, Virgil

    2015-04-22

    A nonplanar, twisted, and flexible tetrachlorinated perylene bisimide (Cl4PBI) was functionalized with two AB3 minidendrons containing hydrogenated or semifluorinated dodecyl groups. The hydrogenated dendron was attached to the imide groups of Cl4PBI via m = 0, 1, and 2 methylenic units, whereas the dendron containing semifluorinated groups was attached via m = 3 or a di(ethylene oxide) linker (m = 2EO). The supramolecular structures of these compounds, determined by a combination of differential scanning calorimetry, X-ray diffraction, and solid-state NMR, were compared with those of nonchlorinated planar and rigid PBI reported previously, which demonstrated the thermodynamically controlled formation of 2D periodic arrays at high temperatures and 3D arrays at low temperatures. The molecularly less ordered Cl4PBI containing hydrogenated dendrons self-organize into exclusively 3D crystalline periodic arrays under thermodynamic control for m = 0 and 2, while the more highly molecularly ordered PBI produced less stable and ordered 3D crystals and also 2D assemblies. This induction of a higher degree of 3D order in supramolecular assemblies of the less well-ordered molecular building blocks was unanticipated. The semifluorinated dendronized Cl4PBI with m = 3 formed a 2D columnar hexagonal array under kinetic control, whereas the compound with m = 2EO formed an unusual 2D honeycomb-like hexagonal phase under thermodynamic control. These Cl4PBI compounds provide a new route to stable crystalline assemblies via thermodynamic control at lower temperatures than previously obtained with PBI, thus generating 3D order in an accessible range of temperature of interest for structural analysis and for technological applications. PMID:25830346

  6. Descriptors, physical properties, and drug-likeness.

    PubMed

    Brüstle, Matthias; Beck, Bernd; Schindler, Torsten; King, William; Mitchell, Timothy; Clark, Timothy

    2002-08-01

    We have investigated techniques for distinguishing between drugs and nondrugs using a set of molecular descriptors derived from semiempirical molecular orbital (AM1) calculations. The "drug" data set of 2105 compounds was derived from the World Drug Index (WDI) using a procedure designed to select real drugs. The "nondrug" data set was the Maybridge database. We have first investigated the dimensionality of physical properties space based on a set of 26 descriptors that we have used successfully to build absorption, distribution, metabolism, and excretion-related quantitative structure-property relationship models. We discuss the general nature of the descriptors for physical property space and the ability of these descriptors to distinguish between drugs and nondrugs. The third most significant principal component of this set of descriptors serves as a useful numerical index of drug-likeness, but no others are able to distinguish between drugs and nondrugs. We have therefore extended our set of descriptors to a total of 66 and have used recursive partitioning to identify the descriptors that can distinguish between drugs and nondrugs. This procedure pointed to two of the descriptors that play an important role in the principal component found above and one more from the set of 40 extra descriptors. These three descriptors were then used to train a Kohonen artificial neural net for the entire Maybridge data set. Projecting the drug database onto the map obtained resulted in a clear distinction not only between drugs and nondrugs but also, for instance, between hormones and other drugs. Projection of 42 131 compounds from the WDI onto the Kohonen map also revealed pronounced clustering in the regions of the map assigned as druglike. PMID:12139446

  7. 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. PMID:26343829

  8. Molecular docking based virtual screening of natural compounds as potential BACE1 inhibitors: 3D QSAR pharmacophore mapping and molecular dynamics analysis.

    PubMed

    Kumar, Akhil; Roy, Sudeep; Tripathi, Shubhandra; Sharma, Ashok

    2016-01-01

    Beta-site APP cleaving enzyme1 (BACE1) catalyzes the rate determining step in the generation of Aβ peptide and is widely considered as a potential therapeutic drug target for Alzheimer's disease (AD). Active site of BACE1 contains catalytic aspartic (Asp) dyad and flap. Asp dyad cleaves the substrate amyloid precursor protein with the help of flap. Currently, there are no marketed drugs available against BACE1 and existing inhibitors are mostly pseudopeptide or synthetic derivatives. There is a need to search for a potent inhibitor with natural scaffold interacting with flap and Asp dyad. This study screens the natural database InterBioScreen, followed by three-dimensional (3D) QSAR pharmacophore modeling, mapping, in silico ADME/T predictions to find the potential BACE1 inhibitors. Further, molecular dynamics of selected inhibitors were performed to observe the dynamic structure of protein after ligand binding. All conformations and the residues of binding region were stable but the flap adopted a closed conformation after binding with the ligand. Bond oligosaccharide interacted with the flap as well as catalytic dyad via hydrogen bond throughout the simulation. This led to stabilize the flap in closed conformation and restricted the entry of substrate. Carbohydrates have been earlier used in the treatment of AD because of their low toxicity, high efficiency, good biocompatibility, and easy permeability through the blood-brain barrier. Our finding will be helpful in identify the potential leads to design novel BACE1 inhibitors for AD therapy. PMID:25707809

  9. 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

  10. Investigation of a novel molecular descriptor for the lead optimization of 4-aminoquinazolines as vascular endothelial growth factor receptor-2 inhibitors: application for quantitative structure-activity relationship analysis in lead optimization.

    PubMed

    Kawakami, Joel K; Martinez, Yannica; Sasaki, Brandi; Harris, Melissa; Kurata, Wendy E; Lau, Alan F

    2011-03-01

    We investigated the use of infrared vibrational frequency of ligands as a potential novel molecular descriptor in three different molecular target and chemical series. The vibrational energy of a ligand was approximated from the sum of infrared (IR) absorptions of each functional group within a molecule and normalized by its molecular weight (MDIR). Calculations were performed on a set of 4-aminoquinazolines with similar docking scores for the VEGFR2/KDR receptor. 4-Aminoquinazolines with MDIR values ranging 192-196 provided compounds with KDR inhibitory activity. The correlation of KDR inhibitory activity was similarly observed in a separate chemical series, the pyrazolo[1,5-a]pyrimidines. Initial exploration of this molecular descriptor supports a tool for rapid lead optimization in the 4-aminoquinazoline chemical series and a potential method for scaffold hopping in pursuit of new inhibitors. PMID:21306896

  11. Investigation of a novel molecular descriptor for the lead optimization of 4-aminoquinazolines as vascular endothelial growth factor receptor – 2 inhibitors: Application for quantitative structure activity relationship analysis in lead optimization

    PubMed Central

    Kawakami, Joel K.; Martinez, Yannica; Sasaki, Brandi; Harris, Melissa; Kurata, Wendy E.; Lau, Alan F.

    2013-01-01

    We investigated the use of infrared vibrational frequency of ligands as a potential novel molecular descriptor in three different molecular target and chemical series. The vibrational energy of a ligand was approximated from the sum of infrared (IR) absorptions of each functional group within a molecule and normalized by its molecular weight (MDIR). Calculations were performed on a set of 4-aminoquinazolines with similar docking scores for the VEGFR2/KDR receptor. 4-Aminoquinazolines with MDIR values ranging 192–196 provided compounds with KDR inhibitory activity. The correlation of KDR inhibitory activity was similarly observed in a separate chemical series, the pyrazolo[1,5-a]pyrimidines. Initial exploration of this molecular descriptor supports a tool for rapid lead optimization in the 4-aminoquinazoline chemical series and a potential method for scaffold hopping in pursuit of new inhibitors. PMID:21306896

  12. Topology dictionary for 3D video understanding.

    PubMed

    Tung, Tony; Matsuyama, Takashi

    2012-08-01

    This paper presents a novel approach that achieves 3D video understanding. 3D video consists of a stream of 3D models of subjects in motion. The acquisition of long sequences requires large storage space (2 GB for 1 min). Moreover, it is tedious to browse data sets and extract meaningful information. We propose the topology dictionary to encode and describe 3D video content. The model consists of a topology-based shape descriptor dictionary which can be generated from either extracted patterns or training sequences. The model relies on 1) topology description and classification using Reeb graphs, and 2) a Markov motion graph to represent topology change states. We show that the use of Reeb graphs as the high-level topology descriptor is relevant. It allows the dictionary to automatically model complex sequences, whereas other strategies would require prior knowledge on the shape and topology of the captured subjects. Our approach serves to encode 3D video sequences, and can be applied for content-based description and summarization of 3D video sequences. Furthermore, topology class labeling during a learning process enables the system to perform content-based event recognition. Experiments were carried out on various 3D videos. We showcase an application for 3D video progressive summarization using the topology dictionary. PMID:22745004

  13. Low temperature H2S removal with 3-D structural mesoporous molecular sieves supported ZnO from gas stream.

    PubMed

    Li, L; Sun, T H; Shu, C H; Zhang, H B

    2016-07-01

    A series of 3-dimensional (3-D) structural mesoporous silica materials, SBA-16, MCM-48 and KIT-6, was synthesized and supported with different ZnO loadings (10, 20, 30, and 40wt%) by the incipient wetness method to evaluate the performances on H2S removal at room temperature. These materials were characterized by N2 adsorption, XRD, and TEM to investigate their textural properties. All the ZnO-loaded adsorbents exhibited the H2S removal capacity of bellow 0.1 ppmv. With the best ZnO loading percentage of 30wt% on MCM-48 and KIT-6, 20wt% on SBA-16 according to the results of breakthrough test, further increasing ZnO loading caused the decrease of the adsorption capacity due to the agglomeration of ZnO. Besides, the H2S adsorption capacities of the supports materials varied in the order of KIT-6>MCM-48>SBA-16, which was influenced primarily by their pore volume and pore size. With the largest pores in these 3-D arrangement materials, KIT-6 showed the best performance of supported material for ZnO, due to its retained superior physical properties as well as large pore diameter to allow faster gas-solid interaction and huge pore volume to disperse ZnO on the surface of it. PMID:26970044

  14. Insights into mechanism of pyrido[2,3-d]pyrimidines as DYRK1A inhibitors based on molecular dynamic simulations.

    PubMed

    Li, Jiao Jiao; Tian, Yue Li; Zhai, Hong Lin; Lv, Min; Zhang, Xiao Yun

    2016-08-01

    DYRK1A is characterized by the early development and regulation of neuronal proliferation, and its over expression gives rise to neurological abnormalities. As the promising DYRK1A inhibitors, the binding mechanism between DYRK1A and pyrido[2,3-d]pyrimidines derivatives at molecular level are still veiled. In this article, it was achieved to get the structural insights into pyrido[2,3-d]pyrimidines derivatives as DYRK1A inhibitors by means of comprehensive computational approaches involving molecular docking, molecular dynamics simulation, free energy calculation, and energy decomposition analysis. The calculated energy values were highly consistent with the experimental activities. Based on the individual energy terms analysis, the van der Waals interaction was the major leading force in the DYRK1A-ligand interaction. Lys188 was the important residue that formed the hydrogen bond, which improved the inhibitory activity. Furthermore, four novel inhibitors with higher predicted activity were designed based on the obtained findings and confirmed by molecular simulations. Our study is expected to provide significant drug design strategy for the development of more promising DYRK1A inhibitors. Proteins 2016; 84:1108-1123. © 2016 Wiley Periodicals, Inc. PMID:27119584

  15. Three-dimensional distribution of the ISM in the Milky Way Galaxy. IV. 3D molecular fraction and Galactic-scale H I-to-H2 transition

    NASA Astrophysics Data System (ADS)

    Sofue, Yoshiaki; Nakanishi, Hiroyuki

    2016-08-01

    Three-dimensional (3D) distribution of the volume-density molecular fraction, defined by f_mol^ρ =ρ _H_2/(ρ _{H I}+ρ _H_2), is studied in the Milky Way Galaxy. The molecular front appears at galacto-centric distance of R ˜ 8 kpc, where the galactic-scale phase transition from atomic to molecular hydrogen occurs with f_mol^ρ dropping from ˜0.8 to 0.2 within a radial interval as narrow as ˜0.5 kpc. The f_mol^ρ front is much sharper than that of the surface density molecular fraction. The f_mol^ρ front also appears in the direction vertical to the galactic plane with a full width of the high-f_mol^ρ disk to be ˜100 pc. The radial and vertical f_mol^ρ profiles, particularly the front behavior, are fitted by theoretical curves calculated using the observed density profile and assumed radiation field and metallicity with exponential gradients. The molecular fraction was found to be enhanced along spiral arms at radii R ˜ 6 to 10 kpc, such as the Perseus arm. This implies that the molecular clouds are produced from H I in the arms and are dissociated in the interarm regions in the transition region around the molecular front. We also show that there is a threshold value of mean H I density, over which H I is transformed into molecular gas.

  16. Three-dimensional distribution of the ISM in the Milky Way Galaxy. IV. 3D molecular fraction and Galactic-scale H I-to-H2 transition

    NASA Astrophysics Data System (ADS)

    Sofue, Yoshiaki; Nakanishi, Hiroyuki

    2016-06-01

    Three-dimensional (3D) distribution of the volume-density molecular fraction, defined by f_mol^ρ=ρ_H_2/(ρ_{H I}+ρ_H_2), is studied in the Milky Way Galaxy. The molecular front appears at galacto-centric distance of R ˜ 8 kpc, where the galactic-scale phase transition from atomic to molecular hydrogen occurs with f_mol^ρ dropping from ˜0.8 to 0.2 within a radial interval as narrow as ˜0.5 kpc. The f_mol^ρ front is much sharper than that of the surface density molecular fraction. The f_mol^ρ front also appears in the direction vertical to the galactic plane with a full width of the high-f_mol^ρ disk to be ˜100 pc. The radial and vertical f_mol^ρ profiles, particularly the front behavior, are fitted by theoretical curves calculated using the observed density profile and assumed radiation field and metallicity with exponential gradients. The molecular fraction was found to be enhanced along spiral arms at radii R ˜ 6 to 10 kpc, such as the Perseus arm. This implies that the molecular clouds are produced from H I in the arms and are dissociated in the interarm regions in the transition region around the molecular front. We also show that there is a threshold value of mean H I density, over which H I is transformed into molecular gas.

  17. DG-AMMOS: A New tool to generate 3D conformation of small molecules using Distance Geometry and Automated Molecular Mechanics Optimization for in silico Screening

    PubMed Central

    2009-01-01

    Background Discovery of new bioactive molecules that could enter drug discovery programs or that could serve as chemical probes is a very complex and costly endeavor. Structure-based and ligand-based in silico screening approaches are nowadays extensively used to complement experimental screening approaches in order to increase the effectiveness of the process and facilitating the screening of thousands or millions of small molecules against a biomolecular target. Both in silico screening methods require as input a suitable chemical compound collection and most often the 3D structure of the small molecules has to be generated since compounds are usually delivered in 1D SMILES, CANSMILES or in 2D SDF formats. Results Here, we describe the new open source program DG-AMMOS which allows the generation of the 3D conformation of small molecules using Distance Geometry and their energy minimization via Automated Molecular Mechanics Optimization. The program is validated on the Astex dataset, the ChemBridge Diversity database and on a number of small molecules with known crystal structures extracted from the Cambridge Structural Database. A comparison with the free program Balloon and the well-known commercial program Omega generating the 3D of small molecules is carried out. The results show that the new free program DG-AMMOS is a very efficient 3D structure generator engine. Conclusion DG-AMMOS provides fast, automated and reliable access to the generation of 3D conformation of small molecules and facilitates the preparation of a compound collection prior to high-throughput virtual screening computations. The validation of DG-AMMOS on several different datasets proves that generated structures are generally of equal quality or sometimes better than structures obtained by other tested methods. PMID:19912625

  18. Recapitulation of Tumor Heterogeneity and Molecular Signatures in a 3D Brain Cancer Model with Decreased Sensitivity to Histone Deacetylase Inhibition

    PubMed Central

    Smith, Stuart J.; Wilson, Martin; Ward, Jennifer H.; Rahman, Cheryl V.; Peet, Andrew C.; Macarthur, Donald C.; Rose, Felicity R. A. J.; Grundy, Richard G.; Rahman, Ruman

    2012-01-01

    Introduction Physiologically relevant pre-clinical ex vivo models recapitulating CNS tumor micro-environmental complexity will aid development of biologically-targeted agents. We present comprehensive characterization of tumor aggregates generated using the 3D Rotary Cell Culture System (RCCS). Methods CNS cancer cell lines were grown in conventional 2D cultures and the RCCS and comparison with a cohort of 53 pediatric high grade gliomas conducted by genome wide gene expression and microRNA arrays, coupled with immunohistochemistry, ex vivo magnetic resonance spectroscopy and drug sensitivity evaluation using the histone deacetylase inhibitor, Vorinostat. Results Macroscopic RCCS aggregates recapitulated the heterogeneous morphology of brain tumors with a distinct proliferating rim, necrotic core and oxygen tension gradient. Gene expression and microRNA analyses revealed significant differences with 3D expression intermediate to 2D cultures and primary brain tumors. Metabolic profiling revealed differential profiles, with an increase in tumor specific metabolites in 3D. To evaluate the potential of the RCCS as a drug testing tool, we determined the efficacy of Vorinostat against aggregates of U87 and KNS42 glioblastoma cells. Both lines demonstrated markedly reduced sensitivity when assaying in 3D culture conditions compared to classical 2D drug screen approaches. Conclusions Our comprehensive characterization demonstrates that 3D RCCS culture of high grade brain tumor cells has profound effects on the genetic, epigenetic and metabolic profiles of cultured cells, with these cells residing as an intermediate phenotype between that of 2D cultures and primary tumors. There is a discrepancy between 2D culture and tumor molecular profiles, and RCCS partially re-capitulates tissue specific features, allowing drug testing in a more relevant ex vivo system. PMID:23272238

  19. 3D-QSAR and molecular docking studies on designing inhibitors of the hepatitis C virus NS5B polymerase

    NASA Astrophysics Data System (ADS)

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

    2016-08-01

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

  20. Analysis of B-Raf[Formula: see text] inhibitors using 2D and 3D-QSAR, molecular docking and pharmacophore studies.

    PubMed

    Aalizadeh, Reza; Pourbasheer, Eslam; Ganjali, Mohammad Reza

    2015-11-01

    In the present work, a molecular modeling study was carried out using 2D and 3D quantitative structure-activity relationships for the various series of compounds known as B-Raf[Formula: see text] inhibitors. For 2D-QSAR analysis, a linear model was developed by MLR based on GA-OLS with appropriate results [Formula: see text], which was validated by several external validation techniques. To perform a 3D-QSAR analysis, CoMFA and CoMSIA methods were used. The selected CoMFA model could provide reliable statistical values [Formula: see text] based on the training set in the biases of the selected alignment. Using the same selected alignment, a statistically reliable CoMSIA model, out of thirty-one different combinations, was also obtained [Formula: see text]. The predictive accuracy of the derived models was rigorously evaluated with the external test set of nineteen compounds based on several validation techniques. Molecular docking simulations and pharmacophore analyses were also performed to derive the true conformations of the most potent inhibitors with B-Raf[Formula: see text] kinase. PMID:26276566

  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

    2016-01-01

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

  2. 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

  3. Molecular Signaling Pathways Controlling Vascular Tube Morphogenesis and Pericyte-Induced Tube Maturation in 3D Extracellular Matrices.

    PubMed

    Bowers, S L K; Norden, P R; Davis, G E

    2016-01-01

    During capillary network formation, ECs establish interconnecting tubes with defined lumens that reside within vascular guidance tunnels (physical spaces generated during EC tubulogenesis). Pericytes are recruited to EC tubes within these tunnels and capillary basement membrane deposition occurs to facilitate tube maturation. Here, we discuss molecular mechanisms controlling EC tubulogenesis demonstrating the involvement of integrins, MT1-MMP, extracellular matrix, Cdc42, Rac1, Rac2, k-Ras, Rap1b, and key downstream effectors including Pak2, Pak4, IQGAP1, MRCKβ, and Rasip1. These molecules activate kinase cascades controlling EC tube formation, in conjunction with growth factor receptor signaling, which involve PKCɛ, Src family, Raf, Mek, and Erk kinases. These molecules and signaling cascades stimulate EC lumen and tube formation by: regulating MT-MMP-dependent lumen expansion and vascular guidance tunnel formation; generation of intracellular vacuoles/vesicles to create EC apical membranes; and establishing cytoskeletal polarity with acetylated tubulin distributed subapically (and F-actin basally) to facilitate vacuole trafficking/fusion in a polarized, perinuclear region. Using defined serum-free models, we have demonstrated that human EC tubulogenesis and EC-pericyte tube coassembly requires five exogenously applied growth factors which are SCF, IL-3, SDF-1α, FGF-2, and insulin (Factors). Also, we have demonstrated that EC-derived PDGF-BB and HB-EGF are necessary for pericytes to proliferate, recruit to tubes, and induce basement membrane assembly. Finally, we have shown that VEGF fails to directly stimulate EC tubulogenesis. In contrast, it acts as an upstream EC primer of downstream "Factor"-induced tubulogenic and EC-pericyte tube coassembly by upregulating c-Kit, IL-3Rα, and CXCR4 as well as PDGF-BB and HB-EGF expression. PMID:27451100

  4. Molecular dynamics studies of side chain effect on the beta-1,3-D-glucan triple helix in aqueous solution.

    PubMed

    Okobira, Tadashi; Miyoshi, Kentaro; Uezu, Kazuya; Sakurai, Kazuo; Shinkai, Seiji

    2008-03-01

    beta-1,3-D-glucans have been isolated from fungi as right-handed 6(1) triple helices. They are categorized by the side chains bound to the main triple helix through beta-(1-->6)-D-glycosyl linkage. Indeed, since a glucose-based side chain is water soluble, the presence and frequency of glucose-based side chains give rise to significant variation in the physical properties of the glucan family. Curdlan has no side chains and self-assembles to form an water-insoluble triple helical structure, while schizophyllan, which has a 1,6-D-glucose side chain on every third glucose unit along the main chain, is completely water soluble. A thermal fluctuation in the optical rotatory dispersion is observed for the side chain, indicating probable co-operative interaction between the side chains and water molecules. This paper documents molecular dynamics simulations in aqueous solution for three models of the beta-1,3-D-glucan series: curdlan (no side chain), schizophyllan (a beta-(1-->6)-D-glycosyl side-chain at every third position), and a hypothetical triple helix with a side chain at every sixth main-chain glucose unit. A decrease was observed in the helical pitch as the population of the side chain increased. Two types of hydrogen bonding via water molecules, the side chain/main chain and the side chain/side chain hydrogen bonding, play an important role in determination of the triple helix conformation. The formation of a one-dimensional cavity of diameter about 3.5 A was observed in the schizophyllan triple helix, while curdlan showed no such cavity. The side chain/side chain hydrogen bonding in schizophyllan and the hypothetical beta-1,3-D-glucan triple helix could cause the tilt of the main-chain glucose residues to the helix. PMID:18257529

  5. Development and molecular characterization of polymeric micro-nanofibrous scaffold of a defined 3-D niche for in vitro chemosensitivity analysis against acute myeloid leukemia cells

    PubMed Central

    Nair, Maya S; Mony, Ullas; Menon, Deepthy; Koyakutty, Manzoor; Sidharthan, Neeraj; Pavithran, Keechilat; Nair, Shantikumar V; Menon, Krishnakumar N

    2015-01-01

    Standard in vitro drug testing employs 2-D tissue culture plate systems to test anti-leukemic drugs against cell adhesion-mediated drug-resistant leukemic cells that harbor in 3-D bone marrow microenvironments. This drawback necessitates the fabrication of 3-D scaffolds that have cell adhesion-mediated drug-resistant properties similar to in vivo niches. We therefore aimed at exploiting the known property of polyurethane (PU)/poly-l-lactic acid (PLLA) in forming a micro-nanofibrous structure to fabricate unique, not presented before, as far as we are aware, 3-D micro-nanofibrous scaffold composites using a thermally induced phase separation technique. Among the different combinations of PU/PLLA composites generated, the unique PU/PLLA 60:40 composite displayed micro-nanofibrous morphology similar to decellularized bone marrow with increased protein and fibronectin adsorption. Culturing of acute myeloid leukemia (AML) KG1a cells in FN-coated PU/PLLA 60:40 shows increased cell adhesion and cell adhesion-mediated drug resistance to the drugs cytarabine and daunorubicin without changing the original CD34+/CD38−/CD33− phenotype for 168 hours compared to fibronectin tissue culture plate systems. Molecularly, as seen in vivo, increased chemoresistance is associated with the upregulation of anti-apoptotic Bcl2 and the cell cycle regulatory protein p27Kip1 leading to cell growth arrest. Abrogation of Bcl2 activity by the Bcl2-specific inhibitor ABT 737 led to cell death in the presence of both cytarabine and daunorubicin, demonstrating that the cell adhesion-mediated drug resistance induced by Bcl2 and p27Kip1 in the scaffold was similar to that seen in vivo. These results thus show the utility of a platform technology, wherein drug testing can be performed before administering to patients without the necessity for stromal cells. PMID:26028971

  6. RELATIONSHIPS BETWEEN DESCRIPTORS FOR HYDROPHOBICITY AND SOFT ELECTROPHILICITY IN PREDICTING TOXICITY

    EPA Science Inventory

    The toxicity of chemicals is orthogonal with individual molecular descriptors used to quantify hydrophobicity and soft electro-philicity when considering large data sets. Estimating the toxicity of reactive chemicals requires descriptors of both passive transport and the stereoel...

  7. 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

  8. Artemisinin activity-based probes identify multiple molecular targets within the asexual stage of the malaria parasites Plasmodium falciparum 3D7

    PubMed Central

    Ismail, Hanafy M.; Barton, Victoria; Phanchana, Matthew; Charoensutthivarakul, Sitthivut; Wong, Michael H. L.; Hemingway, Janet; Biagini, Giancarlo A.; O’Neill, Paul M.; Ward, Stephen A.

    2016-01-01

    The artemisinin (ART)-based antimalarials have contributed significantly to reducing global malaria deaths over the past decade, but we still do not know how they kill parasites. To gain greater insight into the potential mechanisms of ART drug action, we developed a suite of ART activity-based protein profiling probes to identify parasite protein drug targets in situ. Probes were designed to retain biological activity and alkylate the molecular target(s) of Plasmodium falciparum 3D7 parasites in situ. Proteins tagged with the ART probe can then be isolated using click chemistry before identification by liquid chromatography–MS/MS. Using these probes, we define an ART proteome that shows alkylated targets in the glycolytic, hemoglobin degradation, antioxidant defense, and protein synthesis pathways, processes essential for parasite survival. This work reveals the pleiotropic nature of the biological functions targeted by this important class of antimalarial drugs. PMID:26858419

  9. Artemisinin activity-based probes identify multiple molecular targets within the asexual stage of the malaria parasites Plasmodium falciparum 3D7.

    PubMed

    Ismail, Hanafy M; Barton, Victoria; Phanchana, Matthew; Charoensutthivarakul, Sitthivut; Wong, Michael H L; Hemingway, Janet; Biagini, Giancarlo A; O'Neill, Paul M; Ward, Stephen A

    2016-02-23

    The artemisinin (ART)-based antimalarials have contributed significantly to reducing global malaria deaths over the past decade, but we still do not know how they kill parasites. To gain greater insight into the potential mechanisms of ART drug action, we developed a suite of ART activity-based protein profiling probes to identify parasite protein drug targets in situ. Probes were designed to retain biological activity and alkylate the molecular target(s) of Plasmodium falciparum 3D7 parasites in situ. Proteins tagged with the ART probe can then be isolated using click chemistry before identification by liquid chromatography-MS/MS. Using these probes, we define an ART proteome that shows alkylated targets in the glycolytic, hemoglobin degradation, antioxidant defense, and protein synthesis pathways, processes essential for parasite survival. This work reveals the pleiotropic nature of the biological functions targeted by this important class of antimalarial drugs. PMID:26858419

  10. Europeana and 3D

    NASA Astrophysics Data System (ADS)

    Pletinckx, D.

    2011-09-01

    The current 3D hype creates a lot of interest in 3D. People go to 3D movies, but are we ready to use 3D in our homes, in our offices, in our communication? Are we ready to deliver real 3D to a general public and use interactive 3D in a meaningful way to enjoy, learn, communicate? The CARARE project is realising this for the moment in the domain of monuments and archaeology, so that real 3D of archaeological sites and European monuments will be available to the general public by 2012. There are several aspects to this endeavour. First of all is the technical aspect of flawlessly delivering 3D content over all platforms and operating systems, without installing software. We have currently a working solution in PDF, but HTML5 will probably be the future. Secondly, there is still little knowledge on how to create 3D learning objects, 3D tourist information or 3D scholarly communication. We are still in a prototype phase when it comes to integrate 3D objects in physical or virtual museums. Nevertheless, Europeana has a tremendous potential as a multi-facetted virtual museum. Finally, 3D has a large potential to act as a hub of information, linking to related 2D imagery, texts, video, sound. We describe how to create such rich, explorable 3D objects that can be used intuitively by the generic Europeana user and what metadata is needed to support the semantic linking.

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

    PubMed

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

    2014-01-01

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

  12. Representation of chemical information in OASIS centralized 3D database for existing chemicals.

    PubMed

    Nikolov, Nikolai; Grancharov, Vanio; Stoyanova, Galya; Pavlov, Todor; Mekenyan, Ovanes

    2006-01-01

    The present inventory of existing chemicals in regulatory agencies in North America and Europe, encompassing the chemicals of the European Chemicals Bureau (EINECS, with 61 573 discrete chemicals); the Danish EPA (159 448 chemicals); the U.S. EPA (TSCA, 56 882 chemicals; HPVC, 10 546 chemicals) and pesticides' active and inactive ingredients of the U.S. EPA (1379 chemicals); the Organization for Economic Cooperation and Development (HPVC, 4750 chemicals); Environment Canada (DSL, 10851 chemicals); and the Japanese Ministry of Economy, Trade, and Industry (16811), was combined in a centralized 3D database for existing chemicals. The total number of unique chemicals from all of these databases exceeded 185 500. Defined and undefined chemical mixtures and polymers are handled, along with discrete (hydrolyzing and nonhydrolyzing) chemicals. The database manager provides the storage and retrieval of chemical structures with 2D and 3D data, accounting for molecular flexibility by using representative sets of conformers for each chemical. The electronic and geometric structures of all conformers are quantum-chemically optimized and evaluated. Hence, the database contains over 3.7 million 3D records with hundreds of millions of descriptor data items at the levels of structures, conformers, or atoms. The platform contains a highly developed search subsystem--a search is possible on Chemical Abstracts Service numbers; names; 2D and 3D fragment searches; structural, conformational, or atomic properties; affiliation in other chemical databases; structure similarity; logical combinations; saved queries; and search result exports. Models (collections of logically related descriptors) are supported, including information on a model's author, date, bioassay, organs/tissues, conditions, administration, and so forth. Fragments can be interactively constructed using a visual structure editor. A configurable database browser is designed for the inspection and editing of all types of

  13. Student Descriptor Scale Manual.

    ERIC Educational Resources Information Center

    Goetz, Lori; And Others

    The Student Descriptor Scale (SDS) was developed as a validation measure to determine whether students described and counted by states as "severely handicapped" were, indeed, students with severe disabilities. The SDS addresses nine characteristics: intellectual disability, health impairment, need for toileting assistance, upper torso motor…

  14. Learning discriminant face descriptor.

    PubMed

    Lei, Zhen; Pietikäinen, Matti; Li, Stan Z

    2014-02-01

    Local feature descriptor is an important module for face recognition and those like Gabor and local binary patterns (LBP) have proven effective face descriptors. Traditionally, the form of such local descriptors is predefined in a handcrafted way. In this paper, we propose a method to learn a discriminant face descriptor (DFD) in a data-driven way. The idea is to learn the most discriminant local features that minimize the difference of the features between images of the same person and maximize that between images from different people. In particular, we propose to enhance the discriminative ability of face representation in three aspects. First, the discriminant image filters are learned. Second, the optimal neighborhood sampling strategy is soft determined. Third, the dominant patterns are statistically constructed. Discriminative learning is incorporated to extract effective and robust features. We further apply the proposed method to the heterogeneous (cross-modality) face recognition problem and learn DFD in a coupled way (coupled DFD or C-DFD) to reduce the gap between features of heterogeneous face images to improve the performance of this challenging problem. Extensive experiments on FERET, CAS-PEAL-R1, LFW, and HFB face databases validate the effectiveness of the proposed DFD learning on both homogeneous and heterogeneous face recognition problems. The DFD improves POEM and LQP by about 4.5 percent on LFW database and the C-DFD enhances the heterogeneous face recognition performance of LBP by over 25 percent. PMID:24356350

  15. 3D QSAR STUDIES ON A SERIES OF QUINAZOLINE DERRIVATIVES AS TYROSINE KINASE (EGFR) INHIBITOR: THE K-NEAREST NEIGHBOR MOLECULAR FIELD ANALYSIS APPROACH

    PubMed Central

    Noolvi, Malleshappa N.; Patel, Harun M.

    2010-01-01

    Epidermal growth factor receptor (EGFR) protein tyrosine kinases (PTKs) are known for its role in cancer. Quinazoline have been reported to be the molecules of interest, with potent anticancer activity and they act by binding to ATP site of protein kinases. ATP binding site of protein kinases provides an extensive opportunity to design newer analogs. With this background, we report an attempt to discern the structural and physicochemical requirements for inhibition of EGFR tyrosine kinase. The k-Nearest Neighbor Molecular Field Analysis (kNN-MFA), a three dimensional quantitative structure activity relationship (3D- QSAR) method has been used in the present case to study the correlation between the molecular properties and the tyrosine kinase (EGFR) inhibitory activities on a series of quinazoline derivatives. kNNMFA calculations for both electrostatic and steric field were carried out. The master grid maps derived from the best model has been used to display the contribution of electrostatic potential and steric field. The statistical results showed significant correlation coefficient r2 (q2) of 0.846, r2 for external test set (pred_r2) 0.8029, coefficient of correlation of predicted data set (pred_r2se) of 0.6658, degree of freedom 89 and k nearest neighbor of 2. Therefore, this study not only casts light on binding mechanism between EGFR and its inhibitors, but also provides hints for the design of new EGFR inhibitors with observable structural diversity PMID:24825983

  16. Design, synthesis, anti-tumor activity, and molecular modeling of quinazoline and pyrido[2,3-d]pyrimidine derivatives targeting epidermal growth factor receptor.

    PubMed

    Hou, Ju; Wan, Shanhe; Wang, Guangfa; Zhang, Tingting; Li, Zhonghuang; Tian, Yuanxin; Yu, Yonghuan; Wu, Xiaoyun; Zhang, Jiajie

    2016-08-01

    Three series of novel quinazoline and pyrido[2,3-d]pyrimidine derivatives were designed, synthesized and evaluated for their ability to inhibit EGFR tyrosine kinase and a panel of five human cancer cell lines (MCF-7, A549, BT-474, SK-BR-3, and MDA-MB-231). Bioassay results indicated that five of these prepared compounds (12c-12e and 13c-13d) exhibited remarkably higher inhibitory activities against EGFR and SK-BR-3 cell line. Compounds 12c and 12e displayed the most potent EGFR inhibitory activity (IC50 = 2.97 nM and 3.58 nM, respectively) and good anti-proliferative effect against SK-BR-3 cell with the IC50 values of 3.10 μM and 5.87 μM, respectively. Furthermore, molecular docking and molecular dynamics simulation studies verified that compound 12c and 12e shared similar binding pattern with gefitinib in the binding pocket of EGFR. MM-GBSA binding free energy revealed that the compound 12c and 12e have almost the same inhibitory activity against EGFR as gefitinib, and that the dominating effect of van der Waals interactions drives the binding process. PMID:27132165

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

    PubMed

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

    2016-06-01

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

  18. Ligand-based Pharmacophore Modeling; Atom-based 3D-QSAR Analysis and Molecular Docking Studies of Phosphoinositide-Dependent Kinase-1 Inhibitors

    PubMed Central

    Kirubakaran, P.; Muthusamy, K.; Singh, K. H. D.; Nagamani, S.

    2012-01-01

    Phosphoinositide-dependent kinase-1 plays a vital role in the PI3-kinase signaling pathway that regulates gene expression, cell cycle growth and proliferation. The common human cancers include lung, breast, blood and prostate possess over stimulation of the phosphoinositide-dependent kinase-1 signaling and making phosphoinositide-dependent kinase-1 an interesting therapeutic target in oncology. A ligand-based pharmacophore and atom-based 3D-QSAR studies were carried out on a set of 82 inhibitors of PDK1. A six point pharmacophore with two hydrogen bond acceptors (A), three hydrogen bond donors (D) and one hydrophobic group (H) was obtained. The pharmacophore hypothesis yielded a 3D-QSAR model with good partial least square statistics results. The training set correlation is characterized by partial least square factors (R2 = 0.9557, SD = 0.2334, F = 215.5, P = 1.407e-32). The test set correlation is characterized by partial least square factors (Q2 ext = 0.7510, RMSE = 0.5225, Pearson-R =0.8676). The external validation indicated that our QSAR model possess high predictive power with good value of 0.99 and value of 0.88. The docking results show the binding orientations of these inhibitors at active site amino acid residues (Ala162, Thr222, Glu209 and Glu166) of phosphoinositide-dependent kinase-1 protein. The binding free energy interactions of protein-ligand complex have been calculated, which plays an important role in molecular recognition and drug design approach. PMID:23325995

  19. Modular Chemical Descriptor Language (MCDL): Stereochemical modules

    SciTech Connect

    Gakh, Andrei A; Burnett, Michael N; Trepalin, Sergei V.; Yarkov, Alexander V

    2011-01-01

    In our previous papers we introduced the Modular Chemical Descriptor Language (MCDL) for providing a linear representation of chemical information. A subsequent development was the MCDL Java Chemical Structure Editor which is capable of drawing chemical structures from linear representations and generating MCDL descriptors from structures. In this paper we present MCDL modules and accompanying software that incorporate unique representation of molecular stereochemistry based on Cahn-Ingold-Prelog and Fischer ideas in constructing stereoisomer descriptors. The paper also contains additional discussions regarding canonical representation of stereochemical isomers, and brief algorithm descriptions of the open source LINDES, Java applet, and Open Babel MCDL processing module software packages. Testing of the upgraded MCDL Java Chemical Structure Editor on compounds taken from several large and diverse chemical databases demonstrated satisfactory performance for storage and processing of stereochemical information in MCDL format.

  20. 3d-3d correspondence revisited

    NASA Astrophysics Data System (ADS)

    Chung, Hee-Joong; Dimofte, Tudor; Gukov, Sergei; Sułkowski, Piotr

    2016-04-01

    In fivebrane compactifications on 3-manifolds, we point out the importance of all flat connections in the proper definition of the effective 3d {N}=2 theory. The Lagrangians of some theories with the desired properties can be constructed with the help of homological knot invariants that categorify colored Jones polynomials. Higgsing the full 3d theories constructed this way recovers theories found previously by Dimofte-Gaiotto-Gukov. We also consider the cutting and gluing of 3-manifolds along smooth boundaries and the role played by all flat connections in this operation.

  1. Study of differences in the VEGFR2 inhibitory activities between semaxanib and SU5205 using 3D-QSAR, docking, and molecular dynamics simulations.

    PubMed

    Muñoz, Camila; Adasme, Francisco; Alzate-Morales, Jans H; Vergara-Jaque, Ariela; Kniess, Torsten; Caballero, Julio

    2012-02-01

    Semaxanib (SU5416) and 3-[4'-fluorobenzylidene]indolin-2-one (SU5205) are structurally similar drugs that are able to inhibit vascular endothelial growth factor receptor-2 (VEGFR2), but the former is 87 times more effective than the latter. Previously, SU5205 was used as a radiolabelled inhibitor (as surrogate for SU5416) and a radiotracer for positron emission tomography (PET) imaging, but the compound exhibited poor stability and only a moderate IC(50) toward VEGFR2. In the current work, the relationship between the structure and activity of these drugs as VEGFR2 inhibitors was studied using 3D-QSAR, docking and molecular dynamics (MD) simulations. First, comparative molecular field analysis (CoMFA) was performed using 48 2-indolinone derivatives and their VEGFR2 inhibitory activities. The best CoMFA model was carried out over a training set including 40 compounds, and it included steric and electrostatic fields. In addition, this model gave satisfactory cross-validation results and adequately predicted 8 compounds contained in the test set. The plots of the CoMFA fields could explain the structural differences between semaxanib and SU5205. Docking and molecular dynamics simulations showed that both molecules have the same orientation and dynamics inside the VEGFR2 active site. However, the hydrophobic pocket of VEGFR2 was more exposed to the solvent media when it was complexed with SU5205. An energetic analysis, including Embrace and MM-GBSA calculations, revealed that the potency of ligand binding is governed by van der Waals contacts. PMID:22070999

  2. 3D-QSAR, molecular dynamics simulations and molecular docking studies of benzoxazepine moiety as mTOR inhibitor for the treatment of lung cancer.

    PubMed

    Chaube, Udit; Chhatbar, Dhara; Bhatt, Hardik

    2016-02-01

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

  3. 3D and Education

    NASA Astrophysics Data System (ADS)

    Meulien Ohlmann, Odile

    2013-02-01

    Today the industry offers a chain of 3D products. Learning to "read" and to "create in 3D" becomes an issue of education of primary importance. 25 years professional experience in France, the United States and Germany, Odile Meulien set up a personal method of initiation to 3D creation that entails the spatial/temporal experience of the holographic visual. She will present some different tools and techniques used for this learning, their advantages and disadvantages, programs and issues of educational policies, constraints and expectations related to the development of new techniques for 3D imaging. Although the creation of display holograms is very much reduced compared to the creation of the 90ies, the holographic concept is spreading in all scientific, social, and artistic activities of our present time. She will also raise many questions: What means 3D? Is it communication? Is it perception? How the seeing and none seeing is interferes? What else has to be taken in consideration to communicate in 3D? How to handle the non visible relations of moving objects with subjects? Does this transform our model of exchange with others? What kind of interaction this has with our everyday life? Then come more practical questions: How to learn creating 3D visualization, to learn 3D grammar, 3D language, 3D thinking? What for? At what level? In which matter? for whom?

  4. Mono, bi- and trinuclear metal complexes derived from new benzene-1,4-bis(3-pyridin-2-ylurea) ligand. Spectral, magnetic, thermal and 3D molecular modeling studies

    NASA Astrophysics Data System (ADS)

    El-ghamry, Mosad A.; Saleh, Akila A.; Khalil, Saied M. E.; Mohammed, Amira A.

    2013-06-01

    New bis (pyridylurea) ligand, H2L, was synthesized by the reaction of ethylpyridine-2-carbamate (EPC) and p-phenylenediamine. The ligand was characterized by elemental analysis, IR, 1H NMR, electronic and mass spectra. Reaction of the prepared ligand with Co2+, Ni2+, Cu2+, Fe3+, VO2+ and UO22+ ions afforded mono, bi- and trinuclear metal complexes. Also, new mixed ligand complexes of the ligand H2L and 8-hydroxyquinoline (8-HQ) with Co2+, Ni2+, Cu2+ and Fe3+ ions were synthesized. The ligand behaves as bi- and tetradentate toward the transition metal ions, coordination via the pyridine sbnd N, the carbonyl sbnd O and/or the amidic sbnd N atoms in a non, mono- and bis-deprotonated form. The complexes were characterized by elemental and thermal analyses, IR, electronic and mass spectra as well as conductance and magnetic susceptibility measurements. The results showed that the metal complexes exhibited different geometrical arrangements such as square planar, tetrahedral, octahedral and square pyramidal arrangements. The Coats-Redfern equation was used to calculate the kinetic and thermodynamic parameters for the different thermal decomposition steps of some complexes. 3D molecular modeling of the ligand, H2L and a representative complex were studied.

  5. Molecular cloning, expression pattern, and 3D structural prediction of the cold inducible RNA-binding protein (CIRP) in Japanese flounder ( Paralichthys olivaceus)

    NASA Astrophysics Data System (ADS)

    Yang, Xiao; Gao, Jinning; Ma, Liman; Li, Zan; Wang, Wenji; Wang, Zhongkai; Yu, Haiyang; Qi, Jie; Wang, Xubo; Wang, Zhigang; Zhang, Quanqi

    2015-02-01

    Cold-inducible RNA-binding protein (CIRP) is a kind of RNA binding proteins that plays important roles in many physiological processes. The CIRP has been widely studied in mammals and amphibians since it was first cloned from mammals. On the contrary, there are little reports in teleosts. In this study, the Po CIRP gene of the Japanese flounder was cloned and sequenced. The genomic sequence consists of seven exons and six introns. The putative PoCIRP protein of flounder was 198 amino acid residues long containing the RNA recognition motif (RRM). Phylogenetic analysis showed that the flounder PoCIRP is highly conserved with other teleost CIRPs. The 5' flanking sequence was cloned by genome walking and many transcription factor binding sites were identified. There is a CpGs region located in promoter and exon I region and the methylation state is low. Quantitative real-time PCR analysis uncovered that Po CIRP gene was widely expressed in adult tissues with the highest expression level in the ovary. The mRNA of the Po CIRP was maternally deposited and the expression level of the gene was regulated up during the gastrula and neurula stages. In order to gain the information how the protein interacts with mRNA, we performed the modeling of the 3D structure of the flounder PoCIRP. The results showed a cleft existing the surface of the molecular. Taken together, the results indicate that the CIRP is a multifunctional molecular in teleosts and the findings about the structure provide valuable information for understanding the basis of this protein's function.

  6. 3D-RISM-KH molecular theory of solvation and density functional theory investigation of the role of water in the aggregation of model asphaltenes.

    PubMed

    da Costa, L M; Hayaki, S; Stoyanov, S R; Gusarov, S; Tan, X; Gray, M R; Stryker, J M; Tykwinski, R; Carneiro, J Walkimar de M; Sato, H; Seidl, P R; Kovalenko, A

    2012-03-21

    We applied a multiscale modeling approach that involves the statistical-mechanical three-dimensional reference interaction site model with the Kovalenko-Hirata closure approximation (3D-RISM-KH molecular theory of solvation) as well as density functional theory (DFT) of electronic structure to study the role of water in aggregation of the asphaltene model compound 4,4'-bis(2-pyren-1-yl-ethyl)-2,2'-bipyridine (PBP) [X. Tan, H. Fenniri and M. R. Gray, Energy Fuels, 2008, 22, 715]. The solvation free energy and potential of mean force predicted by 3D-RISM-KH reveal favorable pathways for disaggregation of PBP dimers in pure versus water-saturated chloroform solvent. The water density distribution functions elucidate hydrogen bonding preferences and water bridge formation between PBP monomers. The ΔG(298) values of -5 to -7 kcal mol(-1) for transfer of water molecules in chloroform to a state interacting with PBP molecules are in agreement with experimental results. Geometry optimization and thermochemistry analysis of PBP dimers with and without water bridges using WB97Xd/6-31G(d,p) predict that both PBP dimerization and dimer stabilization by water bridges are spontaneous (ΔG(298) < 0). The (1)H NMR chemical shifts of PBP monomers and dimers predicted using the gauge-independent atomic orbital method and polarizable continuum model for solvation in chloroform are in an excellent agreement with the experimental results for dilute and concentrated PBP solutions in chloroform, respectively [X. Tan, H. Fenniri and M. R. Gray, Energy Fuels, 2009, 23, 3687]. The DFT calculations of PBP dimers with explicit water show that bridges containing 1-3 water molecules lead to stabilization of PBP dimers. Additional water molecules form hydrogen bonds with these bridges and de-shield the PBP protons, negating the effect of water on the (1)H(C3) NMR chemical shift of PBP, in agreement with experiment. The ΔG(298) results show that hydrogen bonding to water and water

  7. 3D Imaging.

    ERIC Educational Resources Information Center

    Hastings, S. K.

    2002-01-01

    Discusses 3 D imaging as it relates to digital representations in virtual library collections. Highlights include X-ray computed tomography (X-ray CT); the National Science Foundation (NSF) Digital Library Initiatives; output peripherals; image retrieval systems, including metadata; and applications of 3 D imaging for libraries and museums. (LRW)

  8. Color-invariant three-dimensional feature descriptor for color-shift-model-based image processing

    NASA Astrophysics Data System (ADS)

    Lim, Joohyun; Paik, Joonki

    2011-11-01

    We present a novel color-invariant depth feature descriptor for color-shift-model (CSM)-based image processing. Color images acquired by a single camera equipped with multiple color-filter aperture (MCA) contain depth-dependent color misalignment. The amount and direction of the misalignment provides object's distance from the camera. The CSM-based image processing, which represents the combined image-acquisition and depth-estimation framework, requires a color-invariant feature descriptor that can convey depth information. For improving depth-estimation performance, color boosting is performed on a color image acquired by the MCA camera, and CSM-based channel-shifting descriptor vectors, or channel-shifting vectors (CSVs), are generated by using the feasibility test. Color-invariant features are also extracted in the luminance image. The proposed color-invariant three-dimensional (3-D) feature descriptor is finally obtained by combining the CSVs and luminance features. We present experimental analysis of the proposed feature descriptor and show that the descriptors are proportional to the depth of an object. The proposed descriptor can be used for feature-based image matching in various applications, including 3-D scene modeling, 3-D object recognition, 3-D video tracking, and multifocusing, to name a few.

  9. TRACE 3-D documentation

    SciTech Connect

    Crandall, K.R.

    1987-08-01

    TRACE 3-D is an interactive beam-dynamics program that calculates the envelopes of a bunched beam, including linear space-charge forces, through a user-defined transport system. TRACE 3-D provides an immediate graphics display of the envelopes and the phase-space ellipses and allows nine types of beam-matching options. This report describes the beam-dynamics calculations and gives detailed instruction for using the code. Several examples are described in detail.

  10. Combined 3D-QSAR, Molecular Docking and Molecular Dynamics Study on Derivatives of Peptide Epoxyketone and Tyropeptin-Boronic Acid as Inhibitors Against the β5 Subunit of Human 20S Proteasome

    PubMed Central

    Liu, Jianling; Zhang, Hong; Xiao, Zhengtao; Wang, Fangfang; Wang, Xia; Wang, Yonghua

    2011-01-01

    An abnormal ubiquitin-proteasome is found in many human diseases, especially in cancer, and has received extensive attention as a promising therapeutic target in recent years. In this work, several in silico models have been built with two classes of proteasome inhibitors (PIs) by using 3D-QSAR, homology modeling, molecular docking and molecular dynamics (MD) simulations. The study resulted in two types of satisfactory 3D-QSAR models, i.e., the CoMFA model (Q2 = 0.462, R2pred = 0.820) for epoxyketone inhibitors (EPK) and the CoMSIA model (Q2 = 0.622, R2pred = 0.821) for tyropeptin-boronic acid derivatives (TBA). From the contour maps, some key structural factors responsible for the activity of these two series of PIs are revealed. For EPK inhibitors, the N-cap part should have higher electropositivity; a large substituent such as a benzene ring is favored at the C6-position. In terms of TBA inhibitors, hydrophobic substituents with a larger size anisole group are preferential at the C8-position; higher electropositive substituents like a naphthalene group at the C3-position can enhance the activity of the drug by providing hydrogen bond interaction with the protein target. Molecular docking disclosed that residues Thr60, Thr80, Gly106 and Ser189 play a pivotal role in maintaining the drug-target interactions, which are consistent with the contour maps. MD simulations further indicated that the binding modes of each conformation derived from docking is stable and in accord with the corresponding structure extracted from MD simulation overall. These results can offer useful theoretical references for designing more potent PIs. PMID:21673924

  11. 3D Printed Block Copolymer Nanostructures

    ERIC Educational Resources Information Center

    Scalfani, Vincent F.; Turner, C. Heath; Rupar, Paul A.; Jenkins, Alexander H.; Bara, Jason E.

    2015-01-01

    The emergence of 3D printing has dramatically advanced the availability of tangible molecular and extended solid models. Interestingly, there are few nanostructure models available both commercially and through other do-it-yourself approaches such as 3D printing. This is unfortunate given the importance of nanotechnology in science today. In this…

  12. Molecular cloning, expression pattern, and 3D structural analysis of the MHC class IIB gene in the Chinese longsnout catfish (Leiocassis longirostris).

    PubMed

    Shen, Tong; Xu, Shixia; Yang, Mei; Pang, Shuying; Yang, Guang

    2011-05-15

    stomach, and low or negligible expression in heart. Homology modelling has been applied to create a 3D model of longsnout catfish MHC class IIB, with features evaluated and discussed to investigate its interaction with CD4 participating in antigen recognition. The present findings will provide valuable information for understanding structure, function, expression, and molecular polymorphism of MHC class IIB in adaptive immunity of the Chinese longsnout catfish and teleost. PMID:21377740

  13. 3D-graphite structure

    SciTech Connect

    Belenkov, E. A. Ali-Pasha, V. A.

    2011-01-15

    The structure of clusters of some new carbon 3D-graphite phases have been calculated using the molecular-mechanics methods. It is established that 3D-graphite polytypes {alpha}{sub 1,1}, {alpha}{sub 1,3}, {alpha}{sub 1,5}, {alpha}{sub 2,1}, {alpha}{sub 2,3}, {alpha}{sub 3,1}, {beta}{sub 1,2}, {beta}{sub 1,4}, {beta}{sub 1,6}, {beta}{sub 2,1}, and {beta}{sub 3,2} consist of sp{sup 2}-hybridized atoms, have hexagonal unit cells, and differ in regards to the structure of layers and order of their alternation. A possible way to experimentally synthesize new carbon phases is proposed: the polymerization and carbonization of hydrocarbon molecules.

  14. Radiochromic 3D Detectors

    NASA Astrophysics Data System (ADS)

    Oldham, Mark

    2015-01-01

    Radiochromic materials exhibit a colour change when exposed to ionising radiation. Radiochromic film has been used for clinical dosimetry for many years and increasingly so recently, as films of higher sensitivities have become available. The two principle advantages of radiochromic dosimetry include greater tissue equivalence (radiologically) and the lack of requirement for development of the colour change. In a radiochromic material, the colour change arises direct from ionising interactions affecting dye molecules, without requiring any latent chemical, optical or thermal development, with important implications for increased accuracy and convenience. It is only relatively recently however, that 3D radiochromic dosimetry has become possible. In this article we review recent developments and the current state-of-the-art of 3D radiochromic dosimetry, and the potential for a more comprehensive solution for the verification of complex radiation therapy treatments, and 3D dose measurement in general.

  15. Bootstrapping 3D fermions

    NASA Astrophysics Data System (ADS)

    Iliesiu, Luca; Kos, Filip; Poland, David; Pufu, Silviu S.; Simmons-Duffin, David; Yacoby, Ran

    2016-03-01

    We study the conformal bootstrap for a 4-point function of fermions < ψψψψ> in 3D. We first introduce an embedding formalism for 3D spinors and compute the conformal blocks appearing in fermion 4-point functions. Using these results, we find general bounds on the dimensions of operators appearing in the ψ × ψ OPE, and also on the central charge C T . We observe features in our bounds that coincide with scaling dimensions in the GrossNeveu models at large N . We also speculate that other features could coincide with a fermionic CFT containing no relevant scalar operators.

  16. 3D-QSAR (CoMFA, CoMFA-RG, CoMSIA) and molecular docking study of thienopyrimidine and thienopyridine derivatives to explore structural requirements for aurora-B kinase inhibition.

    PubMed

    Borisa, Ankit; Bhatt, Hardik

    2015-11-15

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

  17. 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.

  18. LigandBox: A database for 3D structures of chemical compounds

    PubMed Central

    Kawabata, Takeshi; Sugihara, Yusuke; Fukunishi, Yoshifumi; Nakamura, Haruki

    2013-01-01

    A database for the 3D structures of available compounds is essential for the virtual screening by molecular docking. We have developed the LigandBox database (http://ligandbox.protein.osaka-u.ac.jp/ligandbox/) containing four million available compounds, collected from the catalogues of 37 commercial suppliers, and approved drugs and biochemical compounds taken from KEGG_DRUG, KEGG_COMPOUND and PDB databases. Each chemical compound in the database has several 3D conformers with hydrogen atoms and atomic charges, which are ready to be docked into receptors using docking programs. The 3D conformations were generated using our molecular simulation program package, myPresto. Various physical properties, such as aqueous solubility (LogS) and carcinogenicity have also been calculated to characterize the ADME-Tox properties of the compounds. The Web database provides two services for compound searches: a property/chemical ID search and a chemical structure search. The chemical structure search is performed by a descriptor search and a maximum common substructure (MCS) search combination, using our program kcombu. By specifying a query chemical structure, users can find similar compounds among the millions of compounds in the database within a few minutes. Our database is expected to assist a wide range of researchers, in the fields of medical science, chemical biology, and biochemistry, who are seeking to discover active chemical compounds by the virtual screening. PMID:27493549

  19. 3D microscope

    NASA Astrophysics Data System (ADS)

    Iizuka, Keigo

    2008-02-01

    In order to circumvent the fact that only one observer can view the image from a stereoscopic microscope, an attachment was devised for displaying the 3D microscopic image on a large LCD monitor for viewing by multiple observers in real time. The principle of operation, design, fabrication, and performance are presented, along with tolerance measurements relating to the properties of the cellophane half-wave plate used in the design.

  20. 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. PMID:27037463

  1. 3D object retrieval using salient views.

    PubMed

    Atmosukarto, Indriyati; Shapiro, Linda G

    2013-06-01

    This paper presents a method for selecting salient 2D views to describe 3D objects for the purpose of retrieval. The views are obtained by first identifying salient points via a learning approach that uses shape characteristics of the 3D points (Atmosukarto and Shapiro in International workshop on structural, syntactic, and statistical pattern recognition, 2008; Atmosukarto and Shapiro in ACM multimedia information retrieval, 2008). The salient views are selected by choosing views with multiple salient points on the silhouette of the object. Silhouette-based similarity measures from Chen et al. (Comput Graph Forum 22(3):223-232, 2003) are then used to calculate the similarity between two 3D objects. Retrieval experiments were performed on three datasets: the Heads dataset, the SHREC2008 dataset, and the Princeton dataset. Experimental results show that the retrieval results using the salient views are comparable to the existing light field descriptor method (Chen et al. in Comput Graph Forum 22(3):223-232, 2003), and our method achieves a 15-fold speedup in the feature extraction computation time. PMID:23833704

  2. 3D object retrieval using salient views

    PubMed Central

    Shapiro, Linda G.

    2013-01-01

    This paper presents a method for selecting salient 2D views to describe 3D objects for the purpose of retrieval. The views are obtained by first identifying salient points via a learning approach that uses shape characteristics of the 3D points (Atmosukarto and Shapiro in International workshop on structural, syntactic, and statistical pattern recognition, 2008; Atmosukarto and Shapiro in ACM multimedia information retrieval, 2008). The salient views are selected by choosing views with multiple salient points on the silhouette of the object. Silhouette-based similarity measures from Chen et al. (Comput Graph Forum 22(3):223–232, 2003) are then used to calculate the similarity between two 3D objects. Retrieval experiments were performed on three datasets: the Heads dataset, the SHREC2008 dataset, and the Princeton dataset. Experimental results show that the retrieval results using the salient views are comparable to the existing light field descriptor method (Chen et al. in Comput Graph Forum 22(3):223–232, 2003), and our method achieves a 15-fold speedup in the feature extraction computation time. PMID:23833704

  3. Filling the gap between the quantum and classical worlds of nanoscale magnetism: giant molecular aggregates based on paramagnetic 3d metal ions.

    PubMed

    Papatriantafyllopoulou, Constantina; Moushi, Eleni E; Christou, George; Tasiopoulos, Anastasios J

    2016-03-14

    In this review, aspects of the syntheses, structures and magnetic properties of giant 3d and 3d/4f paramagnetic metal clusters in moderate oxidation states are discussed. The term "giant clusters" is used herein to denote metal clusters with nuclearity of 30 or greater. Many synthetic strategies towards such species have been developed and are discussed in this paper. Attempts are made to categorize some of the most successful methods to giant clusters, but it will be pointed out that the characteristics of the crystal structures of such compounds including nuclearity, shape, architecture, etc. are unpredictable depending on the specific structural features of the included organic ligands, reaction conditions and other factors. The majority of the described compounds in this review are of special interest not only for their fascinating nanosized structures but also because they sometimes display interesting magnetic phenomena, such as ferromagnetic exchange interactions, large ground state spin values, single-molecule magnetism behaviour or impressively large magnetocaloric effects. In addition, they often possess the properties of both the quantum and the classical world, and thus their systematic study offers the potential for the discovery of new physical phenomena, as well as a better understanding of the existing ones. The research field of giant clusters is under continuous evolution and their intriguing structural characteristics and magnetism properties that attract the interest of synthetic Inorganic Chemists promise a brilliant future for this class of compounds. PMID:26767319

  4. Multiviewer 3D monitor

    NASA Astrophysics Data System (ADS)

    Kostrzewski, Andrew A.; Aye, Tin M.; Kim, Dai Hyun; Esterkin, Vladimir; Savant, Gajendra D.

    1998-09-01

    Physical Optics Corporation has developed an advanced 3-D virtual reality system for use with simulation tools for training technical and military personnel. This system avoids such drawbacks of other virtual reality (VR) systems as eye fatigue, headaches, and alignment for each viewer, all of which are due to the need to wear special VR goggles. The new system is based on direct viewing of an interactive environment. This innovative holographic multiplexed screen technology makes it unnecessary for the viewer to wear special goggles.

  5. 3D Audio System

    NASA Technical Reports Server (NTRS)

    1992-01-01

    Ames Research Center research into virtual reality led to the development of the Convolvotron, a high speed digital audio processing system that delivers three-dimensional sound over headphones. It consists of a two-card set designed for use with a personal computer. The Convolvotron's primary application is presentation of 3D audio signals over headphones. Four independent sound sources are filtered with large time-varying filters that compensate for motion. The perceived location of the sound remains constant. Possible applications are in air traffic control towers or airplane cockpits, hearing and perception research and virtual reality development.

  6. 3D Surgical Simulation

    PubMed Central

    Cevidanes, Lucia; Tucker, Scott; Styner, Martin; Kim, Hyungmin; Chapuis, Jonas; Reyes, Mauricio; Proffit, William; Turvey, Timothy; Jaskolka, Michael

    2009-01-01

    This paper discusses the development of methods for computer-aided jaw surgery. Computer-aided jaw surgery allows us to incorporate the high level of precision necessary for transferring virtual plans into the operating room. We also present a complete computer-aided surgery (CAS) system developed in close collaboration with surgeons. Surgery planning and simulation include construction of 3D surface models from Cone-beam CT (CBCT), dynamic cephalometry, semi-automatic mirroring, interactive cutting of bone and bony segment repositioning. A virtual setup can be used to manufacture positioning splints for intra-operative guidance. The system provides further intra-operative assistance with the help of a computer display showing jaw positions and 3D positioning guides updated in real-time during the surgical procedure. The CAS system aids in dealing with complex cases with benefits for the patient, with surgical practice, and for orthodontic finishing. Advanced software tools for diagnosis and treatment planning allow preparation of detailed operative plans, osteotomy repositioning, bone reconstructions, surgical resident training and assessing the difficulties of the surgical procedures prior to the surgery. CAS has the potential to make the elaboration of the surgical plan a more flexible process, increase the level of detail and accuracy of the plan, yield higher operative precision and control, and enhance documentation of cases. Supported by NIDCR DE017727, and DE018962 PMID:20816308

  7. Molecular, electronic structure and conformational flexibility of the 1,6-dihydropyrimidine, 4,5-dihydrofuro[2,3-d]pyrimidine and their oxo, imino and methylene derivatives

    NASA Astrophysics Data System (ADS)

    Shishkin, Oleg V.; Antonov, Dmitry M.

    1996-11-01

    Molecular and electronic structures of 1,6-dihydropyrimidine, 4,5-dihydrofuro[2,3-d]pyrimidine and their oxo, imino and methylene derivatives have been studied using the semiempirical quantum-chemical method AM1. The equilibrium geometry of all molecules is planar. These results were confirmed by X-ray structural investigations of the 1-oxo- and 1-imino derivatives of 2,5-dimethyl-3-(2,2,2-trichloroethyl)-4,5-dihydrofuro[2,3-d]pyrimidine. However, the dihydropyrimidine ring in all compounds possesses a degree of conformational flexibility. The transition from a planar equilibrium conformation to a distorted sofa with the CNCC torsion angle ± 20° causes an increase of energy less than 1.5 kcal mol -1. The factors that determine this property of the dihydroheterocycle (bending strain, non-aromaticity, conjugation, 1,2-allylic strain) have been considered.

  8. Self-assembled 3D heterometallic Cu(II)/Fe(II) coordination polymers with octahedral net skeletons: structural features, molecular magnetism, thermal and oxidation catalytic properties.

    PubMed

    Karabach, Yauhen Y; Guedes da Silva, M Fátima C; Kopylovich, Maximilian N; Gil-Hernández, Beatriz; Sanchiz, Joaquin; Kirillov, Alexander M; Pombeiro, Armando J L

    2010-12-01

    The new three-dimensional (3D) heterometallic Cu(II)/Fe(II) coordination polymers [Cu(6)(H(2)tea)(6)Fe(CN)(6)](n)(NO(3))(2n)·6nH(2)O (1) and [Cu(6)(Hmdea)(6)Fe(CN)(6)](n)(NO(3))(2n)·7nH(2)O (2) have been easily generated by aqueous-medium self-assembly reactions of copper(II) nitrate with triethanolamine or N-methyldiethanolamine (H(3)tea or H(2)mdea, respectively), in the presence of potassium ferricyanide and sodium hydroxide. They have been isolated as air-stable crystalline solids and fully characterized including by single-crystal X-ray diffraction analyses. The latter reveal the formation of 3D metal-organic frameworks that are constructed from the [Cu(2)(μ-H(2)tea)(2)](2+) or [Cu(2)(μ-Hmdea)(2)](2+) nodes and the octahedral [Fe(CN)(6)](4-) linkers, featuring regular (1) or distorted (2) octahedral net skeletons. Upon dehydration, both compounds show reversible escape and binding processes toward water or methanol molecules. Magnetic susceptibility measurements of 1 and 2 reveal strong antiferromagnetic [J = -199(1) cm(-1)] or strong ferromagnetic [J = +153(1) cm(-1)] couplings between the copper(II) ions through the μ-O-alkoxo atoms in 1 or 2, respectively. The differences in magnetic behavior are explained in terms of the dependence of the magnetic coupling constant on the Cu-O-Cu bridging angle. Compounds 1 and 2 also act as efficient catalyst precursors for the mild oxidation of cyclohexane by aqueous hydrogen peroxide to cyclohexanol and cyclohexanone (homogeneous catalytic system), leading to maximum total yields (based on cyclohexane) and turnover numbers (TONs) up to about 22% and 470, respectively. PMID:21028781

  9. 3D polarimetric purity

    NASA Astrophysics Data System (ADS)

    Gil, José J.; San José, Ignacio

    2010-11-01

    From our previous definition of the indices of polarimetric purity for 3D light beams [J.J. Gil, J.M. Correas, P.A. Melero and C. Ferreira, Monogr. Semin. Mat. G. de Galdeano 31, 161 (2004)], an analysis of their geometric and physical interpretation is presented. It is found that, in agreement with previous results, the first parameter is a measure of the degree of polarization, whereas the second parameter (called the degree of directionality) is a measure of the mean angular aperture of the direction of propagation of the corresponding light beam. This pair of invariant, non-dimensional, indices of polarimetric purity contains complete information about the polarimetric purity of a light beam. The overall degree of polarimetric purity is obtained as a weighted quadratic average of the degree of polarization and the degree of directionality.

  10. 3D field harmonics

    SciTech Connect

    Caspi, S.; Helm, M.; Laslett, L.J.

    1991-03-30

    We have developed an harmonic representation for the three dimensional field components within the windings of accelerator magnets. The form by which the field is presented is suitable for interfacing with other codes that make use of the 3D field components (particle tracking and stability). The field components can be calculated with high precision and reduced cup time at any location (r,{theta},z) inside the magnet bore. The same conductor geometry which is used to simulate line currents is also used in CAD with modifications more readily available. It is our hope that the format used here for magnetic fields can be used not only as a means of delivering fields but also as a way by which beam dynamics can suggest correction to the conductor geometry. 5 refs., 70 figs.

  11. 'Bonneville' in 3-D!

    NASA Technical Reports Server (NTRS)

    2004-01-01

    The Mars Exploration Rover Spirit took this 3-D navigation camera mosaic of the crater called 'Bonneville' after driving approximately 13 meters (42.7 feet) to get a better vantage point. Spirit's current position is close enough to the edge to see the interior of the crater, but high enough and far enough back to get a view of all of the walls. Because scientists and rover controllers are so pleased with this location, they will stay here for at least two more martian days, or sols, to take high resolution panoramic camera images of 'Bonneville' in its entirety. Just above the far crater rim, on the left side, is the rover's heatshield, which is visible as a tiny reflective speck.

  12. Is conformation a fundamental descriptor in QSAR? A case for halogenated anesthetics

    PubMed Central

    Guimarães, Maria C; Duarte, Mariene H; Silla, Josué M

    2016-01-01

    Summary An intriguing question in 3D-QSAR lies on which conformation(s) to use when generating molecular descriptors (MD) for correlation with bioactivity values. This is not a simple task because the bioactive conformation in molecule data sets is usually unknown and, therefore, optimized structures in a receptor-free environment are often used to generate the MD´s. In this case, a wrong conformational choice can cause misinterpretation of the QSAR model. The present computational work reports the conformational analysis of the volatile anesthetic isoflurane (2-chloro-2-(difluoromethoxy)-1,1,1-trifluoroethane) in the gas phase and also in polar and nonpolar implicit and explicit solvents to show that stable minima (ruled by intramolecular interactions) do not necessarily coincide with the bioconformation (ruled by enzyme induced fit). Consequently, a QSAR model based on two-dimensional chemical structures was built and exhibited satisfactory modeling/prediction capability and interpretability, then suggesting that these 2D MD´s can be advantageous over some three-dimensional descriptors. PMID:27340468

  13. 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.

  14. Elucidating the structural basis of diphenyl ether derivatives as highly potent enoyl-ACP reductase inhibitors through molecular dynamics simulations and 3D-QSAR study.

    PubMed

    Kamsri, Pharit; Punkvang, Auradee; Saparpakorn, Patchareenart; Hannongbua, Supa; Irle, Stephan; Pungpo, Pornpan

    2014-07-01

    Diphenyl ether derivatives are good candidates for anti-tuberculosis agents that display a promising potency for inhibition of InhA, an essential enoyl-acyl carrier protein (ACP) reductase involved in fatty acid biosynthesis pathways in Mycobacterium tuberculosis. In this work, key structural features for the inhibition were identified by 3D-QSAR CoMSIA models, constructed based on available experimental binding properties of diphenyl ether inhibitors, and a set of four representative compounds was subjected to MD simulations of inhibitor-InhA complexes for the calculation of binding free energies. The results show that bulky groups are required for the R1 substituent on the phenyl A ring of the inhibitors to favor a hydrophobic pocket formed by residues Phe149, Met155, Pro156, Ala157, Tyr158, Pro193, Met199, Val203, Leu207, Ile215, and Leu218. Small substituents with a hydrophilic property are required at the R3 and R4 positions of the inhibitor phenyl B rings to form hydrogen bonds with the backbones of Gly96 and Met98, respectively. For the R2 substituent, small substituents with simultaneous hydrophilic or hydrophobic properties are required to favor the interaction with the pyrophosphate moiety of NAD(+) and the methyl side chain of Ala198, respectively. The reported data provide structural guidance for the design of new and potent diphenyl ether-based inhibitors with high inhibitory activities against M. tuberculosis InhA. PMID:24935113

  15. Quantifying Modes of 3D Cell Migration.

    PubMed

    Driscoll, Meghan K; Danuser, Gaudenz

    2015-12-01

    Although it is widely appreciated that cells migrate in a variety of diverse environments in vivo, we are only now beginning to use experimental workflows that yield images with sufficient spatiotemporal resolution to study the molecular processes governing cell migration in 3D environments. Since cell migration is a dynamic process, it is usually studied via microscopy, but 3D movies of 3D processes are difficult to interpret by visual inspection. In this review, we discuss the technologies required to study the diversity of 3D cell migration modes with a focus on the visualization and computational analysis tools needed to study cell migration quantitatively at a level comparable to the analyses performed today on cells crawling on flat substrates. PMID:26603943

  16. Modeling Cellular Processes in 3-D

    PubMed Central

    Mogilner, Alex; Odde, David

    2011-01-01

    Summary 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 3-D. Here, we highlight recent advances related to 3-D modeling in cell biology. While some processes require full 3-D analysis, we suggest that others are more naturally described in 2-D or 1-D. Keeping the dimensionality as low as possible reduces computational time and makes models more intuitively comprehensible; however, the ability to test full 3-D models will build greater confidence in models generally and remains an important emerging area of cell biological modeling. PMID:22036197

  17. Macro-molecular data storage with petabyte/cm3 density, highly parallel read/write operations, and genuine 3D storage capability

    NASA Astrophysics Data System (ADS)

    Mansuripur, Masud; Khulbe, Pramod K.

    2004-09-01

    Digital information can be encoded in the building-block sequence of macromolecules, such as RNA and single-stranded DNA. Methods of "writing" and "reading" macromolecular strands are currently available, but they are slow and expensive. In an ideal molecular data storage system, routine operations such as write, read, erase, store, and transfer must be done reliably and at high speed within an integrated chip. As a first step toward demonstrating the feasibility of this concept, we report preliminary results of DNA readout experiments conducted in miniaturized chambers that are scalable to even smaller dimensions. We show that translocation of a single-stranded DNA molecule (consisting of 50 adenosine bases followed by 100 cytosine bases) through an ion-channel yields a characteristic signal that is attributable to the 2-segment structure of the molecule. We also examine the dependence of the rate and speed of molecular translocation on the adjustable parameters of the experiment.

  18. Combining 3-D plasmonic gold nanorod arrays with colloidal nanoparticles as a versatile concept for reliable, sensitive, and selective molecular detection by SERS.

    PubMed

    Yilmaz, Mehmet; Senlik, Erhan; Biskin, Erhan; Yavuz, Mustafa Selman; Tamer, Ugur; Demirel, Gokhan

    2014-03-28

    The detection of molecules at an ultralow level by Surface-Enhanced Raman Spectroscopy (SERS) has recently attracted enormous interest for various applications especially in biological, medical, and environmental fields. Despite the significant progress, SERS systems are still facing challenges for practical applications related to their sensitivity, reliability, and selectivity. To overcome these limitations, in this study, we have proposed a simple yet facile concept by combining 3-D anisotropic gold nanorod arrays with colloidal gold nanoparticles having different shapes for highly reliable, selective, and sensitive detection of some hazardous chemical and biological warfare agents in trace amounts through SERS. The gold nanorod arrays were created on the BK7 glass slides or silicon wafer surfaces via the oblique angle deposition (OAD) technique without using any template material or lithography technique and their surface densities were adjusted by manipulating the deposition angle (α). It is found that gold nanorod arrays fabricated at α = 10° exhibited the highest SERS enhancement in the absence of colloidal gold nanoparticles. Synergetic enhancement was obviously observed in SERS signals when combining gold nanorod arrays with colloidal gold nanoparticles having different shapes (i.e., spherical, rod, and cage). Due to their ability to produce localized surface plasmons (LSPs) in transverse and longitudinal directions, utilization of colloidal gold nanorods as a synergetic agent led to an increase in the enhancement factor by about tenfold compared to plain gold nanorod arrays. Moreover, we have tested our approach to detect some chemical and biological toxins namely dipicolinic acid (DIP), methyl parathion (MP), and diethyl phosphoramidate (DP). For all toxins, Raman spectra with high signal-to-noise ratios and reproducibility were successfully obtained over a broad concentration range (5 ppm-10 ppb). Our results suggest that the slightly tangled and

  19. 3D Structure of Sulfolobus solfataricus Carboxypeptidase Developed by Molecular Modeling is Confirmed by Site-Directed Mutagenesis and Small Angle X-Ray Scattering

    PubMed Central

    Occhipinti, Emanuela; Martelli, Pier Luigi; Spinozzi, Francesco; Corsi, Federica; Formantici, Cristina; Molteni, Laura; Amenitsch, Heintz; Mariani, Paolo; Tortora, Paolo; Casadio, Rita

    2003-01-01

    Sulfolobus solfataricus carboxypeptidase (CPSso) is a thermostable zinc-metalloenzyme with a Mr of 43,000. Taking into account the experimentally determined zinc content of one ion per subunit, we developed two alternative 3D models, starting from the available structures of Thermoactinomyces vulgaris carboxypeptidase (Model A) and Pseudomonas carboxypeptidase G2 (Model B). The former enzyme is monomeric and has one metal ion in the active site, while the latter is dimeric and has two bound zinc ions. The two models were computed by exploiting the structural alignment of the one zinc- with the two zinc-containing active sites of the two templates, and with a threading procedure. Both computed structures resembled the respective template, with only one bound zinc with tetrahedric coordination in the active site. With these models, two different quaternary structures can be modeled: one using Model A with a hexameric symmetry, the other from Model B with a tetrameric symmetry. Mutagenesis experiments directed toward the residues putatively involved in metal chelation in either of the models disproved Model A and supported Model B, in which the metal-binding site comprises His108, Asp109, and His168. We also identified Glu142 as the acidic residue interacting with the water molecule occupying the fourth chelation site. Furthermore, the overall fold and the oligomeric structure of the molecule was validated by small angle x-ray scattering (SAXS). An ab initio original approach was used to reconstruct the shape of the CPSso in solution from the experimental curves. The results clearly support a tetrameric structure. The Monte Carlo method was then used to compare the crystallographic coordinates of the possible quaternary structures for CPSso with the SAXS profiles. The fitting procedure showed that only the model built using the Pseudomonas carboxypeptidase G2 structure as a template fitted the experimental data. PMID:12885660

  20. Prominent rocks - 3D

    NASA Technical Reports Server (NTRS)

    1997-01-01

    Many prominent rocks near the Sagan Memorial Station are featured in this image, taken in stereo by the Imager for Mars Pathfinder (IMP) on Sol 3. 3D glasses are necessary to identify surface detail. Wedge is at lower left; Shark, Half-Dome, and Pumpkin are at center. Flat Top, about four inches high, is at lower right. The horizon in the distance is one to two kilometers away.

    Mars Pathfinder is the second in NASA's Discovery program of low-cost spacecraft with highly focused science goals. The Jet Propulsion Laboratory, Pasadena, CA, developed and manages the Mars Pathfinder mission for NASA's Office of Space Science, Washington, D.C. JPL is an operating division of the California Institute of Technology (Caltech). The Imager for Mars Pathfinder (IMP) was developed by the University of Arizona Lunar and Planetary Laboratory under contract to JPL. Peter Smith is the Principal Investigator.

    Click below to see the left and right views individually. [figure removed for brevity, see original site] Left [figure removed for brevity, see original site] Right

  1. 'Diamond' in 3-D

    NASA Technical Reports Server (NTRS)

    2004-01-01

    This 3-D, microscopic imager mosaic of a target area on a rock called 'Diamond Jenness' was taken after NASA's Mars Exploration Rover Opportunity ground into the surface with its rock abrasion tool for a second time.

    Opportunity has bored nearly a dozen holes into the inner walls of 'Endurance Crater.' On sols 177 and 178 (July 23 and July 24, 2004), the rover worked double-duty on Diamond Jenness. Surface debris and the bumpy shape of the rock resulted in a shallow and irregular hole, only about 2 millimeters (0.08 inch) deep. The final depth was not enough to remove all the bumps and leave a neat hole with a smooth floor. This extremely shallow depression was then examined by the rover's alpha particle X-ray spectrometer.

    On Sol 178, Opportunity's 'robotic rodent' dined on Diamond Jenness once again, grinding almost an additional 5 millimeters (about 0.2 inch). The rover then applied its Moessbauer spectrometer to the deepened hole. This double dose of Diamond Jenness enabled the science team to examine the rock at varying layers. Results from those grindings are currently being analyzed.

    The image mosaic is about 6 centimeters (2.4 inches) across.

  2. A Generally Applicable Computer Algorithm Based on the Group Additivity Method for the Calculation of Seven Molecular Descriptors: Heat of Combustion, LogPO/W, LogS, Refractivity, Polarizability, Toxicity and LogBB of Organic Compounds; Scope and Limits of Applicability.

    PubMed

    Naef, Rudolf

    2015-01-01

    A generally applicable computer algorithm for the calculation of the seven molecular descriptors heat of combustion, logPoctanol/water, logS (water solubility), molar refractivity, molecular polarizability, aqueous toxicity (protozoan growth inhibition) and logBB (log (cblood/cbrain)) is presented. The method, an extendable form of the group-additivity method, is based on the complete break-down of the molecules into their constituting atoms and their immediate neighbourhood. The contribution of the resulting atom groups to the descriptor values is calculated using the Gauss-Seidel fitting method, based on experimental data gathered from literature. The plausibility of the method was tested for each descriptor by means of a k-fold cross-validation procedure demonstrating good to excellent predictive power for the former six descriptors and low reliability of logBB predictions. The goodness of fit (Q²) and the standard deviation of the 10-fold cross-validation calculation was >0.9999 and 25.2 kJ/mol, respectively, (based on N = 1965 test compounds) for the heat of combustion, 0.9451 and 0.51 (N = 2640) for logP, 0.8838 and 0.74 (N = 1419) for logS, 0.9987 and 0.74 (N = 4045) for the molar refractivity, 0.9897 and 0.77 (N = 308) for the molecular polarizability, 0.8404 and 0.42 (N = 810) for the toxicity and 0.4709 and 0.53 (N = 383) for logBB. The latter descriptor revealing a very low Q² for the test molecules (R² was 0.7068 and standard deviation 0.38 for N = 413 training molecules) is included as an example to show the limits of the group-additivity method. An eighth molecular descriptor, the heat of formation, was indirectly calculated from the heat of combustion data and correlated with published experimental heat of formation data with a correlation coefficient R² of 0.9974 (N = 2031). PMID:26457702

  3. 3D-QSAR and molecular docking studies of 1,3,5-triazene-2,4-diamine derivatives against r-RNA: novel bacterial translation inhibitors.

    PubMed

    Sekhar, Y Nataraja; Nayana, M Ravi Shashi; Sivakumari, N; Ravikumar, Muttineni; Mahmood, S K

    2008-06-01

    Aminoglycoside mimetics inhibit bacterial translation by interfering with the ribosomal decoding site. To elucidate the structural properties of these compounds important for antibacterial activity, comparative molecular field analysis (CoMFA) and comparative molecular similarity indices analysis (CoMSIA) were applied to a set of 56 aminoglycosides mimetics. The successful CoMFA model yielded the leave-one-out (LOO) cross-validated correlation coefficient (q(2)) of 0.708 and a non-cross-validated correlation coefficient (r(2)) of 0.967. CoMSIA model gave q(2)=0.556 and r(2)=0.935. The CoMFA and CoMSIA models were validated with 36 test set compounds and showed a good r(pred)(2) of 0.624 and 0.640, respectively. Contour maps of the two QSAR approaches show that electronic effects dominantly determine the binding affinities. These obtained results were agreed well with the experimental observations and docking studies. The results not only lead to a better understanding of structural requirements of bacterial translation inhibitors but also can help in the design of novel bacterial translation inhibitors. PMID:18372201

  4. 3D-dynamic representation of DNA sequences.

    PubMed

    Wąż, Piotr; Bielińska-Wąż, Dorota

    2014-03-01

    A new 3D graphical representation of DNA sequences is introduced. This representation is called 3D-dynamic representation. It is a generalization of the 2D-dynamic dynamic representation. The sequences are represented by sets of "material points" in the 3D space. The resulting 3D-dynamic graphs are treated as rigid bodies. The descriptors characterizing the graphs are analogous to the ones used in the classical dynamics. The classification diagrams derived from this representation are presented and discussed. Due to the third dimension, "the history of the graph" can be recognized graphically because the 3D-dynamic graph does not overlap with itself. Specific parts of the graphs correspond to specific parts of the sequence. This feature is essential for graphical comparisons of the sequences. Numerically, both 2D and 3D approaches are of high quality. In particular, a difference in a single base between two sequences can be identified and correctly described (one can identify which base) by both 2D and 3D methods. PMID:24567158

  5. 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.

  6. Combined experimental (FT-IR, UV-visible spectra, NMR) and theoretical studies on the molecular structure, vibrational spectra, HOMO, LUMO, MESP surfaces, reactivity descriptor and molecular docking of Phomarin

    NASA Astrophysics Data System (ADS)

    Kumar, Abhishek; Srivastava, Ambrish Kumar; Gangwar, Shashi; Misra, Neeraj; Mondal, Avijit; Brahmachari, Goutam

    2015-09-01

    Phomarin is an important natural product belonging to anthraquinone series of compounds. The equilibrium geometry of phomarin has been determined and analyzed at DFT method employing B3LYP/6-311++G(d,p) level of computation. The reactivity of molecule using various descriptors such as Fukui functions, local softness, electrophilicity, electronegativity, Hardness, HOMO-LUMO gap are calculated and discussed. The infrared and UV-vis spectra of phomarin are calculated and compared with the experimentally observed ones. Moreover, 1H and 13C NMR spectra have been calculated by using the gauge independent atomic orbital method. We also notice that phomarin shows remarkable biological activities against malaria parasite. The study suggests further investigation on phomarin for their pharmacological importance.

  7. 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. PMID:27561920

  8. 3D-QSAR and molecular mechanics study for the differences in the azole activity against yeastlike and filamentous fungi and their relation to P450DM inhibition. 1. 3-substituted-4(3H)-quinazolinones.

    PubMed

    Fratev, Filip; Benfenati, Emilio

    2005-01-01

    A combination between 3D-QSAR and molecular mechanics (MM)-docking study was used as a tool to detail and model the mechanism of action of 46 antifungal azoles. Two methods of alignment of the ligands were performed: (i) alignment of the main skeleton without substituents and (ii) alignment of a defined substructure. The best model is characterized by q(2) with the values of 0.70 for yeastlike (yeast), 0.66 for filamentous fungi, and 0.70 for the selectivity against filamentous fungi. 3D-QSAR regression maps derived from six models were used to identify the regions responsible for the differences in the compounds activity against yeast and filamentous fungi. The binding energy of the important substructures (Local Binding Energy-LBE) and its standard deviation were calculated in order to demonstrate quantitatively the contribution of substituents reflecting the diversity of the antifungal activity. The comparisons of these results with the same regions of the contour maps indicated a good correspondence between the 3D-QSAR and MM (LBE) approaches allowing association between the maps and the participating residues in the active sites of P450DM of C. albicans and A. fumigatus. The pi-pi interactions of two or more aromatic groups of the ligands with Phe228 and Tyr132 prove to be most important for the differences in activity against C. albicans. In A. fumigatus there was a better occupation of the inner central I-spiral in the areas around the heme. For the activity against A. fumigatus the pi-pi interactions of aromatic groups of the compounds with Phe509, Phe228, and Tyr132 are significant for the activity. PMID:15921453

  9. Assessment of metal-assisted nucleophile activation in the hepatitis delta virus ribozyme from molecular simulation and 3D-RISM

    PubMed Central

    Radak, Brian K.; Lee, Tai-Sung; Harris, Michael E.

    2015-01-01

    The hepatitis delta virus ribozyme is an efficient catalyst of RNA 2′-O-transphosphorylation and has emerged as a key experimental system for identifying and characterizing fundamental features of RNA catalysis. Recent structural and biochemical data have led to a proposed mechanistic model whereby an active site Mg2+ ion facilitates deprotonation of the O2′ nucleophile, and a protonated cytosine residue (C75) acts as an acid to donate a proton to the O5′ leaving group as noted in a previous study. This model assumes that the active site Mg2+ ion forms an inner-sphere coordination with the O2′ nucleophile and a nonbridging oxygen of the scissile phosphate. These contacts, however, are not fully resolved in the crystal structure, and biochemical data are not able to unambiguously exclude other mechanistic models. In order to explore the feasibility of this model, we exhaustively mapped the free energy surfaces with different active site ion occupancies via quantum mechanical/molecular mechanical (QM/MM) simulations. We further incorporate a three-dimensional reference interaction site model for the solvated ion atmosphere that allows these calculations to consider not only the rate associated with the chemical steps, but also the probability of observing the system in the presumed active state with the Mg2+ ion bound. The QM/MM results predict that a pathway involving metal-assisted nucleophile activation is feasible based on the rate-controlling transition state barrier departing from the presumed metal-bound active state. However, QM/MM results for a similar pathway in the absence of Mg2+ are not consistent with experimental data, suggesting that a structural model in which the crystallographically determined Mg2+ is simply replaced with Na+ is likely incorrect. It should be emphasized, however, that these results hinge upon the assumption of the validity of the presumed Mg2+-bound starting state, which has not yet been definitively verified experimentally

  10. 3D Spectroscopy in Astronomy

    NASA Astrophysics Data System (ADS)

    Mediavilla, Evencio; Arribas, Santiago; Roth, Martin; Cepa-Nogué, Jordi; Sánchez, Francisco

    2011-09-01

    Preface; Acknowledgements; 1. Introductory review and technical approaches Martin M. Roth; 2. Observational procedures and data reduction James E. H. Turner; 3. 3D Spectroscopy instrumentation M. A. Bershady; 4. Analysis of 3D data Pierre Ferruit; 5. Science motivation for IFS and galactic studies F. Eisenhauer; 6. Extragalactic studies and future IFS science Luis Colina; 7. Tutorials: how to handle 3D spectroscopy data Sebastian F. Sánchez, Begona García-Lorenzo and Arlette Pécontal-Rousset.

  11. 3D Elevation Program—Virtual USA in 3D

    USGS Publications Warehouse

    Lukas, Vicki; Stoker, J.M.

    2016-01-01

    The U.S. Geological Survey (USGS) 3D Elevation Program (3DEP) uses a laser system called ‘lidar’ (light detection and ranging) to create a virtual reality map of the Nation that is very accurate. 3D maps have many uses with new uses being discovered all the time.  

  12. Structural requirements of pyrido[2,3-d]pyrimidin-7-one as CDK4/D inhibitors: 2D autocorrelation, CoMFA and CoMSIA analyses.

    PubMed

    Caballero, Julio; Fernández, Michael; González-Nilo, Fernando D

    2008-06-01

    2D autocorrelation, comparative molecular field analysis (CoMFA) and comparative molecular similarity indices analysis (CoMSIA) were undertaken for a series of pyrido[2,3-d]pyrimidin-7-ones to correlate cyclin-dependent kinase (CDK) cyclin D/CDK4 inhibition with 2D and 3D structural properties of 60 known compounds. QSAR models with considerable internal as well as external predictive ability were obtained. The relevant 2D autocorrelation descriptors for modeling CDK4/D inhibitory activity were selected by linear and nonlinear genetic algorithms (GAs) using multiple linear regression (MLR) and Bayesian-regularized genetic neural network (BRGNN) approaches, respectively. Both models showed good predictive statistics; but BRGNN model enables better external predictions. A weight-based input ranking scheme and Kohonen self-organized maps (SOMs) were carried out to interpret the final net weights. The 2D autocorrelation space brings different descriptors for CDK4/D inhibition, and suggests the atomic properties relevant for the inhibitors to interact with CDK4/D active site. CoMFA and CoMSIA analyses were developed with a focus on interpretative ability using coefficient contour maps. CoMSIA produced significantly better results. The results indicate a strong correlation between the inhibitory activity of the modeled compounds and the electrostatic and hydrophobic fields around them. PMID:18468903

  13. CheS-Mapper - Chemical Space Mapping and Visualization in 3D

    PubMed Central

    2012-01-01

    Analyzing chemical datasets is a challenging task for scientific researchers in the field of chemoinformatics. It is important, yet difficult to understand the relationship between the structure of chemical compounds, their physico-chemical properties, and biological or toxic effects. To that respect, visualization tools can help to better comprehend the underlying correlations. Our recently developed 3D molecular viewer CheS-Mapper (Chemical Space Mapper) divides large datasets into clusters of similar compounds and consequently arranges them in 3D space, such that their spatial proximity reflects their similarity. The user can indirectly determine similarity, by selecting which features to employ in the process. The tool can use and calculate different kind of features, like structural fragments as well as quantitative chemical descriptors. These features can be highlighted within CheS-Mapper, which aids the chemist to better understand patterns and regularities and relate the observations to established scientific knowledge. As a final function, the tool can also be used to select and export specific subsets of a given dataset for further analysis. PMID:22424447

  14. Extra dimensions: 3D in PDF documentation

    SciTech Connect

    Graf, Norman A.

    2011-01-11

    Experimental science is replete with multi-dimensional information which is often poorly represented by the two dimensions of presentation slides and print media. Past efforts to disseminate such information to a wider audience have failed for a number of reasons, including a lack of standards which are easy to implement and have broad support. Adobe's Portable Document Format (PDF) has in recent years become the de facto standard for secure, dependable electronic information exchange. It has done so by creating an open format, providing support for multiple platforms and being reliable and extensible. By providing support for the ECMA standard Universal 3D (U3D) file format in its free Adobe Reader software, Adobe has made it easy to distribute and interact with 3D content. By providing support for scripting and animation, temporal data can also be easily distributed to a wide, non-technical audience. We discuss how the field of radiation imaging could benefit from incorporating full 3D information about not only the detectors, but also the results of the experimental analyses, in its electronic publications. In this article, we present examples drawn from high-energy physics, mathematics and molecular biology which take advantage of this functionality. Furthermore, we demonstrate how 3D detector elements can be documented, using either CAD drawings or other sources such as GEANT visualizations as input.

  15. Extra dimensions: 3D in PDF documentation

    DOE PAGESBeta

    Graf, Norman A.

    2011-01-11

    Experimental science is replete with multi-dimensional information which is often poorly represented by the two dimensions of presentation slides and print media. Past efforts to disseminate such information to a wider audience have failed for a number of reasons, including a lack of standards which are easy to implement and have broad support. Adobe's Portable Document Format (PDF) has in recent years become the de facto standard for secure, dependable electronic information exchange. It has done so by creating an open format, providing support for multiple platforms and being reliable and extensible. By providing support for the ECMA standard Universalmore » 3D (U3D) file format in its free Adobe Reader software, Adobe has made it easy to distribute and interact with 3D content. By providing support for scripting and animation, temporal data can also be easily distributed to a wide, non-technical audience. We discuss how the field of radiation imaging could benefit from incorporating full 3D information about not only the detectors, but also the results of the experimental analyses, in its electronic publications. In this article, we present examples drawn from high-energy physics, mathematics and molecular biology which take advantage of this functionality. Furthermore, we demonstrate how 3D detector elements can be documented, using either CAD drawings or other sources such as GEANT visualizations as input.« less

  16. Modular 3-D Transport model

    EPA Science Inventory

    MT3D was first developed by Chunmiao Zheng in 1990 at S.S. Papadopulos & Associates, Inc. with partial support from the U.S. Environmental Protection Agency (USEPA). Starting in 1990, MT3D was released as a pubic domain code from the USEPA. Commercial versions with enhanced capab...

  17. Market study: 3-D eyetracker

    NASA Technical Reports Server (NTRS)

    1977-01-01

    A market study of a proposed version of a 3-D eyetracker for initial use at NASA's Ames Research Center was made. The commercialization potential of a simplified, less expensive 3-D eyetracker was ascertained. Primary focus on present and potential users of eyetrackers, as well as present and potential manufacturers has provided an effective means of analyzing the prospects for commercialization.

  18. LLNL-Earth3D

    2013-10-01

    Earth3D is a computer code designed to allow fast calculation of seismic rays and travel times through a 3D model of the Earth. LLNL is using this for earthquake location and global tomography efforts and such codes are of great interest to the Earth Science community.

  19. [3-D ultrasound in gastroenterology].

    PubMed

    Zoller, W G; Liess, H

    1994-06-01

    Three-dimensional (3D) sonography represents a development of noninvasive diagnostic imaging by real-time two-dimensional (2D) sonography. The use of transparent rotating scans, comparable to a block of glass, generates a 3D effect. The objective of the present study was to optimate 3D presentation of abdominal findings. Additional investigations were made with a new volumetric program to determine the volume of selected findings of the liver. The results were compared with the estimated volumes of 2D sonography and 2D computer tomography (CT). For the processing of 3D images, typical parameter constellations were found for the different findings, which facilitated processing of 3D images. In more than 75% of the cases examined we found an optimal 3D presentation of sonographic findings with respect to the evaluation criteria developed by us for the 3D imaging of processed data. Great differences were found for the estimated volumes of the findings of the liver concerning the three different techniques applied. 3D ultrasound represents a valuable method to judge morphological appearance in abdominal findings. The possibility of volumetric measurements enlarges its potential diagnostic significance. Further clinical investigations are necessary to find out if definite differentiation between benign and malign findings is possible. PMID:7919882

  20. 3D World Building System

    SciTech Connect

    2013-10-30

    This video provides an overview of the Sandia National Laboratories developed 3-D World Model Building capability that provides users with an immersive, texture rich 3-D model of their environment in minutes using a laptop and color and depth camera.

  1. 3D World Building System

    ScienceCinema

    None

    2014-02-26

    This video provides an overview of the Sandia National Laboratories developed 3-D World Model Building capability that provides users with an immersive, texture rich 3-D model of their environment in minutes using a laptop and color and depth camera.

  2. Euro3D Science Conference

    NASA Astrophysics Data System (ADS)

    Walsh, J. R.

    2004-02-01

    The Euro3D RTN is an EU funded Research Training Network to foster the exploitation of 3D spectroscopy in Europe. 3D spectroscopy is a general term for spectroscopy of an area of the sky and derives its name from its two spatial + one spectral dimensions. There are an increasing number of instruments which use integral field devices to achieve spectroscopy of an area of the sky, either using lens arrays, optical fibres or image slicers, to pack spectra of multiple pixels on the sky (``spaxels'') onto a 2D detector. On account of the large volume of data and the special methods required to reduce and analyse 3D data, there are only a few centres of expertise and these are mostly involved with instrument developments. There is a perceived lack of expertise in 3D spectroscopy spread though the astronomical community and its use in the armoury of the observational astronomer is viewed as being highly specialised. For precisely this reason the Euro3D RTN was proposed to train young researchers in this area and develop user tools to widen the experience with this particular type of data in Europe. The Euro3D RTN is coordinated by Martin M. Roth (Astrophysikalisches Institut Potsdam) and has been running since July 2002. The first Euro3D science conference was held in Cambridge, UK from 22 to 23 May 2003. The main emphasis of the conference was, in keeping with the RTN, to expose the work of the young post-docs who are funded by the RTN. In addition the team members from the eleven European institutes involved in Euro3D also presented instrumental and observational developments. The conference was organized by Andy Bunker and held at the Institute of Astronomy. There were over thirty participants and 26 talks covered the whole range of application of 3D techniques. The science ranged from Galactic planetary nebulae and globular clusters to kinematics of nearby galaxies out to objects at high redshift. Several talks were devoted to reporting recent observations with newly

  3. PLOT3D user's manual

    NASA Technical Reports Server (NTRS)

    Walatka, Pamela P.; Buning, Pieter G.; Pierce, Larry; Elson, Patricia A.

    1990-01-01

    PLOT3D is a computer graphics program designed to visualize the grids and solutions of computational fluid dynamics. Seventy-four functions are available. Versions are available for many systems. PLOT3D can handle multiple grids with a million or more grid points, and can produce varieties of model renderings, such as wireframe or flat shaded. Output from PLOT3D can be used in animation programs. The first part of this manual is a tutorial that takes the reader, keystroke by keystroke, through a PLOT3D session. The second part of the manual contains reference chapters, including the helpfile, data file formats, advice on changing PLOT3D, and sample command files.

  4. 3D printing in dentistry.

    PubMed

    Dawood, A; Marti Marti, B; Sauret-Jackson, V; Darwood, A

    2015-12-01

    3D printing has been hailed as a disruptive technology which will change manufacturing. Used in aerospace, defence, art and design, 3D printing is becoming a subject of great interest in surgery. The technology has a particular resonance with dentistry, and with advances in 3D imaging and modelling technologies such as cone beam computed tomography and intraoral scanning, and with the relatively long history of the use of CAD CAM technologies in dentistry, it will become of increasing importance. Uses of 3D printing include the production of drill guides for dental implants, the production of physical models for prosthodontics, orthodontics and surgery, the manufacture of dental, craniomaxillofacial and orthopaedic implants, and the fabrication of copings and frameworks for implant and dental restorations. This paper reviews the types of 3D printing technologies available and their various applications in dentistry and in maxillofacial surgery. PMID:26657435

  5. AGGRESCAN3D (A3D): server for prediction of aggregation properties of protein structures

    PubMed Central

    Zambrano, Rafael; Jamroz, Michal; Szczasiuk, Agata; Pujols, Jordi; Kmiecik, Sebastian; Ventura, Salvador

    2015-01-01

    Protein aggregation underlies an increasing number of disorders and constitutes a major bottleneck in the development of therapeutic proteins. Our present understanding on the molecular determinants of protein aggregation has crystalized in a series of predictive algorithms to identify aggregation-prone sites. A majority of these methods rely only on sequence. Therefore, they find difficulties to predict the aggregation properties of folded globular proteins, where aggregation-prone sites are often not contiguous in sequence or buried inside the native structure. The AGGRESCAN3D (A3D) server overcomes these limitations by taking into account the protein structure and the experimental aggregation propensity scale from the well-established AGGRESCAN method. Using the A3D server, the identified aggregation-prone residues can be virtually mutated to design variants with increased solubility, or to test the impact of pathogenic mutations. Additionally, A3D server enables to take into account the dynamic fluctuations of protein structure in solution, which may influence aggregation propensity. This is possible in A3D Dynamic Mode that exploits the CABS-flex approach for the fast simulations of flexibility of globular proteins. The A3D server can be accessed at http://biocomp.chem.uw.edu.pl/A3D/. PMID:25883144

  6. PLOT3D/AMES, APOLLO UNIX VERSION USING GMR3D (WITH TURB3D)

    NASA Technical Reports Server (NTRS)

    Buning, P.

    1994-01-01

    PLOT3D is an interactive graphics program designed to help scientists visualize computational fluid dynamics (CFD) grids and solutions. Today, supercomputers and CFD algorithms can provide scientists with simulations of such highly complex phenomena that obtaining an understanding of the simulations has become a major problem. Tools which help the scientist visualize the simulations can be of tremendous aid. PLOT3D/AMES offers more functions and features, and has been adapted for more types of computers than any other CFD graphics program. Version 3.6b+ is supported for five computers and graphic libraries. Using PLOT3D, CFD physicists can view their computational models from any angle, observing the physics of problems and the quality of solutions. As an aid in designing aircraft, for example, PLOT3D's interactive computer graphics can show vortices, temperature, reverse flow, pressure, and dozens of other characteristics of air flow during flight. As critical areas become obvious, they can easily be studied more closely using a finer grid. PLOT3D is part of a computational fluid dynamics software cycle. First, a program such as 3DGRAPE (ARC-12620) helps the scientist generate computational grids to model an object and its surrounding space. Once the grids have been designed and parameters such as the angle of attack, Mach number, and Reynolds number have been specified, a "flow-solver" program such as INS3D (ARC-11794 or COS-10019) solves the system of equations governing fluid flow, usually on a supercomputer. Grids sometimes have as many as two million points, and the "flow-solver" produces a solution file which contains density, x- y- and z-momentum, and stagnation energy for each grid point. With such a solution file and a grid file containing up to 50 grids as input, PLOT3D can calculate and graphically display any one of 74 functions, including shock waves, surface pressure, velocity vectors, and particle traces. PLOT3D's 74 functions are organized into

  7. PLOT3D/AMES, APOLLO UNIX VERSION USING GMR3D (WITHOUT TURB3D)

    NASA Technical Reports Server (NTRS)

    Buning, P.

    1994-01-01

    PLOT3D is an interactive graphics program designed to help scientists visualize computational fluid dynamics (CFD) grids and solutions. Today, supercomputers and CFD algorithms can provide scientists with simulations of such highly complex phenomena that obtaining an understanding of the simulations has become a major problem. Tools which help the scientist visualize the simulations can be of tremendous aid. PLOT3D/AMES offers more functions and features, and has been adapted for more types of computers than any other CFD graphics program. Version 3.6b+ is supported for five computers and graphic libraries. Using PLOT3D, CFD physicists can view their computational models from any angle, observing the physics of problems and the quality of solutions. As an aid in designing aircraft, for example, PLOT3D's interactive computer graphics can show vortices, temperature, reverse flow, pressure, and dozens of other characteristics of air flow during flight. As critical areas become obvious, they can easily be studied more closely using a finer grid. PLOT3D is part of a computational fluid dynamics software cycle. First, a program such as 3DGRAPE (ARC-12620) helps the scientist generate computational grids to model an object and its surrounding space. Once the grids have been designed and parameters such as the angle of attack, Mach number, and Reynolds number have been specified, a "flow-solver" program such as INS3D (ARC-11794 or COS-10019) solves the system of equations governing fluid flow, usually on a supercomputer. Grids sometimes have as many as two million points, and the "flow-solver" produces a solution file which contains density, x- y- and z-momentum, and stagnation energy for each grid point. With such a solution file and a grid file containing up to 50 grids as input, PLOT3D can calculate and graphically display any one of 74 functions, including shock waves, surface pressure, velocity vectors, and particle traces. PLOT3D's 74 functions are organized into

  8. A local adaptive image descriptor

    NASA Astrophysics Data System (ADS)

    Zahid Ishraque, S. M.; Shoyaib, Mohammad; Abdullah-Al-Wadud, M.; Monirul Hoque, Md; Chae, Oksam

    2013-12-01

    The local binary pattern (LBP) is a robust but computationally simple approach in texture analysis. However, LBP performs poorly in the presence of noise and large illumination variation. Thus, a local adaptive image descriptor termed as LAID is introduced in this proposal. It is a ternary pattern and is able to generate persistent codes to represent microtextures in a given image, especially in noisy conditions. It can also generate stable texture codes if the pixel intensities change abruptly due to the illumination changes. Experimental results also show the superiority of the proposed method over other state-of-the-art methods.

  9. A Compact Shape Descriptor for Triangular Surface Meshes

    PubMed Central

    Gao, Zhanheng; Yu, Zeyun; Pang, Xiaoli

    2014-01-01

    Three-dimensional shape-based descriptors have been widely used in object recognition and database retrieval. In the current work, we present a novel method called compact Shape-DNA (cShape-DNA) to describe the shape of a triangular surface mesh. While the original Shape-DNA technique provides an effective and isometric-invariant descriptor for surface shapes, the number of eigenvalues used is typically large. To further reduce the space and time consumptions, especially for large-scale database applications, it is of great interest to find a more compact way to describe an arbitrary surface shape. In the present approach, the standard Shape-DNA is first computed from the given mesh and then processed by surface area-based normalization and line subtraction. The proposed cShape-DNA descriptor is composed of some low frequencies of the discrete Fourier transform of the processed Shape-DNA. Several experiments are shown to illustrate the effectiveness and efficiency of the cShape-DNA method on 3D shape analysis, particularly on shape comparison and classification. PMID:24910467

  10. Bioprinting of 3D hydrogels.

    PubMed

    Stanton, M M; Samitier, J; Sánchez, S

    2015-08-01

    Three-dimensional (3D) bioprinting has recently emerged as an extension of 3D material printing, by using biocompatible or cellular components to build structures in an additive, layer-by-layer methodology for encapsulation and culture of cells. These 3D systems allow for cell culture in a suspension for formation of highly organized tissue or controlled spatial orientation of cell environments. The in vitro 3D cellular environments simulate the complexity of an in vivo environment and natural extracellular matrices (ECM). This paper will focus on bioprinting utilizing hydrogels as 3D scaffolds. Hydrogels are advantageous for cell culture as they are highly permeable to cell culture media, nutrients, and waste products generated during metabolic cell processes. They have the ability to be fabricated in customized shapes with various material properties with dimensions at the micron scale. 3D hydrogels are a reliable method for biocompatible 3D printing and have applications in tissue engineering, drug screening, and organ on a chip models. PMID:26066320

  11. Unassisted 3D camera calibration

    NASA Astrophysics Data System (ADS)

    Atanassov, Kalin; Ramachandra, Vikas; Nash, James; Goma, Sergio R.

    2012-03-01

    With the rapid growth of 3D technology, 3D image capture has become a critical part of the 3D feature set on mobile phones. 3D image quality is affected by the scene geometry as well as on-the-device processing. An automatic 3D system usually assumes known camera poses accomplished by factory calibration using a special chart. In real life settings, pose parameters estimated by factory calibration can be negatively impacted by movements of the lens barrel due to shaking, focusing, or camera drop. If any of these factors displaces the optical axes of either or both cameras, vertical disparity might exceed the maximum tolerable margin and the 3D user may experience eye strain or headaches. To make 3D capture more practical, one needs to consider unassisted (on arbitrary scenes) calibration. In this paper, we propose an algorithm that relies on detection and matching of keypoints between left and right images. Frames containing erroneous matches, along with frames with insufficiently rich keypoint constellations, are detected and discarded. Roll, pitch yaw , and scale differences between left and right frames are then estimated. The algorithm performance is evaluated in terms of the remaining vertical disparity as compared to the maximum tolerable vertical disparity.

  12. Arena3D: visualization of biological networks in 3D

    PubMed Central

    Pavlopoulos, Georgios A; O'Donoghue, Seán I; Satagopam, Venkata P; Soldatos, Theodoros G; Pafilis, Evangelos; Schneider, Reinhard

    2008-01-01

    Background Complexity is a key problem when visualizing biological networks; as the number of entities increases, most graphical views become incomprehensible. Our goal is to enable many thousands of entities to be visualized meaningfully and with high performance. Results We present a new visualization tool, Arena3D, which introduces a new concept of staggered layers in 3D space. Related data – such as proteins, chemicals, or pathways – can be grouped onto separate layers and arranged via layout algorithms, such as Fruchterman-Reingold, distance geometry, and a novel hierarchical layout. Data on a layer can be clustered via k-means, affinity propagation, Markov clustering, neighbor joining, tree clustering, or UPGMA ('unweighted pair-group method with arithmetic mean'). A simple input format defines the name and URL for each node, and defines connections or similarity scores between pairs of nodes. The use of Arena3D is illustrated with datasets related to Huntington's disease. Conclusion Arena3D is a user friendly visualization tool that is able to visualize biological or any other network in 3D space. It is free for academic use and runs on any platform. It can be downloaded or lunched directly from . Java3D library and Java 1.5 need to be pre-installed for the software to run. PMID:19040715

  13. Fdf in US3D

    NASA Astrophysics Data System (ADS)

    Otis, Collin; Ferrero, Pietro; Candler, Graham; Givi, Peyman

    2013-11-01

    The scalar filtered mass density function (SFMDF) methodology is implemented into the computer code US3D. This is an unstructured Eulerian finite volume hydrodynamic solver and has proven very effective for simulation of compressible turbulent flows. The resulting SFMDF-US3D code is employed for large eddy simulation (LES) on unstructured meshes. Simulations are conducted of subsonic and supersonic flows under non-reacting and reacting conditions. The consistency and the accuracy of the simulated results are assessed along with appraisal of the overall performance of the methodology. The SFMDF-US3D is now capable of simulating high speed flows in complex configurations.

  14. Local functional descriptors for surface comparison based binding prediction

    PubMed Central

    2012-01-01

    Background Molecular recognition in proteins occurs due to appropriate arrangements of physical, chemical, and geometric properties of an atomic surface. Similar surface regions should create similar binding interfaces. Effective methods for comparing surface regions can be used in identifying similar regions, and to predict interactions without regard to the underlying structural scaffold that creates the surface. Results We present a new descriptor for protein functional surfaces and algorithms for using these descriptors to compare protein surface regions to identify ligand binding interfaces. Our approach uses descriptors of local regions of the surface, and assembles collections of matches to compare larger regions. Our approach uses a variety of physical, chemical, and geometric properties, adaptively weighting these properties as appropriate for different regions of the interface. Our approach builds a classifier based on a training corpus of examples of binding sites of the target ligand. The constructed classifiers can be applied to a query protein providing a probability for each position on the protein that the position is part of a binding interface. We demonstrate the effectiveness of the approach on a number of benchmarks, demonstrating performance that is comparable to the state-of-the-art, with an approach with more generality than these prior methods. Conclusions Local functional descriptors offer a new method for protein surface comparison that is sufficiently flexible to serve in a variety of applications. PMID:23176080

  15. Neuronal nicotinic acetylcholine receptor agonists: pharmacophores, evolutionary QSAR and 3D-QSAR models.

    PubMed

    Nicolotti, Orazio; Altomare, Cosimo; Pellegrini-Calace, Marialuisa; Carotti, Angelo

    2004-01-01

    Neuronal nicotinic acetylcholine ion channel receptors (nAChRs) exist as several subtypes and are involved in a variety of functions and disorders of the central nervous system (CNS), such as Alzheimer's and Parkinson's diseases. The lack of reliable information on the 3D structure of nAChRs prompted us to focus efforts on pharmacophore and structure-affinity relationships (SAFIRs). The use of DISCO (DIStance COmparison) and Catalyst/HipHop led to the formulation of a pharmacophore that is made of three geometrically unrelated features: (i) an ammonium head involved in coulombic and/or H-bond interactions, (ii) a lone pair of a pyridine nitrogen or a carbonyl oxygen, as H-bond acceptor site, and (iii) a hydrophobic molecular region generally constituted by aliphatic cycles. The quantitative SAFIR (QSAFIR) study was carried out on about three hundred nicotinoid agonists, and coherent results were obtained from classical Hansch-type approach, 3D QSAFIRs, based on Comparative Molecular Field Analysis (CoMFA), and trade-off models generated by Multi-objective Genetic QSAR (MoQSAR), a novel evolutionary software that makes use of Genetic Programming (GP) and multi-objective optimization (MO). Within each congeneric series, Hansch-type equations revealed detrimental steric effects as the major factors modulating the receptor affinity, whereas CoMFA allowed us to merge progressively single-class models in a more global one, whose robustness was supported by crossvalidation, high prediction statistics and satisfactory predictions of the affinity data of a true external ligand set (r(2)(pred) = 0.796). Next, MoQSAR was used to analyze a data set of 58 highly active nicotinoids characterized by 56 descriptors, that are log P, MR and 54 low inter-correlated WHIM (Weighted Holistic Invariant Molecular) indices. Equivalent QSAFIR models, that represent different compromises between structural model complexity, fitting and internal model complexity, were found. Our attention was

  16. Three-dimensional Content-Based Cardiac Image Retrieval using global and local descriptors

    PubMed Central

    Bergamasco, Leila C. C.; Nunes, Fátima L. S.

    2015-01-01

    The increase in volume of medical images generated and stored has created difficulties in accurate image retrieval. An alternative is to generate three-dimensional (3D) models from such medical images and use them in the search. Some of the main cardiac illnesses, such as Congestive Heart Failure (CHF), have deformation in the heart’s shape as one of the main symptoms, which can be identified faster in a 3D object than in slices. This article presents techniques developed to retrieve 3D cardiac models using global and local descriptors within a content-based image retrieval system. These techniques were applied in pre-classified 3D models with and without the CHF disease and they were evaluated by using Precision vs. Recall metric. We observed that local descriptors achieved better results than a global descriptor, reaching 85% of accuracy. The results confirmed the potential of using 3D models retrieval in the medical context to aid in the diagnosis. PMID:26958280

  17. Three-dimensional Content-Based Cardiac Image Retrieval using global and local descriptors.

    PubMed

    Bergamasco, Leila C C; Nunes, Fátima L S

    2015-01-01

    The increase in volume of medical images generated and stored has created difficulties in accurate image retrieval. An alternative is to generate three-dimensional (3D) models from such medical images and use them in the search. Some of the main cardiac illnesses, such as Congestive Heart Failure (CHF), have deformation in the heart's shape as one of the main symptoms, which can be identified faster in a 3D object than in slices. This article presents techniques developed to retrieve 3D cardiac models using global and local descriptors within a content-based image retrieval system. These techniques were applied in pre-classified 3D models with and without the CHF disease and they were evaluated by using Precision vs. Recall metric. We observed that local descriptors achieved better results than a global descriptor, reaching 85% of accuracy. The results confirmed the potential of using 3D models retrieval in the medical context to aid in the diagnosis. PMID:26958280

  18. Wavefront construction in 3-D

    SciTech Connect

    Chilcoat, S.R. Hildebrand, S.T.

    1995-12-31

    Travel time computation in inhomogeneous media is essential for pre-stack Kirchhoff imaging in areas such as the sub-salt province in the Gulf of Mexico. The 2D algorithm published by Vinje, et al, has been extended to 3D to compute wavefronts in complicated inhomogeneous media. The 3D wavefront construction algorithm provides many advantages over conventional ray tracing and other methods of computing travel times in 3D. The algorithm dynamically maintains a reasonably consistent ray density without making a priori guesses at the number of rays to shoot. The determination of caustics in 3D is a straight forward geometric procedure. The wavefront algorithm also enables the computation of multi-valued travel time surfaces.

  19. Heterodyne 3D ghost imaging

    NASA Astrophysics Data System (ADS)

    Yang, Xu; Zhang, Yong; Yang, Chenghua; Xu, Lu; Wang, Qiang; Zhao, Yuan

    2016-06-01

    Conventional three dimensional (3D) ghost imaging measures range of target based on pulse fight time measurement method. Due to the limit of data acquisition system sampling rate, range resolution of the conventional 3D ghost imaging is usually low. In order to take off the effect of sampling rate to range resolution of 3D ghost imaging, a heterodyne 3D ghost imaging (HGI) system is presented in this study. The source of HGI is a continuous wave laser instead of pulse laser. Temporal correlation and spatial correlation of light are both utilized to obtain the range image of target. Through theory analysis and numerical simulations, it is demonstrated that HGI can obtain high range resolution image with low sampling rate.

  20. Combinatorial 3D Mechanical Metamaterials

    NASA Astrophysics Data System (ADS)

    Coulais, Corentin; Teomy, Eial; de Reus, Koen; Shokef, Yair; van Hecke, Martin

    2015-03-01

    We present a class of elastic structures which exhibit 3D-folding motion. Our structures consist of cubic lattices of anisotropic unit cells that can be tiled in a complex combinatorial fashion. We design and 3d-print this complex ordered mechanism, in which we combine elastic hinges and defects to tailor the mechanics of the material. Finally, we use this large design space to encode smart functionalities such as surface patterning and multistability.

  1. In silico prediction of major drug clearance pathways by support vector machines with feature-selected descriptors.

    PubMed

    Toshimoto, Kouta; Wakayama, Naomi; Kusama, Makiko; Maeda, Kazuya; Sugiyama, Yuichi; Akiyama, Yutaka

    2014-11-01

    We have previously established an in silico classification method ("CPathPred") to predict the major clearance pathways of drugs based on an empirical decision with only four physicochemical descriptors-charge, molecular weight, octanol-water distribution coefficient, and protein unbound fraction in plasma-using a rectangular method. In this study, we attempted to improve the prediction performance of the method by introducing a support vector machine (SVM) and increasing the number of descriptors. The data set consisted of 141 approved drugs whose major clearance pathways were classified into metabolism by CYP3A4, CYP2C9, or CYP2D6; organic anion transporting polypeptide-mediated hepatic uptake; or renal excretion. With the same four default descriptors as used in CPathPred, the SVM-based predictor (named "default descriptor SVM") resulted in higher prediction performance compared with a rectangular-based predictor judged by 10-fold cross-validation. Two SVM-based predictors were also established by adding some descriptors as follows: 1) 881 descriptors predicted in silico from the chemical structures of drugs in addition to 4 default descriptors ("885 descriptor SVM"); and 2) selected descriptors extracted by a feature selection based on a greedy algorithm with default descriptors ("feature selection SVM"). The prediction accuracies of the rectangular-based predictor, default descriptor SVM, 885 descriptor SVM, and feature selection SVM were 0.49, 0.60, 0.72, and 0.91, respectively, and the overall precision values for these four methods were 0.72, 0.77, 0.86, and 0.98, respectively. In conclusion, we successfully constructed SVM-based predictors with limited numbers of descriptors to classify the major clearance pathways of drugs in humans with high prediction performance. PMID:25128502

  2. From 3D view to 3D print

    NASA Astrophysics Data System (ADS)

    Dima, M.; Farisato, G.; Bergomi, M.; Viotto, V.; Magrin, D.; Greggio, D.; Farinato, J.; Marafatto, L.; Ragazzoni, R.; Piazza, D.

    2014-08-01

    In the last few years 3D printing is getting more and more popular and used in many fields going from manufacturing to industrial design, architecture, medical support and aerospace. 3D printing is an evolution of bi-dimensional printing, which allows to obtain a solid object from a 3D model, realized with a 3D modelling software. The final product is obtained using an additive process, in which successive layers of material are laid down one over the other. A 3D printer allows to realize, in a simple way, very complex shapes, which would be quite difficult to be produced with dedicated conventional facilities. Thanks to the fact that the 3D printing is obtained superposing one layer to the others, it doesn't need any particular work flow and it is sufficient to simply draw the model and send it to print. Many different kinds of 3D printers exist based on the technology and material used for layer deposition. A common material used by the toner is ABS plastics, which is a light and rigid thermoplastic polymer, whose peculiar mechanical properties make it diffusely used in several fields, like pipes production and cars interiors manufacturing. I used this technology to create a 1:1 scale model of the telescope which is the hardware core of the space small mission CHEOPS (CHaracterising ExOPlanets Satellite) by ESA, which aims to characterize EXOplanets via transits observations. The telescope has a Ritchey-Chrétien configuration with a 30cm aperture and the launch is foreseen in 2017. In this paper, I present the different phases for the realization of such a model, focusing onto pros and cons of this kind of technology. For example, because of the finite printable volume (10×10×12 inches in the x, y and z directions respectively), it has been necessary to split the largest parts of the instrument in smaller components to be then reassembled and post-processed. A further issue is the resolution of the printed material, which is expressed in terms of layers

  3. The assess facility descriptor module

    SciTech Connect

    Jordan, S.E.; Winblad, A.; Key, B.; Walker, S.; Renis, T.; Saleh, R.

    1989-01-01

    The Facility Descriptor (Facility) module is part of the Analytic System and Software for Evaluating Safeguards and Security (ASSESS). Facility is the foundational software application in the ASSESS system for modelling a nuclear facility's safeguards and security system to determine the effectiveness against theft of special nuclear material. The Facility module provides the tools for an analyst to define a complete description of a facility's physical protection system which can then be used by other ASSESS software modules to determine vulnerability to a spectrum of insider and outsider threats. The analyst can enter a comprehensive description of the protection system layout including all secured areas, target locations, and detailed safeguards specifications. An extensive safeguard component catalog provides the reference data for calculating delay and detection performance. Multiple target locations within the same physical area may be specified, and the facility may be defined for two different operational states such as dayshift and nightshift. 6 refs., 5 figs.

  4. THESAURUS OF ERIC DESCRIPTORS (INTERIM) JANUARY 1967.

    ERIC Educational Resources Information Center

    1967

    THE "THESAURUS OF ERIC DESCRIPTORS (INTERIM)" SUPERSEDES, AND REPRESENTS A REFINEMENT OF, THE "THESAURUS OF ERIC DESCRIPTORS." THE INTERIM ISSUE IS A PRELIMINARY ERIC SYSTEM TOOL AND IS NOT TO BE CONSIDERED A COMPLETE REPRESENTATION OF THE FINAL PRODUCT. THIS REFINEMENT IS THE RESULT OF TWO MAJOR PROJECTS--(1) THE INCORPORATION OF SUGGESTIONS…

  5. YouDash3D: exploring stereoscopic 3D gaming for 3D movie theaters

    NASA Astrophysics Data System (ADS)

    Schild, Jonas; Seele, Sven; Masuch, Maic

    2012-03-01

    Along with the success of the digitally revived stereoscopic cinema, events beyond 3D movies become attractive for movie theater operators, i.e. interactive 3D games. In this paper, we present a case that explores possible challenges and solutions for interactive 3D games to be played by a movie theater audience. We analyze the setting and showcase current issues related to lighting and interaction. Our second focus is to provide gameplay mechanics that make special use of stereoscopy, especially depth-based game design. Based on these results, we present YouDash3D, a game prototype that explores public stereoscopic gameplay in a reduced kiosk setup. It features live 3D HD video stream of a professional stereo camera rig rendered in a real-time game scene. We use the effect to place the stereoscopic effigies of players into the digital game. The game showcases how stereoscopic vision can provide for a novel depth-based game mechanic. Projected trigger zones and distributed clusters of the audience video allow for easy adaptation to larger audiences and 3D movie theater gaming.

  6. Aircraft noise descriptor and its application

    NASA Astrophysics Data System (ADS)

    Igarashi, Juichi

    The methods and indices used in Japan to evaluate aircraft noise and the government-enforced countermeasures are discussed. The ECPNL descriptor was modified so as to make the new descriptor, WECPNL', approximately equivalent to Lden, and the noise contours were calculated for each airport in Japan. The government enforced the policy of land purchase within the WECPNL' of 85, and the houses within the value of 75 were declared as needing insulation. The noise descriptor Leq or Ldn has been used to describe human responses to various kinds of noises. However, a single value descriptor was found to have a limit of applicability, because the human response is not a linear function of a sound level. Another defect of the descriptor is a failure to represent the human response adequately for a small number of flights. It is noted that the house vibration caused by low-frequency components of aircraft noise cannot yet be evaluated.

  7. Remote 3D Medical Consultation

    NASA Astrophysics Data System (ADS)

    Welch, Greg; Sonnenwald, Diane H.; Fuchs, Henry; Cairns, Bruce; Mayer-Patel, Ketan; Yang, Ruigang; State, Andrei; Towles, Herman; Ilie, Adrian; Krishnan, Srinivas; Söderholm, Hanna M.

    Two-dimensional (2D) video-based telemedical consultation has been explored widely in the past 15-20 years. Two issues that seem to arise in most relevant case studies are the difficulty associated with obtaining the desired 2D camera views, and poor depth perception. To address these problems we are exploring the use of a small array of cameras to synthesize a spatially continuous range of dynamic three-dimensional (3D) views of a remote environment and events. The 3D views can be sent across wired or wireless networks to remote viewers with fixed displays or mobile devices such as a personal digital assistant (PDA). The viewpoints could be specified manually or automatically via user head or PDA tracking, giving the remote viewer virtual head- or hand-slaved (PDA-based) remote cameras for mono or stereo viewing. We call this idea remote 3D medical consultation (3DMC). In this article we motivate and explain the vision for 3D medical consultation; we describe the relevant computer vision/graphics, display, and networking research; we present a proof-of-concept prototype system; and we present some early experimental results supporting the general hypothesis that 3D remote medical consultation could offer benefits over conventional 2D televideo.

  8. Speaking Volumes About 3-D

    NASA Technical Reports Server (NTRS)

    2002-01-01

    In 1999, Genex submitted a proposal to Stennis Space Center for a volumetric 3-D display technique that would provide multiple users with a 360-degree perspective to simultaneously view and analyze 3-D data. The futuristic capabilities of the VolumeViewer(R) have offered tremendous benefits to commercial users in the fields of medicine and surgery, air traffic control, pilot training and education, computer-aided design/computer-aided manufacturing, and military/battlefield management. The technology has also helped NASA to better analyze and assess the various data collected by its satellite and spacecraft sensors. Genex capitalized on its success with Stennis by introducing two separate products to the commercial market that incorporate key elements of the 3-D display technology designed under an SBIR contract. The company Rainbow 3D(R) imaging camera is a novel, three-dimensional surface profile measurement system that can obtain a full-frame 3-D image in less than 1 second. The third product is the 360-degree OmniEye(R) video system. Ideal for intrusion detection, surveillance, and situation management, this unique camera system offers a continuous, panoramic view of a scene in real time.

  9. Spectral Characterization and 3D Molecular Modeling Studies of Metal Complexes Involving the O, N-Donor Environment of Quinazoline-4(3H)-one Schiff Base and Their Biological Studies

    PubMed Central

    Siddappa, Kuruba; Mane, Sunilkumar B.

    2014-01-01

    A simple condensation of 3-amino-2-methylquinazoline-4-one with 2-hydroxy-1-naphthaldehyde produced new tridentate ONO donor Schiff base ligand with efficient yield. The structural characterization of ligand and its Cu(II), Ni(II), Co(II), Mn(II), Zn(II), and Cd(II) complexes were achieved by the aid of elemental analysis, spectral characterization such as (UV-visible, IR, NMR, mass, and ESR), and magnetic data. The analytical and spectroscopic studies suggest the octahedral geometries of Cu(II), Co(II), Ni(II) and Mn(II) complexes and tetrahedral geometry of Zn(II) and Cd(II) complexes with the tridentate ONO Schiff base ligand. Furthermore, the conclusions drawn from these studies afford further support to the mode of bonding discussed on the basis of their 3D molecular modeling studies by considering different bond lengths, bond angles, and bond distance. The ligand and its metal complexes evaluated for their antimicrobial activity against Staphylococcus aureus (MTCC number 7443), Bacillus subtilis (MTCC number 9878), Escherichia coli (MTCC number 1698), Aspergillus niger (MTCC number 281), and Aspergillus flavus (MTCC number 277). The MIC of these compounds was found to be most active at 10 μg/mL concentration in inhibiting the growth of the tested organisms. The DNA cleavage activity of all the complexes was studied by gel electrophoresis method. PMID:24678278

  10. 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).

  11. 3D-Printed Microfluidics.

    PubMed

    Au, Anthony K; Huynh, Wilson; Horowitz, Lisa F; Folch, Albert

    2016-03-14

    The advent of soft lithography allowed for an unprecedented expansion in the field of microfluidics. However, the vast majority of PDMS microfluidic devices are still made with extensive manual labor, are tethered to bulky control systems, and have cumbersome user interfaces, which all render commercialization difficult. On the other hand, 3D printing has begun to embrace the range of sizes and materials that appeal to the developers of microfluidic devices. Prior to fabrication, a design is digitally built as a detailed 3D CAD file. The design can be assembled in modules by remotely collaborating teams, and its mechanical and fluidic behavior can be simulated using finite-element modeling. As structures are created by adding materials without the need for etching or dissolution, processing is environmentally friendly and economically efficient. We predict that in the next few years, 3D printing will replace most PDMS and plastic molding techniques in academia. PMID:26854878

  12. 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…

  13. 3D Computations and Experiments

    SciTech Connect

    Couch, R; Faux, D; Goto, D; Nikkel, D

    2004-04-05

    This project consists of two activities. Task A, Simulations and Measurements, combines all the material model development and associated numerical work with the materials-oriented experimental activities. The goal of this effort is to provide an improved understanding of dynamic material properties and to provide accurate numerical representations of those properties for use in analysis codes. Task B, ALE3D Development, involves general development activities in the ALE3D code with the focus of improving simulation capabilities for problems of mutual interest to DoD and DOE. Emphasis is on problems involving multi-phase flow, blast loading of structures and system safety/vulnerability studies.

  14. 3D Computations and Experiments

    SciTech Connect

    Couch, R; Faux, D; Goto, D; Nikkel, D

    2003-05-12

    This project is in its first full year after the combining of two previously funded projects: ''3D Code Development'' and ''Dynamic Material Properties''. The motivation behind this move was to emphasize and strengthen the ties between the experimental work and the computational model development in the materials area. The next year's activities will indicate the merging of the two efforts. The current activity is structured in two tasks. Task A, ''Simulations and Measurements'', combines all the material model development and associated numerical work with the materials-oriented experimental activities. Task B, ''ALE3D Development'', is a continuation of the non-materials related activities from the previous project.

  15. Nature of magnetic interactions in 3D {[M(II)(pyrazole)4]2[Nb(IV)(CN)8].4H2O}n (M = Mn, Fe, Co, Ni) molecular magnets.

    PubMed

    Pinkowicz, Dawid; Pełka, Robert; Drath, Olga; Nitek, Wojciech; Bałanda, Maria; Majcher, Anna Małgorzata; Poneti, Giordano; Sieklucka, Barbara

    2010-08-16

    The self-assembly of [Nb(IV)(CN)(8)](4-) with different 3d metal centers in an aqueous solution and an excess of pyrazole resulted in the formation of four 3D isostructural compounds {[M(II)(pyrazole)(4)](2)[Nb(IV)(CN)(8)].4H(2)O}(n), where M(II) = Mn, Fe, Co, and Ni for 1-4, respectively. All four assemblies crystallize in the same I4(1)/a space group and show identical cyanido-bridged structures decorated with pyrazole molecules coordinated to M(II) centers. All four compounds show also long-range magnetic ordering below 24, 8, 6, and 13 K, respectively. A thorough analysis of the structural and magnetic data utilizing the molecular field model has allowed for an estimation of the values of coupling constants J(M-Nb) attributed to the one type of M(II)-NC-Nb(IV) linkage existing in 1-4. The J(M-Nb) values increase monotonically from -6.8 for 1 through -3.1 for 2 and +3.5 for 3, to +8.1 cm(-1) for 4 and are strongly correlated with the number of unpaired electrons on the M(II) metal center. Average orbital contributions to the total exchange coupling constants J(M-Nb) have also been identified and calculated: antiferromagnetic J(AF) = -21.6 cm(-1) originating from the d(xy), d(xz), and d(yz) orbitals of M(II) and ferromagnetic J(F) = +15.4 cm(-1) originating from d(z(2)) and d(x(2)-y(2)) orbitals of M(II). Antiferromagnetic interaction is successively weakened in the 1-4 row with each additional electron on the t(2g) level, which results in a change of the sign of J(M-Nb) and the nature of long-range magnetic ordering from ferrimagnetic in 1 and 2 to ferromagnetic in 3 and 4. PMID:20690767

  16. SNL3dFace

    2007-07-20

    This software distribution contains MATLAB and C++ code to enable identity verification using 3D images that may or may not contain a texture component. The code is organized to support system performance testing and system capability demonstration through the proper configuration of the available user interface. Using specific algorithm parameters the face recognition system has been demonstrated to achieve a 96.6% verification rate (Pd) at 0.001 false alarm rate. The system computes robust facial featuresmore » of a 3D normalized face using Principal Component Analysis (PCA) and Fisher Linear Discriminant Analysis (FLDA). A 3D normalized face is obtained by alighning each face, represented by a set of XYZ coordinated, to a scaled reference face using the Iterative Closest Point (ICP) algorithm. The scaled reference face is then deformed to the input face using an iterative framework with parameters that control the deformed surface regulation an rate of deformation. A variety of options are available to control the information that is encoded by the PCA. Such options include the XYZ coordinates, the difference of each XYZ coordinates from the reference, the Z coordinate, the intensity/texture values, etc. In addition to PCA/FLDA feature projection this software supports feature matching to obtain similarity matrices for performance analysis. In addition, this software supports visualization of the STL, MRD, 2D normalized, and PCA synthetic representations in a 3D environment.« less

  17. 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…

  18. SNL3dFace

    SciTech Connect

    Russ, Trina; Koch, Mark; Koudelka, Melissa; Peters, Ralph; Little, Charles; Boehnen, Chris; Peters, Tanya

    2007-07-20

    This software distribution contains MATLAB and C++ code to enable identity verification using 3D images that may or may not contain a texture component. The code is organized to support system performance testing and system capability demonstration through the proper configuration of the available user interface. Using specific algorithm parameters the face recognition system has been demonstrated to achieve a 96.6% verification rate (Pd) at 0.001 false alarm rate. The system computes robust facial features of a 3D normalized face using Principal Component Analysis (PCA) and Fisher Linear Discriminant Analysis (FLDA). A 3D normalized face is obtained by alighning each face, represented by a set of XYZ coordinated, to a scaled reference face using the Iterative Closest Point (ICP) algorithm. The scaled reference face is then deformed to the input face using an iterative framework with parameters that control the deformed surface regulation an rate of deformation. A variety of options are available to control the information that is encoded by the PCA. Such options include the XYZ coordinates, the difference of each XYZ coordinates from the reference, the Z coordinate, the intensity/texture values, etc. In addition to PCA/FLDA feature projection this software supports feature matching to obtain similarity matrices for performance analysis. In addition, this software supports visualization of the STL, MRD, 2D normalized, and PCA synthetic representations in a 3D environment.

  19. 3D Printing: Exploring Capabilities

    ERIC Educational Resources Information Center

    Samuels, Kyle; Flowers, Jim

    2015-01-01

    As 3D printers become more affordable, schools are using them in increasing numbers. They fit well with the emphasis on product design in technology and engineering education, allowing students to create high-fidelity physical models to see and test different iterations in their product designs. They may also help students to "think in three…

  20. Learning spectral descriptors for deformable shape correspondence.

    PubMed

    Litman, R; Bronstein, A M

    2014-01-01

    Informative and discriminative feature descriptors play a fundamental role in deformable shape analysis. For example, they have been successfully employed in correspondence, registration, and retrieval tasks. In recent years, significant attention has been devoted to descriptors obtained from the spectral decomposition of the Laplace-Beltrami operator associated with the shape. Notable examples in this family are the heat kernel signature (HKS) and the recently introduced wave kernel signature (WKS). The Laplacian-based descriptors achieve state-of-the-art performance in numerous shape analysis tasks; they are computationally efficient, isometry-invariant by construction, and can gracefully cope with a variety of transformations. In this paper, we formulate a generic family of parametric spectral descriptors. We argue that to be optimized for a specific task, the descriptor should take into account the statistics of the corpus of shapes to which it is applied (the "signal") and those of the class of transformations to which it is made insensitive (the "noise"). While such statistics are hard to model axiomatically, they can be learned from examples. Following the spirit of the Wiener filter in signal processing, we show a learning scheme for the construction of optimized spectral descriptors and relate it to Mahalanobis metric learning. The superiority of the proposed approach in generating correspondences is demonstrated on synthetic and scanned human figures. We also show that the learned descriptors are robust enough to be learned on synthetic data and transferred successfully to scanned shapes. PMID:24231874

  1. TACO3D. 3-D Finite Element Heat Transfer Code

    SciTech Connect

    Mason, W.E.

    1992-03-04

    TACO3D is a three-dimensional, finite-element program for heat transfer analysis. An extension of the two-dimensional TACO program, it can perform linear and nonlinear analyses and can be used to solve either transient or steady-state problems. The program accepts time-dependent or temperature-dependent material properties, and materials may be isotropic or orthotropic. A variety of time-dependent and temperature-dependent boundary conditions and loadings are available including temperature, flux, convection, and radiation boundary conditions and internal heat generation. Additional specialized features treat enclosure radiation, bulk nodes, and master/slave internal surface conditions (e.g., contact resistance). Data input via a free-field format is provided. A user subprogram feature allows for any type of functional representation of any independent variable. A profile (bandwidth) minimization option is available. The code is limited to implicit time integration for transient solutions. TACO3D has no general mesh generation capability. Rows of evenly-spaced nodes and rows of sequential elements may be generated, but the program relies on separate mesh generators for complex zoning. TACO3D does not have the ability to calculate view factors internally. Graphical representation of data in the form of time history and spatial plots is provided through links to the POSTACO and GRAPE postprocessor codes.

  2. Structural protein descriptors in 1-dimension and their sequence-based predictions.

    PubMed

    Kurgan, Lukasz; Disfani, Fatemeh Miri

    2011-09-01

    The last few decades observed an increasing interest in development and application of 1-dimensional (1D) descriptors of protein structure. These descriptors project 3D structural features onto 1D strings of residue-wise structural assignments. They cover a wide-range of structural aspects including conformation of the backbone, burying depth/solvent exposure and flexibility of residues, and inter-chain residue-residue contacts. We perform first-of-its-kind comprehensive comparative review of the existing 1D structural descriptors. We define, review and categorize ten structural descriptors and we also describe, summarize and contrast over eighty computational models that are used to predict these descriptors from the protein sequences. We show that the majority of the recent sequence-based predictors utilize machine learning models, with the most popular being neural networks, support vector machines, hidden Markov models, and support vector and linear regressions. These methods provide high-throughput predictions and most of them are accessible to a non-expert user via web servers and/or stand-alone software packages. We empirically evaluate several recent sequence-based predictors of secondary structure, disorder, and solvent accessibility descriptors using a benchmark set based on CASP8 targets. Our analysis shows that the secondary structure can be predicted with over 80% accuracy and segment overlap (SOV), disorder with over 0.9 AUC, 0.6 Matthews Correlation Coefficient (MCC), and 75% SOV, and relative solvent accessibility with PCC of 0.7 and MCC of 0.6 (0.86 when homology is used). We demonstrate that the secondary structure predicted from sequence without the use of homology modeling is as good as the structure extracted from the 3D folds predicted by top-performing template-based methods. PMID:21787299

  3. Application of SMILES Notation Based Optimal Descriptors in Drug Discovery and Design.

    PubMed

    Veselinović, Aleksandar M; Veselinović, Jovana B; Živković, Jelena V; Nikolić, Goran M

    2015-01-01

    SMILES notation based optimal descriptors as a universal tool for the QSAR analysis with further application in drug discovery and design is presented. The basis of this QSAR modeling is Monte Carlo method which has important advantages over other methods, like the possibility of analysis of a QSAR as a random event, is discussed. The advantages of SMILES notation based optimal descriptors in comparison to commonly used descriptors are defined. The published results of QSAR modeling with SMILES notation based optimal descriptors applied for various pharmacologically important endpoints are listed. The presented QSAR modeling approach obeys OECD principles and has mechanistic interpretation with possibility to identify molecular fragments that contribute in positive and negative way to studied biological activity, what is of big importance in computer aided drug design of new compounds with desired activity. PMID:25961525

  4. Optoplasmonics: hybridization in 3D

    NASA Astrophysics Data System (ADS)

    Rosa, L.; Gervinskas, G.; Žukauskas, A.; Malinauskas, M.; Brasselet, E.; Juodkazis, S.

    2013-12-01

    Femtosecond laser fabrication has been used to make hybrid refractive and di ractive micro-optical elements in photo-polymer SZ2080. For applications in micro- uidics, axicon lenses were fabricated (both single and arrays), for generation of light intensity patterns extending through the entire depth of a typically tens-of-micrometers deep channel. Further hybridisation of an axicon with a plasmonic slot is fabricated and demonstrated nu- merically. Spiralling chiral grooves were inscribed into a 100-nm-thick gold coating sputtered over polymerized micro-axicon lenses, using a focused ion beam. This demonstrates possibility of hybridisation between optical and plasmonic 3D micro-optical elements. Numerical modelling of optical performance by 3D-FDTD method is presented.

  5. 3-D Relativistic MHD Simulations

    NASA Astrophysics Data System (ADS)

    Nishikawa, K.-I.; Frank, J.; Koide, S.; Sakai, J.-I.; Christodoulou, D. M.; Sol, H.; Mutel, R. L.

    1998-12-01

    We present 3-D numerical simulations of moderately hot, supersonic jets propagating initially along or obliquely to the field lines of a denser magnetized background medium with Lorentz factors of W = 4.56 and evolving in a four-dimensional spacetime. The new results are understood as follows: Relativistic simulations have consistently shown that these jets are effectively heavy and so they do not suffer substantial momentum losses and are not decelerated as efficiently as their nonrelativistic counterparts. In addition, the ambient magnetic field, however strong, can be pushed aside with relative ease by the beam, provided that the degrees of freedom associated with all three spatial dimensions are followed self-consistently in the simulations. This effect is analogous to pushing Japanese ``noren'' or vertical Venetian blinds out of the way while the slats are allowed to bend in 3-D space rather than as a 2-D slab structure.

  6. Forensic 3D Scene Reconstruction

    SciTech Connect

    LITTLE,CHARLES Q.; PETERS,RALPH R.; RIGDON,J. BRIAN; SMALL,DANIEL E.

    1999-10-12

    Traditionally law enforcement agencies have relied on basic measurement and imaging tools, such as tape measures and cameras, in recording a crime scene. A disadvantage of these methods is that they are slow and cumbersome. The development of a portable system that can rapidly record a crime scene with current camera imaging, 3D geometric surface maps, and contribute quantitative measurements such as accurate relative positioning of crime scene objects, would be an asset to law enforcement agents in collecting and recording significant forensic data. The purpose of this project is to develop a feasible prototype of a fast, accurate, 3D measurement and imaging system that would support law enforcement agents to quickly document and accurately record a crime scene.

  7. Forensic 3D scene reconstruction

    NASA Astrophysics Data System (ADS)

    Little, Charles Q.; Small, Daniel E.; Peters, Ralph R.; Rigdon, J. B.

    2000-05-01

    Traditionally law enforcement agencies have relied on basic measurement and imaging tools, such as tape measures and cameras, in recording a crime scene. A disadvantage of these methods is that they are slow and cumbersome. The development of a portable system that can rapidly record a crime scene with current camera imaging, 3D geometric surface maps, and contribute quantitative measurements such as accurate relative positioning of crime scene objects, would be an asset to law enforcement agents in collecting and recording significant forensic data. The purpose of this project is to develop a fieldable prototype of a fast, accurate, 3D measurement and imaging system that would support law enforcement agents to quickly document and accurately record a crime scene.

  8. 360-degree 3D profilometry

    NASA Astrophysics Data System (ADS)

    Song, Yuanhe; Zhao, Hong; Chen, Wenyi; Tan, Yushan

    1997-12-01

    A new method of 360 degree turning 3D shape measurement in which light sectioning and phase shifting techniques are both used is presented in this paper. A sine light field is applied in the projected light stripe, meanwhile phase shifting technique is used to calculate phases of the light slit. Thereafter wrapped phase distribution of the slit is formed and the unwrapping process is made by means of the height information based on the light sectioning method. Therefore phase measuring results with better precision can be obtained. At last the target 3D shape data can be produced according to geometric relationships between phases and the object heights. The principles of this method are discussed in detail and experimental results are shown in this paper.

  9. 3D Printable Graphene Composite.

    PubMed

    Wei, Xiaojun; Li, Dong; Jiang, Wei; Gu, Zheming; Wang, Xiaojuan; Zhang, Zengxing; Sun, Zhengzong

    2015-01-01

    In human being's history, both the Iron Age and Silicon Age thrived after a matured massive processing technology was developed. Graphene is the most recent superior material which could potentially initialize another new material Age. However, while being exploited to its full extent, conventional processing methods fail to provide a link to today's personalization tide. New technology should be ushered in. Three-dimensional (3D) printing fills the missing linkage between graphene materials and the digital mainstream. Their alliance could generate additional stream to push the graphene revolution into a new phase. Here we demonstrate for the first time, a graphene composite, with a graphene loading up to 5.6 wt%, can be 3D printable into computer-designed models. The composite's linear thermal coefficient is below 75 ppm·°C(-1) from room temperature to its glass transition temperature (Tg), which is crucial to build minute thermal stress during the printing process. PMID:26153673

  10. 3D Printed Robotic Hand

    NASA Technical Reports Server (NTRS)

    Pizarro, Yaritzmar Rosario; Schuler, Jason M.; Lippitt, Thomas C.

    2013-01-01

    Dexterous robotic hands are changing the way robots and humans interact and use common tools. Unfortunately, the complexity of the joints and actuations drive up the manufacturing cost. Some cutting edge and commercially available rapid prototyping machines now have the ability to print multiple materials and even combine these materials in the same job. A 3D model of a robotic hand was designed using Creo Parametric 2.0. Combining "hard" and "soft" materials, the model was printed on the Object Connex350 3D printer with the purpose of resembling as much as possible the human appearance and mobility of a real hand while needing no assembly. After printing the prototype, strings where installed as actuators to test mobility. Based on printing materials, the manufacturing cost of the hand was $167, significantly lower than other robotic hands without the actuators since they have more complex assembly processes.

  11. 3D light scanning macrography.

    PubMed

    Huber, D; Keller, M; Robert, D

    2001-08-01

    The technique of 3D light scanning macrography permits the non-invasive surface scanning of small specimens at magnifications up to 200x. Obviating both the problem of limited depth of field inherent to conventional close-up macrophotography and the metallic coating required by scanning electron microscopy, 3D light scanning macrography provides three-dimensional digital images of intact specimens without the loss of colour, texture and transparency information. This newly developed technique offers a versatile, portable and cost-efficient method for the non-invasive digital and photographic documentation of small objects. Computer controlled device operation and digital image acquisition facilitate fast and accurate quantitative morphometric investigations, and the technique offers a broad field of research and educational applications in biological, medical and materials sciences. PMID:11489078

  12. [Real time 3D echocardiography].

    PubMed

    Bauer, F; Shiota, T; Thomas, J D

    2001-07-01

    Three-dimensional representation of the heart is an old concern. Usually, 3D reconstruction of the cardiac mass is made by successive acquisition of 2D sections, the spatial localisation and orientation of which require complex guiding systems. More recently, the concept of volumetric acquisition has been introduced. A matricial emitter-receiver probe complex with parallel data processing provides instantaneous of a pyramidal 64 degrees x 64 degrees volume. The image is restituted in real time and is composed of 3 planes (planes B and C) which can be displaced in all spatial directions at any time during acquisition. The flexibility of this system of acquisition allows volume and mass measurement with greater accuracy and reproducibility, limiting inter-observer variability. Free navigation of the planes of investigation allows reconstruction for qualitative and quantitative analysis of valvular heart disease and other pathologies. Although real time 3D echocardiography is ready for clinical usage, some improvements are still necessary to improve its conviviality. Then real time 3D echocardiography could be the essential tool for understanding, diagnosis and management of patients. PMID:11494630

  13. [Real time 3D echocardiography

    NASA Technical Reports Server (NTRS)

    Bauer, F.; Shiota, T.; Thomas, J. D.

    2001-01-01

    Three-dimensional representation of the heart is an old concern. Usually, 3D reconstruction of the cardiac mass is made by successive acquisition of 2D sections, the spatial localisation and orientation of which require complex guiding systems. More recently, the concept of volumetric acquisition has been introduced. A matricial emitter-receiver probe complex with parallel data processing provides instantaneous of a pyramidal 64 degrees x 64 degrees volume. The image is restituted in real time and is composed of 3 planes (planes B and C) which can be displaced in all spatial directions at any time during acquisition. The flexibility of this system of acquisition allows volume and mass measurement with greater accuracy and reproducibility, limiting inter-observer variability. Free navigation of the planes of investigation allows reconstruction for qualitative and quantitative analysis of valvular heart disease and other pathologies. Although real time 3D echocardiography is ready for clinical usage, some improvements are still necessary to improve its conviviality. Then real time 3D echocardiography could be the essential tool for understanding, diagnosis and management of patients.

  14. Deconstructing field-induced ketene isomerization through Lagrangian descriptors.

    PubMed

    Craven, Galen T; Hernandez, Rigoberto

    2016-02-01

    The time-dependent geometrical separatrices governing state transitions in field-induced ketene isomerization are constructed using the method of Lagrangian descriptors. We obtain the stable and unstable manifolds of time-varying transition states as dynamic phase space objects governing configurational changes when the ketene molecule is subjected to an oscillating electric field. The dynamics of the isomerization reaction are modeled through classical trajectory studies on the Gezelter-Miller potential energy surface and an approximate dipole moment model which is coupled to a time-dependent electric field. We obtain a representation of the reaction geometry, over varying field strengths and oscillation frequencies, by partitioning an initial phase space into basins labeled according to which product state is reached at a given time. The borders between these basins are in agreement with those obtained using Lagrangian descriptors, even in regimes exhibiting chaotic dynamics. Major outcomes of this work are: validation and extension of a transition state theory framework built from Lagrangian descriptors, elaboration of the applicability for this theory to periodically- and aperiodically-driven molecular systems, and prediction of regimes in which isomerization of ketene and its derivatives may be controlled using an external field. PMID:26778728

  15. A novel method to compare protein structures using local descriptors

    PubMed Central

    2011-01-01

    Background Protein structure comparison is one of the most widely performed tasks in bioinformatics. However, currently used methods have problems with the so-called "difficult similarities", including considerable shifts and distortions of structure, sequential swaps and circular permutations. There is a demand for efficient and automated systems capable of overcoming these difficulties, which may lead to the discovery of previously unknown structural relationships. Results We present a novel method for protein structure comparison based on the formalism of local descriptors of protein structure - DEscriptor Defined Alignment (DEDAL). Local similarities identified by pairs of similar descriptors are extended into global structural alignments. We demonstrate the method's capability by aligning structures in difficult benchmark sets: curated alignments in the SISYPHUS database, as well as SISY and RIPC sets, including non-sequential and non-rigid-body alignments. On the most difficult RIPC set of sequence alignment pairs the method achieves an accuracy of 77% (the second best method tested achieves 60% accuracy). Conclusions DEDAL is fast enough to be used in whole proteome applications, and by lowering the threshold of detectable structure similarity it may shed additional light on molecular evolution processes. It is well suited to improving automatic classification of structure domains, helping analyze protein fold space, or to improving protein classification schemes. DEDAL is available online at http://bioexploratorium.pl/EP/DEDAL. PMID:21849047

  16. GPU-Accelerated Denoising in 3D (GD3D)

    2013-10-01

    The raw computational power GPU Accelerators enables fast denoising of 3D MR images using bilateral filtering, anisotropic diffusion, and non-local means. This software addresses two facets of this promising application: what tuning is necessary to achieve optimal performance on a modern GPU? And what parameters yield the best denoising results in practice? To answer the first question, the software performs an autotuning step to empirically determine optimal memory blocking on the GPU. To answer themore » second, it performs a sweep of algorithm parameters to determine the combination that best reduces the mean squared error relative to a noiseless reference image.« less

  17. Evaluation of 3D imaging.

    PubMed

    Vannier, M W

    2000-10-01

    Interactive computer-based simulation is gaining acceptance for craniofacial surgical planning. Subjective visualization without objective measurement capability, however, severely limits the value of simulation since spatial accuracy must be maintained. This study investigated the error sources involved in one method of surgical simulation evaluation. Linear and angular measurement errors were found to be within +/- 1 mm and 1 degree. Surface match of scanned objects was slightly less accurate, with errors up to 3 voxels and 4 degrees, and Boolean subtraction methods were 93 to 99% accurate. Once validated, these testing methods were applied to objectively compare craniofacial surgical simulations to post-operative outcomes, and verified that the form of simulation used in this study yields accurate depictions of surgical outcome. However, to fully evaluate surgical simulation, future work is still required to test the new methods in sufficient numbers of patients to achieve statistically significant results. Once completely validated, simulation cannot only be used in pre-operative surgical planning, but also as a post-operative descriptor of surgical and traumatic physical changes. Validated image comparison methods can also show discrepancy of surgical outcome to surgical plan, thus allowing evaluation of surgical technique. PMID:11098409

  18. Multilayer descriptors for medical image classification.

    PubMed

    Lumini, Alessandra; Nanni, Loris; Brahnam, Sheryl

    2016-05-01

    In this paper, we propose a new method for improving the performance of 2D descriptors by building an n-layer image using different preprocessing approaches from which multilayer descriptors are extracted and used as feature vectors for training a Support Vector Machine. The different preprocessing approaches are used to build different n-layer images (n=3, n=5, etc.). We test both color and gray-level images, two well-known texture descriptors (Local Phase Quantization and Local Binary Pattern), and three of their variants suited for n-layer images (Volume Local Phase Quantization, Local Phase Quantization Three-Orthogonal-Planes, and Volume Local Binary Patterns). Our results show that multilayers and texture descriptors can be combined to outperform the standard single-layer approaches. Experiments on 10 datasets demonstrate the generalizability of the proposed descriptors. Most of these datasets are medical, but in each case the images are very different. Two datasets are completely unrelated to medicine and are included to demonstrate the discriminative power of the proposed descriptors across very different image recognition tasks. A MATLAB version of the complete system developed in this paper will be made available at https://www.dei.unipd.it/node/2357. PMID:26656952

  19. Magmatic Systems in 3-D

    NASA Astrophysics Data System (ADS)

    Kent, G. M.; Harding, A. J.; Babcock, J. M.; Orcutt, J. A.; Bazin, S.; Singh, S.; Detrick, R. S.; Canales, J. P.; Carbotte, S. M.; Diebold, J.

    2002-12-01

    Multichannel seismic (MCS) images of crustal magma chambers are ideal targets for advanced visualization techniques. In the mid-ocean ridge environment, reflections originating at the melt-lens are well separated from other reflection boundaries, such as the seafloor, layer 2A and Moho, which enables the effective use of transparency filters. 3-D visualization of seismic reflectivity falls into two broad categories: volume and surface rendering. Volumetric-based visualization is an extremely powerful approach for the rapid exploration of very dense 3-D datasets. These 3-D datasets are divided into volume elements or voxels, which are individually color coded depending on the assigned datum value; the user can define an opacity filter to reject plotting certain voxels. This transparency allows the user to peer into the data volume, enabling an easy identification of patterns or relationships that might have geologic merit. Multiple image volumes can be co-registered to look at correlations between two different data types (e.g., amplitude variation with offsets studies), in a manner analogous to draping attributes onto a surface. In contrast, surface visualization of seismic reflectivity usually involves producing "fence" diagrams of 2-D seismic profiles that are complemented with seafloor topography, along with point class data, draped lines and vectors (e.g. fault scarps, earthquake locations and plate-motions). The overlying seafloor can be made partially transparent or see-through, enabling 3-D correlations between seafloor structure and seismic reflectivity. Exploration of 3-D datasets requires additional thought when constructing and manipulating these complex objects. As numbers of visual objects grow in a particular scene, there is a tendency to mask overlapping objects; this clutter can be managed through the effective use of total or partial transparency (i.e., alpha-channel). In this way, the co-variation between different datasets can be investigated

  20. Sodium 3D COncentration MApping (COMA 3D) using 23Na and proton MRI

    NASA Astrophysics Data System (ADS)

    Truong, Milton L.; Harrington, Michael G.; Schepkin, Victor D.; Chekmenev, Eduard Y.

    2014-10-01

    Functional changes of sodium 3D MRI signals were converted into millimolar concentration changes using an open-source fully automated MATLAB toolbox. These concentration changes are visualized via 3D sodium concentration maps, and they are overlaid over conventional 3D proton images to provide high-resolution co-registration for easy correlation of functional changes to anatomical regions. Nearly 5000/h concentration maps were generated on a personal computer (ca. 2012) using 21.1 T 3D sodium MRI brain images of live rats with spatial resolution of 0.8 × 0.8 × 0.8 mm3 and imaging matrices of 60 × 60 × 60. The produced concentration maps allowed for non-invasive quantitative measurement of in vivo sodium concentration in the normal rat brain as a functional response to migraine-like conditions. The presented work can also be applied to sodium-associated changes in migraine, cancer, and other metabolic abnormalities that can be sensed by molecular imaging. The MATLAB toolbox allows for automated image analysis of the 3D images acquired on the Bruker platform and can be extended to other imaging platforms. The resulting images are presented in a form of series of 2D slices in all three dimensions in native MATLAB and PDF formats. The following is provided: (a) MATLAB source code for image processing, (b) the detailed processing procedures, (c) description of the code and all sub-routines, (d) example data sets of initial and processed data. The toolbox can be downloaded at: http://www.vuiis.vanderbilt.edu/~truongm/COMA3D/.

  1. Sodium 3D COncentration MApping (COMA 3D) using (23)Na and proton MRI.

    PubMed

    Truong, Milton L; Harrington, Michael G; Schepkin, Victor D; Chekmenev, Eduard Y

    2014-10-01

    Functional changes of sodium 3D MRI signals were converted into millimolar concentration changes using an open-source fully automated MATLAB toolbox. These concentration changes are visualized via 3D sodium concentration maps, and they are overlaid over conventional 3D proton images to provide high-resolution co-registration for easy correlation of functional changes to anatomical regions. Nearly 5000/h concentration maps were generated on a personal computer (ca. 2012) using 21.1T 3D sodium MRI brain images of live rats with spatial resolution of 0.8×0.8×0.8 mm(3) and imaging matrices of 60×60×60. The produced concentration maps allowed for non-invasive quantitative measurement of in vivo sodium concentration in the normal rat brain as a functional response to migraine-like conditions. The presented work can also be applied to sodium-associated changes in migraine, cancer, and other metabolic abnormalities that can be sensed by molecular imaging. The MATLAB toolbox allows for automated image analysis of the 3D images acquired on the Bruker platform and can be extended to other imaging platforms. The resulting images are presented in a form of series of 2D slices in all three dimensions in native MATLAB and PDF formats. The following is provided: (a) MATLAB source code for image processing, (b) the detailed processing procedures, (c) description of the code and all sub-routines, (d) example data sets of initial and processed data. The toolbox can be downloaded at: http://www.vuiis.vanderbilt.edu/~truongm/COMA3D/. PMID:25261742

  2. Sodium 3D COncentration MApping (COMA 3D) Using 23Na and Proton MRI

    PubMed Central

    Truong, Milton L.; Harrington, Michael G.; Schepkin, Victor D.; Chekmenev, Eduard Y.

    2014-01-01

    Functional changes of sodium 3D MRI signals were converted into millimolar concentration changes using an open-source fully automated MATLAB toolbox. These concentration changes are visualized via 3D sodium concentration maps, and they are overlaid over conventional 3D proton images to provide high-resolution co-registration for easy correlation of functional changes to anatomical regions. Nearly 5000/hour concentration maps were generated on a personal computer (ca. 2012) using 21.1 T 3D sodium MRI brain images of live rats with spatial resolution of 0.8×0.8×0.8 mm3 and imaging matrices of 60×60×60. The produced concentration maps allowed for non-invasive quantitative measurement of in vivo sodium concentration in the normal rat brain as a functional response to migraine-like conditions. The presented work can also be applied to sodium-associated changes in migraine, cancer, and other metabolic abnormalities that can be sensed by molecular imaging. The MATLAB toolbox allows for automated image analysis of the 3D images acquired on the Bruker platform and can be extended to other imaging platforms. The resulting images are presented in a form of series of 2D slices in all three dimensions in native MATLAB and PDF formats. The following is provided: (a) MATLAB source code for image processing, (b) the detailed processing procedures, (c) description of the code and all sub-routines, (d) example data sets of initial and processed data. The toolbox can be downloaded at: http://www.vuiis.vanderbilt.edu/~truongm/COMA3D/ PMID:25261742

  3. 3D ear identification based on sparse representation.

    PubMed

    Zhang, Lin; Ding, Zhixuan; Li, Hongyu; Shen, Ying

    2014-01-01

    Biometrics based personal authentication is an effective way for automatically recognizing, with a high confidence, a person's identity. Recently, 3D ear shape has attracted tremendous interests in research field due to its richness of feature and ease of acquisition. However, the existing ICP (Iterative Closet Point)-based 3D ear matching methods prevalent in the literature are not quite efficient to cope with the one-to-many identification case. In this paper, we aim to fill this gap by proposing a novel effective fully automatic 3D ear identification system. We at first propose an accurate and efficient template-based ear detection method. By utilizing such a method, the extracted ear regions are represented in a common canonical coordinate system determined by the ear contour template, which facilitates much the following stages of feature extraction and classification. For each extracted 3D ear, a feature vector is generated as its representation by making use of a PCA-based local feature descriptor. At the stage of classification, we resort to the sparse representation based classification approach, which actually solves an l1-minimization problem. To the best of our knowledge, this is the first work introducing the sparse representation framework into the field of 3D ear identification. Extensive experiments conducted on a benchmark dataset corroborate the effectiveness and efficiency of the proposed approach. The associated Matlab source code and the evaluation results have been made publicly online available at http://sse.tongji.edu.cn/linzhang/ear/srcear/srcear.htm. PMID:24740247

  4. Interactive 3D Mars Visualization

    NASA Technical Reports Server (NTRS)

    Powell, Mark W.

    2012-01-01

    The Interactive 3D Mars Visualization system provides high-performance, immersive visualization of satellite and surface vehicle imagery of Mars. The software can be used in mission operations to provide the most accurate position information for the Mars rovers to date. When integrated into the mission data pipeline, this system allows mission planners to view the location of the rover on Mars to 0.01-meter accuracy with respect to satellite imagery, with dynamic updates to incorporate the latest position information. Given this information so early in the planning process, rover drivers are able to plan more accurate drive activities for the rover than ever before, increasing the execution of science activities significantly. Scientifically, this 3D mapping information puts all of the science analyses to date into geologic context on a daily basis instead of weeks or months, as was the norm prior to this contribution. This allows the science planners to judge the efficacy of their previously executed science observations much more efficiently, and achieve greater science return as a result. The Interactive 3D Mars surface view is a Mars terrain browsing software interface that encompasses the entire region of exploration for a Mars surface exploration mission. The view is interactive, allowing the user to pan in any direction by clicking and dragging, or to zoom in or out by scrolling the mouse or touchpad. This set currently includes tools for selecting a point of interest, and a ruler tool for displaying the distance between and positions of two points of interest. The mapping information can be harvested and shared through ubiquitous online mapping tools like Google Mars, NASA WorldWind, and Worldwide Telescope.

  5. A Clean Adirondack (3-D)

    NASA Technical Reports Server (NTRS)

    2004-01-01

    This is a 3-D anaglyph showing a microscopic image taken of an area measuring 3 centimeters (1.2 inches) across on the rock called Adirondack. The image was taken at Gusev Crater on the 33rd day of the Mars Exploration Rover Spirit's journey (Feb. 5, 2004), after the rover used its rock abrasion tool brush to clean the surface of the rock. Dust, which was pushed off to the side during cleaning, can still be seen to the left and in low areas of the rock.

  6. 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.

  7. What Lies Ahead (3-D)

    NASA Technical Reports Server (NTRS)

    2004-01-01

    This 3-D cylindrical-perspective mosaic taken by the navigation camera on the Mars Exploration Rover Spirit on sol 82 shows the view south of the large crater dubbed 'Bonneville.' The rover will travel toward the Columbia Hills, seen here at the upper left. The rock dubbed 'Mazatzal' and the hole the rover drilled in to it can be seen at the lower left. The rover's position is referred to as 'Site 22, Position 32.' This image was geometrically corrected to make the horizon appear flat.

  8. Vacant Lander in 3-D

    NASA Technical Reports Server (NTRS)

    2004-01-01

    This 3-D image captured by the Mars Exploration Rover Opportunity's rear hazard-identification camera shows the now-empty lander that carried the rover 283 million miles to Meridiani Planum, Mars. Engineers received confirmation that Opportunity's six wheels successfully rolled off the lander and onto martian soil at 3:01 a.m. PST, January 31, 2004, on the seventh martian day, or sol, of the mission. The rover is approximately 1 meter (3 feet) in front of the lander, facing north.

  9. 3D bicipital groove shape analysis and relationship to tendopathy.

    PubMed

    Ward, Aaron D; Hamarneh, Ghassan; Schweitzer, Mark E

    2008-06-01

    The bicipital groove of the proximal humerus is formed by the medial and lateral tuberosities and serves to retain the long biceps tendon in its proper place as the arm moves. Bicipital root and proximal tendon disorders are an important symptom generator in the shoulder. The accuracy of the diagnosis of many shoulder disorders visually without quantitative shape analysis is limited, motivating a clinical need for some ancillary method to assess the proximal biceps. In previous studies, measurements of bicipital groove shape were 2-dimensional (2D), taken from a single axial slice. Because of significant variations in groove shape from one axial slice to another in a single patient, such approaches risk overlooking shape features important to long biceps tendon pathology. In this paper, we present a study of the relationship between bicipital groove shape and long biceps tendon pathology using a novel 3-dimensional (3D) shape descriptor for the bicipital groove. In addition to providing quantitative measures of the shape of the groove and its relation to tendopathy, the new descriptor allows for intuitive, descriptive visualization of the shape of the groove. PMID:17342555

  10. Positional Awareness Map 3D (PAM3D)

    NASA Technical Reports Server (NTRS)

    Hoffman, Monica; Allen, Earl L.; Yount, John W.; Norcross, April Louise

    2012-01-01

    The Western Aeronautical Test Range of the National Aeronautics and Space Administration s Dryden Flight Research Center needed to address the aging software and hardware of its current situational awareness display application, the Global Real-Time Interactive Map (GRIM). GRIM was initially developed in the late 1980s and executes on older PC architectures using a Linux operating system that is no longer supported. Additionally, the software is difficult to maintain due to its complexity and loss of developer knowledge. It was decided that a replacement application must be developed or acquired in the near future. The replacement must provide the functionality of the original system, the ability to monitor test flight vehicles in real-time, and add improvements such as high resolution imagery and true 3-dimensional capability. This paper will discuss the process of determining the best approach to replace GRIM, and the functionality and capabilities of the first release of the Positional Awareness Map 3D.

  11. 3D Printable Graphene Composite

    NASA Astrophysics Data System (ADS)

    Wei, Xiaojun; Li, Dong; Jiang, Wei; Gu, Zheming; Wang, Xiaojuan; Zhang, Zengxing; Sun, Zhengzong

    2015-07-01

    In human being’s history, both the Iron Age and Silicon Age thrived after a matured massive processing technology was developed. Graphene is the most recent superior material which could potentially initialize another new material Age. However, while being exploited to its full extent, conventional processing methods fail to provide a link to today’s personalization tide. New technology should be ushered in. Three-dimensional (3D) printing fills the missing linkage between graphene materials and the digital mainstream. Their alliance could generate additional stream to push the graphene revolution into a new phase. Here we demonstrate for the first time, a graphene composite, with a graphene loading up to 5.6 wt%, can be 3D printable into computer-designed models. The composite’s linear thermal coefficient is below 75 ppm·°C-1 from room temperature to its glass transition temperature (Tg), which is crucial to build minute thermal stress during the printing process.

  12. 3D acoustic atmospheric tomography

    NASA Astrophysics Data System (ADS)

    Rogers, Kevin; Finn, Anthony

    2014-10-01

    This paper presents a method for tomographically reconstructing spatially varying 3D atmospheric temperature profiles and wind velocity fields based. Measurements of the acoustic signature measured onboard a small Unmanned Aerial Vehicle (UAV) are compared to ground-based observations of the same signals. The frequency-shifted signal variations are then used to estimate the acoustic propagation delay between the UAV and the ground microphones, which are also affected by atmospheric temperature and wind speed vectors along each sound ray path. The wind and temperature profiles are modelled as the weighted sum of Radial Basis Functions (RBFs), which also allow local meteorological measurements made at the UAV and ground receivers to supplement any acoustic observations. Tomography is used to provide a full 3D reconstruction/visualisation of the observed atmosphere. The technique offers observational mobility under direct user control and the capacity to monitor hazardous atmospheric environments, otherwise not justifiable on the basis of cost or risk. This paper summarises the tomographic technique and reports on the results of simulations and initial field trials. The technique has practical applications for atmospheric research, sound propagation studies, boundary layer meteorology, air pollution measurements, analysis of wind shear, and wind farm surveys.

  13. 3D Printed Bionic Ears

    PubMed Central

    Mannoor, Manu S.; Jiang, Ziwen; James, Teena; Kong, Yong Lin; Malatesta, Karen A.; Soboyejo, Winston O.; Verma, Naveen; Gracias, David H.; McAlpine, Michael C.

    2013-01-01

    The ability to three-dimensionally interweave biological tissue with functional electronics could enable the creation of bionic organs possessing enhanced functionalities over their human counterparts. Conventional electronic devices are inherently two-dimensional, preventing seamless multidimensional integration with synthetic biology, as the processes and materials are very different. Here, we present a novel strategy for overcoming these difficulties via additive manufacturing of biological cells with structural and nanoparticle derived electronic elements. As a proof of concept, we generated a bionic ear via 3D printing of a cell-seeded hydrogel matrix in the precise anatomic geometry of a human ear, along with an intertwined conducting polymer consisting of infused silver nanoparticles. This allowed for in vitro culturing of cartilage tissue around an inductive coil antenna in the ear, which subsequently enables readout of inductively-coupled signals from cochlea-shaped electrodes. The printed ear exhibits enhanced auditory sensing for radio frequency reception, and complementary left and right ears can listen to stereo audio music. Overall, our approach suggests a means to intricately merge biologic and nanoelectronic functionalities via 3D printing. PMID:23635097

  14. 3-D Relativistic MHD Simulations

    NASA Astrophysics Data System (ADS)

    Nishikaw, K.-I.; Frank, J.; Christodoulou, D. M.; Koide, S.; Sakai, J.-I.; Sol, H.; Mutel, R. L.

    1998-12-01

    We present 3-D numerical simulations of moderately hot, supersonic jets propagating initially along or obliquely to the field lines of a denser magnetized background medium with Lorentz factors of W=4.56 and evolving in a four-dimensional spacetime. The new results are understood as follows: Relativistic simulations have consistently shown that these jets are effectively heavy and so they do not suffer substantial momentum losses and are not decelerated as efficiently as their nonrelativistic counterparts. In addition, the ambient magnetic field, however strong, can be pushed aside with relative ease by the beam, provided that the degrees of freedom associated with all three spatial dimensions are followed self-consistently in the simulations. This effect is analogous to pushing Japanese ``noren'' or vertical Venetian blinds out of the way while the slats are allowed to bend in 3-D space rather than as a 2-D slab structure. We also simulate jets with the more realistic initial conditions for injecting jets for helical mangetic field, perturbed density, velocity, and internal energy, which are supposed to be caused in the process of jet generation. Three possible explanations for the observed variability are (i) tidal disruption of a star falling into the black hole, (ii) instabilities in the relativistic accretion disk, and (iii) jet-related PRocesses. New results will be reported at the meeting.

  15. 3D printed bionic ears.

    PubMed

    Mannoor, Manu S; Jiang, Ziwen; James, Teena; Kong, Yong Lin; Malatesta, Karen A; Soboyejo, Winston O; Verma, Naveen; Gracias, David H; McAlpine, Michael C

    2013-06-12

    The ability to three-dimensionally interweave biological tissue with functional electronics could enable the creation of bionic organs possessing enhanced functionalities over their human counterparts. Conventional electronic devices are inherently two-dimensional, preventing seamless multidimensional integration with synthetic biology, as the processes and materials are very different. Here, we present a novel strategy for overcoming these difficulties via additive manufacturing of biological cells with structural and nanoparticle derived electronic elements. As a proof of concept, we generated a bionic ear via 3D printing of a cell-seeded hydrogel matrix in the anatomic geometry of a human ear, along with an intertwined conducting polymer consisting of infused silver nanoparticles. This allowed for in vitro culturing of cartilage tissue around an inductive coil antenna in the ear, which subsequently enables readout of inductively-coupled signals from cochlea-shaped electrodes. The printed ear exhibits enhanced auditory sensing for radio frequency reception, and complementary left and right ears can listen to stereo audio music. Overall, our approach suggests a means to intricately merge biologic and nanoelectronic functionalities via 3D printing. PMID:23635097

  16. 3D Printable Graphene Composite

    PubMed Central

    Wei, Xiaojun; Li, Dong; Jiang, Wei; Gu, Zheming; Wang, Xiaojuan; Zhang, Zengxing; Sun, Zhengzong

    2015-01-01

    In human being’s history, both the Iron Age and Silicon Age thrived after a matured massive processing technology was developed. Graphene is the most recent superior material which could potentially initialize another new material Age. However, while being exploited to its full extent, conventional processing methods fail to provide a link to today’s personalization tide. New technology should be ushered in. Three-dimensional (3D) printing fills the missing linkage between graphene materials and the digital mainstream. Their alliance could generate additional stream to push the graphene revolution into a new phase. Here we demonstrate for the first time, a graphene composite, with a graphene loading up to 5.6 wt%, can be 3D printable into computer-designed models. The composite’s linear thermal coefficient is below 75 ppm·°C−1 from room temperature to its glass transition temperature (Tg), which is crucial to build minute thermal stress during the printing process. PMID:26153673

  17. 3D medical thermography device

    NASA Astrophysics Data System (ADS)

    Moghadam, Peyman

    2015-05-01

    In this paper, a novel handheld 3D medical thermography system is introduced. The proposed system consists of a thermal-infrared camera, a color camera and a depth camera rigidly attached in close proximity and mounted on an ergonomic handle. As a practitioner holding the device smoothly moves it around the human body parts, the proposed system generates and builds up a precise 3D thermogram model by incorporating information from each new measurement in real-time. The data is acquired in motion, thus it provides multiple points of view. When processed, these multiple points of view are adaptively combined by taking into account the reliability of each individual measurement which can vary due to a variety of factors such as angle of incidence, distance between the device and the subject and environmental sensor data or other factors influencing a confidence of the thermal-infrared data when captured. Finally, several case studies are presented to support the usability and performance of the proposed system.

  18. 3D Ion Temperature Reconstruction

    NASA Astrophysics Data System (ADS)

    Tanabe, Hiroshi; You, Setthivoine; Balandin, Alexander; Inomoto, Michiaki; Ono, Yasushi

    2009-11-01

    The TS-4 experiment at the University of Tokyo collides two spheromaks to form a single high-beta compact toroid. Magnetic reconnection during the merging process heats and accelerates the plasma in toroidal and poloidal directions. The reconnection region has a complex 3D topology determined by the pitch of the spheromak magnetic fields at the merging plane. A pair of multichord passive spectroscopic diagnostics have been established to measure the ion temperature and velocity in the reconnection volume. One setup measures spectral lines across a poloidal plane, retrieving velocity and temperature from Abel inversion. The other, novel setup records spectral lines across another section of the plasma and reconstructs velocity and temperature from 3D vector and 2D scalar tomography techniques. The magnetic field linking both measurement planes is determined from in situ magnetic probe arrays. The ion temperature is then estimated within the volume between the two measurement planes and at the reconnection region. The measurement is followed over several repeatable discharges to follow the heating and acceleration process during the merging reconnection.

  19. LOTT RANCH 3D PROJECT

    SciTech Connect

    Larry Lawrence; Bruce Miller

    2004-09-01

    The Lott Ranch 3D seismic prospect located in Garza County, Texas is a project initiated in September of 1991 by the J.M. Huber Corp., a petroleum exploration and production company. By today's standards the 126 square mile project does not seem monumental, however at the time it was conceived it was the most intensive land 3D project ever attempted. Acquisition began in September of 1991 utilizing GEO-SEISMIC, INC., a seismic data contractor. The field parameters were selected by J.M. Huber, and were of a radical design. The recording instruments used were GeoCor IV amplifiers designed by Geosystems Inc., which record the data in signed bit format. It would not have been practical, if not impossible, to have processed the entire raw volume with the tools available at that time. The end result was a dataset that was thought to have little utility due to difficulties in processing the field data. In 1997, Yates Energy Corp. located in Roswell, New Mexico, formed a partnership to further develop the project. Through discussions and meetings with Pinnacle Seismic, it was determined that the original Lott Ranch 3D volume could be vastly improved upon reprocessing. Pinnacle Seismic had shown the viability of improving field-summed signed bit data on smaller 2D and 3D projects. Yates contracted Pinnacle Seismic Ltd. to perform the reprocessing. This project was initiated with high resolution being a priority. Much of the potential resolution was lost through the initial summing of the field data. Modern computers that are now being utilized have tremendous speed and storage capacities that were cost prohibitive when this data was initially processed. Software updates and capabilities offer a variety of quality control and statics resolution, which are pertinent to the Lott Ranch project. The reprocessing effort was very successful. The resulting processed data-set was then interpreted using modern PC-based interpretation and mapping software. Production data, log data

  20. 3D Printing of Graphene Aerogels.

    PubMed

    Zhang, Qiangqiang; Zhang, Feng; Medarametla, Sai Pradeep; Li, Hui; Zhou, Chi; Lin, Dong

    2016-04-01

    3D printing of a graphene aerogel with true 3D overhang structures is highlighted. The aerogel is fabricated by combining drop-on-demand 3D printing and freeze casting. The water-based GO ink is ejected and freeze-cast into designed 3D structures. The lightweight (<10 mg cm(-3) ) 3D printed graphene aerogel presents superelastic and high electrical conduction. PMID:26861680

  1. ShowMe3D

    2012-01-05

    ShowMe3D is a data visualization graphical user interface specifically designed for use with hyperspectral image obtained from the Hyperspectral Confocal Microscope. The program allows the user to select and display any single image from a three dimensional hyperspectral image stack. By moving a slider control, the user can easily move between images of the stack. The user can zoom into any region of the image. The user can select any pixel or region from themore » displayed image and display the fluorescence spectrum associated with that pixel or region. The user can define up to 3 spectral filters to apply to the hyperspectral image and view the image as it would appear from a filter-based confocal microscope. The user can also obtain statistics such as intensity average and variance from selected regions.« less

  2. ShowMe3D

    SciTech Connect

    Sinclair, Michael B

    2012-01-05

    ShowMe3D is a data visualization graphical user interface specifically designed for use with hyperspectral image obtained from the Hyperspectral Confocal Microscope. The program allows the user to select and display any single image from a three dimensional hyperspectral image stack. By moving a slider control, the user can easily move between images of the stack. The user can zoom into any region of the image. The user can select any pixel or region from the displayed image and display the fluorescence spectrum associated with that pixel or region. The user can define up to 3 spectral filters to apply to the hyperspectral image and view the image as it would appear from a filter-based confocal microscope. The user can also obtain statistics such as intensity average and variance from selected regions.

  3. 3D Elastic Wavefield Tomography

    NASA Astrophysics Data System (ADS)

    Guasch, L.; Warner, M.; Stekl, I.; Umpleby, A.; Shah, N.

    2010-12-01

    Wavefield tomography, or waveform inversion, aims to extract the maximum information from seismic data by matching trace by trace the response of the solid earth to seismic waves using numerical modelling tools. Its first formulation dates from the early 80's, when Albert Tarantola developed a solid theoretical basis that is still used today with little change. Due to computational limitations, the application of the method to 3D problems has been unaffordable until a few years ago, and then only under the acoustic approximation. Although acoustic wavefield tomography is widely used, a complete solution of the seismic inversion problem requires that we account properly for the physics of wave propagation, and so must include elastic effects. We have developed a 3D tomographic wavefield inversion code that incorporates the full elastic wave equation. The bottle neck of the different implementations is the forward modelling algorithm that generates the synthetic data to be compared with the field seismograms as well as the backpropagation of the residuals needed to form the direction update of the model parameters. Furthermore, one or two extra modelling runs are needed in order to calculate the step-length. Our approach uses a FD scheme explicit time-stepping by finite differences that are 4th order in space and 2nd order in time, which is a 3D version of the one developed by Jean Virieux in 1986. We chose the time domain because an explicit time scheme is much less demanding in terms of memory than its frequency domain analogue, although the discussion of wich domain is more efficient still remains open. We calculate the parameter gradients for Vp and Vs by correlating the normal and shear stress wavefields respectively. A straightforward application would lead to the storage of the wavefield at all grid points at each time-step. We tackled this problem using two different approaches. The first one makes better use of resources for small models of dimension equal

  4. Automated building of organometallic complexes from 3D fragments.

    PubMed

    Foscato, Marco; Venkatraman, Vishwesh; Occhipinti, Giovanni; Alsberg, Bjørn K; Jensen, Vidar R

    2014-07-28

    A method for the automated construction of three-dimensional (3D) molecular models of organometallic species in design studies is described. Molecular structure fragments derived from crystallographic structures and accurate molecular-level calculations are used as 3D building blocks in the construction of multiple molecular models of analogous compounds. The method allows for precise control of stereochemistry and geometrical features that may otherwise be very challenging, or even impossible, to achieve with commonly available generators of 3D chemical structures. The new method was tested in the construction of three sets of active or metastable organometallic species of catalytic reactions in the homogeneous phase. The performance of the method was compared with those of commonly available methods for automated generation of 3D models, demonstrating higher accuracy of the prepared 3D models in general, and, in particular, a much wider range with respect to the kind of chemical structures that can be built automatically, with capabilities far beyond standard organic and main-group chemistry. PMID:24998944

  5. Supernova Remnant in 3-D

    NASA Technical Reports Server (NTRS)

    2009-01-01

    wavelengths. Since the amount of the wavelength shift is related to the speed of motion, one can determine how fast the debris are moving in either direction. Because Cas A is the result of an explosion, the stellar debris is expanding radially outwards from the explosion center. Using simple geometry, the scientists were able to construct a 3-D model using all of this information. A program called 3-D Slicer modified for astronomical use by the Astronomical Medicine Project at Harvard University in Cambridge, Mass. was used to display and manipulate the 3-D model. Commercial software was then used to create the 3-D fly-through.

    The blue filaments defining the blast wave were not mapped using the Doppler effect because they emit a different kind of light synchrotron radiation that does not emit light at discrete wavelengths, but rather in a broad continuum. The blue filaments are only a representation of the actual filaments observed at the blast wave.

    This visualization shows that there are two main components to this supernova remnant: a spherical component in the outer parts of the remnant and a flattened (disk-like) component in the inner region. The spherical component consists of the outer layer of the star that exploded, probably made of helium and carbon. These layers drove a spherical blast wave into the diffuse gas surrounding the star. The flattened component that astronomers were unable to map into 3-D prior to these Spitzer observations consists of the inner layers of the star. It is made from various heavier elements, not all shown in the visualization, such as oxygen, neon, silicon, sulphur, argon and iron.

    High-velocity plumes, or jets, of this material are shooting out from the explosion in the plane of the disk-like component mentioned above. Plumes of silicon appear in the northeast and southwest, while those of iron are seen in the southeast and north. These jets were already known and Doppler velocity measurements have been made for these

  6. 3D printing of microscopic bacterial communities

    PubMed Central

    Connell, Jodi L.; Ritschdorff, Eric T.; Whiteley, Marvin; Shear, Jason B.

    2013-01-01

    Bacteria communicate via short-range physical and chemical signals, interactions known to mediate quorum sensing, sporulation, and other adaptive phenotypes. Although most in vitro studies examine bacterial properties averaged over large populations, the levels of key molecular determinants of bacterial fitness and pathogenicity (e.g., oxygen, quorum-sensing signals) may vary over micrometer scales within small, dense cellular aggregates believed to play key roles in disease transmission. A detailed understanding of how cell–cell interactions contribute to pathogenicity in natural, complex environments will require a new level of control in constructing more relevant cellular models for assessing bacterial phenotypes. Here, we describe a microscopic three-dimensional (3D) printing strategy that enables multiple populations of bacteria to be organized within essentially any 3D geometry, including adjacent, nested, and free-floating colonies. In this laser-based lithographic technique, microscopic containers are formed around selected bacteria suspended in gelatin via focal cross-linking of polypeptide molecules. After excess reagent is removed, trapped bacteria are localized within sealed cavities formed by the cross-linked gelatin, a highly porous material that supports rapid growth of fully enclosed cellular populations and readily transmits numerous biologically active species, including polypeptides, antibiotics, and quorum-sensing signals. Using this approach, we show that a picoliter-volume aggregate of Staphylococcus aureus can display substantial resistance to β-lactam antibiotics by enclosure within a shell composed of Pseudomonas aeruginosa. PMID:24101503

  7. Replenishing data descriptors in a DMA injection FIFO buffer

    DOEpatents

    Archer, Charles J.; Blocksome, Michael A.; Cernohous, Bob R.; Heidelberger, Philip; Kumar, Sameer; Parker, Jeffrey J.

    2011-10-11

    Methods, apparatus, and products are disclosed for replenishing data descriptors in a Direct Memory Access (`DMA`) injection first-in-first-out (`FIFO`) buffer that include: determining, by a messaging module on an origin compute node, whether a number of data descriptors in a DMA injection FIFO buffer exceeds a predetermined threshold, each data descriptor specifying an application message for transmission to a target compute node; queuing, by the messaging module, a plurality of new data descriptors in a pending descriptor queue if the number of the data descriptors in the DMA injection FIFO buffer exceeds the predetermined threshold; establishing, by the messaging module, interrupt criteria that specify when to replenish the injection FIFO buffer with the plurality of new data descriptors in the pending descriptor queue; and injecting, by the messaging module, the plurality of new data descriptors into the injection FIFO buffer in dependence upon the interrupt criteria.

  8. Midsagittal plane extraction from brain images based on 3D SIFT

    NASA Astrophysics Data System (ADS)

    Wu, Huisi; Wang, Defeng; Shi, Lin; Wen, Zhenkun; Ming, Zhong

    2014-03-01

    Midsagittal plane (MSP) extraction from 3D brain images is considered as a promising technique for human brain symmetry analysis. In this paper, we present a fast and robust MSP extraction method based on 3D scale-invariant feature transform (SIFT). Unlike the existing brain MSP extraction methods, which mainly rely on the gray similarity, 3D edge registration or parameterized surface matching to determine the fissure plane, our proposed method is based on distinctive 3D SIFT features, in which the fissure plane is determined by parallel 3D SIFT matching and iterative least-median of squares plane regression. By considering the relative scales, orientations and flipped descriptors between two 3D SIFT features, we propose a novel metric to measure the symmetry magnitude for 3D SIFT features. By clustering and indexing the extracted SIFT features using a k-dimensional tree (KD-tree) implemented on graphics processing units, we can match multiple pairs of 3D SIFT features in parallel and solve the optimal MSP on-the-fly. The proposed method is evaluated by synthetic and in vivo datasets, of normal and pathological cases, and validated by comparisons with the state-of-the-art methods. Experimental results demonstrated that our method has achieved a real-time performance with better accuracy yielding an average yaw angle error below 0.91° and an average roll angle error no more than 0.89°.

  9. Supernova Remnant in 3-D

    NASA Technical Reports Server (NTRS)

    2009-01-01

    wavelengths. Since the amount of the wavelength shift is related to the speed of motion, one can determine how fast the debris are moving in either direction. Because Cas A is the result of an explosion, the stellar debris is expanding radially outwards from the explosion center. Using simple geometry, the scientists were able to construct a 3-D model using all of this information. A program called 3-D Slicer modified for astronomical use by the Astronomical Medicine Project at Harvard University in Cambridge, Mass. was used to display and manipulate the 3-D model. Commercial software was then used to create the 3-D fly-through.

    The blue filaments defining the blast wave were not mapped using the Doppler effect because they emit a different kind of light synchrotron radiation that does not emit light at discrete wavelengths, but rather in a broad continuum. The blue filaments are only a representation of the actual filaments observed at the blast wave.

    This visualization shows that there are two main components to this supernova remnant: a spherical component in the outer parts of the remnant and a flattened (disk-like) component in the inner region. The spherical component consists of the outer layer of the star that exploded, probably made of helium and carbon. These layers drove a spherical blast wave into the diffuse gas surrounding the star. The flattened component that astronomers were unable to map into 3-D prior to these Spitzer observations consists of the inner layers of the star. It is made from various heavier elements, not all shown in the visualization, such as oxygen, neon, silicon, sulphur, argon and iron.

    High-velocity plumes, or jets, of this material are shooting out from the explosion in the plane of the disk-like component mentioned above. Plumes of silicon appear in the northeast and southwest, while those of iron are seen in the southeast and north. These jets were already known and Doppler velocity measurements have been made for these

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

    PubMed

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

    2012-01-01

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

  11. 3D multiplexed immunoplasmonics microscopy

    NASA Astrophysics Data System (ADS)

    Bergeron, Éric; Patskovsky, Sergiy; Rioux, David; Meunier, Michel

    2016-07-01

    Selective labelling, identification and spatial distribution of cell surface biomarkers can provide important clinical information, such as distinction between healthy and diseased cells, evolution of a disease and selection of the optimal patient-specific treatment. Immunofluorescence is the gold standard for efficient detection of biomarkers expressed by cells. However, antibodies (Abs) conjugated to fluorescent dyes remain limited by their photobleaching, high sensitivity to the environment, low light intensity, and wide absorption and emission spectra. Immunoplasmonics is a novel microscopy method based on the visualization of Abs-functionalized plasmonic nanoparticles (fNPs) targeting cell surface biomarkers. Tunable fNPs should provide higher multiplexing capacity than immunofluorescence since NPs are photostable over time, strongly scatter light at their plasmon peak wavelengths and can be easily functionalized. In this article, we experimentally demonstrate accurate multiplexed detection based on the immunoplasmonics approach. First, we achieve the selective labelling of three targeted cell surface biomarkers (cluster of differentiation 44 (CD44), epidermal growth factor receptor (EGFR) and voltage-gated K+ channel subunit KV1.1) on human cancer CD44+ EGFR+ KV1.1+ MDA-MB-231 cells and reference CD44- EGFR- KV1.1+ 661W cells. The labelling efficiency with three stable specific immunoplasmonics labels (functionalized silver nanospheres (CD44-AgNSs), gold (Au) NSs (EGFR-AuNSs) and Au nanorods (KV1.1-AuNRs)) detected by reflected light microscopy (RLM) is similar to the one with immunofluorescence. Second, we introduce an improved method for 3D localization and spectral identification of fNPs based on fast z-scanning by RLM with three spectral filters corresponding to the plasmon peak wavelengths of the immunoplasmonics labels in the cellular environment (500 nm for 80 nm AgNSs, 580 nm for 100 nm AuNSs and 700 nm for 40 nm × 92 nm AuNRs). Third, the developed

  12. NIF Ignition Target 3D Point Design

    SciTech Connect

    Jones, O; Marinak, M; Milovich, J; Callahan, D

    2008-11-05

    We have developed an input file for running 3D NIF hohlraums that is optimized such that it can be run in 1-2 days on parallel computers. We have incorporated increasing levels of automation into the 3D input file: (1) Configuration controlled input files; (2) Common file for 2D and 3D, different types of capsules (symcap, etc.); and (3) Can obtain target dimensions, laser pulse, and diagnostics settings automatically from NIF Campaign Management Tool. Using 3D Hydra calculations to investigate different problems: (1) Intrinsic 3D asymmetry; (2) Tolerance to nonideal 3D effects (e.g. laser power balance, pointing errors); and (3) Synthetic diagnostics.

  13. 3D multiplexed immunoplasmonics microscopy.

    PubMed

    Bergeron, Éric; Patskovsky, Sergiy; Rioux, David; Meunier, Michel

    2016-07-21

    Selective labelling, identification and spatial distribution of cell surface biomarkers can provide important clinical information, such as distinction between healthy and diseased cells, evolution of a disease and selection of the optimal patient-specific treatment. Immunofluorescence is the gold standard for efficient detection of biomarkers expressed by cells. However, antibodies (Abs) conjugated to fluorescent dyes remain limited by their photobleaching, high sensitivity to the environment, low light intensity, and wide absorption and emission spectra. Immunoplasmonics is a novel microscopy method based on the visualization of Abs-functionalized plasmonic nanoparticles (fNPs) targeting cell surface biomarkers. Tunable fNPs should provide higher multiplexing capacity than immunofluorescence since NPs are photostable over time, strongly scatter light at their plasmon peak wavelengths and can be easily functionalized. In this article, we experimentally demonstrate accurate multiplexed detection based on the immunoplasmonics approach. First, we achieve the selective labelling of three targeted cell surface biomarkers (cluster of differentiation 44 (CD44), epidermal growth factor receptor (EGFR) and voltage-gated K(+) channel subunit KV1.1) on human cancer CD44(+) EGFR(+) KV1.1(+) MDA-MB-231 cells and reference CD44(-) EGFR(-) KV1.1(+) 661W cells. The labelling efficiency with three stable specific immunoplasmonics labels (functionalized silver nanospheres (CD44-AgNSs), gold (Au) NSs (EGFR-AuNSs) and Au nanorods (KV1.1-AuNRs)) detected by reflected light microscopy (RLM) is similar to the one with immunofluorescence. Second, we introduce an improved method for 3D localization and spectral identification of fNPs based on fast z-scanning by RLM with three spectral filters corresponding to the plasmon peak wavelengths of the immunoplasmonics labels in the cellular environment (500 nm for 80 nm AgNSs, 580 nm for 100 nm AuNSs and 700 nm for 40 nm × 92 nm AuNRs). Third

  14. Analysis of activity space by fragment fingerprints, 2D descriptors, and multitarget dependent transformation of 2D descriptors.

    PubMed

    Givehchi, Alireza; Bender, Andreas; Glen, Robert C

    2006-01-01

    The effect of multitarget dependent descriptor transformation on classification performance is explored in this work. To this end decision trees as well as neural net QSAR in combination with PLS were applied to predict the activity class of 5HT3 ligands, angiotensin converting enzyme inhibitors, 3-hydroxyl-3-methyl glutaryl coenzyme A reductase inhibitors, platelet activating factor antagonists, and thromboxane A2 antagonists. Physicochemical descriptors calculated by MOE and fragment-based descriptors (MOLPRINT 2D) were employed to generate descriptor vectors. In a subsequent step the physicochemical descriptor vectors were transformed to a lower dimensional space using multitarget dependent descriptor transformation. Cross-validation of the original physicochemical descriptors in combination with decision trees and neural net QSAR as well as cross-validation of PLS multitarget transformed descriptors with neural net QSAR were performed. For comparison this was repeated using fragment-based descriptors in combination with decision trees. PMID:16711727

  15. Reduction of Thermal Conductivity by Nanoscale 3D Phononic Crystal

    PubMed Central

    Yang, Lina; Yang, Nuo; Li, Baowen

    2013-01-01

    We studied how the period length and the mass ratio affect the thermal conductivity of isotopic nanoscale three-dimensional (3D) phononic crystal of Si. Simulation results by equilibrium molecular dynamics show isotopic nanoscale 3D phononic crystals can significantly reduce the thermal conductivity of bulk Si at high temperature (1000 K), which leads to a larger ZT than unity. The thermal conductivity decreases as the period length and mass ratio increases. The phonon dispersion curves show an obvious decrease of group velocities in 3D phononic crystals. The phonon's localization and band gap is also clearly observed in spectra of normalized inverse participation ratio in nanoscale 3D phononic crystal. PMID:23378898

  16. Reduction of thermal conductivity by nanoscale 3D phononic crystal.

    PubMed

    Yang, Lina; Yang, Nuo; Li, Baowen

    2013-01-01

    We studied how the period length and the mass ratio affect the thermal conductivity of isotopic nanoscale three-dimensional (3D) phononic crystal of Si. Simulation results by equilibrium molecular dynamics show isotopic nanoscale 3D phononic crystals can significantly reduce the thermal conductivity of bulk Si at high temperature (1000 K), which leads to a larger ZT than unity. The thermal conductivity decreases as the period length and mass ratio increases. The phonon dispersion curves show an obvious decrease of group velocities in 3D phononic crystals. The phonon's localization and band gap is also clearly observed in spectra of normalized inverse participation ratio in nanoscale 3D phononic crystal. PMID:23378898

  17. 3D Kitaev spin liquids

    NASA Astrophysics Data System (ADS)

    Hermanns, Maria

    The Kitaev honeycomb model has become one of the archetypal spin models exhibiting topological phases of matter, where the magnetic moments fractionalize into Majorana fermions interacting with a Z2 gauge field. In this talk, we discuss generalizations of this model to three-dimensional lattice structures. Our main focus is the metallic state that the emergent Majorana fermions form. In particular, we discuss the relation of the nature of this Majorana metal to the details of the underlying lattice structure. Besides (almost) conventional metals with a Majorana Fermi surface, one also finds various realizations of Dirac semi-metals, where the gapless modes form Fermi lines or even Weyl nodes. We introduce a general classification of these gapless quantum spin liquids using projective symmetry analysis. Furthermore, we briefly outline why these Majorana metals in 3D Kitaev systems provide an even richer variety of Dirac and Weyl phases than possible for electronic matter and comment on possible experimental signatures. Work done in collaboration with Kevin O'Brien and Simon Trebst.

  18. Yogi the rock - 3D

    NASA Technical Reports Server (NTRS)

    1997-01-01

    Yogi, a rock taller than rover Sojourner, is the subject of this image, taken in stereo by the deployed Imager for Mars Pathfinder (IMP) on Sol 3. 3D glasses are necessary to identify surface detail. The soil in the foreground has been the location of multiple soil mechanics experiments performed by Sojourner's cleated wheels. Pathfinder scientists were able to control the force inflicted on the soil beneath the rover's wheels, giving them insight into the soil's mechanical properties. The soil mechanics experiments were conducted after this image was taken.

    Mars Pathfinder is the second in NASA's Discovery program of low-cost spacecraft with highly focused science goals. The Jet Propulsion Laboratory, Pasadena, CA, developed and manages the Mars Pathfinder mission for NASA's Office of Space Science, Washington, D.C. JPL is an operating division of the California Institute of Technology (Caltech). The Imager for Mars Pathfinder (IMP) was developed by the University of Arizona Lunar and Planetary Laboratory under contract to JPL. Peter Smith is the Principal Investigator.

    Click below to see the left and right views individually. [figure removed for brevity, see original site] Left [figure removed for brevity, see original site] Right

  19. 3D ultrafast laser scanner

    NASA Astrophysics Data System (ADS)

    Mahjoubfar, A.; Goda, K.; Wang, C.; Fard, A.; Adam, J.; Gossett, D. R.; Ayazi, A.; Sollier, E.; Malik, O.; Chen, E.; Liu, Y.; Brown, R.; Sarkhosh, N.; Di Carlo, D.; Jalali, B.

    2013-03-01

    Laser scanners are essential for scientific research, manufacturing, defense, and medical practice. Unfortunately, often times the speed of conventional laser scanners (e.g., galvanometric mirrors and acousto-optic deflectors) falls short for many applications, resulting in motion blur and failure to capture fast transient information. Here, we present a novel type of laser scanner that offers roughly three orders of magnitude higher scan rates than conventional methods. Our laser scanner, which we refer to as the hybrid dispersion laser scanner, performs inertia-free laser scanning by dispersing a train of broadband pulses both temporally and spatially. More specifically, each broadband pulse is temporally processed by time stretch dispersive Fourier transform and further dispersed into space by one or more diffractive elements such as prisms and gratings. As a proof-of-principle demonstration, we perform 1D line scans at a record high scan rate of 91 MHz and 2D raster scans and 3D volumetric scans at an unprecedented scan rate of 105 kHz. The method holds promise for a broad range of scientific, industrial, and biomedical applications. To show the utility of our method, we demonstrate imaging, nanometer-resolved surface vibrometry, and high-precision flow cytometry with real-time throughput that conventional laser scanners cannot offer due to their low scan rates.

  20. 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.

  1. 3D multiplexed immunoplasmonics microscopy

    NASA Astrophysics Data System (ADS)

    Bergeron, Éric; Patskovsky, Sergiy; Rioux, David; Meunier, Michel

    2016-07-01

    Selective labelling, identification and spatial distribution of cell surface biomarkers can provide important clinical information, such as distinction between healthy and diseased cells, evolution of a disease and selection of the optimal patient-specific treatment. Immunofluorescence is the gold standard for efficient detection of biomarkers expressed by cells. However, antibodies (Abs) conjugated to fluorescent dyes remain limited by their photobleaching, high sensitivity to the environment, low light intensity, and wide absorption and emission spectra. Immunoplasmonics is a novel microscopy method based on the visualization of Abs-functionalized plasmonic nanoparticles (fNPs) targeting cell surface biomarkers. Tunable fNPs should provide higher multiplexing capacity than immunofluorescence since NPs are photostable over time, strongly scatter light at their plasmon peak wavelengths and can be easily functionalized. In this article, we experimentally demonstrate accurate multiplexed detection based on the immunoplasmonics approach. First, we achieve the selective labelling of three targeted cell surface biomarkers (cluster of differentiation 44 (CD44), epidermal growth factor receptor (EGFR) and voltage-gated K+ channel subunit KV1.1) on human cancer CD44+ EGFR+ KV1.1+ MDA-MB-231 cells and reference CD44- EGFR- KV1.1+ 661W cells. The labelling efficiency with three stable specific immunoplasmonics labels (functionalized silver nanospheres (CD44-AgNSs), gold (Au) NSs (EGFR-AuNSs) and Au nanorods (KV1.1-AuNRs)) detected by reflected light microscopy (RLM) is similar to the one with immunofluorescence. Second, we introduce an improved method for 3D localization and spectral identification of fNPs based on fast z-scanning by RLM with three spectral filters corresponding to the plasmon peak wavelengths of the immunoplasmonics labels in the cellular environment (500 nm for 80 nm AgNSs, 580 nm for 100 nm AuNSs and 700 nm for 40 nm × 92 nm AuNRs). Third, the developed

  2. Imidazo[1,2-a]pyrazine inhibitors of phosphoinositide 3-kinase alpha (PI3Kα): 3D-QSAR analysis utilizing the Hybrid Monte Carlo algorithm to refine receptor-ligand complexes for molecular alignment.

    PubMed

    Chadha, N; Jasuja, H; Kaur, M; Singh Bahia, M; Silakari, O

    2014-01-01

    Phosphoinositide 3-kinase alpha (PI3Kα) is a lipid kinase involved in several cellular functions such as cell growth, proliferation, differentiation and survival, and its anomalous regulation leads to cancerous conditions. PI3Kα inhibition completely blocks the cancer signalling pathway, hence it can be explored as an important therapeutic target for cancer treatment. In the present study, docking analysis of 49 selective imidazo[1,2-a]pyrazine inhibitors of PI3Kα was carried out using the QM-Polarized ligand docking (QPLD) program of the Schrödinger software, followed by the refinement of receptor-ligand conformations using the Hybrid Monte Carlo algorithm in the Liaison program, and alignment of refined conformations of inhibitors was utilized for the development of an atom-based 3D-QSAR model in the PHASE program. Among the five generated models, the best model was selected corresponding to PLS factor 2, displaying the highest value of Q(2)test (0.650). The selected model also displayed high values of r(2)train (0.917), F-value (166.5) and Pearson-r (0.877) and a low value of SD (0.265). The contour plots generated for the selected 3D-QSAR model were correlated with the results of docking simulations. Finally, this combined information generated from 3D-QSAR and docking analysis was used to design new congeners. PMID:24601789

  3. Characterization of cerebral aneurysms using 3D moment invariants

    NASA Astrophysics Data System (ADS)

    Millan, Raul D.; Hernandez, Monica; Gallardo, Daniel; Cebral, Juan R.; Putman, Christopher; Dempere-Marco, Laura; Frangi, Alejandro F.

    2005-04-01

    The rupture mechanism of intracranial aneurysms is still not fully understood. Although the size of the aneurysm is the shape index most commonly used to predict rupture, some controversy still exists about its adequateness as an aneurysm rupture predictor. In this work, an automatic method to geometrically characterize the shape of cerebral saccular aneurysms using 3D moment invariants is proposed. Geometric moments are efficiently computed via application of the Divergence Theorem over the aneurysm surface using a non-structured mesh. 3D models of the aneurysm and its connected parent vessels have been reconstructed from segmentations of both 3DRA and CTA images. Two alternative approaches have been used for segmentation, the first one based on isosurface deformable models, and the second one based on the level set method. Several experiments were also conducted to both assess the influence of pre-processing steps in the stability of the aneurysm shape descriptors, and to know the robustness of the proposed method. Moment invariants have proved to be a robust technique while providing a reliable way to discriminate between ruptured and unruptured aneurysms (Sensitivity=0.83, Specificity=0.74) on a data set containing 55 aneurysms. Further investigation over larger databases is necessary to establish their adequateness as reliable predictors of rupture risk.

  4. Ear biometric recognition using local texture descriptors

    NASA Astrophysics Data System (ADS)

    Benzaoui, Amir; Hadid, Abdenour; Boukrouche, Abdelhani

    2014-09-01

    Automated personal identification using the shape of the human ear is emerging as an appealing modality in biometric and forensic domains. This is mainly due to the fact that the ear pattern can provide rich and stable information to differentiate and recognize people. In the literature, there are many approaches and descriptors that achieve relatively good results in constrained environments. The recognition performance tends, however, to significantly decrease under illumination variation, pose variation, and partial occlusion. In this work, we investigate the use of local texture descriptors, namely local binary patterns, local phase quantization, and binarized statistical image features for robust human identification from two-dimensional ear imaging. In contrast to global image descriptors which compute features directly from the entire image, local descriptors representing the features in small local image patches have proven to be more effective in real-world conditions. Our extensive experimental results on the benchmarks IIT Delhi-1, IIT Delhi-2, and USTB ear databases show that local texture features in general and BSIF in particular provide a significant performance improvement compared to the state-of-the-art.

  5. Local Pyramidal Descriptors for Image Recognition.

    PubMed

    Seidenari, Lorenzo; Serra, Giuseppe; Bagdanov, Andrew D; Del Bimbo, Alberto

    2014-05-01

    In this paper, we present a novel method to improve the flexibility of descriptor matching for image recognition by using local multiresolution pyramids in feature space. We propose that image patches be represented at multiple levels of descriptor detail and that these levels be defined in terms of local spatial pooling resolution. Preserving multiple levels of detail in local descriptors is a way of hedging one's bets on which levels will most relevant for matching during learning and recognition. We introduce the Pyramid SIFT (P-SIFT) descriptor and show that its use in four state-of-the-art image recognition pipelines improves accuracy and yields state-of-the-art results. Our technique is applicable independently of spatial pyramid matching and we show that spatial pyramids can be combined with local pyramids to obtain further improvement. We achieve state-of-the-art results on Caltech-101 (80.1%) and Caltech-256 (52.6%) when compared to other approaches based on SIFT features over intensity images. Our technique is efficient and is extremely easy to integrate into image recognition pipelines. PMID:26353235

  6. Local Pyramidal Descriptors for Image Recognition.

    PubMed

    Seidenari, Lorenzo; Serra, Giuseppe; Bagdanov, Andrew D; Del Bimbo, Alberto

    2013-11-22

    In this paper we present a novel method to improve the flexibility of descriptor matching for image recognition by using local multiresolution pyramids in feature space. We propose that image patches be represented at multiple levels of descriptor detail and that these levels be defined in terms of local spatial pooling resolution. Preserving multiple levels of detail in local descriptors is a way of hedging one's bets on which levels will most relevant for matching during learning and recognition. We introduce the Pyramid SIFT (P-SIFT) descriptor and show that its use in four state-of-the-art image recognition pipelines improves accuracy and yields state-of-the-art results. Our technique is applicable independently of spatial pyramid matching and we show that spatial pyramids can be combined with local pyramids to obtain further improvement. We achieve state-of-the-art results on Caltech-101 (80.1%) and Caltech-256 (52.6%) when compared to other approaches based on SIFT features over intensity images. Our technique is efficient and is extremely easy to integrate into image recognition pipelines. PMID:24277944

  7. Entropy descriptors and Entropy Stabilized Oxides

    NASA Astrophysics Data System (ADS)

    Curtarolo, Stefano

    In this presentation we will discuss the development of entropy descriptors for the AFLOWLIB.org ab-initio repository and the path leading to the synthesis of the novel entropy stabilized oxides. [Nat. Comm. 6:8485 (2015)]. Research sponsored by DOD-ONR N000141310635 and N000141512863.

  8. 3-D Cavern Enlargement Analyses

    SciTech Connect

    EHGARTNER, BRIAN L.; SOBOLIK, STEVEN R.

    2002-03-01

    Three-dimensional finite element analyses simulate the mechanical response of enlarging existing caverns at the Strategic Petroleum Reserve (SPR). The caverns are located in Gulf Coast salt domes and are enlarged by leaching during oil drawdowns as fresh water is injected to displace the crude oil from the caverns. The current criteria adopted by the SPR limits cavern usage to 5 drawdowns (leaches). As a base case, 5 leaches were modeled over a 25 year period to roughly double the volume of a 19 cavern field. Thirteen additional leaches where then simulated until caverns approached coalescence. The cavern field approximated the geometries and geologic properties found at the West Hackberry site. This enabled comparisons are data collected over nearly 20 years to analysis predictions. The analyses closely predicted the measured surface subsidence and cavern closure rates as inferred from historic well head pressures. This provided the necessary assurance that the model displacements, strains, and stresses are accurate. However, the cavern field has not yet experienced the large scale drawdowns being simulated. Should they occur in the future, code predictions should be validated with actual field behavior at that time. The simulations were performed using JAS3D, a three dimensional finite element analysis code for nonlinear quasi-static solids. The results examine the impacts of leaching and cavern workovers, where internal cavern pressures are reduced, on surface subsidence, well integrity, and cavern stability. The results suggest that the current limit of 5 oil drawdowns may be extended with some mitigative action required on the wells and later on to surface structure due to subsidence strains. The predicted stress state in the salt shows damage to start occurring after 15 drawdowns with significant failure occurring at the 16th drawdown, well beyond the current limit of 5 drawdowns.

  9. Imaging a Sustainable Future in 3D

    NASA Astrophysics Data System (ADS)

    Schuhr, W.; Lee, J. D.; Kanngieser, E.

    2012-07-01

    It is the intention of this paper, to contribute to a sustainable future by providing objective object information based on 3D photography as well as promoting 3D photography not only for scientists, but also for amateurs. Due to the presentation of this article by CIPA Task Group 3 on "3D Photographs in Cultural Heritage", the presented samples are masterpieces of historic as well as of current 3D photography concentrating on cultural heritage. In addition to a report on exemplarily access to international archives of 3D photographs, samples for new 3D photographs taken with modern 3D cameras, as well as by means of a ground based high resolution XLITE staff camera and also 3D photographs taken from a captive balloon and the use of civil drone platforms are dealt with. To advise on optimum suited 3D methodology, as well as to catch new trends in 3D, an updated synoptic overview of the 3D visualization technology, even claiming completeness, has been carried out as a result of a systematic survey. In this respect, e.g., today's lasered crystals might be "early bird" products in 3D, which, due to lack in resolution, contrast and color, remember to the stage of the invention of photography.

  10. Teaching Geography with 3-D Visualization Technology

    ERIC Educational Resources Information Center

    Anthamatten, Peter; Ziegler, Susy S.

    2006-01-01

    Technology that helps students view images in three dimensions (3-D) can support a broad range of learning styles. "Geo-Wall systems" are visualization tools that allow scientists, teachers, and students to project stereographic images and view them in 3-D. We developed and presented 3-D visualization exercises in several undergraduate courses.…

  11. 3D Printing and Its Urologic Applications

    PubMed Central

    Soliman, Youssef; Feibus, Allison H; Baum, Neil

    2015-01-01

    3D printing is the development of 3D objects via an additive process in which successive layers of material are applied under computer control. This article discusses 3D printing, with an emphasis on its historical context and its potential use in the field of urology. PMID:26028997

  12. 3D Flow Visualization Using Texture Advection

    NASA Technical Reports Server (NTRS)

    Kao, David; Zhang, Bing; Kim, Kwansik; Pang, Alex; Moran, Pat (Technical Monitor)

    2001-01-01

    Texture advection is an effective tool for animating and investigating 2D flows. In this paper, we discuss how this technique can be extended to 3D flows. In particular, we examine the use of 3D and 4D textures on 3D synthetic and computational fluid dynamics flow fields.

  13. 3D Elastic Seismic Wave Propagation Code

    1998-09-23

    E3D is capable of simulating seismic wave propagation in a 3D heterogeneous earth. Seismic waves are initiated by earthquake, explosive, and/or other sources. These waves propagate through a 3D geologic model, and are simulated as synthetic seismograms or other graphical output.

  14. 3D Printing and Its Urologic Applications.

    PubMed

    Soliman, Youssef; Feibus, Allison H; Baum, Neil

    2015-01-01

    3D printing is the development of 3D objects via an additive process in which successive layers of material are applied under computer control. This article discusses 3D printing, with an emphasis on its historical context and its potential use in the field of urology. PMID:26028997

  15. 3-D Perspective Pasadena, California

    NASA Technical Reports Server (NTRS)

    2000-01-01

    This perspective view shows the western part of the city of Pasadena, California, looking north towards the San Gabriel Mountains. Portions of the cities of Altadena and La Canada, Flintridge are also shown. The image was created from three datasets: the Shuttle Radar Topography Mission (SRTM) supplied the elevation data; Landsat data from November 11, 1986 provided the land surface color (not the sky) and U.S. Geological Survey digital aerial photography provides the image detail. The Rose Bowl, surrounded by a golf course, is the circular feature at the bottom center of the image. The Jet Propulsion Laboratory is the cluster of large buildings north of the Rose Bowl at the base of the mountains. A large landfill, Scholl Canyon, is the smooth area in the lower left corner of the scene. This image shows the power of combining data from different sources to create planning tools to study problems that affect large urban areas. In addition to the well-known earthquake hazards, Southern California is affected by a natural cycle of fire and mudflows. Wildfires strip the mountains of vegetation, increasing the hazards from flooding and mudflows for several years afterwards. Data such as shown on this image can be used to predict both how wildfires will spread over the terrain and also how mudflows will be channeled down the canyons. The Shuttle Radar Topography Mission (SRTM), launched on February 11, 2000, uses the same radar instrument that comprised the Spaceborne Imaging Radar-C/X-Band Synthetic Aperture Radar (SIR-C/X-SAR) that flew twice on the Space Shuttle Endeavour in 1994. The mission was designed to collect three dimensional measurements of the Earth's surface. To collect the 3-D data, engineers added a 60-meter-long (200-foot) mast, an additional C-band imaging antenna and improved tracking and navigation devices. The mission is a cooperative project between the National Aeronautics and Space Administration (NASA), the National Imagery and Mapping Agency

  16. The Esri 3D city information model

    NASA Astrophysics Data System (ADS)

    Reitz, T.; Schubiger-Banz, S.

    2014-02-01

    With residential and commercial space becoming increasingly scarce, cities are going vertical. Managing the urban environments in 3D is an increasingly important and complex undertaking. To help solving this problem, Esri has released the ArcGIS for 3D Cities solution. The ArcGIS for 3D Cities solution provides the information model, tools and apps for creating, analyzing and maintaining a 3D city using the ArcGIS platform. This paper presents an overview of the 3D City Information Model and some sample use cases.

  17. The ATLAS3D project - XX. Mass-size and mass-σ distributions of early-type galaxies: bulge fraction drives kinematics, mass-to-light ratio, molecular gas fraction and stellar initial mass function

    NASA Astrophysics Data System (ADS)

    Cappellari, Michele; McDermid, Richard M.; Alatalo, Katherine; Blitz, Leo; Bois, Maxime; Bournaud, Frédéric; Bureau, M.; Crocker, Alison F.; Davies, Roger L.; Davis, Timothy A.; de Zeeuw, P. T.; Duc, Pierre-Alain; Emsellem, Eric; Khochfar, Sadegh; Krajnović, Davor; Kuntschner, Harald; Morganti, Raffaella; Naab, Thorsten; Oosterloo, Tom; Sarzi, Marc; Scott, Nicholas; Serra, Paolo; Weijmans, Anne-Marie; Young, Lisa M.

    2013-07-01

    In the companion Paper XV of this series, we derive accurate total mass-to-light ratios (M/L)_JAM≈ (M/L)({r}= {R_e}) within a sphere of radius r= {R_e} centred on the galaxy, as well as stellar (M/L)stars (with the dark matter removed) for the volume-limited and nearly mass-selected (stellar mass M_star ≳ 6× 10^9 { M_{⊙}}) ATLAS3D sample of 260 early-type galaxies (ETGs, ellipticals Es and lenticulars S0s). Here, we use those parameters to study the two orthogonal projections ({M_JAM}, {σ _e}) and ({M_JAM}, {R_e^maj}) of the thin Mass Plane (MP) ({M_JAM}, {σ _e}, {R_e^maj}) which describes the distribution of the galaxy population, where {M_JAM}≡ L× (M/L)_JAM≈ M_star. The distribution of galaxy properties on both projections of the MP is characterized by: (i) the same zone of exclusion (ZOE), which can be transformed from one projection to the other using the scalar virial equation. The ZOE is roughly described by two power laws, joined by a break at a characteristic mass {M_JAM}≈ 3× 10^{10} { M_{⊙}}, which corresponds to the minimum Re and maximum stellar density. This results in a break in the mean {M_JAM}-{σ _e} relation with trends {M_JAM}∝ σ _e^{2.3} and {M_JAM}∝ σ _e^{4.7} at small and large σe, respectively; (ii) a characteristic mass {M_JAM}≈ 2× 10^{11} { M_{⊙}} which separates a population dominated by flat fast rotator with discs and spiral galaxies at lower masses, from one dominated by quite round slow rotators at larger masses; (iii) below that mass the distribution of ETGs' properties on the two projections of the MP tends to be constant along lines of roughly constant σe, or equivalently along lines with {R_e^maj}∝ {M_JAM}, respectively (or even better parallel to the ZOE: {R_e^maj}∝ M_JAM^{0.75}); (iv) it forms a continuous and parallel sequence with the distribution of spiral galaxies; (v) at even lower masses, the distribution of fast-rotator ETGs and late spirals naturally extends to that of dwarf ETGs (Sph

  18. Case study: Beauty and the Beast 3D: benefits of 3D viewing for 2D to 3D conversion

    NASA Astrophysics Data System (ADS)

    Handy Turner, Tara

    2010-02-01

    From the earliest stages of the Beauty and the Beast 3D conversion project, the advantages of accurate desk-side 3D viewing was evident. While designing and testing the 2D to 3D conversion process, the engineering team at Walt Disney Animation Studios proposed a 3D viewing configuration that not only allowed artists to "compose" stereoscopic 3D but also improved efficiency by allowing artists to instantly detect which image features were essential to the stereoscopic appeal of a shot and which features had minimal or even negative impact. At a time when few commercial 3D monitors were available and few software packages provided 3D desk-side output, the team designed their own prototype devices and collaborated with vendors to create a "3D composing" workstation. This paper outlines the display technologies explored, final choices made for Beauty and the Beast 3D, wish-lists for future development and a few rules of thumb for composing compelling 2D to 3D conversions.

  19. 3D laptop for defense applications

    NASA Astrophysics Data System (ADS)

    Edmondson, Richard; Chenault, David

    2012-06-01

    Polaris Sensor Technologies has developed numerous 3D display systems using a US Army patented approach. These displays have been developed as prototypes for handheld controllers for robotic systems and closed hatch driving, and as part of a TALON robot upgrade for 3D vision, providing depth perception for the operator for improved manipulation and hazard avoidance. In this paper we discuss the prototype rugged 3D laptop computer and its applications to defense missions. The prototype 3D laptop combines full temporal and spatial resolution display with the rugged Amrel laptop computer. The display is viewed through protective passive polarized eyewear, and allows combined 2D and 3D content. Uses include robot tele-operation with live 3D video or synthetically rendered scenery, mission planning and rehearsal, enhanced 3D data interpretation, and simulation.

  20. Landmark detection from 3D mesh facial models for image-based analysis of dysmorphology.

    PubMed

    Chendeb, Marwa; Tortorici, Claudio; Al Muhairi, Hassan; Al Safar, Habiba; Linguraru, Marius; Werghi, Naoufel

    2015-01-01

    Facial landmark detection is a task of interest for facial dysmorphology, an important factor in the diagnosis of genetic conditions. In this paper, we propose a framework for feature points detection from 3D face images. The method is based on 3D Constrained Local Model (CLM) which learns both global variations in the 3D facial scan and local changes around every vertex landmark. Compared to state of the art methods our framework is distinguished by the following novel aspects: 1) It operates on facial surfaces, 2) It allows fusion of shape and color information on the mesh surface, 3) It introduces the use of LBP descriptors on the mesh. We showcase our landmarks detection framework on a set of scans including down syndrome and control cases. We also validate our method through a series of quantitative experiments conducted with the publicly available Bosphorus database. PMID:26736227

  1. Predicting activities without computing descriptors: graph machines for QSAR.

    PubMed

    Goulon, A; Picot, T; Duprat, A; Dreyfus, G

    2007-01-01

    We describe graph machines, an alternative approach to traditional machine-learning-based QSAR, which circumvents the problem of designing, computing and selecting molecular descriptors. In that approach, which is similar in spirit to recursive networks, molecules are considered as structured data, represented as graphs. For each example of the data set, a mathematical function (graph machine) is built, whose structure reflects the structure of the molecule under consideration; it is the combination of identical parameterised functions, called "node functions" (e.g. a feedforward neural network). The parameters of the node functions, shared both within and across the graph machines, are adjusted during training with the "shared weights" technique. Model selection is then performed by traditional cross-validation. Therefore, the designer's main task consists in finding the optimal complexity for the node function. The efficiency of this new approach has been demonstrated in many QSAR or QSPR tasks, as well as in modelling the activities of complex chemicals (e.g. the toxicity of a family of phenols or the anti-HIV activities of HEPT derivatives). It generally outperforms traditional techniques without requiring the selection and computation of descriptors. PMID:17365965

  2. MIND: modality independent neighbourhood descriptor for multi-modal deformable registration.

    PubMed

    Heinrich, Mattias P; Jenkinson, Mark; Bhushan, Manav; Matin, Tahreema; Gleeson, Fergus V; Brady, Sir Michael; Schnabel, Julia A

    2012-10-01

    Deformable registration of images obtained from different modalities remains a challenging task in medical image analysis. This paper addresses this important problem and proposes a modality independent neighbourhood descriptor (MIND) for both linear and deformable multi-modal registration. Based on the similarity of small image patches within one image, it aims to extract the distinctive structure in a local neighbourhood, which is preserved across modalities. The descriptor is based on the concept of image self-similarity, which has been introduced for non-local means filtering for image denoising. It is able to distinguish between different types of features such as corners, edges and homogeneously textured regions. MIND is robust to the most considerable differences between modalities: non-functional intensity relations, image noise and non-uniform bias fields. The multi-dimensional descriptor can be efficiently computed in a dense fashion across the whole image and provides point-wise local similarity across modalities based on the absolute or squared difference between descriptors, making it applicable for a wide range of transformation models and optimisation algorithms. We use the sum of squared differences of the MIND representations of the images as a similarity metric within a symmetric non-parametric Gauss-Newton registration framework. In principle, MIND would be applicable to the registration of arbitrary modalities. In this work, we apply and validate it for the registration of clinical 3D thoracic CT scans between inhale and exhale as well as the alignment of 3D CT and MRI scans. Experimental results show the advantages of MIND over state-of-the-art techniques such as conditional mutual information and entropy images, with respect to clinically annotated landmark locations. PMID:22722056

  3. 3-D Technology Approaches for Biological Ecologies

    NASA Astrophysics Data System (ADS)

    Liu, Liyu; Austin, Robert; U. S-China Physical-Oncology Sciences Alliance (PS-OA) Team

    Constructing three dimensional (3-D) landscapes is an inevitable issue in deep study of biological ecologies, because in whatever scales in nature, all of the ecosystems are composed by complex 3-D environments and biological behaviors. Just imagine if a 3-D technology could help complex ecosystems be built easily and mimic in vivo microenvironment realistically with flexible environmental controls, it will be a fantastic and powerful thrust to assist researchers for explorations. For years, we have been utilizing and developing different technologies for constructing 3-D micro landscapes for biophysics studies in in vitro. Here, I will review our past efforts, including probing cancer cell invasiveness with 3-D silicon based Tepuis, constructing 3-D microenvironment for cell invasion and metastasis through polydimethylsiloxane (PDMS) soft lithography, as well as explorations of optimized stenting positions for coronary bifurcation disease with 3-D wax printing and the latest home designed 3-D bio-printer. Although 3-D technologies is currently considered not mature enough for arbitrary 3-D micro-ecological models with easy design and fabrication, I hope through my talk, the audiences will be able to sense its significance and predictable breakthroughs in the near future. This work was supported by the State Key Development Program for Basic Research of China (Grant No. 2013CB837200), the National Natural Science Foundation of China (Grant No. 11474345) and the Beijing Natural Science Foundation (Grant No. 7154221).

  4. RT3D tutorials for GMS users

    SciTech Connect

    Clement, T.P.; Jones, N.L.

    1998-02-01

    RT3D (Reactive Transport in 3-Dimensions) is a computer code that solves coupled partial differential equations that describe reactive-flow and transport of multiple mobile and/or immobile species in a three dimensional saturated porous media. RT3D was developed from the single-species transport code, MT3D (DoD-1.5, 1997 version). As with MT3D, RT3D also uses the USGS groundwater flow model MODFLOW for computing spatial and temporal variations in groundwater head distribution. This report presents a set of tutorial problems that are designed to illustrate how RT3D simulations can be performed within the Department of Defense Groundwater Modeling System (GMS). GMS serves as a pre- and post-processing interface for RT3D. GMS can be used to define all the input files needed by RT3D code, and later the code can be launched from within GMS and run as a separate application. Once the RT3D simulation is completed, the solution can be imported to GMS for graphical post-processing. RT3D v1.0 supports several reaction packages that can be used for simulating different types of reactive contaminants. Each of the tutorials, described below, provides training on a different RT3D reaction package. Each reaction package has different input requirements, and the tutorials are designed to describe these differences. Furthermore, the tutorials illustrate the various options available in GMS for graphical post-processing of RT3D results. Users are strongly encouraged to complete the tutorials before attempting to use RT3D and GMS on a routine basis.

  5. Feature Point Descriptors: Infrared and Visible Spectra

    PubMed Central

    Ricaurte, Pablo; Chilán, Carmen; Aguilera-Carrasco, Cristhian A.; Vintimilla, Boris X.; Sappa, Angel D.

    2014-01-01

    This manuscript evaluates the behavior of classical feature point descriptors when they are used in images from long-wave infrared spectral band and compare them with the results obtained in the visible spectrum. Robustness to changes in rotation, scaling, blur, and additive noise are analyzed using a state of the art framework. Experimental results using a cross-spectral outdoor image data set are presented and conclusions from these experiments are given. PMID:24566634

  6. A novel biologically inspired local feature descriptor.

    PubMed

    Zhang, Yun; Tian, Tian; Tian, Jinwen; Gong, Junbin; Ming, Delie

    2014-06-01

    Local feature descriptor is a fundamental representation for image patch which has been extensively used in many computer vision applications. In this paper, different from state-of-the-art features, a novel biologically inspired local descriptor (BILD) is proposed based on the visual information processing mechanism of ventral pathway in human brain. The local features used for constructing BILD are extracted by a two-layer network, which corresponds to the simple-to-complex cell hierarchy in the primary visual cortex (V1). It works in a similar way as the simple cell and complex cell do to get responses by applying the lateral inhibition from different orientations and operating an improved cortical pooling. To enhance the distinctiveness of BILD, we combine the local features from different orientations. Extensive evaluations have been performed for image matching and object recognition. Experimental results reveal that our proposed BILD outperforms many widely used descriptors such as SIFT and SURF, which demonstrate its efficiency for representing local regions. PMID:24677037

  7. Image-Based Airborne LiDAR Point Cloud Encoding for 3d Building Model Retrieval

    NASA Astrophysics Data System (ADS)

    Chen, Yi-Chen; Lin, Chao-Hung

    2016-06-01

    With the development of Web 2.0 and cyber city modeling, an increasing number of 3D models have been available on web-based model-sharing platforms with many applications such as navigation, urban planning, and virtual reality. Based on the concept of data reuse, a 3D model retrieval system is proposed to retrieve building models similar to a user-specified query. The basic idea behind this system is to reuse these existing 3D building models instead of reconstruction from point clouds. To efficiently retrieve models, the models in databases are compactly encoded by using a shape descriptor generally. However, most of the geometric descriptors in related works are applied to polygonal models. In this study, the input query of the model retrieval system is a point cloud acquired by Light Detection and Ranging (LiDAR) systems because of the efficient scene scanning and spatial information collection. Using Point clouds with sparse, noisy, and incomplete sampling as input queries is more difficult than that by using 3D models. Because that the building roof is more informative than other parts in the airborne LiDAR point cloud, an image-based approach is proposed to encode both point clouds from input queries and 3D models in databases. The main goal of data encoding is that the models in the database and input point clouds can be consistently encoded. Firstly, top-view depth images of buildings are generated to represent the geometry surface of a building roof. Secondly, geometric features are extracted from depth images based on height, edge and plane of building. Finally, descriptors can be extracted by spatial histograms and used in 3D model retrieval system. For data retrieval, the models are retrieved by matching the encoding coefficients of point clouds and building models. In experiments, a database including about 900,000 3D models collected from the Internet is used for evaluation of data retrieval. The results of the proposed method show a clear superiority

  8. 3D Dynamic Echocardiography with a Digitizer

    NASA Astrophysics Data System (ADS)

    Oshiro, Osamu; Matani, Ayumu; Chihara, Kunihiro

    1998-05-01

    In this paper,a three-dimensional (3D) dynamic ultrasound (US) imaging system,where a US brightness-mode (B-mode) imagetriggered with an R-wave of electrocardiogram (ECG)was obtained with an ultrasound diagnostic deviceand the location and orientation of the US probewere simultaneously measured with a 3D digitizer, is described.The obtained B-mode imagewas then projected onto a virtual 3D spacewith the proposed interpolation algorithm using a Gaussian operator.Furthermore, a 3D image was presented on a cathode ray tube (CRT)and stored in virtual reality modeling language (VRML).We performed an experimentto reconstruct a 3D heart image in systole using this system.The experimental results indicatethat the system enables the visualization ofthe 3D and internal structure of a heart viewed from any angleand has potential for use in dynamic imaging,intraoperative ultrasonography and tele-medicine.

  9. 3D Scientific Visualization with Blender

    NASA Astrophysics Data System (ADS)

    Kent, Brian R.

    2015-03-01

    This is the first book written on using Blender for scientific visualization. It is a practical and interesting introduction to Blender for understanding key parts of 3D rendering and animation that pertain to the sciences via step-by-step guided tutorials. 3D Scientific Visualization with Blender takes you through an understanding of 3D graphics and modelling for different visualization scenarios in the physical sciences.

  10. Software for 3D radiotherapy dosimetry. Validation

    NASA Astrophysics Data System (ADS)

    Kozicki, Marek; Maras, Piotr; Karwowski, Andrzej C.

    2014-08-01

    The subject of this work is polyGeVero® software (GeVero Co., Poland), which has been developed to fill the requirements of fast calculations of 3D dosimetry data with the emphasis on polymer gel dosimetry for radiotherapy. This software comprises four workspaces that have been prepared for: (i) calculating calibration curves and calibration equations, (ii) storing the calibration characteristics of the 3D dosimeters, (iii) calculating 3D dose distributions in irradiated 3D dosimeters, and (iv) comparing 3D dose distributions obtained from measurements with the aid of 3D dosimeters and calculated with the aid of treatment planning systems (TPSs). The main features and functions of the software are described in this work. Moreover, the core algorithms were validated and the results are presented. The validation was performed using the data of the new PABIGnx polymer gel dosimeter. The polyGeVero® software simplifies and greatly accelerates the calculations of raw 3D dosimetry data. It is an effective tool for fast verification of TPS-generated plans for tumor irradiation when combined with a 3D dosimeter. Consequently, the software may facilitate calculations by the 3D dosimetry community. In this work, the calibration characteristics of the PABIGnx obtained through four calibration methods: multi vial, cross beam, depth dose, and brachytherapy, are discussed as well.

  11. Dimensional accuracy of 3D printed vertebra

    NASA Astrophysics Data System (ADS)

    Ogden, Kent; Ordway, Nathaniel; Diallo, Dalanda; Tillapaugh-Fay, Gwen; Aslan, Can

    2014-03-01

    3D printer applications in the biomedical sciences and medical imaging are expanding and will have an increasing impact on the practice of medicine. Orthopedic and reconstructive surgery has been an obvious area for development of 3D printer applications as the segmentation of bony anatomy to generate printable models is relatively straightforward. There are important issues that should be addressed when using 3D printed models for applications that may affect patient care; in particular the dimensional accuracy of the printed parts needs to be high to avoid poor decisions being made prior to surgery or therapeutic procedures. In this work, the dimensional accuracy of 3D printed vertebral bodies derived from CT data for a cadaver spine is compared with direct measurements on the ex-vivo vertebra and with measurements made on the 3D rendered vertebra using commercial 3D image processing software. The vertebra was printed on a consumer grade 3D printer using an additive print process using PLA (polylactic acid) filament. Measurements were made for 15 different anatomic features of the vertebral body, including vertebral body height, endplate width and depth, pedicle height and width, and spinal canal width and depth, among others. It is shown that for the segmentation and printing process used, the results of measurements made on the 3D printed vertebral body are substantially the same as those produced by direct measurement on the vertebra and measurements made on the 3D rendered vertebra.

  12. Stereo 3-D Vision in Teaching Physics

    NASA Astrophysics Data System (ADS)

    Zabunov, Svetoslav

    2012-03-01

    Stereo 3-D vision is a technology used to present images on a flat surface (screen, paper, etc.) and at the same time to create the notion of three-dimensional spatial perception of the viewed scene. A great number of physical processes are much better understood when viewed in stereo 3-D vision compared to standard flat 2-D presentation. The current paper describes the modern stereo 3-D technologies that are applicable to various tasks in teaching physics in schools, colleges, and universities. Examples of stereo 3-D simulations developed by the author can be observed on online.

  13. Accuracy in Quantitative 3D Image Analysis

    PubMed Central

    Bassel, George W.

    2015-01-01

    Quantitative 3D imaging is becoming an increasingly popular and powerful approach to investigate plant growth and development. With the increased use of 3D image analysis, standards to ensure the accuracy and reproducibility of these data are required. This commentary highlights how image acquisition and postprocessing can introduce artifacts into 3D image data and proposes steps to increase both the accuracy and reproducibility of these analyses. It is intended to aid researchers entering the field of 3D image processing of plant cells and tissues and to help general readers in understanding and evaluating such data. PMID:25804539

  14. Non-isothermal 3D SDPD Simulations

    NASA Astrophysics Data System (ADS)

    Yang, Jun; Potami, Raffaele; Gatsonis, Nikolaos

    2012-11-01

    The study of fluids at micro and nanoscale requires new modeling and computational approaches. Smooth Particle Dissipative Dynamics (SDPD) is a mesh-free method that provides a bridge between the continuum equations of hydrodynamics embedded in the Smooth Particle Hydrodynamics approach and the molecular nature embedded in the DPD approach. SDPD is thermodynamically consistent, does not rely on arbitrary coefficients for its thermostat, involves realistic transport coefficients, and includes fluctuation terms. SDPD is implemented in our work for arbitrary 3D geometries with a methodology to model solid wall boundary conditions. We present simulations for isothermal flows for verification of our approach. The entropy equation is implemented with a velocity-entropy Verlet integration algorithm Flows with heat transfer are simulated for verification of the SDPD. We present also the self-diffusion coefficient derived from SDPD simulations for gases and liquids. Results show the scale dependence of self-diffusion coefficient on SDPD particle size. Computational Mathematics Program of the Air Force Office of Scientific Research under grant/contract number FA9550-06-1-0236.

  15. FastScript3D - A Companion to Java 3D

    NASA Technical Reports Server (NTRS)

    Koenig, Patti

    2005-01-01

    FastScript3D is a computer program, written in the Java 3D(TM) programming language, that establishes an alternative language that helps users who lack expertise in Java 3D to use Java 3D for constructing three-dimensional (3D)-appearing graphics. The FastScript3D language provides a set of simple, intuitive, one-line text-string commands for creating, controlling, and animating 3D models. The first word in a string is the name of a command; the rest of the string contains the data arguments for the command. The commands can also be used as an aid to learning Java 3D. Developers can extend the language by adding custom text-string commands. The commands can define new 3D objects or load representations of 3D objects from files in formats compatible with such other software systems as X3D. The text strings can be easily integrated into other languages. FastScript3D facilitates communication between scripting languages [which enable programming of hyper-text markup language (HTML) documents to interact with users] and Java 3D. The FastScript3D language can be extended and customized on both the scripting side and the Java 3D side.

  16. 3D RISM theory with fast reciprocal-space electrostatics

    SciTech Connect

    Heil, Jochen; Kast, Stefan M.

    2015-03-21

    The calculation of electrostatic solute-solvent interactions in 3D RISM (“three-dimensional reference interaction site model”) integral equation theory is recast in a form that allows for a computational treatment analogous to the “particle-mesh Ewald” formalism as used for molecular simulations. In addition, relations that connect 3D RISM correlation functions and interaction potentials with thermodynamic quantities such as the chemical potential and average solute-solvent interaction energy are reformulated in a way that calculations of expensive real-space electrostatic terms on the 3D grid are completely avoided. These methodical enhancements allow for both, a significant speedup particularly for large solute systems and a smoother convergence of predicted thermodynamic quantities with respect to box size, as illustrated for several benchmark systems.

  17. 3D RISM theory with fast reciprocal-space electrostatics.

    PubMed

    Heil, Jochen; Kast, Stefan M

    2015-03-21

    The calculation of electrostatic solute-solvent interactions in 3D RISM ("three-dimensional reference interaction site model") integral equation theory is recast in a form that allows for a computational treatment analogous to the "particle-mesh Ewald" formalism as used for molecular simulations. In addition, relations that connect 3D RISM correlation functions and interaction potentials with thermodynamic quantities such as the chemical potential and average solute-solvent interaction energy are reformulated in a way that calculations of expensive real-space electrostatic terms on the 3D grid are completely avoided. These methodical enhancements allow for both, a significant speedup particularly for large solute systems and a smoother convergence of predicted thermodynamic quantities with respect to box size, as illustrated for several benchmark systems. PMID:25796231

  18. Algorithms for Haptic Rendering of 3D Objects

    NASA Technical Reports Server (NTRS)

    Basdogan, Cagatay; Ho, Chih-Hao; Srinavasan, Mandayam

    2003-01-01

    Algorithms have been developed to provide haptic rendering of three-dimensional (3D) objects in virtual (that is, computationally simulated) environments. The goal of haptic rendering is to generate tactual displays of the shapes, hardnesses, surface textures, and frictional properties of 3D objects in real time. Haptic rendering is a major element of the emerging field of computer haptics, which invites comparison with computer graphics. We have already seen various applications of computer haptics in the areas of medicine (surgical simulation, telemedicine, haptic user interfaces for blind people, and rehabilitation of patients with neurological disorders), entertainment (3D painting, character animation, morphing, and sculpting), mechanical design (path planning and assembly sequencing), and scientific visualization (geophysical data analysis and molecular manipulation).

  19. 3D active surfaces for liver segmentation in multisequence MRI images.

    PubMed

    Bereciartua, Arantza; Picon, Artzai; Galdran, Adrian; Iriondo, Pedro

    2016-08-01

    Biopsies for diagnosis can sometimes be replaced by non-invasive techniques such as CT and MRI. Surgeons require accurate and efficient methods that allow proper segmentation of the organs in order to ensure the most reliable intervention planning. Automated liver segmentation is a difficult and open problem where CT has been more widely explored than MRI. MRI liver segmentation represents a challenge due to the presence of characteristic artifacts, such as partial volumes, noise and low contrast. In this paper, we present a novel method for multichannel MRI automatic liver segmentation. The proposed method consists of the minimization of a 3D active surface by means of the dual approach to the variational formulation of the underlying problem. This active surface evolves over a probability map that is based on a new compact descriptor comprising spatial and multisequence information which is further modeled by means of a liver statistical model. This proposed 3D active surface approach naturally integrates volumetric regularization in the statistical model. The advantages of the compact visual descriptor together with the proposed approach result in a fast and accurate 3D segmentation method. The method was tested on 18 healthy liver studies and results were compared to a gold standard made by expert radiologists. Comparisons with other state-of-the-art approaches are provided by means of nine well established quality metrics. The obtained results improve these methodologies, achieving a Dice Similarity Coefficient of 98.59. PMID:27282235

  20. Fast global interactive volume segmentation with regional supervoxel descriptors

    NASA Astrophysics Data System (ADS)

    Luengo, Imanol; Basham, Mark; French, Andrew P.

    2016-03-01

    In this paper we propose a novel approach towards fast multi-class volume segmentation that exploits supervoxels in order to reduce complexity, time and memory requirements. Current methods for biomedical image segmentation typically require either complex mathematical models with slow convergence, or expensive-to-calculate image features, which makes them non-feasible for large volumes with many objects (tens to hundreds) of different classes, as is typical in modern medical and biological datasets. Recently, graphical models such as Markov Random Fields (MRF) or Conditional Random Fields (CRF) are having a huge impact in different computer vision areas (e.g. image parsing, object detection, object recognition) as they provide global regularization for multiclass problems over an energy minimization framework. These models have yet to find impact in biomedical imaging due to complexities in training and slow inference in 3D images due to the very large number of voxels. Here, we define an interactive segmentation approach over a supervoxel space by first defining novel, robust and fast regional descriptors for supervoxels. Then, a hierarchical segmentation approach is adopted by training Contextual Extremely Random Forests in a user-defined label hierarchy where the classification output of the previous layer is used as additional features to train a new classifier to refine more detailed label information. This hierarchical model yields final class likelihoods for supervoxels which are finally refined by a MRF model for 3D segmentation. Results demonstrate the effectiveness on a challenging cryo-soft X-ray tomography dataset by segmenting cell areas with only a few user scribbles as the input for our algorithm. Further results demonstrate the effectiveness of our method to fully extract different organelles from the cell volume with another few seconds of user interaction.

  1. 3D PDF - a means of public access to geological 3D - objects, using the example of GTA3D

    NASA Astrophysics Data System (ADS)

    Slaby, Mark-Fabian; Reimann, Rüdiger

    2013-04-01

    In geology, 3D modeling has become very important. In the past, two-dimensional data such as isolines, drilling profiles, or cross-sections based on those, were used to illustrate the subsurface geology, whereas now, we can create complex digital 3D models. These models are produced with special software, such as GOCAD ®. The models can be viewed, only through the software used to create them, or through viewers available for free. The platform-independent PDF (Portable Document Format), enforced by Adobe, has found a wide distribution. This format has constantly evolved over time. Meanwhile, it is possible to display CAD data in an Adobe 3D PDF file with the free Adobe Reader (version 7). In a 3D PDF, a 3D model is freely rotatable and can be assembled from a plurality of objects, which can thus be viewed from all directions on their own. In addition, it is possible to create moveable cross-sections (profiles), and to assign transparency to the objects. Based on industry-standard CAD software, 3D PDFs can be generated from a large number of formats, or even be exported directly from this software. In geoinformatics, different approaches to creating 3D PDFs exist. The intent of the Authority for Mining, Energy and Geology to allow free access to the models of the Geotectonic Atlas (GTA3D), could not be realized with standard software solutions. A specially designed code converts the 3D objects to VRML (Virtual Reality Modeling Language). VRML is one of the few formats that allow using image files (maps) as textures, and to represent colors and shapes correctly. The files were merged in Acrobat X Pro, and a 3D PDF was generated subsequently. A topographic map, a display of geographic directions and horizontal and vertical scales help to facilitate the use.

  2. An aerial 3D printing test mission

    NASA Astrophysics Data System (ADS)

    Hirsch, Michael; McGuire, Thomas; Parsons, Michael; Leake, Skye; Straub, Jeremy

    2016-05-01

    This paper provides an overview of an aerial 3D printing technology, its development and its testing. This technology is potentially useful in its own right. In addition, this work advances the development of a related in-space 3D printing technology. A series of aerial 3D printing test missions, used to test the aerial printing technology, are discussed. Through completing these test missions, the design for an in-space 3D printer may be advanced. The current design for the in-space 3D printer involves focusing thermal energy to heat an extrusion head and allow for the extrusion of molten print material. Plastics can be used as well as composites including metal, allowing for the extrusion of conductive material. A variety of experiments will be used to test this initial 3D printer design. High altitude balloons will be used to test the effects of microgravity on 3D printing, as well as parabolic flight tests. Zero pressure balloons can be used to test the effect of long 3D printing missions subjected to low temperatures. Vacuum chambers will be used to test 3D printing in a vacuum environment. The results will be used to adapt a current prototype of an in-space 3D printer. Then, a small scale prototype can be sent into low-Earth orbit as a 3-U cube satellite. With the ability to 3D print in space demonstrated, future missions can launch production hardware through which the sustainability and durability of structures in space will be greatly improved.

  3. 3D ultrafast ultrasound imaging in vivo

    NASA Astrophysics Data System (ADS)

    Provost, Jean; Papadacci, Clement; Esteban Arango, Juan; Imbault, Marion; Fink, Mathias; Gennisson, Jean-Luc; Tanter, Mickael; Pernot, Mathieu

    2014-10-01

    Very high frame rate ultrasound imaging has recently allowed for the extension of the applications of echography to new fields of study such as the functional imaging of the brain, cardiac electrophysiology, and the quantitative imaging of the intrinsic mechanical properties of tumors, to name a few, non-invasively and in real time. In this study, we present the first implementation of Ultrafast Ultrasound Imaging in 3D based on the use of either diverging or plane waves emanating from a sparse virtual array located behind the probe. It achieves high contrast and resolution while maintaining imaging rates of thousands of volumes per second. A customized portable ultrasound system was developed to sample 1024 independent channels and to drive a 32  ×  32 matrix-array probe. Its ability to track in 3D transient phenomena occurring in the millisecond range within a single ultrafast acquisition was demonstrated for 3D Shear-Wave Imaging, 3D Ultrafast Doppler Imaging, and, finally, 3D Ultrafast combined Tissue and Flow Doppler Imaging. The propagation of shear waves was tracked in a phantom and used to characterize its stiffness. 3D Ultrafast Doppler was used to obtain 3D maps of Pulsed Doppler, Color Doppler, and Power Doppler quantities in a single acquisition and revealed, at thousands of volumes per second, the complex 3D flow patterns occurring in the ventricles of the human heart during an entire cardiac cycle, as well as the 3D in vivo interaction of blood flow and wall motion during the pulse wave in the carotid at the bifurcation. This study demonstrates the potential of 3D Ultrafast Ultrasound Imaging for the 3D mapping of stiffness, tissue motion, and flow in humans in vivo and promises new clinical applications of ultrasound with reduced intra—and inter-observer variability.

  4. Extra Dimensions: 3D and Time in PDF Documentation

    SciTech Connect

    Graf, N.A.; /SLAC

    2012-04-11

    Experimental science is replete with multi-dimensional information which is often poorly represented by the two dimensions of presentation slides and print media. Past efforts to disseminate such information to a wider audience have failed for a number of reasons, including a lack of standards which are easy to implement and have broad support. Adobe's Portable Document Format (PDF) has in recent years become the de facto standard for secure, dependable electronic information exchange. It has done so by creating an open format, providing support for multiple platforms and being reliable and extensible. By providing support for the ECMA standard Universal 3D (U3D) file format in its free Adobe Reader software, Adobe has made it easy to distribute and interact with 3D content. By providing support for scripting and animation, temporal data can also be easily distributed to a wide, non-technical audience. We discuss how the field of radiation imaging could benefit from incorporating full 3D information about not only the detectors, but also the results of the experimental analyses, in its electronic publications. In this article, we present examples drawn from high-energy physics, mathematics and molecular biology which take advantage of this functionality. We demonstrate how 3D detector elements can be documented, using either CAD drawings or other sources such as GEANT visualizations as input.

  5. Extra dimensions: 3D and time in PDF documentation

    NASA Astrophysics Data System (ADS)

    Graf, N. A.

    2011-01-01

    Experimental science is replete with multi-dimensional information which is often poorly represented by the two dimensions of presentation slides and print media. Past efforts to disseminate such information to a wider audience have failed for a number of reasons, including a lack of standards which are easy to implement and have broad support. Adobe's Portable Document Format (PDF) has in recent years become the de facto standard for secure, dependable electronic information exchange. It has done so by creating an open format, providing support for multiple platforms and being reliable and extensible. By providing support for the ECMA standard Universal 3D (U3D) file format in its free Adobe Reader software, Adobe has made it easy to distribute and interact with 3D content. By providing support for scripting and animation, temporal data can also be easily distributed to a wide, non-technical audience. We discuss how the field of radiation imaging could benefit from incorporating full 3D information about not only the detectors, but also the results of the experimental analyses, in its electronic publications. In this article, we present examples drawn from high-energy physics, mathematics and molecular biology which take advantage of this functionality. We demonstrate how 3D detector elements can be documented, using either CAD drawings or other sources such as GEANT visualizations as input.

  6. Comparison of protein structures using 3D profile alignment.

    PubMed

    Suyama, M; Matsuo, Y; Nishikawa, K

    1997-01-01

    A novel method for protein structure comparison using 3D profile alignment is presented. The 3D profile is a position-dependent scoring matrix derived from three-dimensional structures and is basically used to estimate sequence-structure compatibility for prediction of protein structure. Our idea is to compare two 3D profiles using a dynamic programming algorithm to obtain optimal alignment and a similarity score between them. When the 3D profile of hemoglobin was compared with each of the profiles in the library, which contained 325 profiles of representative structures, all the profiles of other globins were detected with relatively high scores, and proteins in the same structural class followed the globins. Exhaustive comparison of 3D profiles in the library was also performed to depict protein relatedness in the structure space. Using multidimensional scaling, a planar projection of points in the protein structure space revealed an overall grouping in terms of structural classes, i.e., all-alpha, all-beta, alpha/beta, and alpha+beta. These results differ in implication from those obtained by the conventional structure-structure comparison method. Differences are discussed with respect to the structural divergence of proteins in the course of molecular evolution. PMID:9071025

  7. Molecular characterization of a 13-amino acid deletion in VP1 (1D) protein and novel amino acid substitutions in 3D polymerase protein of foot and mouth disease virus subtype A/Iran87

    PubMed Central

    Jelokhani-Niaraki, Saber; Hashemnejad, Khadije; Kamalzadeh, Morteza; Lotfi, Mohsen

    2011-01-01

    The nucleotide sequence of the VP1 (1D) and partial 3D polymerase (3Dpol) coding regions of the foot and mouth disease virus (FMDV) vaccine strain A/Iran87, a highly passaged isolate (~150 passages), was determined and aligned with previously published FMDV serotype A sequences. Overall analysis of the amino acid substitutions revealed that the partial 3Dpol coding region contained four amino acid alterations. Amino acid sequence comparison of the VP1 coding region of the field isolates revealed deletions in the highly passaged Iranian isolate (A/Iran87). The prominent G-H loop of the FMDV VP1 protein contains the conserved arginine-glycine-aspartic acid (RGD) tripeptide, which is a well-known ligand for a specific cell surface integrin. Despite losing the RGD sequence of the VP1 protein and an Asp26→Glu substitution in a beta sheet located within a small groove of the 3Dpol protein, the virus grew in BHK 21 suspension cell cultures. Since this strain has been used as a vaccine strain, it may be inferred that the RGD deletion has no critical role in virus attachment to the cell during the initiation of infection. It is probable that this FMDV subtype can utilize other pathways for cell attachment. PMID:22122902

  8. 3-D seismology in the Arabian Gulf

    SciTech Connect

    Al-Husseini, M.; Chimblo, R.

    1995-08-01

    Since 1977 when Aramco and GSI (Geophysical Services International) pioneered the first 3-D seismic survey in the Arabian Gulf, under the guidance of Aramco`s Chief Geophysicist John Hoke, 3-D seismology has been effectively used to map many complex subsurface geological phenomena. By the mid-1990s extensive 3-D surveys were acquired in Abu Dhabi, Oman, Qatar and Saudi Arabia. Also in the mid-1990`s Bahrain, Kuwait and Dubai were preparing to record surveys over their fields. On the structural side 3-D has refined seismic maps, focused faults and fractures systems, as well as outlined the distribution of facies, porosity and fluid saturation. In field development, 3D has not only reduced drilling costs significantly, but has also improved the understanding of fluid behavior in the reservoir. In Oman, Petroleum Development Oman (PDO) has now acquired the first Gulf 4-D seismic survey (time-lapse 3D survey) over the Yibal Field. The 4-D survey will allow PDO to directly monitor water encroachment in the highly-faulted Cretaceous Shu`aiba reservoir. In exploration, 3-D seismology has resolved complex prospects with structural and stratigraphic complications and reduced the risk in the selection of drilling locations. The many case studies from Saudi Arabia, Oman, Qatar and the United Arab Emirates, which are reviewed in this paper, attest to the effectiveness of 3D seismology in exploration and producing, in clastics and carbonates reservoirs, and in the Mesozoic and Paleozoic.

  9. A 3D Geostatistical Mapping Tool

    1999-02-09

    This software provides accurate 3D reservoir modeling tools and high quality 3D graphics for PC platforms enabling engineers and geologists to better comprehend reservoirs and consequently improve their decisions. The mapping algorithms are fractals, kriging, sequential guassian simulation, and three nearest neighbor methods.

  10. 3D, or Not to Be?

    ERIC Educational Resources Information Center

    Norbury, Keith

    2012-01-01

    It may be too soon for students to be showing up for class with popcorn and gummy bears, but technology similar to that behind the 3D blockbuster movie "Avatar" is slowly finding its way into college classrooms. 3D classroom projectors are taking students on fantastic voyages inside the human body, to the ruins of ancient Greece--even to faraway…

  11. Stereoscopic Investigations of 3D Coulomb Balls

    SciTech Connect

    Kaeding, Sebastian; Melzer, Andre; Arp, Oliver; Block, Dietmar; Piel, Alexander

    2005-10-31

    In dusty plasmas particles are arranged due to the influence of external forces and the Coulomb interaction. Recently Arp et al. were able to generate 3D spherical dust clouds, so-called Coulomb balls. Here, we present measurements that reveal the full 3D particle trajectories from stereoscopic imaging.

  12. 3-D structures of planetary nebulae

    NASA Astrophysics Data System (ADS)

    Steffen, W.

    2016-07-01

    Recent advances in the 3-D reconstruction of planetary nebulae are reviewed. We include not only results for 3-D reconstructions, but also the current techniques in terms of general methods and software. In order to obtain more accurate reconstructions, we suggest to extend the widely used assumption of homologous nebula expansion to map spectroscopically measured velocity to position along the line of sight.

  13. Wow! 3D Content Awakens the Classroom

    ERIC Educational Resources Information Center

    Gordon, Dan

    2010-01-01

    From her first encounter with stereoscopic 3D technology designed for classroom instruction, Megan Timme, principal at Hamilton Park Pacesetter Magnet School in Dallas, sensed it could be transformative. Last spring, when she began pilot-testing 3D content in her third-, fourth- and fifth-grade classrooms, Timme wasn't disappointed. Students…

  14. Static & Dynamic Response of 3D Solids

    1996-07-15

    NIKE3D is a large deformations 3D finite element code used to obtain the resulting displacements and stresses from multi-body static and dynamic structural thermo-mechanics problems with sliding interfaces. Many nonlinear and temperature dependent constitutive models are available.

  15. Immersive 3D Geovisualization in Higher Education

    ERIC Educational Resources Information Center

    Philips, Andrea; Walz, Ariane; Bergner, Andreas; Graeff, Thomas; Heistermann, Maik; Kienzler, Sarah; Korup, Oliver; Lipp, Torsten; Schwanghart, Wolfgang; Zeilinger, Gerold

    2015-01-01

    In this study, we investigate how immersive 3D geovisualization can be used in higher education. Based on MacEachren and Kraak's geovisualization cube, we examine the usage of immersive 3D geovisualization and its usefulness in a research-based learning module on flood risk, called GEOSimulator. Results of a survey among participating students…

  16. Stereo 3-D Vision in Teaching Physics

    ERIC Educational Resources Information Center

    Zabunov, Svetoslav

    2012-01-01

    Stereo 3-D vision is a technology used to present images on a flat surface (screen, paper, etc.) and at the same time to create the notion of three-dimensional spatial perception of the viewed scene. A great number of physical processes are much better understood when viewed in stereo 3-D vision compared to standard flat 2-D presentation. The…

  17. Pathways for Learning from 3D Technology

    ERIC Educational Resources Information Center

    Carrier, L. Mark; Rab, Saira S.; Rosen, Larry D.; Vasquez, Ludivina; Cheever, Nancy A.

    2012-01-01

    The purpose of this study was to find out if 3D stereoscopic presentation of information in a movie format changes a viewer's experience of the movie content. Four possible pathways from 3D presentation to memory and learning were considered: a direct connection based on cognitive neuroscience research; a connection through "immersion" in that 3D…

  18. Dominant color correlogram descriptor for content-based image retrieval

    NASA Astrophysics Data System (ADS)

    Fierro-Radilla, Atoany; Perez-Daniel, Karina; Nakano-Miyatake, Mariko; Benois, Jenny

    2015-03-01

    Content-based image retrieval (CBIR) has become an interesting and urgent research topic due to the increase of necessity of indexing and classification of multimedia content in large databases. The low level visual descriptors, such as color-based, texture-based and shape-based descriptors, have been used for the CBIR task. In this paper we propose a color-based descriptor which describes well image contents, integrating both global feature provided by dominant color and local features provided by color correlogram. The performance of the proposed descriptor, called Dominant Color Correlogram descriptor (DCCD), is evaluated comparing with some MPEG-7 visual descriptors and other color-based descriptors reported in the literature, using two image datasets with different size and contents. The performance of the proposed descriptor is assessed using three different metrics commonly used in image retrieval task, which are ARP (Average Retrieval Precision), ARR (Average Retrieval Rate) and ANMRR (Average Normalized Modified Retrieval Rank). Also precision-recall curves are provided to show a better performance of the proposed descriptor compared with other color-based descriptors.

  19. Clinical applications of 3-D dosimeters

    NASA Astrophysics Data System (ADS)

    Wuu, Cheng-Shie

    2015-01-01

    Both 3-D gels and radiochromic plastic dosimeters, in conjunction with dose image readout systems (MRI or optical-CT), have been employed to measure 3-D dose distributions in many clinical applications. The 3-D dose maps obtained from these systems can provide a useful tool for clinical dose verification for complex treatment techniques such as IMRT, SRS/SBRT, brachytherapy, and proton beam therapy. These complex treatments present high dose gradient regions in the boundaries between the target and surrounding critical organs. Dose accuracy in these areas can be critical, and may affect treatment outcome. In this review, applications of 3-D gels and PRESAGE dosimeter are reviewed and evaluated in terms of their performance in providing information on clinical dose verification as well as commissioning of various treatment modalities. Future interests and clinical needs on studies of 3-D dosimetry are also discussed.

  20. Biocompatible 3D Matrix with Antimicrobial Properties.

    PubMed

    Ion, Alberto; Andronescu, Ecaterina; Rădulescu, Dragoș; Rădulescu, Marius; Iordache, Florin; Vasile, Bogdan Ștefan; Surdu, Adrian Vasile; Albu, Madalina Georgiana; Maniu, Horia; Chifiriuc, Mariana Carmen; Grumezescu, Alexandru Mihai; Holban, Alina Maria

    2016-01-01

    The aim of this study was to develop, characterize and assess the biological activity of a new regenerative 3D matrix with antimicrobial properties, based on collagen (COLL), hydroxyapatite (HAp), β-cyclodextrin (β-CD) and usnic acid (UA). The prepared 3D matrix was characterized by Scanning Electron Microscopy (SEM), Fourier Transform Infrared Microscopy (FT-IRM), Transmission Electron Microscopy (TEM), and X-ray Diffraction (XRD). In vitro qualitative and quantitative analyses performed on cultured diploid cells demonstrated that the 3D matrix is biocompatible, allowing the normal development and growth of MG-63 osteoblast-like cells and exhibited an antimicrobial effect, especially on the Staphylococcus aureus strain, explained by the particular higher inhibitory activity of usnic acid (UA) against Gram positive bacterial strains. Our data strongly recommend the obtained 3D matrix to be used as a successful alternative for the fabrication of three dimensional (3D) anti-infective regeneration matrix for bone tissue engineering. PMID:26805790

  1. Fabrication of 3D Silicon Sensors

    SciTech Connect

    Kok, A.; Hansen, T.E.; Hansen, T.A.; Lietaer, N.; Summanwar, A.; Kenney, C.; Hasi, J.; Da Via, C.; Parker, S.I.; /Hawaii U.

    2012-06-06

    Silicon sensors with a three-dimensional (3-D) architecture, in which the n and p electrodes penetrate through the entire substrate, have many advantages over planar silicon sensors including radiation hardness, fast time response, active edge and dual readout capabilities. The fabrication of 3D sensors is however rather complex. In recent years, there have been worldwide activities on 3D fabrication. SINTEF in collaboration with Stanford Nanofabrication Facility have successfully fabricated the original (single sided double column type) 3D detectors in two prototype runs and the third run is now on-going. This paper reports the status of this fabrication work and the resulted yield. The work of other groups such as the development of double sided 3D detectors is also briefly reported.

  2. 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.

  3. 3D Visualization Development of SIUE Campus

    NASA Astrophysics Data System (ADS)

    Nellutla, Shravya

    Geographic Information Systems (GIS) has progressed from the traditional map-making to the modern technology where the information can be created, edited, managed and analyzed. Like any other models, maps are simplified representations of real world. Hence visualization plays an essential role in the applications of GIS. The use of sophisticated visualization tools and methods, especially three dimensional (3D) modeling, has been rising considerably due to the advancement of technology. There are currently many off-the-shelf technologies available in the market to build 3D GIS models. One of the objectives of this research was to examine the available ArcGIS and its extensions for 3D modeling and visualization and use them to depict a real world scenario. Furthermore, with the advent of the web, a platform for accessing and sharing spatial information on the Internet, it is possible to generate interactive online maps. Integrating Internet capacity with GIS functionality redefines the process of sharing and processing the spatial information. Enabling a 3D map online requires off-the-shelf GIS software, 3D model builders, web server, web applications and client server technologies. Such environments are either complicated or expensive because of the amount of hardware and software involved. Therefore, the second objective of this research was to investigate and develop simpler yet cost-effective 3D modeling approach that uses available ArcGIS suite products and the free 3D computer graphics software for designing 3D world scenes. Both ArcGIS Explorer and ArcGIS Online will be used to demonstrate the way of sharing and distributing 3D geographic information on the Internet. A case study of the development of 3D campus for the Southern Illinois University Edwardsville is demonstrated.

  4. 3D Ultrafast Ultrasound Imaging In Vivo

    PubMed Central

    Provost, Jean; Papadacci, Clement; Arango, Juan Esteban; Imbault, Marion; Gennisson, Jean-Luc; Tanter, Mickael; Pernot, Mathieu

    2014-01-01

    Very high frame rate ultrasound imaging has recently allowed for the extension of the applications of echography to new fields of study such as the functional imaging of the brain, cardiac electrophysiology, and the quantitative real-time imaging of the intrinsic mechanical properties of tumors, to name a few, non-invasively and in real time. In this study, we present the first implementation of Ultrafast Ultrasound Imaging in three dimensions based on the use of either diverging or plane waves emanating from a sparse virtual array located behind the probe. It achieves high contrast and resolution while maintaining imaging rates of thousands of volumes per second. A customized portable ultrasound system was developed to sample 1024 independent channels and to drive a 32×32 matrix-array probe. Its capability to track in 3D transient phenomena occurring in the millisecond range within a single ultrafast acquisition was demonstrated for 3-D Shear-Wave Imaging, 3-D Ultrafast Doppler Imaging and finally 3D Ultrafast combined Tissue and Flow Doppler. The propagation of shear waves was tracked in a phantom and used to characterize its stiffness. 3-D Ultrafast Doppler was used to obtain 3-D maps of Pulsed Doppler, Color Doppler, and Power Doppler quantities in a single acquisition and revealed, for the first time, the complex 3-D flow patterns occurring in the ventricles of the human heart during an entire cardiac cycle, and the 3-D in vivo interaction of blood flow and wall motion during the pulse wave in the carotid at the bifurcation. This study demonstrates the potential of 3-D Ultrafast Ultrasound Imaging for the 3-D real-time mapping of stiffness, tissue motion, and flow in humans in vivo and promises new clinical applications of ultrasound with reduced intra- and inter-observer variability. PMID:25207828

  5. The psychology of the 3D experience

    NASA Astrophysics Data System (ADS)

    Janicke, Sophie H.; Ellis, Andrew

    2013-03-01

    With 3D televisions expected to reach 50% home saturation as early as 2016, understanding the psychological mechanisms underlying the user response to 3D technology is critical for content providers, educators and academics. Unfortunately, research examining the effects of 3D technology has not kept pace with the technology's rapid adoption, resulting in large-scale use of a technology about which very little is actually known. Recognizing this need for new research, we conducted a series of studies measuring and comparing many of the variables and processes underlying both 2D and 3D media experiences. In our first study, we found narratives within primetime dramas had the power to shift viewer attitudes in both 2D and 3D settings. However, we found no difference in persuasive power between 2D and 3D content. We contend this lack of effect was the result of poor conversion quality and the unique demands of 3D production. In our second study, we found 3D technology significantly increased enjoyment when viewing sports content, yet offered no added enjoyment when viewing a movie trailer. The enhanced enjoyment of the sports content was shown to be the result of heightened emotional arousal and attention in the 3D condition. We believe the lack of effect found for the movie trailer may be genre-related. In our final study, we found 3D technology significantly enhanced enjoyment of two video games from different genres. The added enjoyment was found to be the result of an increased sense of presence.

  6. Active Exploration of Large 3D Model Repositories.

    PubMed

    Gao, Lin; Cao, Yan-Pei; Lai, Yu-Kun; Huang, Hao-Zhi; Kobbelt, Leif; Hu, Shi-Min

    2015-12-01

    With broader availability of large-scale 3D model repositories, the need for efficient and effective exploration becomes more and more urgent. Existing model retrieval techniques do not scale well with the size of the database since often a large number of very similar objects are returned for a query, and the possibilities to refine the search are quite limited. We propose an interactive approach where the user feeds an active learning procedure by labeling either entire models or parts of them as "like" or "dislike" such that the system can automatically update an active set of recommended models. To provide an intuitive user interface, candidate models are presented based on their estimated relevance for the current query. From the methodological point of view, our main contribution is to exploit not only the similarity between a query and the database models but also the similarities among the database models themselves. We achieve this by an offline pre-processing stage, where global and local shape descriptors are computed for each model and a sparse distance metric is derived that can be evaluated efficiently even for very large databases. We demonstrate the effectiveness of our method by interactively exploring a repository containing over 100 K models. PMID:26529460

  7. New set of 2D/3D thermodynamic indices for proteins. A formalism based on “ Molten Globule” theory

    NASA Astrophysics Data System (ADS)

    Ruiz-Blanco Yasser, B.; García, Y.; Sotomayor-Torres, C. M.; Yovani, Marrero-Ponce

    We define eight new macromolecular indices, and several related descriptors for proteins. The coarse grained methodology used for its deduction ensures its fast execution and becomes a powerful potential tool to explore large databases of protein structures. The indices are intended for stability studies, predicting Φ-values, predicting folding rate constants, protein QSAR/QSPR as well as protein alignment studies. Also, these indices could be used as scoring function in protein-protein docking or 3D protein structure prediction algorithms and any others applications which need a numerical code for proteins and/or residues from 2D or 3D format.

  8. Numerical study of wall shear stress-based descriptors in the human left coronary artery.

    PubMed

    Pinto, S I S; Campos, J B L M

    2016-10-01

    The present work is about the application of wall shear stress descriptors - time averaged wall shear stress (TAWSS), oscillating shear index (OSI) and relative residence time (RRT) - to the study of blood flow in the left coronary artery (LCA). These descriptors aid the prediction of disturbed flow conditions in the vessels and play a significant role in the detection of potential zones of atherosclerosis development. Hemodynamic descriptors data were obtained, numerically, through ANSYS® software, for the LCA of a patient-specific geometry and for a 3D idealized model. Comparing both cases, the results are coherent, in terms of location and magnitude. Low TAWSS, high OSI and high RRT values are observed in the bifurcation - potential zone of atherosclerosis appearance. The dissimilarities observed in the TAWSS values, considering blood as a Newtonian or non-Newtonian fluid, releases the importance of the correct blood rheologic caracterization. Moreover, for a higher Reynolds number, the TAWSS values decrease in the bifurcation and along the LAD branch, increasing the probability of plaques deposition. Furthermore, for a stenotic LCA model, very low TAWSS and high RRT values in front and behind the stenosis are observed, indicating the probable extension, in the flow direction, of the lesion. PMID:26883291

  9. Weighted measurement fusion Kalman estimator for multisensor descriptor system

    NASA Astrophysics Data System (ADS)

    Dou, Yinfeng; Ran, Chenjian; Gao, Yuan

    2016-08-01

    For the multisensor linear stochastic descriptor system with correlated measurement noises, the fused measurement can be obtained based on the weighted least square (WLS) method, and the reduced-order state components are obtained applying singular value decomposition method. Then, the multisensor descriptor system is transformed to a fused reduced-order non-descriptor system with correlated noise. And the weighted measurement fusion (WMF) Kalman estimator of this reduced-order subsystem is presented. According to the relationship of the presented non-descriptor system and the original descriptor system, the WMF Kalman estimator and its estimation error variance matrix of the original multisensor descriptor system are presented. The presented WMF Kalman estimator has global optimality, and can avoid computing these cross-variances of the local Kalman estimator, compared with the state fusion method. A simulation example about three-sensors stochastic dynamic input and output systems in economy verifies the effectiveness.

  10. The Classification of HEp-2 Cell Patterns Using Fractal Descriptor.

    PubMed

    Xu, Rudan; Sun, Yuanyuan; Yang, Zhihao; Song, Bo; Hu, Xiaopeng

    2015-07-01

    Indirect immunofluorescence (IIF) with HEp-2 cells is considered as a powerful, sensitive and comprehensive technique for analyzing antinuclear autoantibodies (ANAs). The automatic classification of the HEp-2 cell images from IIF has played an important role in diagnosis. Fractal dimension can be used on the analysis of image representing and also on the property quantification like texture complexity and spatial occupation. In this study, we apply the fractal theory in the application of HEp-2 cell staining pattern classification, utilizing fractal descriptor firstly in the HEp-2 cell pattern classification with the help of morphological descriptor and pixel difference descriptor. The method is applied to the data set of MIVIA and uses the support vector machine (SVM) classifier. Experimental results show that the fractal descriptor combining with morphological descriptor and pixel difference descriptor makes the precisions of six patterns more stable, all above 50%, achieving 67.17% overall accuracy at best with relatively simple feature vectors. PMID:26011888

  11. Invariant Descriptor Learning Using a Siamese Convolutional Neural Network

    NASA Astrophysics Data System (ADS)

    Chen, L.; Rottensteiner, F.; Heipke, C.

    2016-06-01

    In this paper we describe learning of a descriptor based on the Siamese Convolutional Neural Network (CNN) architecture and evaluate our results on a standard patch comparison dataset. The descriptor learning architecture is composed of an input module, a Siamese CNN descriptor module and a cost computation module that is based on the L2 Norm. The cost function we use pulls the descriptors of matching patches close to each other in feature space while pushing the descriptors for non-matching pairs away from each other. Compared to related work, we optimize the training parameters by combining a moving average strategy for gradients and Nesterov's Accelerated Gradient. Experiments show that our learned descriptor reaches a good performance and achieves state-of-art results in terms of the false positive rate at a 95 % recall rate on standard benchmark datasets.

  12. Medical 3D Printing for the Radiologist.

    PubMed

    Mitsouras, Dimitris; Liacouras, Peter; Imanzadeh, Amir; Giannopoulos, Andreas A; Cai, Tianrun; Kumamaru, Kanako K; George, Elizabeth; Wake, Nicole; Caterson, Edward J; Pomahac, Bohdan; Ho, Vincent B; Grant, Gerald T; Rybicki, Frank J

    2015-01-01

    While use of advanced visualization in radiology is instrumental in diagnosis and communication with referring clinicians, there is an unmet need to render Digital Imaging and Communications in Medicine (DICOM) images as three-dimensional (3D) printed models capable of providing both tactile feedback and tangible depth information about anatomic and pathologic states. Three-dimensional printed models, already entrenched in the nonmedical sciences, are rapidly being embraced in medicine as well as in the lay community. Incorporating 3D printing from images generated and interpreted by radiologists presents particular challenges, including training, materials and equipment, and guidelines. The overall costs of a 3D printing laboratory must be balanced by the clinical benefits. It is expected that the number of 3D-printed models generated from DICOM images for planning interventions and fabricating implants will grow exponentially. Radiologists should at a minimum be familiar with 3D printing as it relates to their field, including types of 3D printing technologies and materials used to create 3D-printed anatomic models, published applications of models to date, and clinical benefits in radiology. Online supplemental material is available for this article. PMID:26562233

  13. 3D bioprinting of tissues and organs.

    PubMed

    Murphy, Sean V; Atala, Anthony

    2014-08-01

    Additive manufacturing, otherwise known as three-dimensional (3D) printing, is driving major innovations in many areas, such as engineering, manufacturing, art, education and medicine. Recent advances have enabled 3D printing of biocompatible materials, cells and supporting components into complex 3D functional living tissues. 3D bioprinting is being applied to regenerative medicine to address the need for tissues and organs suitable for transplantation. Compared with non-biological printing, 3D bioprinting involves additional complexities, such as the choice of materials, cell types, growth and differentiation factors, and technical challenges related to the sensitivities of living cells and the construction of tissues. Addressing these complexities requires the integration of technologies from the fields of engineering, biomaterials science, cell biology, physics and medicine. 3D bioprinting has already been used for the generation and transplantation of several tissues, including multilayered skin, bone, vascular grafts, tracheal splints, heart tissue and cartilaginous structures. Other applications include developing high-throughput 3D-bioprinted tissue models for research, drug discovery and toxicology. PMID:25093879

  14. Optically rewritable 3D liquid crystal displays.

    PubMed

    Sun, J; Srivastava, A K; Zhang, W; Wang, L; Chigrinov, V G; Kwok, H S

    2014-11-01

    Optically rewritable liquid crystal display (ORWLCD) is a concept based on the optically addressed bi-stable display that does not need any power to hold the image after being uploaded. Recently, the demand for the 3D image display has increased enormously. Several attempts have been made to achieve 3D image on the ORWLCD, but all of them involve high complexity for image processing on both hardware and software levels. In this Letter, we disclose a concept for the 3D-ORWLCD by dividing the given image in three parts with different optic axis. A quarter-wave plate is placed on the top of the ORWLCD to modify the emerging light from different domains of the image in different manner. Thereafter, Polaroid glasses can be used to visualize the 3D image. The 3D image can be refreshed, on the 3D-ORWLCD, in one-step with proper ORWLCD printer and image processing, and therefore, with easy image refreshing and good image quality, such displays can be applied for many applications viz. 3D bi-stable display, security elements, etc. PMID:25361316

  15. Extra Dimensions: 3D in PDF Documentation

    NASA Astrophysics Data System (ADS)

    Graf, Norman A.

    2012-12-01

    Experimental science is replete with multi-dimensional information which is often poorly represented by the two dimensions of presentation slides and print media. Past efforts to disseminate such information to a wider audience have failed for a number of reasons, including a lack of standards which are easy to implement and have broad support. Adobe's Portable Document Format (PDF) has in recent years become the de facto standard for secure, dependable electronic information exchange. It has done so by creating an open format, providing support for multiple platforms and being reliable and extensible. By providing support for the ECMA standard Universal 3D (U3D) and the ISO PRC file format in its free Adobe Reader software, Adobe has made it easy to distribute and interact with 3D content. Until recently, Adobe's Acrobat software was also capable of incorporating 3D content into PDF files from a variety of 3D file formats, including proprietary CAD formats. However, this functionality is no longer available in Acrobat X, having been spun off to a separate company. Incorporating 3D content now requires the additional purchase of a separate plug-in. In this talk we present alternatives based on open source libraries which allow the programmatic creation of 3D content in PDF format. While not providing the same level of access to CAD files as the commercial software, it does provide physicists with an alternative path to incorporate 3D content into PDF files from such disparate applications as detector geometries from Geant4, 3D data sets, mathematical surfaces or tesselated volumes.

  16. Fingerprint identification using SIFT-based minutia descriptors and improved all descriptor-pair matching.

    PubMed

    Zhou, Ru; Zhong, Dexing; Han, Jiuqiang

    2013-01-01

    The performance of conventional minutiae-based fingerprint authentication algorithms degrades significantly when dealing with low quality fingerprints with lots of cuts or scratches. A similar degradation of the minutiae-based algorithms is observed when small overlapping areas appear because of the quite narrow width of the sensors. Based on the detection of minutiae, Scale Invariant Feature Transformation (SIFT) descriptors are employed to fulfill verification tasks in the above difficult scenarios. However, the original SIFT algorithm is not suitable for fingerprint because of: (1) the similar patterns of parallel ridges; and (2) high computational resource consumption. To enhance the efficiency and effectiveness of the algorithm for fingerprint verification, we propose a SIFT-based Minutia Descriptor (SMD) to improve the SIFT algorithm through image processing, descriptor extraction and matcher. A two-step fast matcher, named improved All Descriptor-Pair Matching (iADM), is also proposed to implement the 1:N verifications in real-time. Fingerprint Identification using SMD and iADM (FISiA) achieved a significant improvement with respect to accuracy in representative databases compared with the conventional minutiae-based method. The speed of FISiA also can meet real-time requirements. PMID:23467056

  17. Fingerprint Identification Using SIFT-Based Minutia Descriptors and Improved All Descriptor-Pair Matching

    PubMed Central

    Zhou, Ru; Zhong, Dexing; Han, Jiuqiang

    2013-01-01

    The performance of conventional minutiae-based fingerprint authentication algorithms degrades significantly when dealing with low quality fingerprints with lots of cuts or scratches. A similar degradation of the minutiae-based algorithms is observed when small overlapping areas appear because of the quite narrow width of the sensors. Based on the detection of minutiae, Scale Invariant Feature Transformation (SIFT) descriptors are employed to fulfill verification tasks in the above difficult scenarios. However, the original SIFT algorithm is not suitable for fingerprint because of: (1) the similar patterns of parallel ridges; and (2) high computational resource consumption. To enhance the efficiency and effectiveness of the algorithm for fingerprint verification, we propose a SIFT-based Minutia Descriptor (SMD) to improve the SIFT algorithm through image processing, descriptor extraction and matcher. A two-step fast matcher, named improved All Descriptor-Pair Matching (iADM), is also proposed to implement the 1:N verifications in real-time. Fingerprint Identification using SMD and iADM (FISiA) achieved a significant improvement with respect to accuracy in representative databases compared with the conventional minutiae-based method. The speed of FISiA also can meet real-time requirements. PMID:23467056

  18. An Efficient Wide-Baseline Dense Matching Descriptor

    NASA Astrophysics Data System (ADS)

    Wan, Yanli; Miao, Zhenjiang; Tang, Zhen; Wan, Lili; Wang, Zhe

    This letter proposes an efficient local descriptor for wide-baseline dense matching. It improves the existing Daisy descriptor by combining intensity-based Haar wavelet response with a new color-based ratio model. The color ratio model is invariant to changes of viewing direction, object geometry, and the direction, intensity and spectral power distribution of the illumination. The experiments show that our descriptor has high discriminative power and robustness.

  19. FUN3D Manual: 12.7

    NASA Technical Reports Server (NTRS)

    Biedron, Robert T.; Carlson, Jan-Renee; Derlaga, Joseph M.; Gnoffo, Peter A.; Hammond, Dana P.; Jones, William T.; Kleb, Bil; Lee-Rausch, Elizabeth M.; Nielsen, Eric J.; Park, Michael A.; Rumsey, Christopher L.; Thomas, James L.; Wood, William A.

    2015-01-01

    This manual describes the installation and execution of FUN3D version 12.7, including optional dependent packages. FUN3D is a suite of computational fluid dynamics simulation and design tools that uses mixed-element unstructured grids in a large number of formats, including structured multiblock and overset grid systems. A discretely-exact adjoint solver enables efficient gradient-based design and grid adaptation to reduce estimated discretization error. FUN3D is available with and without a reacting, real-gas capability. This generic gas option is available only for those persons that qualify for its beta release status.

  20. FUN3D Manual: 12.9

    NASA Technical Reports Server (NTRS)

    Biedron, Robert T.; Carlson, Jan-Renee; Derlaga, Joseph M.; Gnoffo, Peter A.; Hammond, Dana P.; Jones, William T.; Kleb, Bil; Lee-Rausch, Elizabeth M.; Nielsen, Eric J.; Park, Michael A.; Rumsey, Christopher L.; Thomas, James L.; Wood, William A.

    2016-01-01

    This manual describes the installation and execution of FUN3D version 12.9, including optional dependent packages. FUN3D is a suite of computational fluid dynamics simulation and design tools that uses mixed-element unstructured grids in a large number of formats, including structured multiblock and overset grid systems. A discretely-exact adjoint solver enables efficient gradient-based design and grid adaptation to reduce estimated discretization error. FUN3D is available with and without a reacting, real-gas capability. This generic gas option is available only for those persons that qualify for its beta release status.

  1. FUN3D Manual: 13.0

    NASA Technical Reports Server (NTRS)

    Biedron, Robert T.; Carlson, Jan-Renee; Derlaga, Joseph M.; Gnoffo, Peter A.; Hammond, Dana P.; Jones, William T.; Kleb, Bill; Lee-Rausch, Elizabeth M.; Nielsen, Eric J.; Park, Michael A.; Rumsey, Christopher L.; Thomas, James L.; Wood, William A.

    2016-01-01

    This manual describes the installation and execution of FUN3D version 13.0, including optional dependent packages. FUN3D is a suite of computational fluid dynamics simulation and design tools that uses mixed-element unstructured grids in a large number of formats, including structured multiblock and overset grid systems. A discretely-exact adjoint solver enables efficient gradient-based design and grid adaptation to reduce estimated discretization error. FUN3D is available with and without a reacting, real-gas capability. This generic gas option is available only for those persons that qualify for its beta release status.

  2. FUN3D Manual: 12.8

    NASA Technical Reports Server (NTRS)

    Biedron, Robert T.; Carlson, Jan-Renee; Derlaga, Joseph M.; Gnoffo, Peter A.; Hammond, Dana P.; Jones, William T.; Kleb, Bil; Lee-Rausch, Elizabeth M.; Nielsen, Eric J.; Park, Michael A.; Rumsey, Christopher L.; Thomas, James L.; Wood, William A.

    2015-01-01

    This manual describes the installation and execution of FUN3D version 12.8, including optional dependent packages. FUN3D is a suite of computational fluid dynamics simulation and design tools that uses mixed-element unstructured grids in a large number of formats, including structured multiblock and overset grid systems. A discretely-exact adjoint solver enables efficient gradient-based design and grid adaptation to reduce estimated discretization error. FUN3D is available with and without a reacting, real-gas capability. This generic gas option is available only for those persons that qualify for its beta release status.

  3. 3D packaging for integrated circuit systems

    SciTech Connect

    Chu, D.; Palmer, D.W.

    1996-11-01

    A goal was set for high density, high performance microelectronics pursued through a dense 3D packing of integrated circuits. A {open_quotes}tool set{close_quotes} of assembly processes have been developed that enable 3D system designs: 3D thermal analysis, silicon electrical through vias, IC thinning, mounting wells in silicon, adhesives for silicon stacking, pretesting of IC chips before commitment to stacks, and bond pad bumping. Validation of these process developments occurred through both Sandia prototypes and subsequent commercial examples.

  4. A high capacity 3D steganography algorithm.

    PubMed

    Chao, Min-Wen; Lin, Chao-hung; Yu, Cheng-Wei; Lee, Tong-Yee

    2009-01-01

    In this paper, we present a very high-capacity and low-distortion 3D steganography scheme. Our steganography approach is based on a novel multilayered embedding scheme to hide secret messages in the vertices of 3D polygon models. Experimental results show that the cover model distortion is very small as the number of hiding layers ranges from 7 to 13 layers. To the best of our knowledge, this novel approach can provide much higher hiding capacity than other state-of-the-art approaches, while obeying the low distortion and security basic requirements for steganography on 3D models. PMID:19147891

  5. New method of 3-D object recognition

    NASA Astrophysics Data System (ADS)

    He, An-Zhi; Li, Qun Z.; Miao, Peng C.

    1991-12-01

    In this paper, a new method of 3-D object recognition using optical techniques and a computer is presented. We perform 3-D object recognition using moire contour to obtain the object's 3- D coordinates, projecting drawings of the object in three coordinate planes to describe it and using a method of inquiring library of judgement to match objects. The recognition of a simple geometrical entity is simulated by computer and studied experimentally. The recognition of an object which is composed of a few simple geometrical entities is discussed.

  6. Explicit 3-D Hydrodynamic FEM Program

    2000-11-07

    DYNA3D is a nonlinear explicit finite element code for analyzing 3-D structures and solid continuum. The code is vectorized and available on several computer platforms. The element library includes continuum, shell, beam, truss and spring/damper elements to allow maximum flexibility in modeling physical problems. Many materials are available to represent a wide range of material behavior, including elasticity, plasticity, composites, thermal effects and rate dependence. In addition, DYNA3D has a sophisticated contact interface capability, includingmore » frictional sliding, single surface contact and automatic contact generation.« less

  7. How We 3D-Print Aerogel

    SciTech Connect

    2015-04-23

    A new type of graphene aerogel will make for better energy storage, sensors, nanoelectronics, catalysis and separations. Lawrence Livermore National Laboratory researchers have made graphene aerogel microlattices with an engineered architecture via a 3D printing technique known as direct ink writing. The research appears in the April 22 edition of the journal, Nature Communications. The 3D printed graphene aerogels have high surface area, excellent electrical conductivity, are lightweight, have mechanical stiffness and exhibit supercompressibility (up to 90 percent compressive strain). In addition, the 3D printed graphene aerogel microlattices show an order of magnitude improvement over bulk graphene materials and much better mass transport.

  8. An Improved Version of TOPAZ 3D

    SciTech Connect

    Krasnykh, Anatoly

    2003-07-29

    An improved version of the TOPAZ 3D gun code is presented as a powerful tool for beam optics simulation. In contrast to the previous version of TOPAZ 3D, the geometry of the device under test is introduced into TOPAZ 3D directly from a CAD program, such as Solid Edge or AutoCAD. In order to have this new feature, an interface was developed, using the GiD software package as a meshing code. The article describes this method with two models to illustrate the results.

  9. FUN3D Manual: 12.4

    NASA Technical Reports Server (NTRS)

    Biedron, Robert T.; Derlaga, Joseph M.; Gnoffo, Peter A.; Hammond, Dana P.; Jones, William T.; Kleb, Bil; Lee-Rausch, Elizabeth M.; Nielsen, Eric J.; Park, Michael A.; Rumsey, Christopher L.; Thomas, James L.; Wood, William A.

    2014-01-01

    This manual describes the installation and execution of FUN3D version 12.4, including optional dependent packages. FUN3D is a suite of computational fluid dynamics simulation and design tools that uses mixedelement unstructured grids in a large number of formats, including structured multiblock and overset grid systems. A discretely-exact adjoint solver enables efficient gradient-based design and grid adaptation to reduce estimated discretization error. FUN3D is available with and without a reacting, real-gas capability. This generic gas option is available only for those persons that qualify for its beta release status.

  10. FUN3D Manual: 12.5

    NASA Technical Reports Server (NTRS)

    Biedron, Robert T.; Derlaga, Joseph M.; Gnoffo, Peter A.; Hammond, Dana P.; Jones, William T.; Kleb, William L.; Lee-Rausch, Elizabeth M.; Nielsen, Eric J.; Park, Michael A.; Rumsey, Christopher L.; Thomas, James L.; Wood, William A.

    2014-01-01

    This manual describes the installation and execution of FUN3D version 12.5, including optional dependent packages. FUN3D is a suite of computational uid dynamics simulation and design tools that uses mixed-element unstructured grids in a large number of formats, including structured multiblock and overset grid systems. A discretely-exact adjoint solver enables ecient gradient-based design and grid adaptation to reduce estimated discretization error. FUN3D is available with and without a reacting, real-gas capability. This generic gas option is available only for those persons that qualify for its beta release status.

  11. FUN3D Manual: 12.6

    NASA Technical Reports Server (NTRS)

    Biedron, Robert T.; Derlaga, Joseph M.; Gnoffo, Peter A.; Hammond, Dana P.; Jones, William T.; Kleb, William L.; Lee-Rausch, Elizabeth M.; Nielsen, Eric J.; Park, Michael A.; Rumsey, Christopher L.; Thomas, James L.; Wood, William A.

    2015-01-01

    This manual describes the installation and execution of FUN3D version 12.6, including optional dependent packages. FUN3D is a suite of computational fluid dynamics simulation and design tools that uses mixed-element unstructured grids in a large number of formats, including structured multiblock and overset grid systems. A discretely-exact adjoint solver enables efficient gradient-based design and grid adaptation to reduce estimated discretization error. FUN3D is available with and without a reacting, real-gas capability. This generic gas option is available only for those persons that qualify for its beta release status.

  12. Explicit 3-D Hydrodynamic FEM Program

    SciTech Connect

    2000-11-07

    DYNA3D is a nonlinear explicit finite element code for analyzing 3-D structures and solid continuum. The code is vectorized and available on several computer platforms. The element library includes continuum, shell, beam, truss and spring/damper elements to allow maximum flexibility in modeling physical problems. Many materials are available to represent a wide range of material behavior, including elasticity, plasticity, composites, thermal effects and rate dependence. In addition, DYNA3D has a sophisticated contact interface capability, including frictional sliding, single surface contact and automatic contact generation.

  13. Non-Iterative Rigid 2D/3D Point-Set Registration Using Semidefinite Programming

    NASA Astrophysics Data System (ADS)

    Khoo, Yuehaw; Kapoor, Ankur

    2016-07-01

    We describe a convex programming framework for pose estimation in 2D/3D point-set registration with unknown point correspondences. We give two mixed-integer nonlinear program (MINP) formulations of the 2D/3D registration problem when there are multiple 2D images, and propose convex relaxations for both of the MINPs to semidefinite programs (SDP) that can be solved efficiently by interior point methods. Our approach to the 2D/3D registration problem is non-iterative in nature as we jointly solve for pose and correspondence. Furthermore, these convex programs can readily incorporate feature descriptors of points to enhance registration results. We prove that the convex programs exactly recover the solution to the original nonconvex 2D/3D registration problem under noiseless condition. We apply these formulations to the registration of 3D models of coronary vessels to their 2D projections obtained from multiple intra-operative fluoroscopic images. For this application, we experimentally corroborate the exact recovery property in the absence of noise and further demonstrate robustness of the convex programs in the presence of noise.

  14. XML3D and Xflow: combining declarative 3D for the Web with generic data flows.

    PubMed

    Klein, Felix; Sons, Kristian; Rubinstein, Dmitri; Slusallek, Philipp

    2013-01-01

    Researchers have combined XML3D, which provides declarative, interactive 3D scene descriptions based on HTML5, with Xflow, a language for declarative, high-performance data processing. The result lets Web developers combine a 3D scene graph with data flows for dynamic meshes, animations, image processing, and postprocessing. PMID:24808080

  15. JAR3D Webserver: Scoring and aligning RNA loop sequences to known 3D motifs.

    PubMed

    Roll, James; Zirbel, Craig L; Sweeney, Blake; Petrov, Anton I; Leontis, Neocles

    2016-07-01

    Many non-coding RNAs have been identified and may function by forming 2D and 3D structures. RNA hairpin and internal loops are often represented as unstructured on secondary structure diagrams, but RNA 3D structures show that most such loops are structured by non-Watson-Crick basepairs and base stacking. Moreover, different RNA sequences can form the same RNA 3D motif. JAR3D finds possible 3D geometries for hairpin and internal loops by matching loop sequences to motif groups from the RNA 3D Motif Atlas, by exact sequence match when possible, and by probabilistic scoring and edit distance for novel sequences. The scoring gauges the ability of the sequences to form the same pattern of interactions observed in 3D structures of the motif. The JAR3D webserver at http://rna.bgsu.edu/jar3d/ takes one or many sequences of a single loop as input, or else one or many sequences of longer RNAs with multiple loops. Each sequence is scored against all current motif groups. The output shows the ten best-matching motif groups. Users can align input sequences to each of the motif groups found by JAR3D. JAR3D will be updated with every release of the RNA 3D Motif Atlas, and so its performance is expected to improve over time. PMID:27235417

  16. Heliconia phenotypic diversity based on qualitative descriptors.

    PubMed

    Guimarães, W N R; Martins, L S S; Castro, C E F; Carvalho Filho, J L S; Loges, V

    2014-01-01

    The aim of this study was to characterize Heliconia genotypes phenotypically using 26 qualitative descriptors. The evaluations were conducted in five flowering stems per clump in three replicates of 22 Heliconia genotypes. Data were subjected to multivariate analysis, the Mahalanobis dissimilarity measure was estimated, and the dendrogram was generated using the nearest neighbor method. From the values generated by the dissimilarity matrix and the clusters formed among the Heliconia genotypes studied, the phenotypic characterizations that best differentiated the genotypes were: pseudostem and wax green tone (light or dark green), leaf-wax petiole, the petiole hair, cleft margin at the base of the petiole, midrib underside shade of green, wax midrib underside, color sheet (light or dark green), unequal lamina base, torn limb, inflorescence-wax, position of inflorescence, bract leaf in apex, twisting of the rachis, and type of bloom. These results will be applied in the preparation of a catalog for Heliconia descriptors, in the selection of different genotypes with most promising characteristics for crosses, and for the characterization of new genotypes to be introduced in germplasm collections. PMID:24782170

  17. Hierarchical and binary spatial descriptors for lung nodule image retrieval.

    PubMed

    Ng, Gillian; Song, Yang; Cai, Weidong; Zhou, Yun; Liu, Sidong; Feng, David Dagan

    2014-01-01

    With the increasing amount of image data available for cancer staging and diagnosis, it is clear that content-based image retrieval techniques are becoming more important to assist physicians in making diagnoses and tracking disease. Domain-specific feature descriptors have been previously shown to be effective in the retrieval of lung tumors. This work proposes a method to improve the rotation invariance of the hierarchical spatial descriptor, as well as presents a new binary descriptor for the retrieval of lung nodule images. The descriptors were evaluated on the ELCAP public access database, exhibiting good performance overall. PMID:25571476

  18. Admissible consensus for heterogeneous descriptor multi-agent systems

    NASA Astrophysics Data System (ADS)

    Yang, Xin-Rong; Liu, Guo-Ping

    2016-09-01

    This paper focuses on the admissible consensus problem for heterogeneous descriptor multi-agent systems. Based on algebra, graph and descriptor system theory, the necessary and sufficient conditions are proposed for heterogeneous descriptor multi-agent systems achieving admissible consensus. The provided conditions depend on not only the structure properties of each agent dynamics but also the topologies within the descriptor multi-agent systems. Moreover, an algorithm is given to design the novel consensus protocol. A numerical example demonstrates the effectiveness of the proposed design approach.

  19. Axisymmetric Implementation for 3D-Based DSMC Codes

    NASA Technical Reports Server (NTRS)

    Stewart, Benedicte; Lumpkin, F. E.; LeBeau, G. J.

    2011-01-01

    The primary objective in developing NASA s DSMC Analysis Code (DAC) was to provide a high fidelity modeling tool for 3D rarefied flows such as vacuum plume impingement and hypersonic re-entry flows [1]. The initial implementation has been expanded over time to offer other capabilities including a novel axisymmetric implementation. Because of the inherently 3D nature of DAC, this axisymmetric implementation uses a 3D Cartesian domain and 3D surfaces. Molecules are moved in all three dimensions but their movements are limited by physical walls to a small wedge centered on the plane of symmetry (Figure 1). Unfortunately, far from the axis of symmetry, the cell size in the direction perpendicular to the plane of symmetry (the Z-direction) may become large compared to the flow mean free path. This frequently results in inaccuracies in these regions of the domain. A new axisymmetric implementation is presented which aims to solve this issue by using Bird s approach for the molecular movement while preserving the 3D nature of the DAC software [2]. First, the computational domain is similar to that previously used such that a wedge must still be used to define the inflow surface and solid walls within the domain. As before molecules are created inside the inflow wedge triangles but they are now rotated back to the symmetry plane. During the move step, molecules are moved in 3D but instead of interacting with the wedge walls, the molecules are rotated back to the plane of symmetry at the end of the move step. This new implementation was tested for multiple flows over axisymmetric shapes, including a sphere, a cone, a double cone and a hollow cylinder. Comparisons to previous DSMC solutions and experiments, when available, are made.

  20. 3D-printed bioanalytical devices

    NASA Astrophysics Data System (ADS)

    Bishop, Gregory W.; Satterwhite-Warden, Jennifer E.; Kadimisetty, Karteek; Rusling, James F.

    2016-07-01

    While 3D printing technologies first appeared in the 1980s, prohibitive costs, limited materials, and the relatively small number of commercially available printers confined applications mainly to prototyping for manufacturing purposes. As technologies, printer cost, materials, and accessibility continue to improve, 3D printing has found widespread implementation in research and development in many disciplines due to ease-of-use and relatively fast design-to-object workflow. Several 3D printing techniques have been used to prepare devices such as milli- and microfluidic flow cells for analyses of cells and biomolecules as well as interfaces that enable bioanalytical measurements using cellphones. This review focuses on preparation and applications of 3D-printed bioanalytical devices.

  1. Nonlaser-based 3D surface imaging

    SciTech Connect

    Lu, Shin-yee; Johnson, R.K.; Sherwood, R.J.

    1994-11-15

    3D surface imaging refers to methods that generate a 3D surface representation of objects of a scene under viewing. Laser-based 3D surface imaging systems are commonly used in manufacturing, robotics and biomedical research. Although laser-based systems provide satisfactory solutions for most applications, there are situations where non laser-based approaches are preferred. The issues that make alternative methods sometimes more attractive are: (1) real-time data capturing, (2) eye-safety, (3) portability, and (4) work distance. The focus of this presentation is on generating a 3D surface from multiple 2D projected images using CCD cameras, without a laser light source. Two methods are presented: stereo vision and depth-from-focus. Their applications are described.

  2. Tropical Cyclone Jack in Satellite 3-D

    NASA Video Gallery

    This 3-D flyby from NASA's TRMM satellite of Tropical Cyclone Jack on April 21 shows that some of the thunderstorms were shown by TRMM PR were still reaching height of at least 17 km (10.5 miles). ...

  3. 3D Printing for Tissue Engineering

    PubMed Central

    Jia, Jia; Yao, Hai; Mei, Ying

    2016-01-01

    Tissue engineering aims to fabricate functional tissue for applications in regenerative medicine and drug testing. More recently, 3D printing has shown great promise in tissue fabrication with a structural control from micro- to macro-scale by using a layer-by-layer approach. Whether through scaffold-based or scaffold-free approaches, the standard for 3D printed tissue engineering constructs is to provide a biomimetic structural environment that facilitates tissue formation and promotes host tissue integration (e.g., cellular infiltration, vascularization, and active remodeling). This review will cover several approaches that have advanced the field of 3D printing through novel fabrication methods of tissue engineering constructs. It will also discuss the applications of synthetic and natural materials for 3D printing facilitated tissue fabrication. PMID:26869728

  4. 3D Visualization of Recent Sumatra Earthquake

    NASA Astrophysics Data System (ADS)

    Nayak, Atul; Kilb, Debi

    2005-04-01

    Scientists and visualization experts at the Scripps Institution of Oceanography have created an interactive three-dimensional visualization of the 28 March 2005 magnitude 8.7 earthquake in Sumatra. The visualization shows the earthquake's hypocenter and aftershocks recorded until 29 March 2005, and compares it with the location of the 26 December 2004 magnitude 9 event and the consequent seismicity in that region. The 3D visualization was created using the Fledermaus software developed by Interactive Visualization Systems (http://www.ivs.unb.ca/) and stored as a ``scene'' file. To view this visualization, viewers need to download and install the free viewer program iView3D (http://www.ivs3d.com/products/iview3d).

  5. Future Engineers 3-D Print Timelapse

    NASA Video Gallery

    NASA Challenges K-12 students to create a model of a container for space using 3-D modeling software. Astronauts need containers of all kinds - from advanced containers that can study fruit flies t...

  6. 3-D Flyover Visualization of Veil Nebula

    NASA Video Gallery

    This 3-D visualization flies across a small portion of the Veil Nebula as photographed by the Hubble Space Telescope. This region is a small part of a huge expanding remnant from a star that explod...

  7. 3D-patterned polymer brush surfaces

    NASA Astrophysics Data System (ADS)

    Zhou, Xuechang; Liu, Xuqing; Xie, Zhuang; Zheng, Zijian

    2011-12-01

    Polymer brush-based three-dimensional (3D) structures are emerging as a powerful platform to engineer a surface by providing abundant spatially distributed chemical and physical properties. In this feature article, we aim to give a summary of the recent progress on the fabrication of 3D structures with polymer brushes, with a particular focus on the micro- and nanoscale. We start with a brief introduction on polymer brushes and the challenges to prepare their 3D structures. Then, we highlight the recent advances of the fabrication approaches on the basis of traditional polymerization time and grafting density strategies, and a recently developed feature density strategy. Finally, we provide some perspective outlooks on the future directions of engineering the 3D structures with polymer brushes.

  8. Eyes on the Earth 3D

    NASA Technical Reports Server (NTRS)

    Kulikov, anton I.; Doronila, Paul R.; Nguyen, Viet T.; Jackson, Randal K.; Greene, William M.; Hussey, Kevin J.; Garcia, Christopher M.; Lopez, Christian A.

    2013-01-01

    Eyes on the Earth 3D software gives scientists, and the general public, a realtime, 3D interactive means of accurately viewing the real-time locations, speed, and values of recently collected data from several of NASA's Earth Observing Satellites using a standard Web browser (climate.nasa.gov/eyes). Anyone with Web access can use this software to see where the NASA fleet of these satellites is now, or where they will be up to a year in the future. The software also displays several Earth Science Data sets that have been collected on a daily basis. This application uses a third-party, 3D, realtime, interactive game engine called Unity 3D to visualize the satellites and is accessible from a Web browser.

  9. 3-D Animation of Typhoon Bopha

    NASA Video Gallery

    This 3-D animation of NASA's TRMM satellite data showed Typhoon Bopha tracking over the Philippines on Dec. 3 and moving into the Sulu Sea on Dec. 4, 2012. TRMM saw heavy rain (red) was falling at ...

  10. 3-D TRMM Flyby of Hurricane Amanda

    NASA Video Gallery

    The TRMM satellite flew over Hurricane Amanda on Tuesday, May 27 at 1049 UTC (6:49 a.m. EDT) and captured rainfall rates and cloud height data that was used to create this 3-D simulated flyby. Cred...

  11. Cyclone Rusty's Landfall in 3-D

    NASA Video Gallery

    This 3-D image derived from NASA's TRMM satellite Precipitation Radar data on February 26, 2013 at 0654 UTC showed that the tops of some towering thunderstorms in Rusty's eye wall were reaching hei...

  12. TRMM 3-D Flyby of Ingrid

    NASA Video Gallery

    This 3-D flyby of Tropical Storm Ingrid's rainfall was created from TRMM satellite data for Sept. 16. Heaviest rainfall appears in red towers over the Gulf of Mexico, while moderate rainfall stretc...

  13. 3D-printed bioanalytical devices.

    PubMed

    Bishop, Gregory W; Satterwhite-Warden, Jennifer E; Kadimisetty, Karteek; Rusling, James F

    2016-07-15

    While 3D printing technologies first appeared in the 1980s, prohibitive costs, limited materials, and the relatively small number of commercially available printers confined applications mainly to prototyping for manufacturing purposes. As technologies, printer cost, materials, and accessibility continue to improve, 3D printing has found widespread implementation in research and development in many disciplines due to ease-of-use and relatively fast design-to-object workflow. Several 3D printing techniques have been used to prepare devices such as milli- and microfluidic flow cells for analyses of cells and biomolecules as well as interfaces that enable bioanalytical measurements using cellphones. This review focuses on preparation and applications of 3D-printed bioanalytical devices. PMID:27250897

  14. Palacios field: A 3-D case history

    SciTech Connect

    McWhorter, R.; Torguson, B.

    1994-12-31

    In late 1992, Mitchell Energy Corporation acquired a 7.75 sq mi (20.0 km{sup 2}) 3-D seismic survey over Palacios field. Matagorda County, Texas. The company shot the survey to help evaluate the field for further development by delineating the fault pattern of the producing Middle Oligocene Frio interval. They compare the mapping of the field before and after the 3-D survey. This comparison shows that the 3-D volume yields superior fault imaging and interpretability compared to the dense 2-D data set. The problems with the 2-D data set are improper imaging of small and oblique faults and insufficient coverage over a complex fault pattern. Whereas the 2-D data set validated a simple fault model, the 3-D volume revealed a more complex history of faulting that includes three different fault systems. This discovery enabled them to reconstruct the depositional and structural history of Palacios field.

  15. Radiosity diffusion model in 3D

    NASA Astrophysics Data System (ADS)

    Riley, Jason D.; Arridge, Simon R.; Chrysanthou, Yiorgos; Dehghani, Hamid; Hillman, Elizabeth M. C.; Schweiger, Martin

    2001-11-01

    We present the Radiosity-Diffusion model in three dimensions(3D), as an extension to previous work in 2D. It is a method for handling non-scattering spaces in optically participating media. We present the extension of the model to 3D including an extension to the model to cope with increased complexity of the 3D domain. We show that in 3D more careful consideration must be given to the issues of meshing and visibility to model the transport of light within reasonable computational bounds. We demonstrate the model to be comparable to Monte-Carlo simulations for selected geometries, and show preliminary results of comparisons to measured time-resolved data acquired on resin phantoms.

  16. Viewpoint independent representation and recognition of polygonal faced in 3-D

    SciTech Connect

    Bunke, H.; Glauser, T.

    1993-08-01

    The recognition of polygons in 3-D space is an important task in robot vision. Two particular problems are addressed in the paper. First a new set of local shape descriptors for polygons are proposed that are invariant under affine transformation. Furthermore, they are complete in the sense that they allow the reconstruction of any polygon in 3-D space from three consecutive vertices. The second problem discussed in this paper is the recognition of 2-D polygonal objects under affine transformation and the presence of partial occlusion. A recognition procedure that is based on the matching of edge length ratios is introduced using a simplified version of the standard dynamic programming procedure commonly employed for string matching. The algorithm is conceptually very simple, easy to implement and has a low computational complexity. It will be shown in a set of experiments that the method is reliable and robust.

  17. 3D-HST results and prospects

    NASA Astrophysics Data System (ADS)

    Van Dokkum, Pieter G.

    2015-01-01

    The 3D-HST survey is providing a comprehensive census of the distant Universe, combining HST WFC3 imaging and grism spectroscopy with a myriad of other ground- and space-based datasets. This talk constitutes an overview of science results from the survey, with a focus on ongoing work and ways to exploit the rich public release of the 3D-HST data.

  18. Molecular magnetism of M6 hexagon ring in D(3d) symmetric [(MCl)6(XW9O33)2](12-) (M = Cu(II) and Mn(II), X = Sb(III) and As(III)).

    PubMed

    Yamase, Toshihiro; Ishikawa, Hirofumi; Abe, Hiroko; Fukaya, Keisuke; Nojiri, Hiroyuki; Takeuchi, Hideo

    2012-04-16

    Ferromagnetic [n-BuNH(3)](12)[(CuCl)(6)(SbW(9)O(33))(2)]·6H(2)O (1) and antiferromagnetic [n-BuNH(3)](12)[(MnCl)(6)(AsW(9)O(33))(2)]·6H(2)O (4) have been synthesized and structurally and magnetically characterized. Two complexes are structural analogues of [n-BuNH(3)](12)[(CuCl)(6)(AsW(9)O(33))(2)]·6H(2)O (2) and [n-BuNH(3)](12)[(MnCl)(6)(SbW(9)O(33))(2)]·6H(2)O (3) with their ferromagnetic interactions, first reported by us in 2006. (1) When variable temperature (T) direct current (dc) magnetic susceptibility (χ(M)) data are analyzed with the isotropic exchange Hamiltonian for the magnetic exchange interactions, χ(M)T vs T curves fitted by a full matrix diagonalization (for 1) and by the Kambe vector coupling method/Van Vleck's approximation (for 4) yield J = +29.5 and -0.09 cm(-1) and g = 2.3 and 1.9, respectively. These J values were significantly distinguished from +61.0 and +0.14 cm(-1) for 2 and 3, respectively. The magnetization under the pulsed field (up to 10(3) T/s) at 0.5 K exhibits hysteresis loops in the adiabatic process, and the differential magnetization (dM/dB) plots against the pulsed field display peaks characteristic of resonant quantum tunneling of magnetization (QTM) at Zeeman crossed fields, indicating single-molecule magnets for 1-3. High-frequency ESR (HFESR) spectroscopy on polycrystalline samples provides g(∥) = 2.30, g(⊥) = 2.19, and D = -0.147 cm(-1) for 1 (S = 3 ground state), g(∥) = 2.29, g(⊥) = 2.20, and D = -0.145 cm(-1) for 2 (S = 3), and g(∥) = 2.03 and D = -0.007 cm(-1) for 3 (S = 15). An attempt to rationalize the magnetostructural correlation among 1-4, the structurally and magnetically modified D(3d)-symmetric M (=Cu(II) and Mn(II))(6) hexagons sandwiched by two diamagnetic α-B-[XW(9)O(33)](9-) (X = Sb(III) and As(III)) ligands through M-(μ(3)-O)-W linkages, is made. The strongest ferromagnetic coupling for the Cu(6) hexagon of 2, the structure of which approximately provides the Cu(6)(μ(3)-O)(12

  19. Assessing 3d Photogrammetry Techniques in Craniometrics

    NASA Astrophysics Data System (ADS)

    Moshobane, M. C.; de Bruyn, P. J. N.; Bester, M. N.

    2016-06-01

    Morphometrics (the measurement of morphological features) has been revolutionized by the creation of new techniques to study how organismal shape co-varies with several factors such as ecophenotypy. Ecophenotypy refers to the divergence of phenotypes due to developmental changes induced by local environmental conditions, producing distinct ecophenotypes. None of the techniques hitherto utilized could explicitly address organismal shape in a complete biological form, i.e. three-dimensionally. This study investigates the use of the commercial software, Photomodeler Scanner® (PMSc®) three-dimensional (3D) modelling software to produce accurate and high-resolution 3D models. Henceforth, the modelling of Subantarctic fur seal (Arctocephalus tropicalis) and Antarctic fur seal (Arctocephalus gazella) skulls which could allow for 3D measurements. Using this method, sixteen accurate 3D skull models were produced and five metrics were determined. The 3D linear measurements were compared to measurements taken manually with a digital caliper. In addition, repetitive measurements were recorded by varying researchers to determine repeatability. To allow for comparison straight line measurements were taken with the software, assuming that close accord with all manually measured features would illustrate the model's accurate replication of reality. Measurements were not significantly different demonstrating that realistic 3D skull models can be successfully produced to provide a consistent basis for craniometrics, with the additional benefit of allowing non-linear measurements if required.

  20. 3D model reconstruction of underground goaf

    NASA Astrophysics Data System (ADS)

    Fang, Yuanmin; Zuo, Xiaoqing; Jin, Baoxuan

    2005-10-01

    Constructing 3D model of underground goaf, we can control the process of mining better and arrange mining work reasonably. However, the shape of goaf and the laneway among goafs are very irregular, which produce great difficulties in data-acquiring and 3D model reconstruction. In this paper, we research on the method of data-acquiring and 3D model construction of underground goaf, building topological relation among goafs. The main contents are as follows: a) The paper proposed an efficient encoding rule employed to structure the field measurement data. b) A 3D model construction method of goaf is put forward, which by means of combining several TIN (triangulated irregular network) pieces, and an efficient automatic processing algorithm of boundary of TIN is proposed. c) Topological relation of goaf models is established. TIN object is the basic modeling element of goaf 3D model, and the topological relation among goaf is created and maintained by building the topological relation among TIN objects. Based on this, various 3D spatial analysis functions can be performed including transect and volume calculation of goaf. A prototype is developed, which can realized the model and algorithm proposed in this paper.

  1. 3D steerable wavelets in practice.

    PubMed

    Chenouard, Nicolas; Unser, Michael

    2012-11-01

    We introduce a systematic and practical design for steerable wavelet frames in 3D. Our steerable wavelets are obtained by applying a 3D version of the generalized Riesz transform to a primary isotropic wavelet frame. The novel transform is self-reversible (tight frame) and its elementary constituents (Riesz wavelets) can be efficiently rotated in any 3D direction by forming appropriate linear combinations. Moreover, the basis functions at a given location can be linearly combined to design custom (and adaptive) steerable wavelets. The features of the proposed method are illustrated with the processing and analysis of 3D biomedical data. In particular, we show how those wavelets can be used to characterize directional patterns and to detect edges by means of a 3D monogenic analysis. We also propose a new inverse-problem formalism along with an optimization algorithm for reconstructing 3D images from a sparse set of wavelet-domain edges. The scheme results in high-quality image reconstructions which demonstrate the feature-reduction ability of the steerable wavelets as well as their potential for solving inverse problems. PMID:22752138

  2. DYNA3D example problem manual

    SciTech Connect

    Lovejoy, S.C.; Whirley, R.G.

    1990-10-10

    This manual describes in detail the solution of ten example problems using the explicit nonlinear finite element code DYNA3D. The sample problems include solid, shell, and beam element types, and a variety of linear and nonlinear material models. For each example, there is first an engineering description of the physical problem to be studied. Next, the analytical techniques incorporated in the model are discussed and key features of DYNA3D are highlighted. INGRID commands used to generate the mesh are listed, and sample plots from the DYNA3D analysis are given. Finally, there is a description of the TAURUS post-processing commands used to generate the plots of the solution. This set of example problems is useful in verifying the installation of DYNA3D on a new computer system. In addition, these documented analyses illustrate the application of DYNA3D to a variety of engineering problems, and thus this manual should be helpful to new analysts getting started with DYNA3D. 7 refs., 56 figs., 9 tabs.

  3. Recording stereoscopic 3D neurosurgery with a head-mounted 3D camera system.

    PubMed

    Lee, Brian; Chen, Brian R; Chen, Beverly B; Lu, James Y; Giannotta, Steven L

    2015-06-01

    Stereoscopic three-dimensional (3D) imaging can present more information to the viewer and further enhance the learning experience over traditional two-dimensional (2D) video. Most 3D surgical videos are recorded from the operating microscope and only feature the crux, or the most important part of the surgery, leaving out other crucial parts of surgery including the opening, approach, and closing of the surgical site. In addition, many other surgeries including complex spine, trauma, and intensive care unit procedures are also rarely recorded. We describe and share our experience with a commercially available head-mounted stereoscopic 3D camera system to obtain stereoscopic 3D recordings of these seldom recorded aspects of neurosurgery. The strengths and limitations of using the GoPro(®) 3D system as a head-mounted stereoscopic 3D camera system in the operating room are reviewed in detail. Over the past several years, we have recorded in stereoscopic 3D over 50 cranial and spinal surgeries and created a library for education purposes. We have found the head-mounted stereoscopic 3D camera system to be a valuable asset to supplement 3D footage from a 3D microscope. We expect that these comprehensive 3D surgical videos will become an important facet of resident education and ultimately lead to improved patient care. PMID:25620087

  4. RAG-3D: a search tool for RNA 3D substructures.

    PubMed

    Zahran, Mai; Sevim Bayrak, Cigdem; Elmetwaly, Shereef; Schlick, Tamar

    2015-10-30

    To address many challenges in RNA structure/function prediction, the characterization of RNA's modular architectural units is required. Using the RNA-As-Graphs (RAG) database, we have previously explored the existence of secondary structure (2D) submotifs within larger RNA structures. Here we present RAG-3D-a dataset of RNA tertiary (3D) structures and substructures plus a web-based search tool-designed to exploit graph representations of RNAs for the goal of searching for similar 3D structural fragments. The objects in RAG-3D consist of 3D structures translated into 3D graphs, cataloged based on the connectivity between their secondary structure elements. Each graph is additionally described in terms of its subgraph building blocks. The RAG-3D search tool then compares a query RNA 3D structure to those in the database to obtain structurally similar structures and substructures. This comparison reveals conserved 3D RNA features and thus may suggest functional connections. Though RNA search programs based on similarity in sequence, 2D, and/or 3D structural elements are available, our graph-based search tool may be advantageous for illuminating similarities that are not obvious; using motifs rather than sequence space also reduces search times considerably. Ultimately, such substructuring could be useful for RNA 3D structure prediction, structure/function inference and inverse folding. PMID:26304547

  5. 3-D SAR image formation from sparse aperture data using 3-D target grids

    NASA Astrophysics Data System (ADS)

    Bhalla, Rajan; Li, Junfei; Ling, Hao

    2005-05-01

    The performance of ATR systems can potentially be improved by using three-dimensional (3-D) SAR images instead of the traditional two-dimensional SAR images or one-dimensional range profiles. 3-D SAR image formation of targets from radar backscattered data collected on wide angle, sparse apertures has been identified by AFRL as fundamental to building an object detection and recognition capability. A set of data has been released as a challenge problem. This paper describes a technique based on the concept of 3-D target grids aimed at the formation of 3-D SAR images of targets from sparse aperture data. The 3-D target grids capture the 3-D spatial and angular scattering properties of the target and serve as matched filters for SAR formation. The results of 3-D SAR formation using the backhoe public release data are presented.

  6. Rapid 360 degree imaging and stitching of 3D objects using multiple precision 3D cameras

    NASA Astrophysics Data System (ADS)

    Lu, Thomas; Yin, Stuart; Zhang, Jianzhong; Li, Jiangan; Wu, Frank

    2008-02-01

    In this paper, we present the system architecture of a 360 degree view 3D imaging system. The system consists of multiple 3D sensors synchronized to take 3D images around the object. Each 3D camera employs a single high-resolution digital camera and a color-coded light projector. The cameras are synchronized to rapidly capture the 3D and color information of a static object or a live person. The color encoded structure lighting ensures the precise reconstruction of the depth of the object. A 3D imaging system architecture is presented. The architecture employs the displacement of the camera and the projector to triangulate the depth information. The 3D camera system has achieved high depth resolution down to 0.1mm on a human head sized object and 360 degree imaging capability.

  7. CFL3D, FUN3d, and NSU3D Contributions to the Fifth Drag Prediction Workshop

    NASA Technical Reports Server (NTRS)

    Park, Michael A.; Laflin, Kelly R.; Chaffin, Mark S.; Powell, Nicholas; Levy, David W.

    2013-01-01

    Results presented at the Fifth Drag Prediction Workshop using CFL3D, FUN3D, and NSU3D are described. These are calculations on the workshop provided grids and drag adapted grids. The NSU3D results have been updated to reflect an improvement to skin friction calculation on skewed grids. FUN3D results generated after the workshop are included for custom participant generated grids and a grid from a previous workshop. Uniform grid refinement at the design condition shows a tight grouping in calculated drag, where the variation in the pressure component of drag is larger than the skin friction component. At this design condition, A fine-grid drag value was predicted with a smaller drag adjoint adapted grid via tetrahedral adaption to a metric and mixed-element subdivision. The buffet study produced larger variation than the design case, which is attributed to large differences in the predicted side-of-body separation extent. Various modeling and discretization approaches had a strong impact on predicted side-of-body separation. This large wing root separation bubble was not observed in wind tunnel tests indicating that more work is necessary in modeling wing root juncture flows to predict experiments.

  8. High efficient methods of content-based 3D model retrieval

    NASA Astrophysics Data System (ADS)

    Wu, Yuanhao; Tian, Ling; Li, Chenggang

    2013-03-01

    Content-based 3D model retrieval is of great help to facilitate the reuse of existing designs and to inspire designers during conceptual design. However, there is still a gap to apply it in industry due to the low time efficiency. This paper presents two new methods with high efficiency to build a Content-based 3D model retrieval system. First, an improvement is made on the "Shape Distribution (D2)" algorithm, and a new algorithm named "Quick D2" is proposed. Four sample 3D mechanical models are used in an experiment to compare the time cost of the two algorithms. The result indicates that the time cost of Quick D2 is much lower than that of D2, while the descriptors extracted by the two algorithms are almost the same. Second, an expandable 3D model repository index method with high performance, namely, RBK index, is presented. On the basis of RBK index, the search space is pruned effectively during the search process, leading to a speed up of the whole system. The factors that influence the values of the key parameters of RBK index are discussed and an experimental method to find the optimal values of the key parameters is given. Finally, "3D Searcher", a content-based 3D model retrieval system is developed. By using the methods proposed, the time cost for the system to respond one query online is reduced by 75% on average. The system has been implemented in a manufacturing enterprise, and practical query examples during a case of the automobile rear axle design are also shown. The research method presented shows a new research perspective and can effectively improve the content-based 3D model retrieval efficiency.

  9. PLOT3D Export Tool for Tecplot

    NASA Technical Reports Server (NTRS)

    Alter, Stephen

    2010-01-01

    The PLOT3D export tool for Tecplot solves the problem of modified data being impossible to output for use by another computational science solver. The PLOT3D Exporter add-on enables the use of the most commonly available visualization tools to engineers for output of a standard format. The exportation of PLOT3D data from Tecplot has far reaching effects because it allows for grid and solution manipulation within a graphical user interface (GUI) that is easily customized with macro language-based and user-developed GUIs. The add-on also enables the use of Tecplot as an interpolation tool for solution conversion between different grids of different types. This one add-on enhances the functionality of Tecplot so significantly, it offers the ability to incorporate Tecplot into a general suite of tools for computational science applications as a 3D graphics engine for visualization of all data. Within the PLOT3D Export Add-on are several functions that enhance the operations and effectiveness of the add-on. Unlike Tecplot output functions, the PLOT3D Export Add-on enables the use of the zone selection dialog in Tecplot to choose which zones are to be written by offering three distinct options - output of active, inactive, or all zones (grid blocks). As the user modifies the zones to output with the zone selection dialog, the zones to be written are similarly updated. This enables the use of Tecplot to create multiple configurations of a geometry being analyzed. For example, if an aircraft is loaded with multiple deflections of flaps, by activating and deactivating different zones for a specific flap setting, new specific configurations of that aircraft can be easily generated by only writing out specific zones. Thus, if ten flap settings are loaded into Tecplot, the PLOT3D Export software can output ten different configurations, one for each flap setting.

  10. A microfluidic device for 2D to 3D and 3D to 3D cell navigation

    NASA Astrophysics Data System (ADS)

    Shamloo, Amir; Amirifar, Leyla

    2016-01-01

    Microfluidic devices have received wide attention and shown great potential in the field of tissue engineering and regenerative medicine. Investigating cell response to various stimulations is much more accurate and comprehensive with the aid of microfluidic devices. In this study, we introduced a microfluidic device by which the matrix density as a mechanical property and the concentration profile of a biochemical factor as a chemical property could be altered. Our microfluidic device has a cell tank and a cell culture chamber to mimic both 2D to 3D and 3D to 3D migration of three types of cells. Fluid shear stress is negligible on the cells and a stable concentration gradient can be obtained by diffusion. The device was designed by a numerical simulation so that the uniformity of the concentration gradients throughout the cell culture chamber was obtained. Adult neural cells were cultured within this device and they showed different branching and axonal navigation phenotypes within varying nerve growth factor (NGF) concentration profiles. Neural stem cells were also cultured within varying collagen matrix densities while exposed to NGF concentrations and they experienced 3D to 3D collective migration. By generating vascular endothelial growth factor concentration gradients, adult human dermal microvascular endothelial cells also migrated in a 2D to 3D manner and formed a stable lumen within a specific collagen matrix density. It was observed that a minimum absolute concentration and concentration gradient were required to stimulate migration of all types of the cells. This device has the advantage of changing multiple parameters simultaneously and is expected to have wide applicability in cell studies.

  11. RAG-3D: A search tool for RNA 3D substructures

    DOE PAGESBeta

    Zahran, Mai; Sevim Bayrak, Cigdem; Elmetwaly, Shereef; Schlick, Tamar

    2015-08-24

    In this study, to address many challenges in RNA structure/function prediction, the characterization of RNA's modular architectural units is required. Using the RNA-As-Graphs (RAG) database, we have previously explored the existence of secondary structure (2D) submotifs within larger RNA structures. Here we present RAG-3D—a dataset of RNA tertiary (3D) structures and substructures plus a web-based search tool—designed to exploit graph representations of RNAs for the goal of searching for similar 3D structural fragments. The objects in RAG-3D consist of 3D structures translated into 3D graphs, cataloged based on the connectivity between their secondary structure elements. Each graph is additionally describedmore » in terms of its subgraph building blocks. The RAG-3D search tool then compares a query RNA 3D structure to those in the database to obtain structurally similar structures and substructures. This comparison reveals conserved 3D RNA features and thus may suggest functional connections. Though RNA search programs based on similarity in sequence, 2D, and/or 3D structural elements are available, our graph-based search tool may be advantageous for illuminating similarities that are not obvious; using motifs rather than sequence space also reduces search times considerably. Ultimately, such substructuring could be useful for RNA 3D structure prediction, structure/function inference and inverse folding.« less

  12. RAG-3D: A search tool for RNA 3D substructures

    SciTech Connect

    Zahran, Mai; Sevim Bayrak, Cigdem; Elmetwaly, Shereef; Schlick, Tamar

    2015-08-24

    In this study, to address many challenges in RNA structure/function prediction, the characterization of RNA's modular architectural units is required. Using the RNA-As-Graphs (RAG) database, we have previously explored the existence of secondary structure (2D) submotifs within larger RNA structures. Here we present RAG-3D—a dataset of RNA tertiary (3D) structures and substructures plus a web-based search tool—designed to exploit graph representations of RNAs for the goal of searching for similar 3D structural fragments. The objects in RAG-3D consist of 3D structures translated into 3D graphs, cataloged based on the connectivity between their secondary structure elements. Each graph is additionally described in terms of its subgraph building blocks. The RAG-3D search tool then compares a query RNA 3D structure to those in the database to obtain structurally similar structures and substructures. This comparison reveals conserved 3D RNA features and thus may suggest functional connections. Though RNA search programs based on similarity in sequence, 2D, and/or 3D structural elements are available, our graph-based search tool may be advantageous for illuminating similarities that are not obvious; using motifs rather than sequence space also reduces search times considerably. Ultimately, such substructuring could be useful for RNA 3D structure prediction, structure/function inference and inverse folding.

  13. RAG-3D: a search tool for RNA 3D substructures

    PubMed Central

    Zahran, Mai; Sevim Bayrak, Cigdem; Elmetwaly, Shereef; Schlick, Tamar

    2015-01-01

    To address many challenges in RNA structure/function prediction, the characterization of RNA's modular architectural units is required. Using the RNA-As-Graphs (RAG) database, we have previously explored the existence of secondary structure (2D) submotifs within larger RNA structures. Here we present RAG-3D—a dataset of RNA tertiary (3D) structures and substructures plus a web-based search tool—designed to exploit graph representations of RNAs for the goal of searching for similar 3D structural fragments. The objects in RAG-3D consist of 3D structures translated into 3D graphs, cataloged based on the connectivity between their secondary structure elements. Each graph is additionally described in terms of its subgraph building blocks. The RAG-3D search tool then compares a query RNA 3D structure to those in the database to obtain structurally similar structures and substructures. This comparison reveals conserved 3D RNA features and thus may suggest functional connections. Though RNA search programs based on similarity in sequence, 2D, and/or 3D structural elements are available, our graph-based search tool may be advantageous for illuminating similarities that are not obvious; using motifs rather than sequence space also reduces search times considerably. Ultimately, such substructuring could be useful for RNA 3D structure prediction, structure/function inference and inverse folding. PMID:26304547

  14. Automatic needle segmentation in 3D ultrasound images using 3D Hough transform

    NASA Astrophysics Data System (ADS)

    Zhou, Hua; Qiu, Wu; Ding, Mingyue; Zhang, Songgeng

    2007-12-01

    3D ultrasound (US) is a new technology that can be used for a variety of diagnostic applications, such as obstetrical, vascular, and urological imaging, and has been explored greatly potential in the applications of image-guided surgery and therapy. Uterine adenoma and uterine bleeding are the two most prevalent diseases in Chinese woman, and a minimally invasive ablation system using an RF button electrode which is needle-like is being used to destroy tumor cells or stop bleeding currently. Now a 3D US guidance system has been developed to avoid accidents or death of the patient by inaccurate localizations of the electrode and the tumor position during treatment. In this paper, we described two automated techniques, the 3D Hough Transform (3DHT) and the 3D Randomized Hough Transform (3DRHT), which is potentially fast, accurate, and robust to provide needle segmentation in 3D US image for use of 3D US imaging guidance. Based on the representation (Φ , θ , ρ , α ) of straight lines in 3D space, we used the 3DHT algorithm to segment needles successfully assumed that the approximate needle position and orientation are known in priori. The 3DRHT algorithm was developed to detect needles quickly without any information of the 3D US images. The needle segmentation techniques were evaluated using the 3D US images acquired by scanning water phantoms. The experiments demonstrated the feasibility of two 3D needle segmentation algorithms described in this paper.

  15. 3D Printers Can Provide an Added Dimension for Teaching Structure-Energy Relationships

    ERIC Educational Resources Information Center

    Blauch, David N.; Carroll, Felix A.

    2014-01-01

    A 3D printer is used to prepare a variety of models representing potential energy as a function of two geometric coordinates. These models facilitate the teaching of structure-energy relationships in molecular conformations and in chemical reactions.

  16. ICER-3D Hyperspectral Image Compression Software

    NASA Technical Reports Server (NTRS)

    Xie, Hua; Kiely, Aaron; Klimesh, matthew; Aranki, Nazeeh

    2010-01-01

    Software has been developed to implement the ICER-3D algorithm. ICER-3D effects progressive, three-dimensional (3D), wavelet-based compression of hyperspectral images. If a compressed data stream is truncated, the progressive nature of the algorithm enables reconstruction of hyperspectral data at fidelity commensurate with the given data volume. The ICER-3D software is capable of providing either lossless or lossy compression, and incorporates an error-containment scheme to limit the effects of data loss during transmission. The compression algorithm, which was derived from the ICER image compression algorithm, includes wavelet-transform, context-modeling, and entropy coding subalgorithms. The 3D wavelet decomposition structure used by ICER-3D exploits correlations in all three dimensions of sets of hyperspectral image data, while facilitating elimination of spectral ringing artifacts, using a technique summarized in "Improving 3D Wavelet-Based Compression of Spectral Images" (NPO-41381), NASA Tech Briefs, Vol. 33, No. 3 (March 2009), page 7a. Correlation is further exploited by a context-modeling subalgorithm, which exploits spectral dependencies in the wavelet-transformed hyperspectral data, using an algorithm that is summarized in "Context Modeler for Wavelet Compression of Hyperspectral Images" (NPO-43239), which follows this article. An important feature of ICER-3D is a scheme for limiting the adverse effects of loss of data during transmission. In this scheme, as in the similar scheme used by ICER, the spatial-frequency domain is partitioned into rectangular error-containment regions. In ICER-3D, the partitions extend through all the wavelength bands. The data in each partition are compressed independently of those in the other partitions, so that loss or corruption of data from any partition does not affect the other partitions. Furthermore, because compression is progressive within each partition, when data are lost, any data from that partition received

  17. Shim3d Helmholtz Solution Package

    2009-01-29

    This suite of codes solves the Helmholtz Equation for the steady-state propagation of single-frequency electromagnetic radiation in an arbitrary 2D or 3D dielectric medium. Materials can be either transparent or absorptive (including metals) and are described entirely by their shape and complex dielectric constant. Dielectric boundaries are assumed to always fall on grid boundaries and the material within a single grid cell is considered to be uniform. Input to the problem is in the formmore » of a Dirichlet boundary condition on a single boundary, and may be either analytic (Gaussian) in shape, or a mode shape computed using a separate code (such as the included eigenmode solver vwave20), and written to a file. Solution is via the finite difference method using Jacobi iteration for 3D problems or direct matrix inversion for 2D problems. Note that 3D problems that include metals will require different iteration parameters than described in the above reference. For structures with curved boundaries not easily modeled on a rectangular grid, the auxillary codes helmholtz11(2D), helm3d (semivectoral), and helmv3d (full vectoral) are provided. For these codes the finite difference equations are specified on a topological regular triangular grid and solved using Jacobi iteration or direct matrix inversion as before. An automatic grid generator is supplied.« less

  18. 3D Spray Droplet Distributions in Sneezes

    NASA Astrophysics Data System (ADS)

    Techet, Alexandra; Scharfman, Barry; Bourouiba, Lydia

    2015-11-01

    3D spray droplet clouds generated during human sneezing are investigated using the Synthetic Aperture Feature Extraction (SAFE) method, which relies on light field imaging (LFI) and synthetic aperture (SA) refocusing computational photographic techniques. An array of nine high-speed cameras are used to image sneeze droplets and tracked the droplets in 3D space and time (3D + T). An additional high-speed camera is utilized to track the motion of the head during sneezing. In the SAFE method, the raw images recorded by each camera in the array are preprocessed and binarized, simplifying post processing after image refocusing and enabling the extraction of feature sizes and positions in 3D + T. These binary images are refocused using either additive or multiplicative methods, combined with thresholding. Sneeze droplet centroids, radii, distributions and trajectories are determined and compared with existing data. The reconstructed 3D droplet centroids and radii enable a more complete understanding of the physical extent and fluid dynamics of sneeze ejecta. These measurements are important for understanding the infectious disease transmission potential of sneezes in various indoor environments.

  19. T-HEMP3D user manual

    SciTech Connect

    Turner, D.

    1983-08-01

    The T-HEMP3D (Transportable HEMP3D) computer program is a derivative of the STEALTH three-dimensional thermodynamics code developed by Science Applications, Inc., under the direction of Ron Hofmann. STEALTH, in turn, is based entirely on the original HEMP3D code written at Lawrence Livermore National Laboratory. The primary advantage STEALTH has over its predecessors is that it was designed using modern structured design techniques, with rigorous programming standards enforced. This yields two benefits. First, the code is easily changeable; this is a necessity for a physics code used for research. The second benefit is that the code is easily transportable between different types of computers. The STEALTH program was transferred to LLNL under a cooperative development agreement. Changes were made primarily in three areas: material specification, coordinate generation, and the addition of sliding surface boundary conditions. The code was renamed T-HEMP3D to avoid confusion with other versions of STEALTH. This document summarizes the input to T-HEMP3D, as used at LLNL. It does not describe the physics simulated by the program, nor the numerical techniques employed. Furthermore, it does not describe the separate job steps of coordinate generation and post-processing, including graphical display of results. (WHK)

  20. Magnetic Properties of 3D Printed Toroids

    NASA Astrophysics Data System (ADS)

    Bollig, Lindsey; Otto, Austin; Hilpisch, Peter; Mowry, Greg; Nelson-Cheeseman, Brittany; Renewable Energy; Alternatives Lab (REAL) Team

    Transformers are ubiquitous in electronics today. Although toroidal geometries perform most efficiently, transformers are traditionally made with rectangular cross-sections due to the lower manufacturing costs. Additive manufacturing techniques (3D printing) can easily achieve toroidal geometries by building up a part through a series of 2D layers. To get strong magnetic properties in a 3D printed transformer, a composite filament is used containing Fe dispersed in a polymer matrix. How the resulting 3D printed toroid responds to a magnetic field depends on two structural factors of the printed 2D layers: fill factor (planar density) and fill pattern. In this work, we investigate how the fill factor and fill pattern affect the magnetic properties of 3D printed toroids. The magnetic properties of the printed toroids are measured by a custom circuit that produces a hysteresis loop for each toroid. Toroids with various fill factors and fill patterns are compared to determine how these two factors can affect the magnetic field the toroid can produce. These 3D printed toroids can be used for numerous applications in order to increase the efficiency of transformers by making it possible for manufacturers to make a toroidal geometry.

  1. 3D dynamic roadmapping for abdominal catheterizations.

    PubMed

    Bender, Frederik; Groher, Martin; Khamene, Ali; Wein, Wolfgang; Heibel, Tim Hauke; Navab, Nassir

    2008-01-01

    Despite rapid advances in interventional imaging, the navigation of a guide wire through abdominal vasculature remains, not only for novice radiologists, a difficult task. Since this navigation is mostly based on 2D fluoroscopic image sequences from one view, the process is slowed down significantly due to missing depth information and patient motion. We propose a novel approach for 3D dynamic roadmapping in deformable regions by predicting the location of the guide wire tip in a 3D vessel model from the tip's 2D location, respiratory motion analysis, and view geometry. In a first step, the method compensates for the apparent respiratory motion in 2D space before backprojecting the 2D guide wire tip into three dimensional space, using a given projection matrix. To countervail the error connected to the projection parameters and the motion compensation, as well as the ambiguity caused by vessel deformation, we establish a statistical framework, which computes a reliable estimate of the guide wire tip location within the 3D vessel model. With this 2D-to-3D transfer, the navigation can be performed from arbitrary viewing angles, disconnected from the static perspective view of the fluoroscopic sequence. Tests on a realistic breathing phantom and on synthetic data with a known ground truth clearly reveal the superiority of our approach compared to naive methods for 3D roadmapping. The concepts and information presented in this paper are based on research and are not commercially available. PMID:18982662

  2. Lifting Object Detection Datasets into 3D.

    PubMed

    Carreira, Joao; Vicente, Sara; Agapito, Lourdes; Batista, Jorge

    2016-07-01

    While data has certainly taken the center stage in computer vision in recent years, it can still be difficult to obtain in certain scenarios. In particular, acquiring ground truth 3D shapes of objects pictured in 2D images remains a challenging feat and this has hampered progress in recognition-based object reconstruction from a single image. Here we propose to bypass previous solutions such as 3D scanning or manual design, that scale poorly, and instead populate object category detection datasets semi-automatically with dense, per-object 3D reconstructions, bootstrapped from:(i) class labels, (ii) ground truth figure-ground segmentations and (iii) a small set of keypoint annotations. Our proposed algorithm first estimates camera viewpoint using rigid structure-from-motion and then reconstructs object shapes by optimizing over visual hull proposals guided by loose within-class shape similarity assumptions. The visual hull sampling process attempts to intersect an object's projection cone with the cones of minimal subsets of other similar objects among those pictured from certain vantage points. We show that our method is able to produce convincing per-object 3D reconstructions and to accurately estimate cameras viewpoints on one of the most challenging existing object-category detection datasets, PASCAL VOC. We hope that our results will re-stimulate interest on joint object recognition and 3D reconstruction from a single image. PMID:27295458

  3. 3D camera tracking from disparity images

    NASA Astrophysics Data System (ADS)

    Kim, Kiyoung; Woo, Woontack

    2005-07-01

    In this paper, we propose a robust camera tracking method that uses disparity images computed from known parameters of 3D camera and multiple epipolar constraints. We assume that baselines between lenses in 3D camera and intrinsic parameters are known. The proposed method reduces camera motion uncertainty encountered during camera tracking. Specifically, we first obtain corresponding feature points between initial lenses using normalized correlation method. In conjunction with matching features, we get disparity images. When the camera moves, the corresponding feature points, obtained from each lens of 3D camera, are robustly tracked via Kanade-Lukas-Tomasi (KLT) tracking algorithm. Secondly, relative pose parameters of each lens are calculated via Essential matrices. Essential matrices are computed from Fundamental matrix calculated using normalized 8-point algorithm with RANSAC scheme. Then, we determine scale factor of translation matrix by d-motion. This is required because the camera motion obtained from Essential matrix is up to scale. Finally, we optimize camera motion using multiple epipolar constraints between lenses and d-motion constraints computed from disparity images. The proposed method can be widely adopted in Augmented Reality (AR) applications, 3D reconstruction using 3D camera, and fine surveillance systems which not only need depth information, but also camera motion parameters in real-time.

  4. Full-color holographic 3D printer

    NASA Astrophysics Data System (ADS)

    Takano, Masami; Shigeta, Hiroaki; Nishihara, Takashi; Yamaguchi, Masahiro; Takahashi, Susumu; Ohyama, Nagaaki; Kobayashi, Akihiko; Iwata, Fujio

    2003-05-01

    A holographic 3D printer is a system that produces a direct hologram with full-parallax information using the 3-dimensional data of a subject from a computer. In this paper, we present a proposal for the reproduction of full-color images with the holographic 3D printer. In order to realize the 3-dimensional color image, we selected the 3 laser wavelength colors of red (λ=633nm), green (λ=533nm), and blue (λ=442nm), and we built a one-step optical system using a projection system and a liquid crystal display. The 3-dimensional color image is obtained by synthesizing in a 2D array the multiple exposure with these 3 wavelengths made on each 250mm elementary hologram, and moving recording medium on a x-y stage. For the natural color reproduction in the holographic 3D printer, we take the approach of the digital processing technique based on the color management technology. The matching between the input and output colors is performed by investigating first, the relation between the gray level transmittance of the LCD and the diffraction efficiency of the hologram and second, by measuring the color displayed by the hologram to establish a correlation. In our first experimental results a non-linear functional relation for single and multiple exposure of the three components were found. These results are the first step in the realization of a natural color 3D image produced by the holographic color 3D printer.

  5. The importance of 3D dosimetry

    NASA Astrophysics Data System (ADS)

    Low, Daniel

    2015-01-01

    Radiation therapy has been getting progressively more complex for the past 20 years. Early radiation therapy techniques needed only basic dosimetry equipment; motorized water phantoms, ionization chambers, and basic radiographic film techniques. As intensity modulated radiation therapy and image guided therapy came into widespread practice, medical physicists were challenged with developing effective and efficient dose measurement techniques. The complex 3-dimensional (3D) nature of the dose distributions that were being delivered demanded the development of more quantitative and more thorough methods for dose measurement. The quality assurance vendors developed a wide array of multidetector arrays that have been enormously useful for measuring and characterizing dose distributions, and these have been made especially useful with the advent of 3D dose calculation systems based on the array measurements, as well as measurements made using film and portal imagers. Other vendors have been providing 3D calculations based on data from the linear accelerator or the record and verify system, providing thorough evaluation of the dose but lacking quality assurance (QA) of the dose delivery process, including machine calibration. The current state of 3D dosimetry is one of a state of flux. The vendors and professional associations are trying to determine the optimal balance between thorough QA, labor efficiency, and quantitation. This balance will take some time to reach, but a necessary component will be the 3D measurement and independent calculation of delivered radiation therapy dose distributions.

  6. Visual inertia of rotating 3-D objects.

    PubMed

    Jiang, Y; Pantle, A J; Mark, L S

    1998-02-01

    Five experiments were designed to determine whether a rotating, transparent 3-D cloud of dots (simulated sphere) could influence the perceived direction of rotation of a subsequent sphere. Experiment 1 established conditions under which the direction of rotation of a virtual sphere was perceived unambiguously. When a near-far luminance difference and perspective depth cues were present, observers consistently saw the sphere rotate in the intended direction. In Experiment 2, a near-far luminance difference was used to create an unambiguous rotation sequence that was followed by a directionally ambiguous rotation sequence that lacked both the near-far luminance cue and the perspective cue. Observers consistently saw the second sequence as rotating in the same direction as the first, indicating the presence of 3-D visual inertia. Experiment 3 showed that 3-D visual inertia was sufficiently powerful to bias the perceived direction of a rotation sequence made unambiguous by a near-far luminance cue. Experiment 5 showed that 3-D visual inertia could be obtained using an occlusion depth cue to create an unambiguous inertia-inducing sequence. Finally, Experiments 2, 4, and 5 all revealed a fast-decay phase of inertia that lasted for approximately 800 msec, followed by an asymptotic phase that lasted for periods as long as 1,600 msec. The implications of these findings are examined with respect to motion mechanisms of 3-D visual inertia. PMID:9529911

  7. Integral 3D display using multiple LCDs

    NASA Astrophysics Data System (ADS)

    Okaichi, Naoto; Miura, Masato; Arai, Jun; Mishina, Tomoyuki

    2015-03-01

    The quality of the integral 3D images created by a 3D imaging system was improved by combining multiple LCDs to utilize a greater number of pixels than that possible with one LCD. A prototype of the display device was constructed by using four HD LCDs. An integral photography (IP) image displayed by the prototype is four times larger than that reconstructed by a single display. The pixel pitch of the HD display used is 55.5 μm, and the number of elemental lenses is 212 horizontally and 119 vertically. The 3D image pixel count is 25,228, and the viewing angle is 28°. Since this method is extensible, it is possible to display an integral 3D image of higher quality by increasing the number of LCDs. Using this integral 3D display structure makes it possible to make the whole device thinner than a projector-based display system. It is therefore expected to be applied to the home television in the future.

  8. 3D bioprinting for engineering complex tissues.

    PubMed

    Mandrycky, Christian; Wang, Zongjie; Kim, Keekyoung; Kim, Deok-Ho

    2016-01-01

    Bioprinting is a 3D fabrication technology used to precisely dispense cell-laden biomaterials for the construction of complex 3D functional living tissues or artificial organs. While still in its early stages, bioprinting strategies have demonstrated their potential use in regenerative medicine to generate a variety of transplantable tissues, including skin, cartilage, and bone. However, current bioprinting approaches still have technical challenges in terms of high-resolution cell deposition, controlled cell distributions, vascularization, and innervation within complex 3D tissues. While no one-size-fits-all approach to bioprinting has emerged, it remains an on-demand, versatile fabrication technique that may address the growing organ shortage as well as provide a high-throughput method for cell patterning at the micrometer scale for broad biomedical engineering applications. In this review, we introduce the basic principles, materials, integration strategies and applications of bioprinting. We also discuss the recent developments, current challenges and future prospects of 3D bioprinting for engineering complex tissues. Combined with recent advances in human pluripotent stem cell technologies, 3D-bioprinted tissue models could serve as an enabling platform for high-throughput predictive drug screening and more effective regenerative therapies. PMID:26724184

  9. Miniaturized 3D microscope imaging system

    NASA Astrophysics Data System (ADS)

    Lan, Yung-Sung; Chang, Chir-Weei; Sung, Hsin-Yueh; Wang, Yen-Chang; Chang, Cheng-Yi

    2015-05-01

    We designed and assembled a portable 3-D miniature microscopic image system with the size of 35x35x105 mm3 . By integrating a microlens array (MLA) into the optical train of a handheld microscope, the biological specimen's image will be captured for ease of use in a single shot. With the light field raw data and program, the focal plane can be changed digitally and the 3-D image can be reconstructed after the image was taken. To localize an object in a 3-D volume, an automated data analysis algorithm to precisely distinguish profundity position is needed. The ability to create focal stacks from a single image allows moving or specimens to be recorded. Applying light field microscope algorithm to these focal stacks, a set of cross sections will be produced, which can be visualized using 3-D rendering. Furthermore, we have developed a series of design rules in order to enhance the pixel using efficiency and reduce the crosstalk between each microlens for obtain good image quality. In this paper, we demonstrate a handheld light field microscope (HLFM) to distinguish two different color fluorescence particles separated by a cover glass in a 600um range, show its focal stacks, and 3-D position.

  10. 3D optical measuring technologies and systems

    NASA Astrophysics Data System (ADS)

    Chugui, Yuri V.

    2005-02-01

    The results of the R & D activity of TDI SIE SB RAS in the field of the 3D optical measuring technologies and systems for noncontact 3D optical dimensional inspection applied to atomic and railway industry safety problems are presented. This activity includes investigations of diffraction phenomena on some 3D objects, using the original constructive calculation method. The efficient algorithms for precise determining the transverse and longitudinal sizes of 3D objects of constant thickness by diffraction method, peculiarities on formation of the shadow and images of the typical elements of the extended objects were suggested. Ensuring the safety of nuclear reactors and running trains as well as their high exploitation reliability requires a 100% noncontact precise inspection of geometrical parameters of their components. To solve this problem we have developed methods and produced the technical vision measuring systems LMM, CONTROL, PROFIL, and technologies for noncontact 3D dimensional inspection of grid spacers and fuel elements for the nuclear reactor VVER-1000 and VVER-440, as well as automatic laser diagnostic COMPLEX for noncontact inspection of geometric parameters of running freight car wheel pairs. The performances of these systems and the results of industrial testing are presented and discussed. The created devices are in pilot operation at Atomic and Railway Companies.

  11. 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.

  12. Isotropic 3D Nuclear Morphometry of Normal, Fibrocystic and Malignant Breast Epithelial Cells Reveals New Structural Alterations

    PubMed Central

    Nandakumar, Vivek; Kelbauskas, Laimonas; Hernandez, Kathryn F.; Lintecum, Kelly M.; Senechal, Patti; Bussey, Kimberly J.; Davies, Paul C. W.; Johnson, Roger H.; Meldrum, Deirdre R.

    2012-01-01

    Background Grading schemes for breast cancer diagnosis are predominantly based on pathologists' qualitative assessment of altered nuclear structure from 2D brightfield microscopy images. However, cells are three-dimensional (3D) objects with features that are inherently 3D and thus poorly characterized in 2D. Our goal is to quantitatively characterize nuclear structure in 3D, assess its variation with malignancy, and investigate whether such variation correlates with standard nuclear grading criteria. Methodology We applied micro-optical computed tomographic imaging and automated 3D nuclear morphometry to quantify and compare morphological variations between human cell lines derived from normal, benign fibrocystic or malignant breast epithelium. To reproduce the appearance and contrast in clinical cytopathology images, we stained cells with hematoxylin and eosin and obtained 3D images of 150 individual stained cells of each cell type at sub-micron, isotropic resolution. Applying volumetric image analyses, we computed 42 3D morphological and textural descriptors of cellular and nuclear structure. Principal Findings We observed four distinct nuclear shape categories, the predominant being a mushroom cap shape. Cell and nuclear volumes increased from normal to fibrocystic to metastatic type, but there was little difference in the volume ratio of nucleus to cytoplasm (N/C ratio) between the lines. Abnormal cell nuclei had more nucleoli, markedly higher density and clumpier chromatin organization compared to normal. Nuclei of non-tumorigenic, fibrocystic cells exhibited larger textural variations than metastatic cell nuclei. At p<0.0025 by ANOVA and Kruskal-Wallis tests, 90% of our computed descriptors statistically differentiated control from abnormal cell populations, but only 69% of these features statistically differentiated the fibrocystic from the metastatic cell populations. Conclusions Our results provide a new perspective on nuclear structure variations

  13. Ultra-High Resolution 3D Imaging of Whole Cells.

    PubMed

    Huang, Fang; Sirinakis, George; Allgeyer, Edward S; Schroeder, Lena K; Duim, Whitney C; Kromann, Emil B; Phan, Thomy; Rivera-Molina, Felix E; Myers, Jordan R; Irnov, Irnov; Lessard, Mark; Zhang, Yongdeng; Handel, Mary Ann; Jacobs-Wagner, Christine; Lusk, C Patrick; Rothman, James E; Toomre, Derek; Booth, Martin J; Bewersdorf, Joerg

    2016-08-11

    Fluorescence nanoscopy, or super-resolution microscopy, has become an important tool in cell biological research. However, because of its usually inferior resolution in the depth direction (50-80 nm) and rapidly deteriorating resolution in thick samples, its practical biological application has been effectively limited to two dimensions and thin samples. Here, we present the development of whole-cell 4Pi single-molecule switching nanoscopy (W-4PiSMSN), an optical nanoscope that allows imaging of three-dimensional (3D) structures at 10- to 20-nm resolution throughout entire mammalian cells. We demonstrate the wide applicability of W-4PiSMSN across diverse research fields by imaging complex molecular architectures ranging from bacteriophages to nuclear pores, cilia, and synaptonemal complexes in large 3D cellular volumes. PMID:27397506

  14. The 3D Genome as Moderator of Chromosomal Communication.

    PubMed

    Dekker, Job; Mirny, Leonid

    2016-03-10

    Proper expression of genes requires communication with their regulatory elements that can be located elsewhere along the chromosome. The physics of chromatin fibers imposes a range of constraints on such communication. The molecular and biophysical mechanisms by which chromosomal communication is established, or prevented, have become a topic of intense study, and important roles for the spatial organization of chromosomes are being discovered. Here we present a view of the interphase 3D genome characterized by extensive physical compartmentalization and insulation on the one hand and facilitated long-range interactions on the other. We propose the existence of topological machines dedicated to set up and to exploit a 3D genome organization to both promote and censor communication along and between chromosomes. PMID:26967279

  15. Real-time monitoring of 3D cell culture using a 3D capacitance biosensor.

    PubMed

    Lee, Sun-Mi; Han, Nalae; Lee, Rimi; Choi, In-Hong; Park, Yong-Beom; Shin, Jeon-Soo; Yoo, Kyung-Hwa

    2016-03-15

    Three-dimensional (3D) cell cultures have recently received attention because they represent a more physiologically relevant environment compared to conventional two-dimensional (2D) cell cultures. However, 2D-based imaging techniques or cell sensors are insufficient for real-time monitoring of cellular behavior in 3D cell culture. Here, we report investigations conducted with a 3D capacitance cell sensor consisting of vertically aligned pairs of electrodes. When GFP-expressing human breast cancer cells (GFP-MCF-7) encapsulated in alginate hydrogel were cultured in a 3D cell culture system, cellular activities, such as cell proliferation and apoptosis at different heights, could be monitored non-invasively and in real-time by measuring the change in capacitance with the 3D capacitance sensor. Moreover, we were able to monitor cell migration of human mesenchymal stem cells (hMSCs) with our 3D capacitance sensor. PMID:26386332

  16. 3D scene reconstruction based on 3D laser point cloud combining UAV images

    NASA Astrophysics Data System (ADS)

    Liu, Huiyun; Yan, Yangyang; Zhang, Xitong; Wu, Zhenzhen

    2016-03-01

    It is a big challenge capturing and modeling 3D information of the built environment. A number of techniques and technologies are now in use. These include GPS, and photogrammetric application and also remote sensing applications. The experiment uses multi-source data fusion technology for 3D scene reconstruction based on the principle of 3D laser scanning technology, which uses the laser point cloud data as the basis and Digital Ortho-photo Map as an auxiliary, uses 3DsMAX software as a basic tool for building three-dimensional scene reconstruction. The article includes data acquisition, data preprocessing, 3D scene construction. The results show that the 3D scene has better truthfulness, and the accuracy of the scene meet the need of 3D scene construction.

  17. 3D whiteboard: collaborative sketching with 3D-tracked smart phones

    NASA Astrophysics Data System (ADS)

    Lue, James; Schulze, Jürgen P.

    2014-02-01

    We present the results of our investigation of the feasibility of a new approach for collaborative drawing in 3D, based on Android smart phones. Our approach utilizes a number of fiduciary markers, placed in the working area where they can be seen by the smart phones' cameras, in order to estimate the pose of each phone in the room. Our prototype allows two users to draw 3D objects with their smart phones by moving their phones around in 3D space. For example, 3D lines are drawn by recording the path of the phone as it is moved around in 3D space, drawing line segments on the screen along the way. Each user can see the virtual drawing space on their smart phones' displays, as if the display was a window into this space. Besides lines, our prototype application also supports 3D geometry creation, geometry transformation operations, and it shows the location of the other user's phone.

  18. 3D face analysis for demographic biometrics

    SciTech Connect

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

    2015-01-01

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

  19. 3D Printed Multimaterial Microfluidic Valve.

    PubMed

    Keating, Steven J; Gariboldi, Maria Isabella; Patrick, William G; Sharma, Sunanda; Kong, David S; Oxman, Neri

    2016-01-01

    We present a novel 3D printed multimaterial microfluidic proportional valve. The microfluidic valve is a fundamental primitive that enables the development of programmable, automated devices for controlling fluids in a precise manner. We discuss valve characterization results, as well as exploratory design variations in channel width, membrane thickness, and membrane stiffness. Compared to previous single material 3D printed valves that are stiff, these printed valves constrain fluidic deformation spatially, through combinations of stiff and flexible materials, to enable intricate geometries in an actuated, functionally graded device. Research presented marks a shift towards 3D printing multi-property programmable fluidic devices in a single step, in which integrated multimaterial valves can be used to control complex fluidic reactions for a variety of applications, including DNA assembly and analysis, continuous sampling and sensing, and soft robotics. PMID:27525809

  20. Angular description for 3D scattering centers

    NASA Astrophysics Data System (ADS)

    Bhalla, Rajan; Raynal, Ann Marie; Ling, Hao; Moore, John; Velten, Vincent J.

    2006-05-01

    The electromagnetic scattered field from an electrically large target can often be well modeled as if it is emanating from a discrete set of scattering centers (see Fig. 1). In the scattering center extraction tool we developed previously based on the shooting and bouncing ray technique, no correspondence is maintained amongst the 3D scattering center extracted at adjacent angles. In this paper we present a multi