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Sample records for initio protein tertiary

  1. Ab-initio phasing in protein crystallography

    NASA Astrophysics Data System (ADS)

    van der Plas, J. L.; Millane, Rick P.

    2000-11-01

    The central problem in the determination of protein structures form x-ray diffraction dada (x-ray crystallography) corresponds to a phase retrieval problem with undersampled amplitude data. Algorithms for this problem that have an increased radius of convergence have the potential for reducing the amount of experimental work, and cost, involved in determining protein structures. We describe such an algorithm. Application of the algorithm to a simulated crystallographic problem shows that it converges to the correct solution, with no initial phase information, where currently used algorithms fail. The results lend support to the possibility of ab initio phasing in protein crystallography.

  2. A Deep Learning Network Approach to ab initio Protein Secondary Structure Prediction.

    PubMed

    Spencer, Matt; Eickholt, Jesse; Jianlin Cheng

    2015-01-01

    Ab initio protein secondary structure (SS) predictions are utilized to generate tertiary structure predictions, which are increasingly demanded due to the rapid discovery of proteins. Although recent developments have slightly exceeded previous methods of SS prediction, accuracy has stagnated around 80 percent and many wonder if prediction cannot be advanced beyond this ceiling. Disciplines that have traditionally employed neural networks are experimenting with novel deep learning techniques in attempts to stimulate progress. Since neural networks have historically played an important role in SS prediction, we wanted to determine whether deep learning could contribute to the advancement of this field as well. We developed an SS predictor that makes use of the position-specific scoring matrix generated by PSI-BLAST and deep learning network architectures, which we call DNSS. Graphical processing units and CUDA software optimize the deep network architecture and efficiently train the deep networks. Optimal parameters for the training process were determined, and a workflow comprising three separately trained deep networks was constructed in order to make refined predictions. This deep learning network approach was used to predict SS for a fully independent test dataset of 198 proteins, achieving a Q3 accuracy of 80.7 percent and a Sov accuracy of 74.2 percent.

  3. Efficient conformational space exploration in ab initio protein folding simulation

    PubMed Central

    Ullah, Ahammed; Ahmed, Nasif; Pappu, Subrata Dey; Shatabda, Swakkhar; Ullah, A. Z. M. Dayem; Rahman, M. Sohel

    2015-01-01

    Ab initio protein folding simulation largely depends on knowledge-based energy functions that are derived from known protein structures using statistical methods. These knowledge-based energy functions provide us with a good approximation of real protein energetics. However, these energy functions are not very informative for search algorithms and fail to distinguish the types of amino acid interactions that contribute largely to the energy function from those that do not. As a result, search algorithms frequently get trapped into the local minima. On the other hand, the hydrophobic–polar (HP) model considers hydrophobic interactions only. The simplified nature of HP energy function makes it limited only to a low-resolution model. In this paper, we present a strategy to derive a non-uniform scaled version of the real 20×20 pairwise energy function. The non-uniform scaling helps tackle the difficulty faced by a real energy function, whereas the integration of 20×20 pairwise information overcomes the limitations faced by the HP energy function. Here, we have applied a derived energy function with a genetic algorithm on discrete lattices. On a standard set of benchmark protein sequences, our approach significantly outperforms the state-of-the-art methods for similar models. Our approach has been able to explore regions of the conformational space which all the previous methods have failed to explore. Effectiveness of the derived energy function is presented by showing qualitative differences and similarities of the sampled structures to the native structures. Number of objective function evaluation in a single run of the algorithm is used as a comparison metric to demonstrate efficiency. PMID:26361554

  4. Efficient conformational space exploration in ab initio protein folding simulation.

    PubMed

    Ullah, Ahammed; Ahmed, Nasif; Pappu, Subrata Dey; Shatabda, Swakkhar; Ullah, A Z M Dayem; Rahman, M Sohel

    2015-08-01

    Ab initio protein folding simulation largely depends on knowledge-based energy functions that are derived from known protein structures using statistical methods. These knowledge-based energy functions provide us with a good approximation of real protein energetics. However, these energy functions are not very informative for search algorithms and fail to distinguish the types of amino acid interactions that contribute largely to the energy function from those that do not. As a result, search algorithms frequently get trapped into the local minima. On the other hand, the hydrophobic-polar (HP) model considers hydrophobic interactions only. The simplified nature of HP energy function makes it limited only to a low-resolution model. In this paper, we present a strategy to derive a non-uniform scaled version of the real 20×20 pairwise energy function. The non-uniform scaling helps tackle the difficulty faced by a real energy function, whereas the integration of 20×20 pairwise information overcomes the limitations faced by the HP energy function. Here, we have applied a derived energy function with a genetic algorithm on discrete lattices. On a standard set of benchmark protein sequences, our approach significantly outperforms the state-of-the-art methods for similar models. Our approach has been able to explore regions of the conformational space which all the previous methods have failed to explore. Effectiveness of the derived energy function is presented by showing qualitative differences and similarities of the sampled structures to the native structures. Number of objective function evaluation in a single run of the algorithm is used as a comparison metric to demonstrate efficiency.

  5. Tertiary alphabet for the observable protein structural universe.

    PubMed

    Mackenzie, Craig O; Zhou, Jianfu; Grigoryan, Gevorg

    2016-11-22

    Here, we systematically decompose the known protein structural universe into its basic elements, which we dub tertiary structural motifs (TERMs). A TERM is a compact backbone fragment that captures the secondary, tertiary, and quaternary environments around a given residue, comprising one or more disjoint segments (three on average). We seek the set of universal TERMs that capture all structure in the Protein Data Bank (PDB), finding remarkable degeneracy. Only ∼600 TERMs are sufficient to describe 50% of the PDB at sub-Angstrom resolution. However, more rare geometries also exist, and the overall structural coverage grows logarithmically with the number of TERMs. We go on to show that universal TERMs provide an effective mapping between sequence and structure. We demonstrate that TERM-based statistics alone are sufficient to recapitulate close-to-native sequences given either NMR or X-ray backbones. Furthermore, sequence variability predicted from TERM data agrees closely with evolutionary variation. Finally, locations of TERMs in protein chains can be predicted from sequence alone based on sequence signatures emergent from TERM instances in the PDB. For multisegment motifs, this method identifies spatially adjacent fragments that are not contiguous in sequence-a major bottleneck in structure prediction. Although all TERMs recur in diverse proteins, some appear specialized for certain functions, such as interface formation, metal coordination, or even water binding. Structural biology has benefited greatly from previously observed degeneracies in structure. The decomposition of the known structural universe into a finite set of compact TERMs offers exciting opportunities toward better understanding, design, and prediction of protein structure.

  6. TOUCHSTONE II: a new approach to ab initio protein structure prediction.

    PubMed

    Zhang, Yang; Kolinski, Andrzej; Skolnick, Jeffrey

    2003-08-01

    We have developed a new combined approach for ab initio protein structure prediction. The protein conformation is described as a lattice chain connecting C(alpha) atoms, with attached C(beta) atoms and side-chain centers of mass. The model force field includes various short-range and long-range knowledge-based potentials derived from a statistical analysis of the regularities of protein structures. The combination of these energy terms is optimized through the maximization of correlation for 30 x 60,000 decoys between the root mean square deviation (RMSD) to native and energies, as well as the energy gap between native and the decoy ensemble. To accelerate the conformational search, a newly developed parallel hyperbolic sampling algorithm with a composite movement set is used in the Monte Carlo simulation processes. We exploit this strategy to successfully fold 41/100 small proteins (36 approximately 120 residues) with predicted structures having a RMSD from native below 6.5 A in the top five cluster centroids. To fold larger-size proteins as well as to improve the folding yield of small proteins, we incorporate into the basic force field side-chain contact predictions from our threading program PROSPECTOR where homologous proteins were excluded from the data base. With these threading-based restraints, the program can fold 83/125 test proteins (36 approximately 174 residues) with structures having a RMSD to native below 6.5 A in the top five cluster centroids. This shows the significant improvement of folding by using predicted tertiary restraints, especially when the accuracy of side-chain contact prediction is >20%. For native fold selection, we introduce quantities dependent on the cluster density and the combination of energy and free energy, which show a higher discriminative power to select the native structure than the previously used cluster energy or cluster size, and which can be used in native structure identification in blind simulations. These

  7. Exploring the speed and performance of molecular replacement with AMPLE using QUARK ab initio protein models.

    PubMed

    Keegan, Ronan M; Bibby, Jaclyn; Thomas, Jens; Xu, Dong; Zhang, Yang; Mayans, Olga; Winn, Martyn D; Rigden, Daniel J

    2015-02-01

    AMPLE clusters and truncates ab initio protein structure predictions, producing search models for molecular replacement. Here, an interesting degree of complementarity is shown between targets solved using the different ab initio modelling programs QUARK and ROSETTA. Search models derived from either program collectively solve almost all of the all-helical targets in the test set. Initial solutions produced by Phaser after only 5 min perform surprisingly well, improving the prospects for in situ structure solution by AMPLE during synchrotron visits. Taken together, the results show the potential for AMPLE to run more quickly and successfully solve more targets than previously suspected.

  8. The Energy Computation Paradox and ab initio Protein Folding

    PubMed Central

    Faver, John C.; Benson, Mark L.; He, Xiao; Roberts, Benjamin P.; Wang, Bing; Marshall, Michael S.; Sherrill, C. David; Merz, Kenneth M.

    2011-01-01

    The routine prediction of three-dimensional protein structure from sequence remains a challenge in computational biochemistry. It has been intuited that calculated energies from physics-based scoring functions are able to distinguish native from nonnative folds based on previous performance with small proteins and that conformational sampling is the fundamental bottleneck to successful folding. We demonstrate that as protein size increases, errors in the computed energies become a significant problem. We show, by using error probability density functions, that physics-based scores contain significant systematic and random errors relative to accurate reference energies. These errors propagate throughout an entire protein and distort its energy landscape to such an extent that modern scoring functions should have little chance of success in finding the free energy minima of large proteins. Nonetheless, by understanding errors in physics-based score functions, they can be reduced in a post-hoc manner, improving accuracy in energy computation and fold discrimination. PMID:21541343

  9. Specific interactions between DNA and regulatory protein controlled by ligand-binding: Ab initio molecular simulation

    NASA Astrophysics Data System (ADS)

    Matsushita, Y.; Murakawa, T.; Shimamura, K.; Oishi, M.; Ohyama, T.; Kurita, N.

    2015-02-01

    The catabolite activator protein (CAP) is one of the regulatory proteins controlling the transcription mechanism of gene. Biochemical experiments elucidated that the complex of CAP with cyclic AMP (cAMP) is indispensable for controlling the mechanism, while previous molecular simulations for the monomer of CAP+cAMP complex revealed the specific interactions between CAP and cAMP. However, the effect of cAMP-binding to CAP on the specific interactions between CAP and DNA is not elucidated at atomic and electronic levels. We here considered the ternary complex of CAP, cAMP and DNA in solvating water molecules and investigated the specific interactions between them at atomic and electronic levels using ab initio molecular simulations based on classical molecular dynamics and ab initio fragment molecular orbital methods. The results highlight the important amino acid residues of CAP for the interactions between CAP and cAMP and between CAP and DNA.

  10. Specific interactions between DNA and regulatory protein controlled by ligand-binding: Ab initio molecular simulation

    SciTech Connect

    Matsushita, Y. Murakawa, T. Shimamura, K. Oishi, M. Ohyama, T. Kurita, N.

    2015-02-27

    The catabolite activator protein (CAP) is one of the regulatory proteins controlling the transcription mechanism of gene. Biochemical experiments elucidated that the complex of CAP with cyclic AMP (cAMP) is indispensable for controlling the mechanism, while previous molecular simulations for the monomer of CAP+cAMP complex revealed the specific interactions between CAP and cAMP. However, the effect of cAMP-binding to CAP on the specific interactions between CAP and DNA is not elucidated at atomic and electronic levels. We here considered the ternary complex of CAP, cAMP and DNA in solvating water molecules and investigated the specific interactions between them at atomic and electronic levels using ab initio molecular simulations based on classical molecular dynamics and ab initio fragment molecular orbital methods. The results highlight the important amino acid residues of CAP for the interactions between CAP and cAMP and between CAP and DNA.

  11. Ab initio protein structure assembly using continuous structure fragments and optimized knowledge-based force field.

    PubMed

    Xu, Dong; Zhang, Yang

    2012-07-01

    Ab initio protein folding is one of the major unsolved problems in computational biology owing to the difficulties in force field design and conformational search. We developed a novel program, QUARK, for template-free protein structure prediction. Query sequences are first broken into fragments of 1-20 residues where multiple fragment structures are retrieved at each position from unrelated experimental structures. Full-length structure models are then assembled from fragments using replica-exchange Monte Carlo simulations, which are guided by a composite knowledge-based force field. A number of novel energy terms and Monte Carlo movements are introduced and the particular contributions to enhancing the efficiency of both force field and search engine are analyzed in detail. QUARK prediction procedure is depicted and tested on the structure modeling of 145 nonhomologous proteins. Although no global templates are used and all fragments from experimental structures with template modeling score >0.5 are excluded, QUARK can successfully construct 3D models of correct folds in one-third cases of short proteins up to 100 residues. In the ninth community-wide Critical Assessment of protein Structure Prediction experiment, QUARK server outperformed the second and third best servers by 18 and 47% based on the cumulative Z-score of global distance test-total scores in the FM category. Although ab initio protein folding remains a significant challenge, these data demonstrate new progress toward the solution of the most important problem in the field.

  12. Dual folding pathways of an α /β protein from all-atom ab initio folding simulations

    NASA Astrophysics Data System (ADS)

    Lei, Hongxing; Wang, Zhi-Xiang; Wu, Chun; Duan, Yong

    2009-10-01

    Successful ab initio folding of proteins with both α-helix and β-sheet requires a delicate balance among a variety of forces in the simulation model, which may explain that the successful folding of any α /β proteins to within experimental error has yet to be reported. Here we demonstrate that it is an achievable goal to fold α /β proteins with a force field emphasizing the balance between the two major secondary structures. Using our newly developed force field, we conducted extensive ab initio folding simulations on an α /β protein full sequence design (FSD) employing both conventional molecular dynamics and replica exchange molecular dynamics in combination with a generalized-Born solvation model. In these simulations, the folding of FSD to the native state with high population (>64.2%) and high fidelity (Cα-Root Mean Square Deviation of 1.29 Å for the most sampled conformation when compared to the experimental structure) was achieved. The folding of FSD was found to follow two pathways. In the major pathway, the folding started from the formation of the helix. In the minor pathway, however, folding of the β-hairpin started first. Further examination revealed that the helix initiated from the C-terminus and propagated toward the N-terminus. The formation of the hydrophobic contacts coincided with the global folding. Therefore the hydrophobic force does not appear to be the driving force of the folding of this protein.

  13. An amino acid code to define a protein's tertiary packing surface.

    PubMed

    Fraga, Keith J; Joo, Hyun; Tsai, Jerry

    2016-02-01

    One difficult aspect of the protein-folding problem is characterizing the nonspecific interactions that define packing in protein tertiary structure. To better understand tertiary structure, this work extends the knob-socket model by classifying the interactions of a single knob residue packed into a set of contiguous sockets, or a pocket made up of 4 or more residues. The knob-socket construct allows for a symbolic two-dimensional mapping of pockets. The two-dimensional mapping of pockets provides a simple method to investigate the variety of pocket shapes to understand the geometry of protein tertiary surfaces. The diversity of pocket geometries can be organized into groups of pockets that share a common core, which suggests that some interactions in pockets are ancillary to packing. Further analysis of pocket geometries displays a preferred configuration that is right-handed in α-helices and left-handed in β-sheets. The amino acid composition of pockets illustrates the importance of nonpolar amino acids in packing as well as position specificity. As expected, all pocket shapes prefer to pack with hydrophobic knobs; however, knobs are not selective for the pockets they pack. Investigating side-chain rotamer preferences for certain pocket shapes uncovers no strong correlations. These findings allow a simple vocabulary based on knobs and sockets to describe protein tertiary packing that supports improved analysis, design, and prediction of protein structure.

  14. CoMOGrad and PHOG: From Computer Vision to Fast and Accurate Protein Tertiary Structure Retrieval

    PubMed Central

    Karim, Rezaul; Aziz, Mohd. Momin Al; Shatabda, Swakkhar; Rahman, M. Sohel; Mia, Md. Abul Kashem; Zaman, Farhana; Rakin, Salman

    2015-01-01

    The number of entries in a structural database of proteins is increasing day by day. Methods for retrieving protein tertiary structures from such a large database have turn out to be the key to comparative analysis of structures that plays an important role to understand proteins and their functions. In this paper, we present fast and accurate methods for the retrieval of proteins having tertiary structures similar to a query protein from a large database. Our proposed methods borrow ideas from the field of computer vision. The speed and accuracy of our methods come from the two newly introduced features- the co-occurrence matrix of the oriented gradient and pyramid histogram of oriented gradient- and the use of Euclidean distance as the distance measure. Experimental results clearly indicate the superiority of our approach in both running time and accuracy. Our method is readily available for use from this website: http://research.buet.ac.bd:8080/Comograd/. PMID:26293226

  15. DEAD-Box Helicase Proteins Disrupt RNA Tertiary Structure Through Helix Capture

    PubMed Central

    Pan, Cynthia; Potratz, Jeffrey P.; Cannon, Brian; Simpson, Zachary B.; Ziehr, Jessica L.; Tijerina, Pilar; Russell, Rick

    2014-01-01

    DEAD-box helicase proteins accelerate folding and rearrangements of highly structured RNAs and RNA–protein complexes (RNPs) in many essential cellular processes. Although DEAD-box proteins have been shown to use ATP to unwind short RNA helices, it is not known how they disrupt RNA tertiary structure. Here, we use single molecule fluorescence to show that the DEAD-box protein CYT-19 disrupts tertiary structure in a group I intron using a helix capture mechanism. CYT-19 binds to a helix within the structured RNA only after the helix spontaneously loses its tertiary contacts, and then CYT-19 uses ATP to unwind the helix, liberating the product strands. Ded1, a multifunctional yeast DEAD-box protein, gives analogous results with small but reproducible differences that may reflect its in vivo roles. The requirement for spontaneous dynamics likely targets DEAD-box proteins toward less stable RNA structures, which are likely to experience greater dynamic fluctuations, and provides a satisfying explanation for previous correlations between RNA stability and CYT-19 unfolding efficiency. Biologically, the ability to sense RNA stability probably biases DEAD-box proteins to act preferentially on less stable misfolded structures and thereby to promote native folding while minimizing spurious interactions with stable, natively folded RNAs. In addition, this straightforward mechanism for RNA remodeling does not require any specific structural environment of the helicase core and is likely to be relevant for DEAD-box proteins that promote RNA rearrangements of RNP complexes including the spliceosome and ribosome. PMID:25350280

  16. Assembly of protein tertiary structures from secondary structures using optimized potentials.

    PubMed

    Hoang, Trinh Xuan; Seno, Flavio; Banavar, Jayanth R; Cieplak, Marek; Maritan, Amos

    2003-08-01

    We present a simulated annealing-based method for the prediction of the tertiary structures of proteins given knowledge of the secondary structure associated with each amino acid in the sequence. The backbone is represented in a detailed fashion whereas the sidechains and pairwise interactions are modeled in a simplified way, following the LINUS model of Srinivasan and Rose. A perceptron-based technique is used to optimize the interaction potentials for a training set of three proteins. For these proteins, the procedure is able to reproduce the tertiary structures to below 3 A in root mean square deviation (rmsd) from the PDB targets. We present the results of tests on twelve other proteins. For half of these, the lowest energy decoy has a rmsd from the native state below 6 A and, in 9 out of 12 cases, we obtain decoys whose rmsd from the native states are also well below 5 A.

  17. Hypochlorous acid-mediated protein oxidation: how important are chloramine transfer reactions and protein tertiary structure?

    PubMed

    Pattison, David I; Hawkins, Clare L; Davies, Michael J

    2007-08-28

    Hypochlorous acid (HOCl) is a powerful oxidant generated from H2O2 and Cl- by the heme enzyme myeloperoxidase, which is released from activated leukocytes. HOCl possesses potent antibacterial properties, but excessive production can lead to host tissue damage that occurs in numerous human pathologies. As proteins and amino acids are highly abundant in vivo and react rapidly with HOCl, they are likely to be major targets for HOCl. In this study, two small globular proteins, lysozyme and insulin, have been oxidized with increasing excesses of HOCl to determine whether the pattern of HOCl-mediated amino acid consumption is consistent with reported kinetic data for isolated amino acids and model compounds. Identical experiments have been carried out with mixtures of N-acetyl amino acids (to prevent reaction at the alpha-amino groups) that mimic the protein composition to examine the role of protein structure on reactivity. The results indicate that tertiary structure facilitates secondary chlorine transfer reactions of chloramines formed on His and Lys side chains. In light of these data, second-order rate constants for reactions of Lys side chain and Gly chloramines with Trp side chains and disulfide bonds have been determined, together with those for further oxidation of Met sulfoxide by HOCl and His side chain chloramines. Computational kinetic models incorporating these additional rate constants closely predict the experimentally observed amino acid consumption. These studies provide insight into the roles of chloramine formation and three-dimensional structure on the reactions of HOCl with isolated proteins and demonstrate that kinetic models can predict the outcome of HOCl-mediated protein oxidation.

  18. Automated protein structure modeling in CASP9 by I-TASSER pipeline combined with QUARK-based ab initio folding and FG-MD-based structure refinement.

    PubMed

    Xu, Dong; Zhang, Jian; Roy, Ambrish; Zhang, Yang

    2011-01-01

    I-TASSER is an automated pipeline for protein tertiary structure prediction using multiple threading alignments and iterative structure assembly simulations. In CASP9 experiments, two new algorithms, QUARK and fragment-guided molecular dynamics (FG-MD), were added to the I-TASSER pipeline for improving the structural modeling accuracy. QUARK is a de novo structure prediction algorithm used for structure modeling of proteins that lack detectable template structures. For distantly homologous targets, QUARK models are found useful as a reference structure for selecting good threading alignments and guiding the I-TASSER structure assembly simulations. FG-MD is an atomic-level structural refinement program that uses structural fragments collected from the PDB structures to guide molecular dynamics simulation and improve the local structure of predicted model, including hydrogen-bonding networks, torsion angles, and steric clashes. Despite considerable progress in both the template-based and template-free structure modeling, significant improvements on protein target classification, domain parsing, model selection, and ab initio folding of β-proteins are still needed to further improve the I-TASSER pipeline.

  19. On potential energy models for EA-based ab initio protein structure prediction.

    PubMed

    Mijajlovic, Milan; Biggs, Mark J; Djurdjevic, Dusan P

    2010-01-01

    Ab initio protein structure prediction involves determination of the three-dimensional (3D) conformation of proteins on the basis of their amino acid sequence, a potential energy (PE) model that captures the physics of the interatomic interactions, and a method to search for and identify the global minimum in the PE (or free energy) surface such as an evolutionary algorithm (EA). Many PE models have been proposed over the past three decades and more. There is currently no understanding of how the behavior of an EA is affected by the PE model used. The study reported here shows that the EA behavior can be profoundly affected: the EA performance obtained when using the ECEPP PE model is significantly worse than that obtained when using the Amber, OPLS, and CVFF PE models, and the optimal EA control parameter values for the ECEPP model also differ significantly from those associated with the other models.

  20. Ab Initio Calculations of the Electronic Structures and Biological Functions of Protein Molecules

    NASA Astrophysics Data System (ADS)

    Zheng, Haoping

    The self-consistent cluster-embedding (SCCE) calculation method reduces the computational effort from M3 to about M1 (M is the number of atoms in the system) with precise calculations. Thus the ab initio, all-electron calculation of the electronic structure and biological function of protein molecule has become a reality, which will promote new proteomics considerably. The calculated results of two real protein molecules, the trypsin inhibitor from the seeds of squash Cucurbita maxima (CMTI-I, 436 atoms) and the ascaris trypsin inhibitor (912 atoms, two three-dimensional structures), will be presented in this paper. The reactive sites of the inhibitors are determined and explained. The accuracy of structure determination of the inhibitors are tested theoretically.

  1. Ab Initio Calculations of the Electronic Structures and Biological Functions of Protein Molecules

    NASA Astrophysics Data System (ADS)

    Zheng, Haoping

    2003-04-01

    The self-consistent cluster-embedding (SCCE) calculation method reduces the computational effort from M3 to about M1 (M is the number of atoms in the system) with unchanged calculation precision. So the ab initio, all-electron calculation of the electronic structure and biological function of protein molecule becomes a reality, which will promote new proteomics considerably. The calculated results of two real protein molecules, the trypsin inhibitor from the seeds of squash Cucurbita maxima (CMTI-I, 436 atoms) and the Ascaris trypsin inhibitor (912 atoms, two three-dimensional structures), are presented. The reactive sites of the inhibitors are determined and explained. The precision of structure determination of inhibitors are tested theoretically.

  2. Integration of QUARK and I-TASSER for Ab Initio Protein Structure Prediction in CASP11.

    PubMed

    Zhang, Wenxuan; Yang, Jianyi; He, Baoji; Walker, Sara Elizabeth; Zhang, Hongjiu; Govindarajoo, Brandon; Virtanen, Jouko; Xue, Zhidong; Shen, Hong-Bin; Zhang, Yang

    2016-09-01

    We tested two pipelines developed for template-free protein structure prediction in the CASP11 experiment. First, the QUARK pipeline constructs structure models by reassembling fragments of continuously distributed lengths excised from unrelated proteins. Five free-modeling (FM) targets have the model successfully constructed by QUARK with a TM-score above 0.4, including the first model of T0837-D1, which has a TM-score = 0.736 and RMSD = 2.9 Å to the native. Detailed analysis showed that the success is partly attributed to the high-resolution contact map prediction derived from fragment-based distance-profiles, which are mainly located between regular secondary structure elements and loops/turns and help guide the orientation of secondary structure assembly. In the Zhang-Server pipeline, weakly scoring threading templates are re-ordered by the structural similarity to the ab initio folding models, which are then reassembled by I-TASSER based structure assembly simulations; 60% more domains with length up to 204 residues, compared to the QUARK pipeline, were successfully modeled by the I-TASSER pipeline with a TM-score above 0.4. The robustness of the I-TASSER pipeline can stem from the composite fragment-assembly simulations that combine structures from both ab initio folding and threading template refinements. Despite the promising cases, challenges still exist in long-range beta-strand folding, domain parsing, and the uncertainty of secondary structure prediction; the latter of which was found to affect nearly all aspects of FM structure predictions, from fragment identification, target classification, structure assembly, to final model selection. Significant efforts are needed to solve these problems before real progress on FM could be made. Proteins 2016; 84(Suppl 1):76-86. © 2015 Wiley Periodicals, Inc.

  3. Revealing Missing Human Protein Isoforms Based on Ab Initio Prediction, RNA-seq and Proteomics

    PubMed Central

    Hu, Zhiqiang; Scott, Hamish S.; Qin, Guangrong; Zheng, Guangyong; Chu, Xixia; Xie, Lu; Adelson, David L.; Oftedal, Bergithe E.; Venugopal, Parvathy; Babic, Milena; Hahn, Christopher N.; Zhang, Bing; Wang, Xiaojing; Li, Nan; Wei, Chaochun

    2015-01-01

    Biological and biomedical research relies on comprehensive understanding of protein-coding transcripts. However, the total number of human proteins is still unknown due to the prevalence of alternative splicing. In this paper, we detected 31,566 novel transcripts with coding potential by filtering our ab initio predictions with 50 RNA-seq datasets from diverse tissues/cell lines. PCR followed by MiSeq sequencing showed that at least 84.1% of these predicted novel splice sites could be validated. In contrast to known transcripts, the expression of these novel transcripts were highly tissue-specific. Based on these novel transcripts, at least 36 novel proteins were detected from shotgun proteomics data of 41 breast samples. We also showed L1 retrotransposons have a more significant impact on the origin of new transcripts/genes than previously thought. Furthermore, we found that alternative splicing is extraordinarily widespread for genes involved in specific biological functions like protein binding, nucleoside binding, neuron projection, membrane organization and cell adhesion. In the end, the total number of human transcripts with protein-coding potential was estimated to be at least 204,950. PMID:26156868

  4. Ab initio protein folding simulations using atomic burials as informational intermediates between sequence and structure.

    PubMed

    van der Linden, Marx Gomes; Ferreira, Diogo César; de Oliveira, Leandro Cristante; Onuchic, José N; de Araújo, Antônio F Pereira

    2014-07-01

    The three-dimensional structure of proteins is determined by their linear amino acid sequences but decipherment of the underlying protein folding code has remained elusive. Recent studies have suggested that burials, as expressed by atomic distances to the molecular center, are sufficiently informative for structural determination while potentially obtainable from sequences. Here we provide direct evidence for this distinctive role of burials in the folding code, demonstrating that burial propensities estimated from local sequence can indeed be used to fold globular proteins in ab initio simulations. We have used a statistical scheme based on a Hidden Markov Model (HMM) to classify all heavy atoms of a protein into a small number of burial atomic types depending on sequence context. Molecular dynamics simulations were then performed with a potential that forces all atoms of each type towards their predicted burial level, while simple geometric constraints were imposed on covalent structure and hydrogen bond formation. The correct folded conformation was obtained and distinguished in simulations that started from extended chains for a selection of structures comprising all three folding classes and high burial prediction quality. These results demonstrate that atomic burials can act as informational intermediates between sequence and structure, providing a new conceptual framework for improving structural prediction and understanding the fundamentals of protein folding.

  5. Interplay of I-TASSER and QUARK for template-based and ab initio protein structure prediction in CASP10.

    PubMed

    Zhang, Yang

    2014-02-01

    We develop and test a new pipeline in CASP10 to predict protein structures based on an interplay of I-TASSER and QUARK for both free-modeling (FM) and template-based modeling (TBM) targets. The most noteworthy observation is that sorting through the threading template pool using the QUARK-based ab initio models as probes allows the detection of distant-homology templates which might be ignored by the traditional sequence profile-based threading alignment algorithms. Further template assembly refinement by I-TASSER resulted in successful folding of two medium-sized FM targets with >150 residues. For TBM, the multiple threading alignments from LOMETS are, for the first time, incorporated into the ab initio QUARK simulations, which were further refined by I-TASSER assembly refinement. Compared with the traditional threading assembly refinement procedures, the inclusion of the threading-constrained ab initio folding models can consistently improve the quality of the full-length models as assessed by the GDT-HA and hydrogen-bonding scores. Despite the success, significant challenges still exist in domain boundary prediction and consistent folding of medium-size proteins (especially beta-proteins) for nonhomologous targets. Further developments of sensitive fold-recognition and ab initio folding methods are critical for solving these problems.

  6. Environment-specific amino acid substitution tables: tertiary templates and prediction of protein folds.

    PubMed Central

    Overington, J.; Donnelly, D.; Johnson, M. S.; Sali, A.; Blundell, T. L.

    1992-01-01

    The local environment of an amino acid in a folded protein determines the acceptability of mutations at that position. In order to characterize and quantify these structural constraints, we have made a comparative analysis of families of homologous proteins. Residues in each structure are classified according to amino acid type, secondary structure, accessibility of the side chain, and existence of hydrogen bonds from the side chains. Analysis of the pattern of observed substitutions as a function of local environment shows that there are distinct patterns, especially for buried polar residues. The substitution data tables are available on diskette with Protein Science. Given the fold of a protein, one is able to predict sequences compatible with the fold (profiles or templates) and potentially to discriminate between a correctly folded and misfolded protein. Conversely, analysis of residue variation across a family of aligned sequences in terms of substitution profiles can allow prediction of secondary structure or tertiary environment. PMID:1304904

  7. An All-Atom Force Field for Tertiary Structure Prediction of Helical Proteins

    PubMed Central

    Herges, T.; Wenzel, W.

    2004-01-01

    We have developed an all-atom free-energy force field (PFF01) for protein tertiary structure prediction. PFF01 is based on physical interactions and was parameterized using experimental structures of a family of proteins believed to span a wide variety of possible folds. It contains empirical, although sequence-independent terms for hydrogen bonding. Its solvent-accessible surface area solvent model was first fit to transfer energies of small peptides. The parameters of the solvent model were then further optimized to stabilize the native structure of a single protein, the autonomously folding villin headpiece, against competing low-energy decoys. Here we validate the force field for five nonhomologous helical proteins with 20–60 amino acids. For each protein, decoys with 2–3 Å backbone root mean-square deviation and correct experimental Cβ–Cβ distance constraints emerge as those with the lowest energy. PMID:15507688

  8. Protein Tertiary Structure Prediction Based on Main Chain Angle Using a Hybrid Bees Colony Optimization Algorithm

    NASA Astrophysics Data System (ADS)

    Mahmood, Zakaria N.; Mahmuddin, Massudi; Mahmood, Mohammed Nooraldeen

    Encoding proteins of amino acid sequence to predict classified into their respective families and subfamilies is important research area. However for a given protein, knowing the exact action whether hormonal, enzymatic, transmembranal or nuclear receptors does not depend solely on amino acid sequence but on the way the amino acid thread folds as well. This study provides a prototype system that able to predict a protein tertiary structure. Several methods are used to develop and evaluate the system to produce better accuracy in protein 3D structure prediction. The Bees Optimization algorithm which inspired from the honey bees food foraging method, is used in the searching phase. In this study, the experiment is conducted on short sequence proteins that have been used by the previous researches using well-known tools. The proposed approach shows a promising result.

  9. Can DNA-binding proteins of replisome tautomerize nucleotide bases? Ab initio model study.

    PubMed

    Brovarets', Ol'ha O; Yurenko, Yevgen P; Dubey, Igor Ya; Hovorun, Dmytro M

    2012-01-01

    Ab initio quantum-chemical study of specific point contacts of replisome proteins with DNA modeled by acetic acid with canonical and mutagenic tautomers of DNA bases methylated at the glycosidic nitrogen atoms was performed in vacuo and continuum with a low dielectric constant (ϵ ∼ 4) corresponding to a hydrophobic interface of protein-nucleic acid interaction. All tautomerized complexes were found to be dynamically unstable, because the electronic energies of their back-reaction barriers do not exceed zero-point vibrational energies associated with the vibrational modes whose harmonic vibrational frequencies become imaginary in the transition states of the tautomerization reaction. Additionally, based on the physicochemical arguments, it was demonstrated that the effects of biomolecular environment cannot ensure dynamic stabilization. This result allows suggesting that hypothetically generated by DNA-binding proteins of replisome rare tautomers will have no impact on the total spontaneous mutation due to the low reverse barrier allowing a quick return to the canonical form.

  10. Paired natural cysteine mutation mapping: aid to constraining models of protein tertiary structure.

    PubMed Central

    Kreisberg, R.; Buchner, V.; Arad, D.

    1995-01-01

    This paper discusses the benefit of mapping paired cysteine mutation patterns as a guide to identifying the positions of protein disulfide bonds. This information can facilitate the computer modeling of protein tertiary structure. First, a simple, paired natural-cysteine-mutation map is presented that identifies the positions of putative disulfide bonds in protein families. The method is based on the observation that if, during the process of evolution, a disulfide-bonded cysteine residue is not conserved, then it is likely that its counterpart will also be mutated. For each target protein, protein databases were searched for the primary amino acid sequences of all known members of distinct protein families. Primary sequence alignment was carried out using PileUp algorithms in the GCG package. To search for correlated mutations, we listed only the positions where cysteine residues were highly conserved and emphasized the mutated residues. In proteins of known three-dimensional structure, a striking pattern of paired cysteine mutations correlated with the positions of known disulfide bridges. For proteins of unknown architecture, the mutation maps showed several positions where disulfide bridging might occur. PMID:8563638

  11. Ab initio/GIAO-CCSD(T) (13)C NMR study of the rearrangement and dynamic aspects of rapidly equilibrating tertiary carbocations, C6H13(+) and C7H15(+).

    PubMed

    Olah, George A; Prakash, G K Surya; Rasul, Golam

    2016-01-05

    The rearrangement pathways of the equilibrating tertiary carbocations, 2,3-dimethyl-2-butyl cation (C6H13(+), 1), 2,3,3-trimethyl-2-butyl cation (C7H15(+), 5) and 2,3-dimethyl-2-pentyl cation (C7H15(+), 8 and 9) were investigated using the ab initio/GIAO-CCSD(T) (13)C NMR method. Comparing the calculated and experimental (13)C NMR chemical shifts of a series of carbocations indicates that excellent prediction of δ(13)C could be achieved through scaling. In the case of symmetrical equilibrating cations (1 and 5) the Wagner-Meerwein 1,2-hydride and 1,2-methide shifts, respectively, produce the same structure. This indicates that the overall (13)C NMR chemical shifts are conserved and independent of temperature. However, in the case of unsymmetrical equilibrating cations (8 and 9) the Wagner-Meerwein shift produces different tertiary structures, which have slightly different thermodynamic stabilities and, thus, different spectra. At the MP4(SDTQ)/cc-pVTZ//MP2/cc-pVTZ + ZPE level structure 8 is only 90 calories/mol more stable than structure 9. Based on computed (13)C NMR chemical shift calculations, mole fractions of these isomers were determined by assuming the observed chemical shifts are due to the weighted average of the chemical shifts of the static ions.

  12. Ab initio Study of Transition metal binding to the Prion Protein

    NASA Astrophysics Data System (ADS)

    Cox, Daniel L.; Singh, Rajiv R. P.; Pan, Jianping

    2004-03-01

    Fundamental understanding of the prion protein (PrP) is of critical public health importance in view of mad cow and chronic wasting diseases. In recent years, it has been shown that the normal form (PrP^c) binds copper^1), and the structure of the copper binding domain has been elaborated. Hypotheses about toxicity associated with binding of other metals (notably manganese) have been put forward, Accordingly, using the ab initio SIESTA density functional theory code^2), we calculated the binding energy E_B(M) of M-(PrP) complexes relative to initially uncomplexed M ions, with M=Cu,Ni,Zn,Mn and (PrP)^* the minimal binding domain. The binding energy trend is E_B(Ni)>E_B(Cu)>E_B(Zn)>E_B(Mn), consistent with recent experiments apart from the surprising stability of Ni. We will also present preliminary results for binding of initially complexed M ions. *-Supported by U.S. DOE, Office of Basic Energy Sciences, Division of Materials Research 1) G.S. Jackson et al., Proc. Nat. Acad. Sci. (USA) 98, 8531 (2001). 2) P. Ordejón, et al., Phys. Rev. B53, R10441 (1996); J.M. Soler et al., J. Phys. Cond. Matt. 14, 2745 (2002).

  13. Phylogenetic Gaussian process model for the inference of functionally important regions in protein tertiary structures.

    PubMed

    Huang, Yi-Fei; Golding, G Brian

    2014-01-01

    A critical question in biology is the identification of functionally important amino acid sites in proteins. Because functionally important sites are under stronger purifying selection, site-specific substitution rates tend to be lower than usual at these sites. A large number of phylogenetic models have been developed to estimate site-specific substitution rates in proteins and the extraordinarily low substitution rates have been used as evidence of function. Most of the existing tools, e.g. Rate4Site, assume that site-specific substitution rates are independent across sites. However, site-specific substitution rates may be strongly correlated in the protein tertiary structure, since functionally important sites tend to be clustered together to form functional patches. We have developed a new model, GP4Rate, which incorporates the Gaussian process model with the standard phylogenetic model to identify slowly evolved regions in protein tertiary structures. GP4Rate uses the Gaussian process to define a nonparametric prior distribution of site-specific substitution rates, which naturally captures the spatial correlation of substitution rates. Simulations suggest that GP4Rate can potentially estimate site-specific substitution rates with a much higher accuracy than Rate4Site and tends to report slowly evolved regions rather than individual sites. In addition, GP4Rate can estimate the strength of the spatial correlation of substitution rates from the data. By applying GP4Rate to a set of mammalian B7-1 genes, we found a highly conserved region which coincides with experimental evidence. GP4Rate may be a useful tool for the in silico prediction of functionally important regions in the proteins with known structures.

  14. ProteMiner-SSM: a web server for efficient analysis of similar protein tertiary substructures

    PubMed Central

    Chang, Darby Tien-Hau; Chen, Chien-Yu; Chung, Wen-Chin; Oyang, Yen-Jen; Juan, Hsueh-Fen; Huang, Hsuan-Cheng

    2004-01-01

    Analysis of protein–ligand interactions is a fundamental issue in drug design. As the detailed and accurate analysis of protein–ligand interactions involves calculation of binding free energy based on thermodynamics and even quantum mechanics, which is highly expensive in terms of computing time, conformational and structural analysis of proteins and ligands has been widely employed as a screening process in computer-aided drug design. In this paper, a web server called ProteMiner-SSM designed for efficient analysis of similar protein tertiary substructures is presented. In one experiment reported in this paper, the web server has been exploited to obtain some clues about a biochemical hypothesis. The main distinction in the software design of the web server is the filtering process incorporated to expedite the analysis. The filtering process extracts the residues located in the caves of the protein tertiary structure for analysis and operates with O(nlogn) time complexity, where n is the number of residues in the protein. In comparison, the α-hull algorithm, which is a widely used algorithm in computer graphics for identifying those instances that are on the contour of a three-dimensional object, features O(n2) time complexity. Experimental results show that the filtering process presented in this paper is able to speed up the analysis by a factor ranging from 3.15 to 9.37 times. The ProteMiner-SSM web server can be found at http://proteminer.csie.ntu.edu.tw/. There is a mirror site at http://p4.sbl.bc.sinica.edu.tw/proteminer/. PMID:15215355

  15. Ab initio study of the role of lysine 16 for the molecular switching mechanism of Ras protein p21.

    PubMed Central

    Futatsugi, N; Hata, M; Hoshino, T; Tsuda, M

    1999-01-01

    Quantum chemical computations using the ab initio molecular orbital (MO) method have been performed to investigate the molecular switching mechanism of Ras protein p21, which has an important role in intracellular signal cascades. Lys(16) was demonstrated to be crucial to the function of Ras p21, and the hydrolysis of GTP to GDP was found to be an one-step reaction. The potential energy barrier of this hydrolysis reaction from GTP to (GDP + P) was calculated to be approximately 42 kcal/mol. The role of GAP (GTPase-activating protein) was also discussed in terms of the delivery of the water molecules required for the hydrolysis. PMID:10585950

  16. Conformational analysis of processivity clamps in solution demonstrates that tertiary structure does not correlate with protein dynamics.

    PubMed

    Fang, Jing; Nevin, Philip; Kairys, Visvaldas; Venclovas, Ceslovas; Engen, John R; Beuning, Penny J

    2014-04-08

    The relationship between protein sequence, structure, and dynamics has been elusive. Here, we report a comprehensive analysis using an in-solution experimental approach to study how the conservation of tertiary structure correlates with protein dynamics. Hydrogen exchange measurements of eight processivity clamp proteins from different species revealed that, despite highly similar three-dimensional structures, clamp proteins display a wide range of dynamic behavior. Differences were apparent both for structurally similar domains within proteins and for corresponding domains of different proteins. Several of the clamps contained regions that underwent local unfolding with different half-lives. We also observed a conserved pattern of alternating dynamics of the α helices lining the inner pore of the clamps as well as a correlation between dynamics and the number of salt bridges in these α helices. Our observations reveal that tertiary structure and dynamics are not directly correlated and that primary structure plays an important role in dynamics.

  17. Conformational analysis of processivity clamps in solution demonstrates that tertiary structure does not correlate with protein dynamics

    PubMed Central

    Kairys, Visvaldas; Venclovas, Česlovas; Engen, John R.; Beuning, Penny J.

    2014-01-01

    Summary The relationship between protein sequence, structure, and dynamics has been elusive. We report one of the first comprehensive analyses using an in-solution experimental approach to study how the conservation of tertiary structure correlates with protein dynamics. Hydrogen exchange measurements of eight processivity clamp proteins from different species revealed that, despite highly similar three-dimensional structures, clamp proteins display a wide range of dynamic behavior. Differences were apparent both for structurally similar domains within proteins and for corresponding domains of different proteins. Several of the clamps contained regions that underwent local unfolding with different half-lives. We also observed a conserved pattern of alternating dynamics of the α-helices lining the inner pore of the clamps as well as a correlation between dynamics and the number of salt bridges in these α-helices. Our observations reveal that tertiary structure and dynamics are not directly correlated and that primary structure plays an important role in dynamics. PMID:24613485

  18. An improved hybrid global optimization method for protein tertiary structure prediction

    PubMed Central

    McAllister, Scott R.

    2009-01-01

    First principles approaches to the protein structure prediction problem must search through an enormous conformational space to identify low-energy, near-native structures. In this paper, we describe the formulation of the tertiary structure prediction problem as a nonlinear constrained minimization problem, where the goal is to minimize the energy of a protein conformation subject to constraints on torsion angles and interatomic distances. The core of the proposed algorithm is a hybrid global optimization method that combines the benefits of the αBB deterministic global optimization approach with conformational space annealing. These global optimization techniques employ a local minimization strategy that combines torsion angle dynamics and rotamer optimization to identify and improve the selection of initial conformations and then applies a sequential quadratic programming approach to further minimize the energy of the protein conformations subject to constraints. The proposed algorithm demonstrates the ability to identify both lower energy protein structures, as well as larger ensembles of low-energy conformations. PMID:20357906

  19. Vibrational study of new Pt(II) and Pd(II) complexes with functionalized nitrogen-containing tertiary phosphine oxides. Ab initio study of ortho-, meta- and para-dimethylphosphinylmethyleneoxyaniline.

    PubMed

    Trendafilova, N; Bauer, G; Georgieva, I; Tosheva, T; Varbanov, S

    2003-01-01

    Vibrational study of new Pt(II) and Pd(II) complexes of functionalized nitrogen-containing tertiary phosphine oxides, namely ortho-, meta- and para-dimethylphosphinylmethyleneoxyaniline (o-, m- and p-dpmoa), (CH3)2P(O)CH2OC6H4NH2, have been presented. Geometry optimization of the ligands was performed at HF/6-31G* and B3LYP/6-31G* levels of the theory. Harmonic frequencies were calculated at HF/6-31G* optimized geometries. Relative gas-phase and solution-phase (H2O and CH3CN) basicities of o-, m- and p-dpmoa ligands have been determined by ab initio calculations at STO-3G level with the Onsager reaction field model. On the basis of the vibrational study, physical and analytical data it was suggested that the ligands in the complexes studied coordinate through the amino group and form square-planar platinum and palladium complexes of the general formula ML2Cl2 (M = Pt, Pd, L = o-, m- and p-dpmoa).

  20. Vibrational study of new Pt(II) and Pd(II) complexes with functionalized nitrogen-containing tertiary phosphine oxides. Ab initio study of ortho-, meta- and para-dimethylphosphinylmethyleneoxyaniline

    NASA Astrophysics Data System (ADS)

    Trendafilova, N.; Bauer, G.; Georgieva, I.; Tosheva, T.; Varbanov, S.

    2003-01-01

    Vibrational study of new Pt(II) and Pd(II) complexes of functionalized nitrogen-containing tertiary phosphine oxides, namely ortho-, meta- and para-dimethylphosphinylmethyleneoxyaniline ( o-, m- and p-dpmoa), (CH 3) 2P(O)CH 2OC 6H 4NH 2, have been presented. Geometry optimization of the ligands was performed at HF/6-31G* and B3LYP/6-31G* levels of the theory. Harmonic frequencies were calculated at HF/6-31G* optimized geometries. Relative gas-phase and solution-phase (H 2O and CH 3CN) basicities of o-, m- and p-dpmoa ligands have been determined by ab initio calculations at STO-3G level with the Onsager reaction field model. On the basis of the vibrational study, physical and analytical data it was suggested that the ligands in the complexes studied coordinate through the amino group and form square-planar platinum and palladium complexes of the general formula ML 2Cl 2 (M=Pt, Pd, L= o-, m- and p-dpmoa).

  1. MEGADOCK: An All-to-All Protein-Protein Interaction Prediction System Using Tertiary Structure Data

    PubMed Central

    Ohue, Masahito; Matsuzaki, Yuri; Uchikoga, Nobuyuki; Ishida, Takashi; Akiyama, Yutaka

    2014-01-01

    The elucidation of protein-protein interaction (PPI) networks is important for understanding cellular structure and function and structure-based drug design. However, the development of an effective method to conduct exhaustive PPI screening represents a computational challenge. We have been investigating a protein docking approach based on shape complementarity and physicochemical properties. We describe here the development of the protein-protein docking software package “MEGADOCK” that samples an extremely large number of protein dockings at high speed. MEGADOCK reduces the calculation time required for docking by using several techniques such as a novel scoring function called the real Pairwise Shape Complementarity (rPSC) score. We showed that MEGADOCK is capable of exhaustive PPI screening by completing docking calculations 7.5 times faster than the conventional docking software, ZDOCK, while maintaining an acceptable level of accuracy. When MEGADOCK was applied to a subset of a general benchmark dataset to predict 120 relevant interacting pairs from 120 x 120 = 14,400 combinations of proteins, an F-measure value of 0.231 was obtained. Further, we showed that MEGADOCK can be applied to a large-scale protein-protein interaction-screening problem with accuracy better than random. When our approach is combined with parallel high-performance computing systems, it is now feasible to search and analyze protein-protein interactions while taking into account three-dimensional structures at the interactome scale. MEGADOCK is freely available at http://www.bi.cs.titech.ac.jp/megadock. PMID:23855673

  2. Reduction in lipophilicity improved the solubility, plasma–protein binding, and permeability of tertiary sulfonamide RORc inverse agonists

    SciTech Connect

    Fauber, Benjamin P.; René, Olivier; de Leon Boenig, Gladys; Burton, Brenda; Deng, Yuzhong; Eidenschenk, Céline; Everett, Christine; Gobbi, Alberto; Hymowitz, Sarah G.; Johnson, Adam R.; La, Hank; Liimatta, Marya; Lockey, Peter; Norman, Maxine; Ouyang, Wenjun; Wang, Weiru; Wong, Harvey

    2014-08-01

    Using structure-based drug design principles, we identified opportunities to reduce the lipophilicity of our tertiary sulfonamide RORc inverse agonists. The new analogs possessed improved RORc cellular potencies with >77-fold selectivity for RORc over other nuclear receptors in our cell assay suite. The reduction in lipophilicity also led to an increased plasma–protein unbound fraction and improvements in cellular permeability and aqueous solubility.

  3. Development of a Polarizable Force Field for Proteins Via Ab Initio Quantum Chemistry: First Generation Model and Gas Phase Tests

    SciTech Connect

    Kaminski, George A.; Stern, Harry A.; Berne, Bruce J.; Friesner, Richard A.; Cao, Yixiang; Murphy, Robert B.; Zhou, Ruhong; Halgren, Thomas A.

    2002-12-01

    We present results of developing a methodology suitable for producing molecular mechanics force fields with explicit treatment of electrostatic polarization for proteins and other molecular system of biological interest. The technique allows simulation of realistic-size systems. Employing high-level ab initio data as a target for fitting allows us to avoid the problem of the lack of detailed experimental data. Using the fast and reliable quantum mechanical methods supplies robust fitting data for the resulting parameter sets. As a result, gas-phase many-body effects for dipeptides are captured within the average RMSD of 0.22 kcal/mol from their ab initio values, and conformational energies for the di- and tetrapeptides are reproduced within the average RMSD of 0.43 kcal/mol from their quantum mechanical counterparts. The latter is achieved in part because of application of a novel torsional fitting technique recently developed in our group, which has already been used to greatly improve accuracy of the peptide conformational equilibrium prediction with the OPLS-AA force field.1 Finally, we have employed the newly developed first-generation model in computing gas-phase conformations of real proteins, as well as in molecular dynamics studies of the systems. The results show that, although the overall accuracy is no better than what can be achieved with a fixed-charges model, the methodology produces robust results, permits reasonably low computational cost, and avoids other computational problems typical for polarizable force fields. It can be considered as a solid basis for building a more accurate and complete second-generation model.

  4. Development of a Polarizable Force Field For Proteins via Ab Initio Quantum Chemistry: First Generation Model and Gas Phase Tests

    PubMed Central

    KAMINSKI, GEORGE A.; STERN, HARRY A.; BERNE, B. J.; FRIESNER, RICHARD A.; CAO, YIXIANG X.; MURPHY, ROBERT B.; ZHOU, RUHONG; HALGREN, THOMAS A.

    2014-01-01

    We present results of developing a methodology suitable for producing molecular mechanics force fields with explicit treatment of electrostatic polarization for proteins and other molecular system of biological interest. The technique allows simulation of realistic-size systems. Employing high-level ab initio data as a target for fitting allows us to avoid the problem of the lack of detailed experimental data. Using the fast and reliable quantum mechanical methods supplies robust fitting data for the resulting parameter sets. As a result, gas-phase many-body effects for dipeptides are captured within the average RMSD of 0.22 kcal/mol from their ab initio values, and conformational energies for the di- and tetrapeptides are reproduced within the average RMSD of 0.43 kcal/mol from their quantum mechanical counterparts. The latter is achieved in part because of application of a novel torsional fitting technique recently developed in our group, which has already been used to greatly improve accuracy of the peptide conformational equilibrium prediction with the OPLS-AA force field.1 Finally, we have employed the newly developed first-generation model in computing gas-phase conformations of real proteins, as well as in molecular dynamics studies of the systems. The results show that, although the overall accuracy is no better than what can be achieved with a fixed-charges model, the methodology produces robust results, permits reasonably low computational cost, and avoids other computational problems typical for polarizable force fields. It can be considered as a solid basis for building a more accurate and complete second-generation model. PMID:12395421

  5. Ab initio protein phasing at 1.4 A resolution: the new phasing approach of SIR2003-N.

    PubMed

    Burla, Maria C; Carrozzini, Benedetta; Caliandro, Rocco; Cascarano, Giovanni L; De Caro, Liberato; Giacovazzo, Carmelo; Polidori, Giampiero

    2003-11-01

    New algorithms for solving ab initio protein crystal structures have been identified and implemented in a modified version of the program SIR2002. They succeed in solving numerous protein structures diffracting at atomic resolution; the solution was also attained when data were cut at 1.4 A resolution. The direct-space refinement procedure of SIR2003-N takes advantage of using the envelope of the protein, calculated during the phasing process from the current phases. The electron-density map is modified by assuming different weights for pixels within the envelope or out of it, so tentatively depleting the intensities of the false peaks. The map is then inverted and the resulting phase sets may improve their values. The new phasing strategy is also based on an optimal use of some figures of merit, one of which may be successfully applied in the early stages of the phasing process: only the most promising trials are submitted to the complete phasing procedure, so saving computing time. SIR2003-N has been successfully applied also in solving some protein structures diffracting at 1.4-1.5 A resolution.

  6. Planes formed with four intron-positions in tertiary structures of retinol binding protein and calpain domain VI.

    PubMed

    Nosaka, Michiko; Hirata, Katsuki; Tsuji, Ryotarou; Sunaba, Syunya

    2014-01-07

    Eukaryotic genes have intervening sequences, introns, in their coding regions. Since introns are spliced out from m-RNA before translation, they are considered to have no effect on the protein structure. Here, we report a novel relationship between introns and the tertiary structures of retinol binding protein and calpain domain VI. We identified "intron-positions" as amino acid residues on which or just after which introns are found in their corresponding nucleotide sequences, and then found that four intron-positions form a plane. We also found that the four intron-positions of retinol-binding protein encloses its ligand retinol. The tertiary structure of calpain domain VI changes after Ca(2+) binding, and the four intron-positions form a plane that includes its ligand calpastatin. To evaluate the statistical significance of the planarity, we calculated the mean distance of each intron-position from the plane defined by the other three intron-positions, and showed that it is significantly smaller than the one calculated for randomly generated locations based on exon size distribution. On the basis of this finding, we discuss the evolution of retinol binding protein and the origin of introns.

  7. Accurate ab initio prediction of NMR chemical shifts of nucleic acids and nucleic acids/protein complexes

    PubMed Central

    Victora, Andrea; Möller, Heiko M.; Exner, Thomas E.

    2014-01-01

    NMR chemical shift predictions based on empirical methods are nowadays indispensable tools during resonance assignment and 3D structure calculation of proteins. However, owing to the very limited statistical data basis, such methods are still in their infancy in the field of nucleic acids, especially when non-canonical structures and nucleic acid complexes are considered. Here, we present an ab initio approach for predicting proton chemical shifts of arbitrary nucleic acid structures based on state-of-the-art fragment-based quantum chemical calculations. We tested our prediction method on a diverse set of nucleic acid structures including double-stranded DNA, hairpins, DNA/protein complexes and chemically-modified DNA. Overall, our quantum chemical calculations yield highly/very accurate predictions with mean absolute deviations of 0.3–0.6 ppm and correlation coefficients (r2) usually above 0.9. This will allow for identifying misassignments and validating 3D structures. Furthermore, our calculations reveal that chemical shifts of protons involved in hydrogen bonding are predicted significantly less accurately. This is in part caused by insufficient inclusion of solvation effects. However, it also points toward shortcomings of current force fields used for structure determination of nucleic acids. Our quantum chemical calculations could therefore provide input for force field optimization. PMID:25404135

  8. Residue contacts predicted by evolutionary covariance extend the application of ab initio molecular replacement to larger and more challenging protein folds.

    PubMed

    Simkovic, Felix; Thomas, Jens M H; Keegan, Ronan M; Winn, Martyn D; Mayans, Olga; Rigden, Daniel J

    2016-07-01

    For many protein families, the deluge of new sequence information together with new statistical protocols now allow the accurate prediction of contacting residues from sequence information alone. This offers the possibility of more accurate ab initio (non-homology-based) structure prediction. Such models can be used in structure solution by molecular replacement (MR) where the target fold is novel or is only distantly related to known structures. Here, AMPLE, an MR pipeline that assembles search-model ensembles from ab initio structure predictions ('decoys'), is employed to assess the value of contact-assisted ab initio models to the crystallographer. It is demonstrated that evolutionary covariance-derived residue-residue contact predictions improve the quality of ab initio models and, consequently, the success rate of MR using search models derived from them. For targets containing β-structure, decoy quality and MR performance were further improved by the use of a β-strand contact-filtering protocol. Such contact-guided decoys achieved 14 structure solutions from 21 attempted protein targets, compared with nine for simple Rosetta decoys. Previously encountered limitations were superseded in two key respects. Firstly, much larger targets of up to 221 residues in length were solved, which is far larger than the previously benchmarked threshold of 120 residues. Secondly, contact-guided decoys significantly improved success with β-sheet-rich proteins. Overall, the improved performance of contact-guided decoys suggests that MR is now applicable to a significantly wider range of protein targets than were previously tractable, and points to a direct benefit to structural biology from the recent remarkable advances in sequencing.

  9. Residue contacts predicted by evolutionary covariance extend the application of ab initio molecular replacement to larger and more challenging protein folds

    PubMed Central

    Simkovic, Felix; Thomas, Jens M. H.; Keegan, Ronan M.; Winn, Martyn D.; Mayans, Olga; Rigden, Daniel J.

    2016-01-01

    For many protein families, the deluge of new sequence information together with new statistical protocols now allow the accurate prediction of contacting residues from sequence information alone. This offers the possibility of more accurate ab initio (non-homology-based) structure prediction. Such models can be used in structure solution by molecular replacement (MR) where the target fold is novel or is only distantly related to known structures. Here, AMPLE, an MR pipeline that assembles search-model ensembles from ab initio structure predictions (‘decoys’), is employed to assess the value of contact-assisted ab initio models to the crystallographer. It is demonstrated that evolutionary covariance-derived residue–residue contact predictions improve the quality of ab initio models and, consequently, the success rate of MR using search models derived from them. For targets containing β-structure, decoy quality and MR performance were further improved by the use of a β-strand contact-filtering protocol. Such contact-guided decoys achieved 14 structure solutions from 21 attempted protein targets, compared with nine for simple Rosetta decoys. Previously encountered limitations were superseded in two key respects. Firstly, much larger targets of up to 221 residues in length were solved, which is far larger than the previously benchmarked threshold of 120 residues. Secondly, contact-guided decoys significantly improved success with β-sheet-rich proteins. Overall, the improved performance of contact-guided decoys suggests that MR is now applicable to a significantly wider range of protein targets than were previously tractable, and points to a direct benefit to structural biology from the recent remarkable advances in sequencing. PMID:27437113

  10. Oxyanion selectivity in sulfate and molybdate transport proteins: an ab initio/CDM study.

    PubMed

    Dudev, Todor; Lim, Carmay

    2004-08-25

    A striking feature of sulfate (SO(4)(2-)) and molybdate (MoO(4)(2-)) transport proteins, such as SBP and ModA, which specifically bind SO(4)(2-) and MoO(4)(2-), respectively, is their ability to discriminate very similar anions with the same net charge, geometry, and hydrogen-bonding properties. Here, we determine to what extent (1) oxyanion-solvent interactions, (2) oxyanion-amino acid interactions, and (3) the anion-binding pocket sizes of the cognate protein contribute to the anion selectivity process in SO(4)(2-) and MoO(4)(2-) transport proteins by computing the free energies for replacing SO(4)(2-) with MoO(4)(2)(-)/WO(4)(2-) in model SO(4)(2-)-binding sites of varying degrees of solvent exposure using a combined quantum mechanical/continuum dielectric approach. The calculations reveal that MoO(4)(2-) transport proteins, such as ModA, specifically bind MoO(4)(2-)/WO(4)(2-) but not SO(4)(2-), mainly because the desolvation penalty of MoO(4)(2-)/WO(4)(2-) is significantly less than that of SO(4)(2-) and, to a lesser extent, because the large and rigid cavity in these proteins attenuates ligand interactions with SO(4)(2-), as compared to MoO(4)(2-). On the other hand, SO(4)(2-) transport proteins prefer SO(4)(2-) to MoO(4)(2-)/WO(4)(2-) because the small anion-binding pocket characteristic of these proteins inhibits binding of the larger MoO(4)(2-) and WO(4)(2-) anions. The calculations also help to explain the absence of positively charged Lys/Arg side chains in the anion-binding sites of SBP and ModA. During evolution, these transport proteins may have excluded cationic ligands from their binding sites because, on one hand, Lys/Arg do not contribute to the selectivity of the binding pocket and, on the other, they substantially stabilize the complex between the oxyanion and protein ligands, which in turn would prohibit the rapid release of the bound oxyanion at a certain stage during the transport process.

  11. Identification of tertiary structure resemblance in proteins using a maximal common subgraph isomorphism algorithm.

    PubMed

    Grindley, H M; Artymiuk, P J; Rice, D W; Willett, P

    1993-02-05

    A program called PROTEP is described that permits the rapid comparison of pairs of three-dimensional protein structures to identify the patterns of secondary structure elements that they have in common. The representation of the protein structures as labelled graphs, where the secondary structure elements in a protein and the spatial and angular relationships between them correspond to the nodes and edges of a graph, was developed for use with an earlier program, called POSSUM, which identified subgraph isomorphisms in protein structures. PROTEP takes this representation and uses a different and more flexible approach to locating structural patterns in pairs of proteins, using a maximal common subgraph isomorphism algorithm that is based on a clique detection procedure. A range of searches is described to demonstrate that areas of common structural overlap between protein structures taken from the Protein Data Bank can be identified both effectively and efficiently.

  12. Making the Bend: DNA Tertiary Structure and Protein-DNA Interactions

    PubMed Central

    Harteis, Sabrina; Schneider, Sabine

    2014-01-01

    DNA structure functions as an overlapping code to the DNA sequence. Rapid progress in understanding the role of DNA structure in gene regulation, DNA damage recognition and genome stability has been made. The three dimensional structure of both proteins and DNA plays a crucial role for their specific interaction, and proteins can recognise the chemical signature of DNA sequence (“base readout”) as well as the intrinsic DNA structure (“shape recognition”). These recognition mechanisms do not exist in isolation but, depending on the individual interaction partners, are combined to various extents. Driving force for the interaction between protein and DNA remain the unique thermodynamics of each individual DNA-protein pair. In this review we focus on the structures and conformations adopted by DNA, both influenced by and influencing the specific interaction with the corresponding protein binding partner, as well as their underlying thermodynamics. PMID:25026169

  13. Folding processes of the B domain of protein A to the native state observed in all-atom ab initio folding simulations

    NASA Astrophysics Data System (ADS)

    Lei, Hongxing; Wu, Chun; Wang, Zhi-Xiang; Zhou, Yaoqi; Duan, Yong

    2008-06-01

    Reaching the native states of small proteins, a necessary step towards a comprehensive understanding of the folding mechanisms, has remained a tremendous challenge to ab initio protein folding simulations despite the extensive effort. In this work, the folding process of the B domain of protein A (BdpA) has been simulated by both conventional and replica exchange molecular dynamics using AMBER FF03 all-atom force field. Started from an extended chain, a total of 40 conventional (each to 1.0 μs) and two sets of replica exchange (each to 200.0 ns per replica) molecular dynamics simulations were performed with different generalized-Born solvation models and temperature control schemes. The improvements in both the force field and solvent model allowed successful simulations of the folding process to the native state as demonstrated by the 0.80 A˚ Cα root mean square deviation (RMSD) of the best folded structure. The most populated conformation was the native folded structure with a high population. This was a significant improvement over the 2.8 A˚ Cα RMSD of the best nativelike structures from previous ab initio folding studies on BdpA. To the best of our knowledge, our results demonstrate, for the first time, that ab initio simulations can reach the native state of BdpA. Consistent with experimental observations, including Φ-value analyses, formation of helix II/III hairpin was a crucial step that provides a template upon which helix I could form and the folding process could complete. Early formation of helix III was observed which is consistent with the experimental results of higher residual helical content of isolated helix III among the three helices. The calculated temperature-dependent profile and the melting temperature were in close agreement with the experimental results. The simulations further revealed that phenylalanine 31 may play critical to achieve the correct packing of the three helices which is consistent with the experimental observation

  14. Mixed ab initio quantum mechanics/molecular mechanics methods using frozen orbitals with applications to peptides and proteins

    NASA Astrophysics Data System (ADS)

    Philipp, Dean Michael

    Methodology is discussed for mixed ab initio quantum mechanics/molecular mechanics modeling of systems where the quantum mechanics (QM) and molecular mechanics (MM) regions are within the same molecule. The ab initio QM calculations are at the restricted Hartree-Fock level using the pseudospectral method of the Jaguar program while the MM part is treated with the OPLS force fields implemented in the IMPACT program. The interface between the QM and MM regions, in particular, is elaborated upon, as it is dealt with by ``breaking'' bonds at the boundaries and using Boys-localized orbitals found from model molecules in place of the bonds. These orbitals are kept frozen during QM calculations. The mixed modeling presented here can be used for single point energy calculations and geometry optimizations. Results from tests of the method to find relative conformational energies and geometries of alanine tetrapeptides are presented along with comparisons to pure QM and pure MM calculations.

  15. Probing protein environment in an enzymatic process: All-electron quantum chemical analysis combined with ab initio quantum mechanical/molecular mechanical modeling of chorismate mutase

    NASA Astrophysics Data System (ADS)

    Ishida, Toyokazu

    2008-09-01

    In this study, we investigated the electronic character of protein environment in enzymatic processes by performing all-electron QM calculations based on the fragment molecular orbital (FMO) method. By introducing a new computational strategy combining all-electron QM analysis with ab initio QM/MM modeling, we investigated the details of molecular interaction energy between a reactive substrate and amino acid residues at a catalytic site. For a practical application, we selected the chorismate mutase catalyzed reaction as an example. Because the computational time required to perform all-electron QM reaction path searches was very large, we employed the ab initio QM/MM modeling technique to construct reliable reaction profiles and performed all-electron FMO calculations for the selected geometries. The main focus of the paper is to analyze the details of electrostatic stabilization, which is considered to be the major feature of enzymatic catalyses, and to clarify how the electronic structure of proteins is polarized in response to the change in electron distribution of the substrate. By performing interaction energy decomposition analysis from a quantum chemical viewpoint, we clarified the relationship between the location of amino acid residues on the protein domain and the degree of electronic polarization of each residue. In particular, in the enzymatic transition state, Arg7, Glu78, and Arg90 are highly polarized in response to the delocalized electronic character of the substrate, and as a result, a large amount of electrostatic stabilization energy is stored in the molecular interaction between the enzyme and the substrate and supplied for transition state stabilization.

  16. Probing protein environment in an enzymatic process: All-electron quantum chemical analysis combined with ab initio quantum mechanical/molecular mechanical modeling of chorismate mutase.

    PubMed

    Ishida, Toyokazu

    2008-09-28

    In this study, we investigated the electronic character of protein environment in enzymatic processes by performing all-electron QM calculations based on the fragment molecular orbital (FMO) method. By introducing a new computational strategy combining all-electron QM analysis with ab initio QM/MM modeling, we investigated the details of molecular interaction energy between a reactive substrate and amino acid residues at a catalytic site. For a practical application, we selected the chorismate mutase catalyzed reaction as an example. Because the computational time required to perform all-electron QM reaction path searches was very large, we employed the ab initio QM/MM modeling technique to construct reliable reaction profiles and performed all-electron FMO calculations for the selected geometries. The main focus of the paper is to analyze the details of electrostatic stabilization, which is considered to be the major feature of enzymatic catalyses, and to clarify how the electronic structure of proteins is polarized in response to the change in electron distribution of the substrate. By performing interaction energy decomposition analysis from a quantum chemical viewpoint, we clarified the relationship between the location of amino acid residues on the protein domain and the degree of electronic polarization of each residue. In particular, in the enzymatic transition state, Arg7, Glu78, and Arg90 are highly polarized in response to the delocalized electronic character of the substrate, and as a result, a large amount of electrostatic stabilization energy is stored in the molecular interaction between the enzyme and the substrate and supplied for transition state stabilization.

  17. Ab initio structural modeling of and experimental validation for Chlamydia trachomatis protein CT296 reveal structural similarity to Fe(II) 2-oxoglutarate-dependent enzymes

    SciTech Connect

    Kemege, Kyle E.; Hickey, John M.; Lovell, Scott; Battaile, Kevin P.; Zhang, Yang; Hefty, P. Scott

    2012-02-13

    Chlamydia trachomatis is a medically important pathogen that encodes a relatively high percentage of proteins with unknown function. The three-dimensional structure of a protein can be very informative regarding the protein's functional characteristics; however, determining protein structures experimentally can be very challenging. Computational methods that model protein structures with sufficient accuracy to facilitate functional studies have had notable successes. To evaluate the accuracy and potential impact of computational protein structure modeling of hypothetical proteins encoded by Chlamydia, a successful computational method termed I-TASSER was utilized to model the three-dimensional structure of a hypothetical protein encoded by open reading frame (ORF) CT296. CT296 has been reported to exhibit functional properties of a divalent cation transcription repressor (DcrA), with similarity to the Escherichia coli iron-responsive transcriptional repressor, Fur. Unexpectedly, the I-TASSER model of CT296 exhibited no structural similarity to any DNA-interacting proteins or motifs. To validate the I-TASSER-generated model, the structure of CT296 was solved experimentally using X-ray crystallography. Impressively, the ab initio I-TASSER-generated model closely matched (2.72-{angstrom} C{alpha} root mean square deviation [RMSD]) the high-resolution (1.8-{angstrom}) crystal structure of CT296. Modeled and experimentally determined structures of CT296 share structural characteristics of non-heme Fe(II) 2-oxoglutarate-dependent enzymes, although key enzymatic residues are not conserved, suggesting a unique biochemical process is likely associated with CT296 function. Additionally, functional analyses did not support prior reports that CT296 has properties shared with divalent cation repressors such as Fur.

  18. A Novel Method Using Abstract Convex Underestimation in Ab-Initio Protein Structure Prediction for Guiding Search in Conformational Feature Space.

    PubMed

    Hao, Xiao-Hu; Zhang, Gui-Jun; Zhou, Xiao-Gen; Yu, Xu-Feng

    2016-01-01

    To address the searching problem of protein conformational space in ab-initio protein structure prediction, a novel method using abstract convex underestimation (ACUE) based on the framework of evolutionary algorithm was proposed. Computing such conformations, essential to associate structural and functional information with gene sequences, is challenging due to the high-dimensionality and rugged energy surface of the protein conformational space. As a consequence, the dimension of protein conformational space should be reduced to a proper level. In this paper, the high-dimensionality original conformational space was converted into feature space whose dimension is considerably reduced by feature extraction technique. And, the underestimate space could be constructed according to abstract convex theory. Thus, the entropy effect caused by searching in the high-dimensionality conformational space could be avoided through such conversion. The tight lower bound estimate information was obtained to guide the searching direction, and the invalid searching area in which the global optimal solution is not located could be eliminated in advance. Moreover, instead of expensively calculating the energy of conformations in the original conformational space, the estimate value is employed to judge if the conformation is worth exploring to reduce the evaluation time, thereby making computational cost lower and the searching process more efficient. Additionally, fragment assembly and the Monte Carlo method are combined to generate a series of metastable conformations by sampling in the conformational space. The proposed method provides a novel technique to solve the searching problem of protein conformational space. Twenty small-to-medium structurally diverse proteins were tested, and the proposed ACUE method was compared with It Fix, HEA, Rosetta and the developed method LEDE without underestimate information. Test results show that the ACUE method can more rapidly and more

  19. The RNA-binding domain of ribosomal protein L11 recognizes an rRNA tertiary structure stabilized by both thiostrepton and magnesium ion

    PubMed Central

    Blyn, Lawrence B.; Risen, Lisa M.; Griffey, Richard H.; Draper, David E.

    2000-01-01

    Antibiotics that inhibit ribosomal function may do so by one of several mechanisms, including the induction of incorrect RNA folding or prevention of protein and/or RNA conformational transitions. Thiostrepton, which binds to the ‘GTPase center’ of the large subunit, has been postulated to prevent conformational changes in either the L11 protein or rRNA to which it binds. Scintillation proximity assays designed to look at the binding of the L11 C-terminal RNA-binding domain to a 23S ribosomal RNA (rRNA) fragment, as well as the ability of thiostrepton to induce that binding, were used to demonstrate the role of Mg2+, L11 and thiostrepton in the formation and maintenance of the rRNA fragment tertiary structure. Experiments using these assays with both an Escherichia coli rRNA fragment and a thermostable variant of that RNA show that Mg2+, L11 and thiostrepton all induce the RNA to fold to an essentially identical tertiary structure. PMID:10734197

  20. Dimeric structure of the N-terminal domain of PriB protein from Thermoanaerobacter tengcongensis solved ab initio

    SciTech Connect

    Liebschner, Dorothee; Brzezinski, Krzysztof; Dauter, Miroslawa; Dauter, Zbigniew; Nowak, Marta; Kur, Józef; Olszewski, Marcin

    2012-12-01

    The N-terminal domain of the PriB protein from the thermophilic bacterium T. tengcongensis (TtePriB) was expressed and its crystal structure has been solved at the atomic resolution of 1.09 Å by direct methods. PriB is one of the components of the bacterial primosome, which catalyzes the reactivation of stalled replication forks at sites of DNA damage. The N-terminal domain of the PriB protein from the thermophilic bacterium Thermoanaerobacter tengcongensis (TtePriB) was expressed and its crystal structure was solved at the atomic resolution of 1.09 Å by direct methods. The protein chain, which encompasses the first 104 residues of the full 220-residue protein, adopts the characteristic oligonucleotide/oligosaccharide-binding (OB) structure consisting of a five-stranded β-barrel filled with hydrophobic residues and equipped with four loops extending from the barrel. In the crystal two protomers dimerize, forming a six-stranded antiparallel β-sheet. The structure of the N-terminal OB domain of T. tengcongensis shows significant differences compared with mesophile PriBs. While in all other known structures of PriB a dimer is formed by two identical OB domains in separate chains, TtePriB contains two consecutive OB domains in one chain. However, sequence comparison of both the N-terminal and the C-terminal domains of TtePriB suggests that they have analogous structures and that the natural protein possesses a structure similar to a dimer of two N-terminal domains.

  1. Controlled crystal dehydration triggers a space-group switch and shapes the tertiary structure of cytomegalovirus immediate-early 1 (IE1) protein.

    PubMed

    Klingl, Stefan; Scherer, Myriam; Stamminger, Thomas; Muller, Yves A

    2015-07-01

    Cytomegalovirus immediate-early 1 (IE1) protein is a key viral effector protein that reprograms host cells. Controlled dehydration experiments with IE1 crystals not only extended their diffraction limit from 2.85 to 2.3 Å resolution but also triggered a monoclinic to tetragonal space-group transition with only minor alterations in the unit-cell parameters. An analysis of the pre-dehydration and post-dehydration crystal structures shows how dehydration rearranges the packing of IE1 molecules to meet the unit-cell constraints of the higher lattice symmetry. The transition from P21 to P43 reduces the number of copies in the asymmetric unit from four to two, and molecules previously related by noncrystallographic symmetry merge into identical crystallographic copies in the tetragonal space group. At the same time, dehydration considerably alters the tertiary structure of one of the two remaining IE1 chains in the asymmetric unit. It appears that this conformational switch is required to compensate for a transition that is assumed to be unfavourable, namely from a highly preferred to a rarely observed space group. At the same time, the dehydration-triggered molecular reshaping could reveal an inherent molecular flexibility that possibly informs on the biological function of IE1, namely on its binding to target proteins from the host cell.

  2. An assessment of vertical inheritance versus endosymbiont transfer of nucleus-encoded genes for mitochondrial proteins following tertiary endosymbiosis in Karlodinium micrum.

    PubMed

    Danne, Jillian C; Gornik, Sebastian G; Waller, Ross F

    2012-01-01

    Most photosynthetic dinoflagellates harbour a red alga-derived secondary plastid. In the dinoflagellate Karlodinium micrum, this plastid was replaced by a subsequent endosymbiosis, resulting in a tertiary plastid derived from a haptophyte. Evolution of endosymbionts entails substantial relocation of endosymbiont genes to the host nucleus: a process called endosymbiotic gene transfer (EGT). In K. micrum, numerous plastid genes from the haptophyte nucleus are found in the host nucleus, providing evidence for EGT in this system. In other cases of endosymbiosis, notably ancient primary endosymbiotic events, EGT has been inferred to contribute to remodeling of other cell functions by expression of proteins in compartments other than the endosymbiont from which they derived. K. micrum provides a more recently derived endosymbiotic system to test for evidence of EGT and gain of function in non-plastid compartments. In this study, we test for gain of haptophyte-derived proteins for mitochondrial function in K. micrum. Using molecular phylogenies we have analysed whether nucleus-encoded mitochondrial proteins were inherited by EGT from the haptophyte endosymbiont, or vertically inherited from the dinoflagellate host lineage. From this dataset we found no evidence of haptophyte-derived mitochondrial genes, and the only cases of non-vertical inheritance were genes derived from lateral gene transfer events.

  3. Primary, secondary, and tertiary structure of the core of a histone H1-like protein from the sperm of Mytilus.

    PubMed

    Jutglar, L; Borrell, J I; Ausió, J

    1991-05-05

    We have analyzed the structure of the trypsin-resistant core of the protein PL-II* of the sperm from Mytilus californianus. The peptide has a molecular mass of 8436 Da and its primary sequence is ATGGAKKP STLSMIVAAIQAMKNRKGSSVQAIRKYILANNKG INTSRLGSAMKLAFAKGLKSGVLVRPKTSAGA SGATGSFRVG. This sequence bears an enormous homology and fulfills the constraints of the consensus sequence of the trypsin-resistant peptides of the proteins of the histone H1 family. Secondary structure analysis using Fourier-transform infared spectroscopy as well as predictive methods indicate the presence of 20-30% beta-structure and approximately 25% alpha-helix for this peptide. As in the case of histone H1 proteins, the protein PL-II* core exhibits a compact globular structure as deduced from hydrodynamic measurements. The presence of a histone H1 protein with protamine-like features, seems to be thus, a common general feature of the chromatin composition in the sperm of the bivalve molluscs.

  4. Interplay among tertiary contacts, secondary structure formation and side-chain packing in the protein folding mechanism: all-atom representation study of protein L.

    PubMed

    Clementi, Cecilia; García, Angel E; Onuchic, José N

    2003-02-21

    Experimental and theoretical results suggest that, since proteins are energetically minimally frustrated, the native fold, or topology, plays a primary role in determining the structure of the transition state ensemble and on-pathway intermediate states in protein folding. Although the central role of native state topology in determining the folding mechanism is thought to be a quite general result-at least for small two-state folding proteins-there are remarkable exceptions. Recent experimental findings have shown that topology alone cannot always determine the folding mechanism, and demonstrated that the balance between topology and energetics is very delicate. This balance seems to be particularly critical in proteins with a highly symmetrical native structure, such as proteins L and G, which have similar native structure topology but fold by different mechanisms. Simplified, C(alpha)-atom only protein models have shown not be sufficient to differentiate these mechanisms. An all-atom Gō model provides a valuable intermediate model between structurally simplified protein representations and all-atom protein simulations with explicit/implicit solvent descriptions. We present here a detailed study of an all-atom Gō-like representation of protein L, in close comparison with the experimental results and with the results obtained from a simple C(alpha)-atom representation of the same protein. We also perform simulations for protein G, where we obtain a folding mechanism in which the protein symmetry is broken exactly in the opposite way to protein L as has been observed experimentally. A detailed analysis for protein L also shows that the role of specific residues is correctly and quantitatively reproduced by the all-atom Gō model over almost the entire protein.

  5. Relation between proteins tertiary structure, tryptophan fluorescence lifetimes and tryptophan S(o)→(1)L(b) and S(o)→(1)L(a) transitions. Studies on α1-acid glycoprotein and β-lactoglobulin.

    PubMed

    Albani, Jihad René

    2011-05-01

    We measured fluorescence lifetimes and fluorescence spectra (excitation and emission) of tryptophan residues of α(1)-acid glycoprotein (three Trp residues) and β-lactoglobulin (two Trp residues) in absence and presence of 450 μM progesterone. Progesterone binds only to α(1)-acid glycoprotein. In absence of progesterone, each of the two proteins displays three fluorescence lifetimes. Addition of progesterone induces a partial inhibition of the S(o) → (1)L(a) transition without affecting fluorescence lifetimes. The same experiments performed in presence of denatured proteins in 6 M guanidine show that addition of progesterone inhibits partially the S(o) → (1)L(a) transition and its peak is 15 nm shifted to the red compared to that obtained for native proteins. However, the S(o) → (1)L(b) transition position peak is not affected by protein denaturation. Thus, the tertiary structure of the protein plays an important role by modulating the tryptophan electronic transitions. Fluorescence emission decay recorded in absence and presence of progesterone yields three fluorescence lifetimes whether proteins are denatured or not. Thus, protein tertiary structure is not responsible for the presence of three fluorescence lifetimes. These characterize tryptophan substructures reached at the excited states and which population (pre-exponential values) depend on the tryptophan residues interaction with their microenvironment(s) and thus on the global conformation of the protein.

  6. Tertiary interactions within the ribosomal exit tunnel.

    PubMed

    Kosolapov, Andrey; Deutsch, Carol

    2009-04-01

    Although tertiary folding of whole protein domains is prohibited by the cramped dimensions of the ribosomal tunnel, dynamic tertiary interactions may permit folding of small elementary units within the tunnel. To probe this possibility, we used a beta-hairpin and an alpha-helical hairpin from the cytosolic N terminus of a voltage-gated potassium channel and determined a probability of folding for each at defined locations inside and outside the tunnel. Minimalist tertiary structures can form near the exit port of the tunnel, a region that provides an entropic window for initial exploration of local peptide conformations. Tertiary subdomains of the nascent peptide fold sequentially, but not independently, during translation. These studies offer an approach for diagnosing the molecular basis for folding defects that lead to protein malfunction and provide insight into the role of the ribosome during early potassium channel biogenesis.

  7. Gut Microbiota in Type 2 Diabetes Individuals and Correlation with Monocyte Chemoattractant Protein1 and Interferon Gamma from Patients Attending a Tertiary Care Centre in Chennai, India

    PubMed Central

    Pushpanathan, Premalatha; Srikanth, Padma; Seshadri, Krishna G.; Selvarajan, Sribal; Pitani, Ravi Shankar; Kumar, Thomas David; Janarthanan, R.

    2016-01-01

    Background: Type 2 diabetes mellitus (T2DM) and obesity are associated with changes in gut microbiota and characterized by chronic low-grade inflammation. Monocyte chemoattractant protein-1 (MCP-1) and interferon gamma (IFNγ) are proinflammatory cytokines which play an important role in the development of T2DM. We undertook this study to analyze the gut microbiota of T2DM and nondiabetic subjects and to determine the profile of MCP 1 and IFNγ in the same subjects attending a tertiary care center in Chennai, Tamil Nadu, India. Methods: The study included 30 subjects with clinical details. Stool and blood samples were collected from all the subjects. DNA was extracted from fecal samples and polymerase chain reaction was done using fusion primers. Metagenomic analysis was performed using ion torrent sequencing. The reads obtained were in FASTA format and reported as operational taxonomic units. Human MCP 1 and IFNγ enzyme linked immunosorbent assay (ELISA) were performed for 23 serum samples. Results: The study consisted of 30 subjects; 17 were T2DM and 13 were nondiabetics. The gut microbiota among T2DM consisted predominantly of Gram negative bacteria; Escherichia and Prevotella, when compared with the nondiabetic group with predominantly Gram positive organisms suchas Faecalibacterium, Eubacterium, and Bifidobacterium. The mean MCP-1 values in the diabetic group were 232.8 pg/ml and in the nondiabetic group 170.84 pg/ml. IFNγ (mean 385.5 pg/ml) was raised in glycated hemoglobin (HbA1c) group of 6.5–7.5% which was statistically significant. Association of Escherichia with T2DM and association of Bifidobacteria in the nondiabetics were also statistically significant. Conclusion: Escherichia counts were elevated in T2DM with HbA1c of 6.5–8.5% which was statistically significant suggesting that lipopolysaccharides present in the cell wall of Gram-negative bacteria may be responsible for low-grade inflammation as evidenced by elevated MCP-1 and IFNγ levels in T

  8. West Hackberry Tertiary Project

    SciTech Connect

    Gillham, Travis; Yannimaras, Demetrios

    1999-11-03

    The West Hackberry Tertiary Project is a field test of the concept that air injection can generate tertiary oil recovery through the Double Displacement Process. The Double Displacement Process is the gas displacement of a water invaded oil column for the purpose of recovering tertiary oil through gravity drainage. The novel aspect of this project is the use of air as the injection fluid. In Gulf Coast oil reservoirs with pronounced bed dip, reservoir performance has shown that gravity drainage recoveries average 80% to 90% of the original oil in place while water drive recoveries average 50% to 60% of the original oil in place. The target for tertiary oil recovery with the Double Displacement Process is the incremental oil between the 50% to 60% water drive recoveries and the 80% to 90% gravity drainage recoveries. The use of air injection in this process combines the benefits of air's low cost and universal accessibility with the potential for improved oil recovery resulting from spontaneous in situ combustion. If successful, this project will demonstrate that utilizing air injection in the Double Displacement Process will result in an economically viable tertiary process in many Gulf Coast oil reservoirs where other tertiary processes are presently uneconomic. The West Hackberry Tertiary Project receives matching funds from the United States Department of Energy (DOE) as part of the DOE's Class 1 Program for the development of advance recovery technologies in fluvial dominated deltaic reservoirs. In addition, the Petroleum Engineering Department at Louisiana State University (LSU) provides independent study and technology transfer.

  9. Forcefield_NCAA: Ab Initio Charge Parameters to Aid in the Discovery and Design of Therapeutic Proteins and Peptides with Unnatural Amino Acids and Their Application to Complement Inhibitors of the Compstatin Family

    PubMed Central

    2015-01-01

    We describe the development and testing of ab initio derived, AMBER ff03 compatible charge parameters for a large library of 147 noncanonical amino acids including β- and N-methylated amino acids for use in applications such as protein structure prediction and de novo protein design. The charge parameter derivation was performed using the RESP fitting approach. Studies were performed assessing the suitability of the derived charge parameters in discriminating the activity/inactivity between 63 analogs of the complement inhibitor Compstatin on the basis of previously published experimental IC50 data and a screening procedure involving short simulations and binding free energy calculations. We found that both the approximate binding affinity (K*) and the binding free energy calculated through MM-GBSA are capable of discriminating between active and inactive Compstatin analogs, with MM-GBSA performing significantly better. Key interactions between the most potent Compstatin analog that contains a noncanonical amino acid are presented and compared to the most potent analog containing only natural amino acids and native Compstatin. We make the derived parameters and an associated web interface that is capable of performing modifications on proteins using Forcefield_NCAA and outputting AMBER-ready topology and parameter files freely available for academic use at http://selene.princeton.edu/FFNCAA. The forcefield allows one to incorporate these customized amino acids into design applications with control over size, van der Waals, and electrostatic interactions. PMID:24932669

  10. Striped tertiary storage arrays

    NASA Technical Reports Server (NTRS)

    Drapeau, Ann L.

    1993-01-01

    Data stripping is a technique for increasing the throughput and reducing the response time of large access to a storage system. In striped magnetic or optical disk arrays, a single file is striped or interleaved across several disks; in a striped tape system, files are interleaved across tape cartridges. Because a striped file can be accessed by several disk drives or tape recorders in parallel, the sustained bandwidth to the file is greater than in non-striped systems, where access to the file are restricted to a single device. It is argued that applying striping to tertiary storage systems will provide needed performance and reliability benefits. The performance benefits of striping for applications using large tertiary storage systems is discussed. It will introduce commonly available tape drives and libraries, and discuss their performance limitations, especially focusing on the long latency of tape accesses. This section will also describe an event-driven tertiary storage array simulator that is being used to understand the best ways of configuring these storage arrays. The reliability problems of magnetic tape devices are discussed, and plans for modeling the overall reliability of striped tertiary storage arrays to identify the amount of error correction required are described. Finally, work being done by other members of the Sequoia group to address latency of accesses, optimizing tertiary storage arrays that perform mostly writes, and compression is discussed.

  11. Tertiary Education in Portugal

    ERIC Educational Resources Information Center

    OECD Publishing (NJ3), 2008

    2008-01-01

    Portugal's tertiary education sector has expanded significantly over the last 20 years, but participation and overall educational attainment levels remain below European standards and enrolment rates have begun to decline. The OECD review recommends that Portugal's national government should focus on strategic direction and leave higher education…

  12. Electronic Absorption Spectra from MM and ab initio QM/MM Molecular Dynamics: Environmental Effects on the Absorption Spectrum of Photoactive Yellow Protein

    PubMed Central

    Isborn, Christine M.; Götz, Andreas W.; Clark, Matthew A.; Walker, Ross C.; Martínez, Todd J.

    2012-01-01

    We describe a new interface of the GPU parallelized TeraChem electronic structure package and the Amber molecular dynamics package for quantum mechanical (QM) and mixed QM and molecular mechanical (MM) molecular dynamics simulations. This QM/MM interface is used for computation of the absorption spectra of the photoactive yellow protein (PYP) chromophore in vacuum, aqueous solution, and protein environments. The computed excitation energies of PYP require a very large QM region (hundreds of atoms) covalently bonded to the chromophore in order to achieve agreement with calculations that treat the entire protein quantum mechanically. We also show that 40 or more surrounding water molecules must be included in the QM region in order to obtain converged excitation energies of the solvated PYP chromophore. These results indicate that large QM regions (with hundreds of atoms) are a necessity in QM/MM calculations. PMID:23476156

  13. West Hackberry Tertiary Project

    SciTech Connect

    Kenneth Haley; Travis Gillham; Demetrios Yannimaras

    1999-03-31

    The West Hackberry Tertiary Project is a field test of the concept that air injection can be combined with the Double Displacement Process to produce a tertiary recovery process that is both low cost and economic at current oil prices. The Double Displacement Process is the gas displacement of a water invaded oil column for the purpose of recovering tertiary oil by gravity drainage. In reservoirs with pronounced bed dip such as those found in West Hackberry and other Gulf Coast salt dome fields, reservoir performance has shown that gravity drainage recoveries average 80% to 90% of the original oil in place while waterdrive recoveries average 50% to 60% of the original oil in place. The target for tertiary oil recovery in the Double Displacement Process is the incremental oil between the 50% to 60% waterdrive recoveries and the 80% to 90% gravity drainage recoveries. In previous field tests, the Double Displacement Process has proven successful in generating tertiary oil recovery. The use of air injection in this process combines the benefits of air's low cost and universal accessibility with the potential for accelerated oil recovery from the combustion process. If successful, this project will demonstrate that utilizing air injection in the Double Displacement Process will result in an economically viable tertiary process in reservoirs (such as Gulf Coast salt dome reservoirs) where any other tertiary process is presently uneconomic. Air injection on the West Hank began in November of 1994. Although West Flank air injection has increased reservoir pressure by 500 pounds per square inch (psi), production response has not yet occurred. The gas cap on the West Flank has not expanded sufficiently to push the oil rim down to the nearest down structure well. Cumulative injection to date is 1.6 BCF, only approximately 50% of the projected volume required to establish oil production response. Additional air injection is required to further expand the gas cap and thereby

  14. Ethiopian Tertiary dike swarms

    NASA Technical Reports Server (NTRS)

    Mohr, P. A.

    1971-01-01

    Mapping of the Ethiopian rift and Afar margins revealed the existence of Tertiary dike swarms. The structural relations of these swarms and the fed lava pile to monoclinal warping of the margins partly reflect a style of continental margin tectonics found in other parts of the world. In Ethiopia, however, conjugate dike trends appear to be unusually strongly developed. Relation of dikes to subsequent margin faulting is ambiguous, and there are instances where the two phenomena are spatially separate and of differing trends. There is no evidence for lateral migration with time of dike injection toward the rift zone. No separate impingement of Red Sea, Gulf of Aden, and African rift system stress fields on the Ethiopian region can be demonstrated from the Tertiary dike swarms. Rather, a single, regional paleostress field existed, suggestive of a focus beneath the central Ethiopian plateau. This stress field was dominated by tension: there is no cogent evidence for shearing along the rift margins. A gentle compression along the rift floor is indicated. A peculiar sympathy of dike hade directions at given localities is evident.

  15. From Compact to String—The Role of Secondary and Tertiary Structure in Charge-Induced Unzipping of Gas-Phase Proteins

    NASA Astrophysics Data System (ADS)

    Warnke, Stephan; Hoffmann, Waldemar; Seo, Jongcheol; De Genst, Erwin; von Helden, Gert; Pagel, Kevin

    2016-12-01

    In the gas phase, protein ions can adopt a broad range of structures, which have been investigated extensively in the past using ion mobility-mass spectrometry (IM-MS)-based methods. Compact ions with low number of charges undergo a Coulomb-driven transition to partially folded species when the charge increases, and finally form extended structures with presumably little or no defined structure when the charge state is high. However, with respect to the secondary structure, IM-MS methods are essentially blind. Infrared (IR) spectroscopy, on the other hand, is sensitive to such structural details and there is increasing evidence that helices as well as β-sheet-like structures can exist in the gas phase, especially for ions in low charge states. Very recently, we showed that also the fully extended form of highly charged protein ions can adopt a distinct type of secondary structure that features a characteristic C5-type hydrogen bond pattern. Here we use a combination of IM-MS and IR spectroscopy to further investigate the influence of the initial, native conformation on the formation of these structures. Our results indicate that when intramolecular Coulomb-repulsion is large enough to overcome the stabilization energies of the genuine secondary structure, all proteins, regardless of their sequence or native conformation, form C5-type hydrogen bond structures. Furthermore, our results suggest that in highly charged proteins the positioning of charges along the sequence is only marginally influenced by the basicity of individual residues.

  16. AB INITIO AND CALPHAD THERMODYNAMICS OF MATERIALS

    SciTech Connect

    Turchi, P A

    2004-04-14

    Ab initio electronic structure methods can supplement CALPHAD in two major ways for subsequent applications to stability in complex alloys. The first one is rather immediate and concerns the direct input of ab initio energetics in CALPHAD databases. The other way, more involved, is the assessment of ab initio thermodynamics {acute a} la CALPHAD. It will be shown how these results can be used within CALPHAD to predict the equilibrium properties of multi-component alloys.

  17. Structural basis of light chain amyloidogenicity: comparison of the thermodynamic properties, fibrillogenic potential and tertiary structural features of four vλ6 proteins

    SciTech Connect

    Wall, J.S.; Gupta, V.; Wilkerson, M.; Schell, M.; Loris, R.; Adams, P.; Solomon, A.; Stevens, F.; Dealwis, C.

    2004-04-01

    Primary (AL) amyloidosis results from the pathologic deposition of monoclonal light chains as amyloid fibrils. Studies of recombinant-derived variable region (V{sub L}) fragments of these proteins have shown an inverse relationship between thermodynamic stability and fibrillogenic potential. Further, ionic interactions within the V{sub L} domain were predicted to influence the kinetics of light chain fibrillogenicity, as evidenced from our analyses of a relatively stable V{sub {lambda}}6 protein (Jto) with a long range electrostatic interaction between Asp and Arg side chains at position 29 and 68, respectively, and an unstable, highly fibrillogenic V{sub {lambda}}6 protein (Wil) that had neutral amino acids at these locations. To test this hypothesis, we have generated two Jto-related mutants designed to disrupt the interaction between Asp 29 and Arg 68 (JtoD29A and JtoR68S). Although the thermodynamic stabilities of unfolding for these two molecules were identical, they exhibited very different kinetics of fibril formation: the rate of JtoD29A fibrillogenesis was slow and comparable to the parent molecule, whereas that of JtoR68S was significantly faster. High-resolution X-ray diffraction analyses of crystals prepared from the two mutants having the same space group and unit cell dimensions revealed no significant main-chain conformational changes. However, several notable side-chain alterations were observed in JtoR68S, as compared with JtoD29A, that resulted in the solvent exposure of a greater hydrophobic surface and modifications in the electrostatic potential surface. We posit that these differences contributed to the enhanced fibrillogenic potential of the Arg 68 mutant, since both Jto mutants lacked the intrachain ionic interaction and were equivalently unstable. The information gleaned from our studies has provided insight into structural parameters that in addition to overall thermodynamic stability, contribute to the fibril forming propensity of

  18. Primary, secondary, and tertiary hyperparathyroidism.

    PubMed

    Ahmad, Rehan; Hammond, James M

    2004-08-01

    Primary, secondary, and tertiary hyperparathyroidism have evolved since their original description. What was once a debilitating disease has now become one with few symptoms on initial presentation. Complications from these disorders have decreased significantly because of earlier detection. Improved management of patients with chronic renal disease has also limited complications among those with secondary and tertiary hyperparathyroidism. Appropriate management is essential even in the early phase of the disorder to minimize the morbidities that may result if left untreated.

  19. Forcefield_PTM: Ab Initio Charge and AMBER Forcefield Parameters for Frequently Occurring Post-Translational Modifications.

    PubMed

    Khoury, George A; Thompson, Jeff P; Smadbeck, James; Kieslich, Chris A; Floudas, Christodoulos A

    2013-12-10

    In this work, we introduce Forcefield_PTM, a set of AMBER forcefield parameters consistent with ff03 for 32 common post-translational modifications. Partial charges were calculated through ab initio calculations and a two-stage RESP-fitting procedure in an ether-like implicit solvent environment. The charges were found to be generally consistent with others previously reported for phosphorylated amino acids, and trimethyllysine, using different parameterization methods. Pairs of modified and their corresponding unmodified structures were curated from the PDB for both single and multiple modifications. Background structural similarity was assessed in the context of secondary and tertiary structures from the global dataset. Next, the charges derived for Forcefield_PTM were tested on a macroscopic scale using unrestrained all-atom Langevin molecular dynamics simulations in AMBER for 34 (17 pairs of modified/unmodified) systems in implicit solvent. Assessment was performed in the context of secondary structure preservation, stability in energies, and correlations between the modified and unmodified structure trajectories on the aggregate. As an illustration of their utility, the parameters were used to compare the structural stability of the phosphorylated and dephosphorylated forms of OdhI. Microscopic comparisons between quantum and AMBER single point energies along key χ torsions on several PTMs were performed and corrections to improve their agreement in terms of mean squared errors and squared correlation coefficients were parameterized. This forcefield for post-translational modifications in condensed-phase simulations can be applied to a number of biologically relevant and timely applications including protein structure prediction, protein and peptide design, docking, and to study the effect of PTMs on folding and dynamics. We make the derived parameters and an associated interactive webtool capable of performing post-translational modifications on proteins

  20. Addressing the Role of Conformational Diversity in Protein Structure Prediction

    PubMed Central

    Parisi, Gustavo; Fornasari, Maria Silvina

    2016-01-01

    Computational modeling of tertiary structures has become of standard use to study proteins that lack experimental characterization. Unfortunately, 3D structure prediction methods and model quality assessment programs often overlook that an ensemble of conformers in equilibrium populates the native state of proteins. In this work we collected sets of publicly available protein models and the corresponding target structures experimentally solved and studied how they describe the conformational diversity of the protein. For each protein, we assessed the quality of the models against known conformers by several standard measures and identified those models ranked best. We found that model rankings are defined by both the selected target conformer and the similarity measure used. 70% of the proteins in our datasets show that different models are structurally closest to different conformers of the same protein target. We observed that model building protocols such as template-based or ab initio approaches describe in similar ways the conformational diversity of the protein, although for template-based methods this description may depend on the sequence similarity between target and template sequences. Taken together, our results support the idea that protein structure modeling could help to identify members of the native ensemble, highlight the importance of considering conformational diversity in protein 3D quality evaluations and endorse the study of the variability of the native structure for a meaningful biological analysis. PMID:27159429

  1. Tertiary climatic fluctuations and methods of analysis of tertiary floras

    USGS Publications Warehouse

    Wolfe, J.A.

    1971-01-01

    On theoretical grounds, an analysis of the physiognomy of a Tertiary leaf assemblage is more direct and reliable than a circuitous floristic analysis in assigning thermal regimes to fossil assemblages. Using primarily foliar physiognomy and secondarily floristic composition, it can be shown that: (1) some middle latitude Tertiary assemblages probably lived under meteoroligically tropical climates; (2) a major and rapid climatic deterioration occurred in the Oligocene; and (3) a major climatic fluctuation probably occurred in the Late Eocene. These analyses thus substantiate the conclusions of several other paleobotanists regarding climatic fluctuations. Recent criticisms of these analyses are shown to be invalid and to be based largely on misinterpretations. ?? 1971.

  2. Regulation and 3 dimensional culture of tertiary follicle growth.

    PubMed

    Cheon, Yong-Pil

    2012-09-01

    It has been revealed that multiple cohorts of tertiary follicles develop during some animal estrous cycle and the human menstrual cycle. To reach developmental competence, oocytes need the support of somatic cells. During embryogenesis, the primordial germ cells appear, travel to the gonadal rudiments, and form follicles. The female germ cells develop within the somatic cells of the ovary, granulosa cells, and theca cells. How the oocyte and follicle cells support each other has been seriously studied. The latest technologies in genes and proteins and genetic engineering have allowed us to collect a great deal of information about folliculogenesis. For example, a few web pages (http://www.ncbi.nlm.nih.gov; http://mrg.genetics.washington.edu) provide access to databases of genomes, sequences of transcriptomes, and various tools for analyzing and discovering genes important in ovarian development. Formation of the antrum (tertiary follicle) is the final phase of folliculogenesis and the transition from intraovarian to extraovian regulation. This final step coordinates with the hypothalamic-pituitary-ovarian axis. On the other hand, currently, follicle physiology is under intense investigation, as little is known about how to overcome women's ovarian problems or how to develop competent oocytes from in vitro follicle culture or transplantation. In this review, some of the known roles of hormones and some of the genes involved in tertiary follicle growth and the general characteristics of tertiary follicles are summarized. In addition, in vitro culture of tertiary follicles is also discussed as a study model and an assisted reproductive technology model.

  3. Ab initio dynamical vertex approximation

    NASA Astrophysics Data System (ADS)

    Galler, Anna; Thunström, Patrik; Gunacker, Patrik; Tomczak, Jan M.; Held, Karsten

    2017-03-01

    Diagrammatic extensions of dynamical mean-field theory (DMFT) such as the dynamical vertex approximation (DΓ A) allow us to include nonlocal correlations beyond DMFT on all length scales and proved their worth for model calculations. Here, we develop and implement an Ab initio DΓ A approach (AbinitioDΓ A ) for electronic structure calculations of materials. The starting point is the two-particle irreducible vertex in the two particle-hole channels which is approximated by the bare nonlocal Coulomb interaction and all local vertex corrections. From this, we calculate the full nonlocal vertex and the nonlocal self-energy through the Bethe-Salpeter equation. The AbinitioDΓ A approach naturally generates all local DMFT correlations and all nonlocal G W contributions, but also further nonlocal correlations beyond: mixed terms of the former two and nonlocal spin fluctuations. We apply this new methodology to the prototypical correlated metal SrVO3.

  4. Buckets and Fire: Metaphors in Tertiary Teaching

    ERIC Educational Resources Information Center

    Emerson, Lisa; Mansvelt, Juliana

    2015-01-01

    This paper examines New Zealand tertiary teachers' use of metaphor and their attitudes to the consumer metaphor in relation to teaching. Based on interviews with 16 tertiary teachers, this study shows that although teachers believe the consumer metaphor is accepted by students, tertiary institutions and policy makers, and that it has affected…

  5. Tertiary Literacy on the Cusp.

    ERIC Educational Resources Information Center

    Absalom, Doug; Golebiowski, Zosia

    2002-01-01

    Outlines recent concerns regarding a perceived decline in literacy standards in Australia, with reference to changing literacy abilities and standards in tertiary education. Summarizes and critiques current discussions on changes in literacy expectations and contemporary notions of literacy. Concludes with discussion of three important agents of…

  6. Protein Structure

    ERIC Educational Resources Information Center

    Asmus, Elaine Garbarino

    2007-01-01

    Individual students model specific amino acids and then, through dehydration synthesis, a class of students models a protein. The students clearly learn amino acid structure, primary, secondary, tertiary, and quaternary structure in proteins and the nature of the bonds maintaining a protein's shape. This activity is fun, concrete, inexpensive and…

  7. Protein Folding and Structure Prediction from the Ground Up: The Atomistic Associative Memory, Water Mediated, Structure and Energy Model.

    PubMed

    Chen, Mingchen; Lin, Xingcheng; Zheng, Weihua; Onuchic, José N; Wolynes, Peter G

    2016-08-25

    The associative memory, water mediated, structure and energy model (AWSEM) is a coarse-grained force field with transferable tertiary interactions that incorporates local in sequence energetic biases using bioinformatically derived structural information about peptide fragments with locally similar sequences that we call memories. The memory information from the protein data bank (PDB) database guides proper protein folding. The structural information about available sequences in the database varies in quality and can sometimes lead to frustrated free energy landscapes locally. One way out of this difficulty is to construct the input fragment memory information from all-atom simulations of portions of the complete polypeptide chain. In this paper, we investigate this approach first put forward by Kwac and Wolynes in a more complete way by studying the structure prediction capabilities of this approach for six α-helical proteins. This scheme which we call the atomistic associative memory, water mediated, structure and energy model (AAWSEM) amounts to an ab initio protein structure prediction method that starts from the ground up without using bioinformatic input. The free energy profiles from AAWSEM show that atomistic fragment memories are sufficient to guide the correct folding when tertiary forces are included. AAWSEM combines the efficiency of coarse-grained simulations on the full protein level with the local structural accuracy achievable from all-atom simulations of only parts of a large protein. The results suggest that a hybrid use of atomistic fragment memory and database memory in structural predictions may well be optimal for many practical applications.

  8. Ab initio phonon limited transport

    NASA Astrophysics Data System (ADS)

    Verstraete, Matthieu

    We revisit the thermoelectric (TE) transport properties of two champion materials, PbTe and SnSe, using fully first principles methods. In both cases the performance of the material is due to subtle combinations of structural effects, scattering, and phase space reduction. In PbTe anharmonic effects are completely opposite to the predicted quasiharmonic evolution of phonon frequencies and to frequently (and incorrectly) cited extrapolations of experiments. This stabilizes the material at high T, but also tends to enhance its thermal conductivity, in a non linear manner, above 600 Kelvin. This explains why PbTe is in practice limited to room temperature applications. SnSe has recently been shown to be the most efficient TE material in bulk form. This is mainly due to a strongly enhanced carrier concentration and electrical conductivity, after going through a phase transition from 600 to 800 K. We calculate the transport coefficients as well as the defect concentrations ab initio, showing excellent agreement with experiment, and elucidating the origin of the double phase transition as well as the new charge carriers. AH Romero, EKU Gross, MJ Verstraete, and O Hellman PRB 91, 214310 (2015) O. Hellman, IA Abrikosov, and SI Simak, PRB 84 180301 (2011)

  9. Brønsted acidity of protic ionic liquids: a modern ab initio valence bond theory perspective.

    PubMed

    Patil, Amol Baliram; Mahadeo Bhanage, Bhalchandra

    2016-09-21

    Room temperature ionic liquids (ILs), especially protic ionic liquids (PILs), are used in many areas of the chemical sciences. Ionicity, the extent of proton transfer, is a key parameter which determines many physicochemical properties and in turn the suitability of PILs for various applications. The spectrum of computational chemistry techniques applied to investigate ionic liquids includes classical molecular dynamics, Monte Carlo simulations, ab initio molecular dynamics, Density Functional Theory (DFT), CCSD(t) etc. At the other end of the spectrum is another computational approach: modern ab initio Valence Bond Theory (VBT). VBT differs from molecular orbital theory based methods in the expression of the molecular wave function. The molecular wave function in the valence bond ansatz is expressed as a linear combination of valence bond structures. These structures include covalent and ionic structures explicitly. Modern ab initio valence bond theory calculations of representative primary and tertiary ammonium protic ionic liquids indicate that modern ab initio valence bond theory can be employed to assess the acidity and ionicity of protic ionic liquids a priori.

  10. Well-characterized sequence features of eukaryote genomes and implications for ab initio gene prediction.

    PubMed

    Huang, Ying; Chen, Shi-Yi; Deng, Feilong

    2016-01-01

    In silico analysis of DNA sequences is an important area of computational biology in the post-genomic era. Over the past two decades, computational approaches for ab initio prediction of gene structure from genome sequence alone have largely facilitated our understanding on a variety of biological questions. Although the computational prediction of protein-coding genes has already been well-established, we are also facing challenges to robustly find the non-coding RNA genes, such as miRNA and lncRNA. Two main aspects of ab initio gene prediction include the computed values for describing sequence features and used algorithm for training the discriminant function, and by which different combinations are employed into various bioinformatic tools. Herein, we briefly review these well-characterized sequence features in eukaryote genomes and applications to ab initio gene prediction. The main purpose of this article is to provide an overview to beginners who aim to develop the related bioinformatic tools.

  11. Ab Initio potential grid based docking: From High Performance Computing to In Silico Screening

    NASA Astrophysics Data System (ADS)

    de Jonge, Marc R.; Vinkers, H. Maarten; van Lenthe, Joop H.; Daeyaert, Frits; Bush, Ian J.; van Dam, Huub J. J.; Sherwood, Paul; Guest, Martyn F.

    2007-09-01

    We present a new and completely parallel method for protein ligand docking. The potential of the docking target structure is obtained directly from the electron density derived through an ab initio computation. A large subregion of the crystal structure of Isocitrate Lyase, was selected as docking target. To allow the full ab initio treatment of this region special care was taken to assign optimal basis functions. The electrostatic potential is tested by docking a small charged molecule (succinate) into the binding site. The ab initio grid yields a superior result by producing the best binding orientation and position, and by recognizing it as the best. In contrast the same docking procedure, but using a classical point-charge based potential, produces a number of additional incorrect binding poses, and does not recognize the correct pose as the best solution.

  12. Tertiary carbonate reservoirs in Indonesia

    SciTech Connect

    Nayoan, G.A.S.; Arpandi; Siregar, M.

    1981-01-01

    Hydrocarbon production from Tertiary carbonate reservoirs accounted for ca. 10% of daily Indonesian production at the beginning of 1978. Environmentally, the reservoirs appear as parts of reef complexes and high-energy carbonate deposits within basinal areas situated mainly in the back arc of the archipelago. Good porosities of the reservoirs are represented by vugular/moldic and intergranular porosity types. The reservoirs are capable of producing prolific amounts of hydrocarbons: production tests in Salawati-Irian Jaya reaches maximum values of 32,000 bpd, and in Arun-North Sumatra tests recorded 200 MMCF gas/day. Significant hydrocarbon accumulations are related to good reservoir rocks in carbonates deposited as patch reefs, pinnacle reefs, and platform complexes. Exploration efforts expand continuously within carbonate formations which are extensive horizontally as well as vertically in the Tertiary stratigraphic column.

  13. Proteins: sequence to structure and function--current status.

    PubMed

    Shenoy, Sandhya R; Jayaram, B

    2010-11-01

    In an era that has been dominated by Structural Biology for the last 30-40 years, a dramatic change of focus towards sequence analysis has spurred the advent of the genome projects and the resultant diverging sequence/structure deficit. The central challenge of Computational Structural Biology is therefore to rationalize the mass of sequence information into biochemical and biophysical knowledge and to decipher the structural, functional and evolutionary clues encoded in the language of biological sequences. In investigating the meaning of sequences, two distinct analytical themes have emerged: in the first approach, pattern recognition techniques are used to detect similarity between sequences and hence to infer related structures and functions; in the second ab initio prediction methods are used to deduce 3D structure, and ultimately to infer function, directly from the linear sequence. In this article, we attempt to provide a critical assessment of what one may and may not expect from the biological sequences and to identify major issues yet to be resolved. The presentation is organized under several subtitles like protein sequences, pattern recognition techniques, protein tertiary structure prediction, membrane protein bioinformatics, human proteome, protein-protein interactions, metabolic networks, potential drug targets based on simple sequence properties, disordered proteins, the sequence-structure relationship and chemical logic of protein sequences.

  14. Ab Initio Study of Polonium

    SciTech Connect

    Zabidi, Noriza Ahmad; Kassim, Hasan Abu; Shrivastava, Keshav N.

    2008-05-20

    Polonium is the only element with a simple cubic (sc) crystal structure. Atoms in solid polonium sit at the corners of a simple cubic unit cell and no where else. Polonium has a valence electron configuration 6s{sup 2}6p{sup 4} (Z = 84). The low temperature {alpha}-phase transforms into the rhombohedral (trigonal) {beta} structure at {approx}348 K. The sc {alpha}-Po unit cell constant is a = 3.345 A. The beta form of polonium ({beta}-Po) has the lattice parameters, a{sub R} = 3.359 A and a rhombohedral angle 98 deg. 13'. We have performed an ab initio electronic structure calculation by using the density functional theory. We have performed the calculation with and without spin-orbit (SO) coupling by using both the LDA and the GGA for the exchange-correlations. The k-points in a simple cubic BZ are determined by R (0.5, 0.5, 0.5), {gamma} (0, 0, 0), X (0.5, 0, 0), M (0.5, 0.5, 0) and {gamma} (0, 0, 0). Other directions of k-points are {gamma} (0, 0, 0), X (0.5, 0, 0), R (0.5, 0.5, 0.5) and {gamma} (0, 0, 0). The SO splittings of p states at the {gamma} point in the GGA+SO scheme for {alpha}-Po are 0.04 eV and 0.02 eV while for the {beta}-Po these are 0.03 eV and 0.97 eV. We have also calculated the vibrational spectra for the unit cells in both the structures. We find that exchanging of a Po atom by Pb atom produces several more bands and destabilizes the {beta} phase.

  15. Ab initio study of cyanoguanidine isomers

    NASA Astrophysics Data System (ADS)

    Arbuznikov, A. V.; Sheludyakova, L. A.; Burgina, E. B.

    1995-06-01

    An ab initio quantum chemical study of the geometric structure and stability of cyanoguanidine isomers was carried out at the Hartree-Fock and Møller-Plesset levels of theory. Two stable separable isomers ('cyanioime' and 'cyanoamine') are found. This gives evidence in favour of the vibrational spectroscopy data showing the existence of both isomers.

  16. Ab initio study of cyanoguanidine isomers

    NASA Astrophysics Data System (ADS)

    Arbuznikov, A. V.; Sheludyakova, L. A.; Burgina, E. B.

    1995-06-01

    An ab initio quantum chemical study of the geometric structure and stability of cyanoguanidine isomers was carried out at the Hartree-Fock and Møller-Plesset levels of theory. Two stable separable isomers (‘cyanioime' and ‘cyanoamine') are found. This gives evidence in favour of the vibrational spectroscopy data showing the existence of both isomers.

  17. Asymmetric synthesis of tertiary thiols and thioethers

    PubMed Central

    MacLellan, Paul

    2011-01-01

    Summary Enantiomerically pure tertiary thiols provide a major synthetic challenge, and despite the importance of chiral sulfur-containing compounds in biological and medicinal chemistry, surprisingly few effective methods are suitable for the asymmetric synthesis of tertiary thiols. This review details the most practical of the methods available. PMID:21647256

  18. Nodular tertiary syphilis in an immunocompetent patient*

    PubMed Central

    Bittencourt, Maraya de Jesus Semblano; de Brito, Arival Cardoso; Nascimento, Bianca Angelina Macêdodo; Carvalho, Alessandra Haber; Drago, Marion Guimarães

    2016-01-01

    Acquired syphilis can be divided into primary, secondary, latent, and tertiary stages. About 25% of patients with untreated primary syphilis will develop late signs that generally occur after three to five years, with involvement of several organs. The authors present an immunocompetent female who developed a tertiary stage syphilis presenting with long-standing nodular plaques. PMID:27579755

  19. Tertiary Education and Training in Australia, 2010

    ERIC Educational Resources Information Center

    National Centre for Vocational Education Research (NCVER), 2012

    2012-01-01

    This publication presents information on tertiary education and training during 2010, including statistics on participation and outcomes. The definition of tertiary education and training adopted for this publication is formal study in vocational education and training (VET) and higher education, including enrolments in Australian Qualifications…

  20. Understanding Secondary-Tertiary Transition in Mathematics

    ERIC Educational Resources Information Center

    Clark, Megan; Lovric, Miroslav

    2009-01-01

    In Clark and Lovric ("Suggestion for a theoretical model for secondary-tertiary transition in mathematics", "Math. Educ. Res. J." 20(2) (2008), pp. 25-37) we began developing a model for the secondary-tertiary transition in mathematics, based on the anthropological notion of a rite of passage. We articulated several reasons why we believe that the…

  1. Mixed-Sector Tertiary Education. Research Overview

    ERIC Educational Resources Information Center

    Moodie, Gavin

    2012-01-01

    This research overview provides the key messages arising from two related projects investigating tertiary education institutions that have recently begun to offer tertiary programs outside the sector of their initial establishment and the sector of the majority of their enrolments. These are TAFE institutes offering higher education programs,…

  2. Ab initio infrared and Raman spectra

    NASA Astrophysics Data System (ADS)

    Fredkin, Donald R.; Komornicki, Andrew; White, Steven R.; Wilson, Kent R.

    1983-06-01

    We discuss several ways in which molecular absorption and scattering spectra can be computed ab initio, from the fundamental constants of nature. These methods can be divided into two general categories. In the first, or sequential, type of approach, one first solves the electronic part of the Schrödinger equation in the Born-Oppenheimer approximation, mapping out the potential energy, dipole moment vector (for infrared absorption) and polarizability tensor (for Raman scattering) as functions of nuclear coordinates. Having completed the electronic part of the calculation, one then solves the nuclear part of the problem either classically or quantum mechanically. As an example of the sequential ab initio approach, the infrared and Raman rotational and vibrational-rotational spectral band contours for the water molecule are computed in the simplest rigid rotor, normal mode approximation. Quantum techniques are used to calculate the necessary potential energy, dipole moment, and polarizability information at the equilibrium geometry. A new quick, accurate, and easy to program classical technique involving no reference to Euler angles or special functions is developed to compute the infrared and Raman band contours for any rigid rotor, including asymmetric tops. A second, or simultaneous, type of ab initio approach is suggested for large systems, particularly those for which normal mode analysis is inappropriate, such as liquids, clusters, or floppy molecules. Then the curse of dimensionality prevents mapping out in advance the complete potential, dipole moment, and polarizability functions over the whole space of nuclear positions of all atoms, and a solution in which the electronic and nuclear parts of the Born-Oppenheimer approximation are simultaneously solved is needed. A quantum force classical trajectory (QFCT) molecular dynamic method, based on linear response theory, is described, in which the forces, dipole moment, and polarizability are computed quantum

  3. Ab initio infrared and Raman spectra

    NASA Technical Reports Server (NTRS)

    Fredkin, D. R.; White, S. R.; Wilson, K. R.; Komornicki, A.

    1983-01-01

    It is pointed out that with increased computer power and improved computational techniques, such as the gradients developed in recent years, it is becoming practical to compute spectra ab initio, from the fundamental constants of nature, for systems of increasing complexity. The present investigation has the objective to explore several possible ab initio approaches to spectra, giving particular attention to infrared and nonresonance Raman. Two approaches are discussed. The sequential approach, in which first the electronic part and then later the nuclear part of the Born-Oppenheimer approximation is solved, is appropriate for small systems. The simultaneous approach, in which the electronic and nuclear parts are solved at the same time, is more appropriate for many-atom systems. A review of the newer quantum gradient techniques is provided, and the infrared and Raman spectral band contours for the water molecule are computed.

  4. Ab initio Theory of Semiconductor Nanocrystals

    NASA Astrophysics Data System (ADS)

    Wang, Lin-Wang

    2007-03-01

    With blooming experimental synthesis of various nanostructures out of many semiconductor materials, there is an urgent need to calculate the electronic structures and optical properties of these nanosystems based on reliable ab initio methods. Unfortunately, due to the O(N^3) scaling of the conventional ab initio calculation methods based on the density functional theory (DFT), and the >1000 atom sizes of the most experimental nanosystems, the direct applications of these conventional ab intio methods are often difficult. Here we will present the calculated results using our O(N) scaling charge patching method (CPM) [1,2] to nanosystems up to 10,000 atoms. The CPM yields the charge density of a nanosystem by patching the charge motifs generated from small prototype systems. The CPM electron/hole eigen energies differ from the directly calculated results by only ˜10-20 meV. We will present the optical band gaps of quantum dots and wires, quantum rods, quantum dot/quantum well, and quantum dots doped with impurities. Besides good agreements with experimental measurements, we will demonstrate why it is important to perform ab initio calculations, in contrast with the continuum model k.p calculations. We will show the effects of surface polarization potentials and the internal electric fields. Finally, a linear scaling 3 dimensional fragment (LS3DF) method will be discussed. The LS3DF method can be used to calculate the total energy and atomic forces of a large nanosystem, with the results practically the same as the direct DFT method. Our work demonstrates that, with the help of supercomputers, it is now feasible to calculate the electronic structures and optical properties of >10,000 atom nanocrystals with ab initio accuracy. [1] L.W. Wang, Phys. Rev. Lett. 88, 256402 (2002). [2] J. Li, L.W. Wang, Phys. Rev. B 72, 125325 (2005).

  5. Tertiary structural propensities reveal fundamental sequence/structure relationships.

    PubMed

    Zheng, Fan; Zhang, Jian; Grigoryan, Gevorg

    2015-05-05

    Extracting useful generalizations from the continually growing Protein Data Bank (PDB) is of central importance. We hypothesize that the PDB contains valuable quantitative information on the level of local tertiary structural motifs (TERMs). We show that by breaking a protein structure into its constituent TERMs, and querying the PDB to characterize the natural ensemble matching each, we can estimate the compatibility of the structure with a given amino acid sequence through a metric we term "structure score." Considering submissions from recent Critical Assessment of Structure Prediction (CASP) experiments, we found a strong correlation (R = 0.69) between structure score and model accuracy, with poorly predicted regions readily identifiable. This performance exceeds that of leading atomistic statistical energy functions. Furthermore, TERM-based analysis of two prototypical multi-state proteins rapidly produced structural insights fully consistent with prior extensive experimental studies. We thus find that TERM-based analysis should have considerable utility for protein structural biology.

  6. Ab Initio Crystal Field for Lanthanides.

    PubMed

    Ungur, Liviu; Chibotaru, Liviu F

    2017-03-13

    An ab initio methodology for the first-principle derivation of crystal-field (CF) parameters for lanthanides is described. The methodology is applied to the analysis of CF parameters in [Tb(Pc)2 ](-) (Pc=phthalocyanine) and Dy4 K2 ([Dy(4) K(2) O(OtBu)(12) ]) complexes, and compared with often used approximate and model descriptions. It is found that the application of geometry symmetrization, and the use of electrostatic point-charge and phenomenological CF models, lead to unacceptably large deviations from predictions based on ab initio calculations for experimental geometry. It is shown how the predictions of standard CASSCF (Complete Active Space Self-Consistent Field) calculations (with 4f orbitals in the active space) can be systematically improved by including effects of dynamical electronic correlation (CASPT2 step) and by admixing electronic configurations of the 5d shell. This is exemplified for the well-studied Er-trensal complex (H3 trensal=2,2',2"-tris(salicylideneimido)trimethylamine). The electrostatic contributions to CF parameters in this complex, calculated with true charge distributions in the ligands, yield less than half of the total CF splitting, thus pointing to the dominant role of covalent effects. This analysis allows the conclusion that ab initio crystal field is an essential tool for the decent description of lanthanides.

  7. AB initio infrared and Raman spectra

    NASA Astrophysics Data System (ADS)

    Fredkin, D. R.; Komornicki, A.; White, S. R.; Wilson, K. R.

    1982-08-01

    We discuss several ways in which molecular absorption and scattering spectra can be computed ab initio, from the fundamental constants of nature. These methods can be divided into two general categories. In the first, or sequential, type of approach, one first solves the electronic part of the Schroedinger equation in the Born-Oppenheimer approximation, mapping out the potential energy, dipole moment vector (for infrared absorption) and polarizability tensor (for Raman scattering) as functions of nuclear coordinates. Having completed the electronic part of the calculation, one then solves the nuclear part of the problem either classically or quantum mechanically. As an example of the sequential ab initio approach, the infrared and Raman rotational and vibrational-rotational spectral band contours for the water molecule are computed in the simplest rigid rotor, normal mode approximation. Quantum techniques, are used to calculate the necessary potential energy, dipole moment, and polarizability information at the equilibrium geometry. A new quick, accurate, and easy to program classical technique involving no reference to Euler angles or special functions is developed to compute the infrared and Raman angles or special functions is developed to compute the infrared and Raman band contours for any rigid rotor, including asymmetric tops. A second, or simultaneous, type of ab initio approach is suggested for large systems, particularly those for which normal mode analysis is inappropriate, such as liquids, clusters, or floppy molecules.

  8. Discrete Molecular Dynamics Can Predict Helical Prestructured Motifs in Disordered Proteins

    PubMed Central

    Han, Kyou-Hoon; Dokholyan, Nikolay V.; Tompa, Péter; Kalmár, Lajos; Hegedűs, Tamás

    2014-01-01

    Intrinsically disordered proteins (IDPs) lack a stable tertiary structure, but their short binding regions termed Pre-Structured Motifs (PreSMo) can form transient secondary structure elements in solution. Although disordered proteins are crucial in many biological processes and designing strategies to modulate their function is highly important, both experimental and computational tools to describe their conformational ensembles and the initial steps of folding are sparse. Here we report that discrete molecular dynamics (DMD) simulations combined with replica exchange (RX) method efficiently samples the conformational space and detects regions populating α-helical conformational states in disordered protein regions. While the available computational methods predict secondary structural propensities in IDPs based on the observation of protein-protein interactions, our ab initio method rests on physical principles of protein folding and dynamics. We show that RX-DMD predicts α-PreSMos with high confidence confirmed by comparison to experimental NMR data. Moreover, the method also can dissect α-PreSMos in close vicinity to each other and indicate helix stability. Importantly, simulations with disordered regions forming helices in X-ray structures of complexes indicate that a preformed helix is frequently the binding element itself, while in other cases it may have a role in initiating the binding process. Our results indicate that RX-DMD provides a breakthrough in the structural and dynamical characterization of disordered proteins by generating the structural ensembles of IDPs even when experimental data are not available. PMID:24763499

  9. Specific interactions between amyloid-β peptide and curcumin derivatives: Ab initio molecular simulations

    NASA Astrophysics Data System (ADS)

    Ishimura, Hiromi; Kadoya, Ryushi; Suzuki, Tomoya; Murakawa, Takeru; Shulga, Sergiy; Kurita, Noriyuki

    2015-07-01

    Alzheimer's disease is caused by accumulation of amyloid-β (Aβ) peptides in a brain. To suppress the production of Aβ peptides, it is effective to inhibit the cleavage of amyloid precursor protein (APP) by secretases. However, because the secretases also play important roles to produce vital proteins for human body, inhibitors for the secretases may have side effects. To propose new agents for protecting the cleavage site of APP from the attacking of the γ-secretase, we have investigated here the specific interactions between a short APP peptide and curcumin derivatives, using protein-ligand docking as well as ab initio molecular simulations.

  10. Salts employed in hydrophobic interaction chromatography can change protein structure - insights from protein-ligand interaction thermodynamics, circular dichroism spectroscopy and small angle X-ray scattering.

    PubMed

    Komaromy, Andras Z; Kulsing, Chadin; Boysen, Reinhard I; Hearn, Milton T W

    2015-03-01

    Key requirements of protein purification by hydrophobic interaction chromatography (HIC) are preservation of the tertiary/quaternary structure, maintenance of biological function, and separation of the correctly folded protein from its unfolded forms or aggregates. This study examines the relationship between the HIC retention behavior of hen egg white lysozyme (HEWL) in high concentrations of several kosmotropic salts and its conformation, assessed by circular dichroism (CD) spectroscopy. Further, the physicochemical properties of HEWL in the presence of high concentrations of ammonium sulfate, sodium chloride and magnesium chloride were investigated by small angle X-ray scattering (SAXS) at different temperatures. Radii of gyration were extrapolated from Guinier approximations and the indirect transform program GNOM with protein-protein interaction and contrast variation taken into account. A bead model simulation provided information on protein structural changes using ab initio reconstruction with GASBOR. These results correlated to the secondary structure content obtained from CD spectroscopy of HEWL. These changes in SAXS and CD data were consistent with heat capacity ΔCp -values obtained from van't Hoff plot analyses of the retention data. Collectively, these insights enable informed decisions to be made on the choice of chromatographic conditions, leading to improved separation selectivity and opportunities for innovative column-assisted protein refolding methods.

  11. The first solvation shell of magnesium ion in a model protein environment with formate, water, and X-NH3, H2S, imidazole, formaldehyde, and chloride as ligands: an Ab initio study.

    PubMed

    Deerfield, D W; Fox, D J; Head-Gordon, M; Hiskey, R G; Pedersen, L G

    1995-03-01

    The first coordination shell of an Mg(II) ion in a model protein environment is studied. Complexes containing a model carboxylate, an Mg(II) ion, various ligands (NH3, H2S, imidazole, and formaldehyde) and water of hydration about the divalent metal ion were geometry optimized. We find that for complexes with the same coordination number, the unidentate carboxylate-Mg(II) ion is greater than 10 kcal mol-1 more stable than the bidentate orientation. Imidazole was found to be the most stable ligand, followed in order by NH3, formaldehyde, H2O, and H2S.

  12. Progresses in Ab Initio QM/MM Free Energy Simulations of Electrostatic Energies in Proteins: Accelerated QM/MM Studies of pKa, Redox Reactions and Solvation Free Energies

    SciTech Connect

    Kamerlin, Shina C. L.; Haranczyk, Maciej; Warshel, Arieh

    2009-03-01

    Hybrid quantum mechanical / molecular mechanical (QM/MM) approaches have been used to provide a general scheme for chemical reactions in proteins. However, such approaches still present a major challenge to computational chemists, not only because of the need for very large computer time in order to evaluate the QM energy but also because of the need for propercomputational sampling. This review focuses on the sampling issue in QM/MM evaluations of electrostatic energies in proteins. We chose this example since electrostatic energies play a major role in controlling the function of proteins and are key to the structure-function correlation of biological molecules. Thus, the correct treatment of electrostatics is essential for the accurate simulation of biological systems. Although we will be presenting here different types of QM/MM calculations of electrostatic energies (and related properties), our focus will be on pKa calculations. This reflects the fact that pKa of ionizable groups in proteins provide one of the most direct benchmarks for the accuracy of electrostatic models of macromolecules. While pKa calculations by semimacroscopic models have given reasonable results in many cases, existing attempts to perform pKa calculations using QM/MM-FEP have led to large discrepancies between calculated and experimental values. In this work, we accelerate our QM/MM calculations using an updated mean charge distribution and a classical reference potential. We examine both a surface residue (Asp3) of the bovine pancreatic trypsin inhibitor, as well as a residue buried in a hydrophobic pocket (Lys102) of the T4-lysozyme mutant. We demonstrate that by using this approach, we are able to reproduce the relevant sidechain pKas with an accuracy of 3 kcal/mol. This is well within the 7 kcal/mol energy difference observed in studies of enzymatic catalysis, and is thus sufficient accuracy to determine the main contributions to the catalytic energies of enzymes. We also provide an

  13. Asymmetric Synthesis of Tertiary Benzylic Alcohols

    PubMed Central

    Antczak, Monika I.; Cai, Feng; Ready, Joseph M.

    2010-01-01

    Vinyl, aryl and alkynyl organometallics add to ketones containing a stereogenic sulfoxide. Tertiary alcohols are generated in diastereomerically and enantiomerically pure form. Reductive lithiation converts the sulfoxide into a variety of useful functional groups. PMID:21142190

  14. Computational Prediction of RNA Tertiary Structure

    NASA Astrophysics Data System (ADS)

    Zhao, Yunjie; Gong, Zhou; Chen, Changjun; Xiao, Yi

    2012-02-01

    RNAs have been found to be involved in the biological processes. The large RNA usually consists of two basic elements: RNA hairpins and duplex. Due to the experimental determination difficulties, the few RNA tertiary structures limit our understanding of the specific regulation mechanisms and functions. Therefore, RNA tertiary structure prediction is very important for understanding RNA biological functions. Since RNA often folds hierarchically, one of the possible RNA structure prediction approaches is through the hierarchical steps. Here, we focus on the prediction method of RNA tertiary hairpin and duplex structures in which assembles the small tertiary structure fragments from well-defined RNA structural motifs. In a benchmark test with known experiment structures, more than half of the cases agree with the experimental structure better than 3 å RMSD over all the heavy atoms. The prediction results also reproduce the native like complementary base pairs of the secondary structures. Most importantly, the method performs the atomic accuracy of tertiary structures by about several minutes. We expect that the method will be a useful resource for RNA tertiary structure prediction and helpful to the biological research community.

  15. Resolution of ab initio shapes determined from small-angle scattering.

    PubMed

    Tuukkanen, Anne T; Kleywegt, Gerard J; Svergun, Dmitri I

    2016-11-01

    Spatial resolution is an important characteristic of structural models, and the authors of structures determined by X-ray crystallography or electron cryo-microscopy always provide the resolution upon publication and deposition. Small-angle scattering of X-rays or neutrons (SAS) has recently become a mainstream structural method providing the overall three-dimensional structures of proteins, nucleic acids and complexes in solution. However, no quantitative resolution measure is available for SAS-derived models, which significantly hampers their validation and further use. Here, a method is derived for resolution assessment for ab initio shape reconstruction from scattering data. The inherent variability of the ab initio shapes is utilized and it is demonstrated how their average Fourier shell correlation function is related to the model resolution. The method is validated against simulated data for proteins with known high-resolution structures and its efficiency is demonstrated in applications to experimental data. It is proposed that henceforth the resolution be reported in publications and depositions of ab initio SAS models.

  16. Resolution of ab initio shapes determined from small-angle scattering

    PubMed Central

    Tuukkanen, Anne T.; Kleywegt, Gerard J.; Svergun, Dmitri I.

    2016-01-01

    Spatial resolution is an important characteristic of structural models, and the authors of structures determined by X-ray crystallography or electron cryo-microscopy always provide the resolution upon publication and deposition. Small-angle scattering of X-rays or neutrons (SAS) has recently become a mainstream structural method providing the overall three-dimensional structures of proteins, nucleic acids and complexes in solution. However, no quantitative resolution measure is available for SAS-derived models, which significantly hampers their validation and further use. Here, a method is derived for resolution assessment for ab initio shape reconstruction from scattering data. The inherent variability of the ab initio shapes is utilized and it is demonstrated how their average Fourier shell correlation function is related to the model resolution. The method is validated against simulated data for proteins with known high-resolution structures and its efficiency is demonstrated in applications to experimental data. It is proposed that henceforth the resolution be reported in publications and depositions of ab initio SAS models. PMID:27840683

  17. Structural properties of liquid N-methylacetamide via ab initio, path integral, and classical molecular dynamics

    NASA Astrophysics Data System (ADS)

    Whitfield, T. W.; Crain, J.; Martyna, G. J.

    2006-03-01

    In order to better understand the physical interactions that stabilize protein secondary structure, the neat liquid state of a peptidic fragment, N-methylacetamide (NMA), was studied using computer simulation. Three different descriptions of the molecular liquid were examined: an empirical force field treatment with classical nuclei, an empirical force field treatment with quantum mechanical nuclei, and an ab initio density functional theory (DFT) treatment. The DFT electronic structure was evaluated using the BLYP approximate functional and a plane wave basis set. The different physical effects probed by the three models, such as quantum dispersion, many-body polarization, and nontrivial charge distributions on the liquid properties, were compared. Much of the structural ordering in the liquid is characterized by hydrogen bonded chains of NMA molecules. Modest structural differences are present among the three models of liquid NMA. The average molecular dipole in the liquid under the ab initio treatment, however, is enhanced by 60% over the gas phase value.

  18. Germacrene D Cyclization: An Ab Initio Investigation

    PubMed Central

    Setzer, William N.

    2008-01-01

    Essential oils that contain large concentrations of germacrene D are typically accompanied by cadinane sesquiterpenoids. The acid-catalyzed cyclization of germacrene D to give cadinane and selinane sesquiterpenes has been computationally investigated using both density functional (B3LYP/6-31G*) and post Hartree-Fock (MP2/6-31G* *) ab initio methods. The calculated energies are in general agreement with experimentally observed product distributions, both from acid-catalyzed cyclizations as well as distribution of the compounds in essential oils. PMID:19325722

  19. Ab initio quantum chemistry: Methodology and applications

    PubMed Central

    Friesner, Richard A.

    2005-01-01

    This Perspective provides an overview of state-of-the-art ab initio quantum chemical methodology and applications. The methods that are discussed include coupled cluster theory, localized second-order Moller–Plesset perturbation theory, multireference perturbation approaches, and density functional theory. The accuracy of each approach for key chemical properties is summarized, and the computational performance is analyzed, emphasizing significant advances in algorithms and implementation over the past decade. Incorporation of a condensed-phase environment by means of mixed quantum mechanical/molecular mechanics or self-consistent reaction field techniques, is presented. A wide range of illustrative applications, focusing on materials science and biology, are discussed briefly. PMID:15870212

  20. Molecular associations from ab initio pair potentials

    NASA Astrophysics Data System (ADS)

    Iglesias, E.; Sordo, T. L.; Sordo, J. A.

    1991-12-01

    A method of building up stable molecular associations by using pair potentials from ab initio calculations is presented. The Matsuoka-Clementi-Yoshimine potential has been chosen to emulate the water-water interactions while 1-6-12 potentials are used to compute both solute-solvent and solute-solute interactions. Parameters for neutral-amino-acid-water and neutral- amino-acid-neutral-amino-acid interactions are provided by the program. Supermolecules are constructed by minimization of the interaction energy of the molecules involved. Both steepest-decent and Fletcher-Powell algorithms are available to carry out such a minimization.

  1. Ab-initio Studies Of Lithium Oxide

    NASA Astrophysics Data System (ADS)

    Gupta, M. K.; Goel, Prabhatasree; Mittal, R.; Chaplot, S. L.

    2010-12-01

    Lithium oxide is an important material because of its high thermal conductivity and superionic behavior at high temperature. It behaves like a superionic conductor above 1200 K. Phonon frequencies have been calculated using ab-initio method. The calculations of phonon dispersion relation near unit cell volume corresponding to the superionic transition indicate softening of zone boundary transverse acoustic phonon mode along (110). The instability of phonon mode could lead to the dynamical disorder of lithium sub lattice. Thermal expansion and equation of states are also computed. The results compare well with our previous semi-empirical potential calculations.

  2. Assessing Predicted Contacts for Building Protein Three-Dimensional Models.

    PubMed

    Adhikari, Badri; Bhattacharya, Debswapna; Cao, Renzhi; Cheng, Jianlin

    2017-01-01

    Recent successes of contact-guided protein structure prediction methods have revived interest in solving the long-standing problem of ab initio protein structure prediction. With homology modeling failing for many protein sequences that do not have templates, contact-guided structure prediction has shown promise, and consequently, contact prediction has gained a lot of interest recently. Although a few dozen contact prediction tools are already currently available as web servers and downloadables, not enough research has been done towards using existing measures like precision and recall to evaluate these contacts with the goal of building three-dimensional models. Moreover, when we do not have a native structure for a set of predicted contacts, the only analysis we can perform is a simple contact map visualization of the predicted contacts. A wider and more rigorous assessment of the predicted contacts is needed, in order to build tertiary structure models. This chapter discusses instructions and protocols for using tools and applying techniques in order to assess predicted contacts for building three-dimensional models.

  3. Towards Accurate Ab Initio Predictions of the Spectrum of Methane

    NASA Technical Reports Server (NTRS)

    Schwenke, David W.; Kwak, Dochan (Technical Monitor)

    2001-01-01

    We have carried out extensive ab initio calculations of the electronic structure of methane, and these results are used to compute vibrational energy levels. We include basis set extrapolations, core-valence correlation, relativistic effects, and Born- Oppenheimer breakdown terms in our calculations. Our ab initio predictions of the lowest lying levels are superb.

  4. Molecular Dynamics Simulation of Bacteriorhodopsin's Photoisomerization Using Ab Initio Forces for the Excited Chromophore

    PubMed Central

    Hayashi, Shigehiko; Tajkhorshid, Emad; Schulten, Klaus

    2003-01-01

    Retinal proteins are photoreceptors found in many living organisms. They possess a common chromophore, retinal, that upon absorption of light isomerizes and thereby triggers biological functions ranging from light energy conversion to phototaxis and vision. The photoisomerization of retinal is extremely fast, highly selective inside the protein matrix, and characterized through optimal sensitivity to incoming light. This article describes the first report of an ab initio quantum mechanical description of the in situ isomerization dynamics of retinal in bacteriorhodopsin, a microbial retinal protein that functions as a light-driven proton pump. The description combines ab initio multi-electronic state molecular dynamics of a truncated retinal chromophore model (N-methyl-γ-methylpenta-2,4-dieniminium cation fragment) with molecular mechanics of the protein motion and unveils in complete detail the photoisomerization process. The results illustrate the essential role of the protein for the characteristic kinetics and high selectivity of the photoisomerization: the protein arrests inhomogeneous photoisomerization paths and funnels them into a single path that initiates the functional process. Supported by comparison with dynamic spectral modulations observed in femtosecond spectroscopy, the results identify the principal molecular motion during photoisomerization. PMID:12944261

  5. Tertiary model of a plant cellulose synthase

    PubMed Central

    Sethaphong, Latsavongsakda; Haigler, Candace H.; Kubicki, James D.; Zimmer, Jochen; Bonetta, Dario; DeBolt, Seth; Yingling, Yaroslava G.

    2013-01-01

    A 3D atomistic model of a plant cellulose synthase (CESA) has remained elusive despite over forty years of experimental effort. Here, we report a computationally predicted 3D structure of 506 amino acids of cotton CESA within the cytosolic region. Comparison of the predicted plant CESA structure with the solved structure of a bacterial cellulose-synthesizing protein validates the overall fold of the modeled glycosyltransferase (GT) domain. The coaligned plant and bacterial GT domains share a six-stranded β-sheet, five α-helices, and conserved motifs similar to those required for catalysis in other GT-2 glycosyltransferases. Extending beyond the cross-kingdom similarities related to cellulose polymerization, the predicted structure of cotton CESA reveals that plant-specific modules (plant-conserved region and class-specific region) fold into distinct subdomains on the periphery of the catalytic region. Computational results support the importance of the plant-conserved region and/or class-specific region in CESA oligomerization to form the multimeric cellulose–synthesis complexes that are characteristic of plants. Relatively high sequence conservation between plant CESAs allowed mapping of known mutations and two previously undescribed mutations that perturb cellulose synthesis in Arabidopsis thaliana to their analogous positions in the modeled structure. Most of these mutation sites are near the predicted catalytic region, and the confluence of other mutation sites supports the existence of previously undefined functional nodes within the catalytic core of CESA. Overall, the predicted tertiary structure provides a platform for the biochemical engineering of plant CESAs. PMID:23592721

  6. Ab initio based polarizable force field parametrization

    NASA Astrophysics Data System (ADS)

    Masia, Marco

    2008-05-01

    Experimental and simulation studies of anion-water systems have pointed out the importance of molecular polarization for many phenomena ranging from hydrogen-bond dynamics to water interfaces structure. The study of such systems at molecular level is usually made with classical molecular dynamics simulations. Structural and dynamical features are deeply influenced by molecular and ionic polarizability, which parametrization in classical force field has been an object of long-standing efforts. Although when classical models are compared to ab initio calculations at condensed phase, it is found that the water dipole moments are underestimated by ˜30%, while the anion shows an overpolarization at short distances. A model for chloride-water polarizable interaction is parametrized here, making use of Car-Parrinello simulations at condensed phase. The results hint to an innovative approach in polarizable force fields development, based on ab initio simulations, which do not suffer for the mentioned drawbacks. The method is general and can be applied to the modeling of different systems ranging from biomolecular to solid state simulations.

  7. Ab initio non-relativistic spin dynamics

    SciTech Connect

    Ding, Feizhi; Goings, Joshua J.; Li, Xiaosong; Frisch, Michael J.

    2014-12-07

    Many magnetic materials do not conform to the (anti-)ferromagnetic paradigm where all electronic spins are aligned to a global magnetization axis. Unfortunately, most electronic structure methods cannot describe such materials with noncollinear electron spin on account of formally requiring spin alignment. To overcome this limitation, it is necessary to generalize electronic structure methods and allow each electron spin to rotate freely. Here, we report the development of an ab initio time-dependent non-relativistic two-component spinor (TDN2C), which is a generalization of the time-dependent Hartree-Fock equations. Propagating the TDN2C equations in the time domain allows for the first-principles description of spin dynamics. A numerical tool based on the Hirshfeld partitioning scheme is developed to analyze the time-dependent spin magnetization. In this work, we also introduce the coupling between electron spin and a homogenous magnetic field into the TDN2C framework to simulate the response of the electronic spin degrees of freedom to an external magnetic field. This is illustrated for several model systems, including the spin-frustrated Li{sub 3} molecule. Exact agreement is found between numerical and analytic results for Larmor precession of hydrogen and lithium atoms. The TDN2C method paves the way for the ab initio description of molecular spin transport and spintronics in the time domain.

  8. Freezing-induced perturbation of tertiary structure of a monoclonal antibody.

    PubMed

    Liu, Lu; Braun, Latoya Jones; Wang, Wei; Randolph, Theodore W; Carpenter, John F

    2014-07-01

    We studied the effects of pH and solution additives on freezing-induced perturbations in the tertiary structure of a monoclonal antibody (mAb) by intrinsic tryptophan fluorescence spectroscopy. In general, freezing caused perturbations in the tertiary structure of the mAb, which were reversible or irreversible depending on the pH or excipients present in the formulation. Protein aggregation occurred in freeze-thawed samples in which perturbations of the tertiary structure were observed, but the levels of protein aggregates formed were not proportional to the degree of structural perturbation. Protein aggregation also occurred in freeze-thawed samples without obvious structural perturbations, most likely because of freeze concentration of protein and salts, and thus reduced protein colloidal stability. Therefore, freezing-induced protein aggregation may or may not first involve the perturbation of its native structure, followed by the assembly processes to form aggregates. Depending on the solution conditions, either step can be rate limiting. Finally, this study demonstrates the potential of fluorescence spectroscopy as a valuable tool for screening therapeutic protein formulations subjected to freeze-thaw stress.

  9. Cooperative Tertiary Interaction Network Guides RNA Folding

    SciTech Connect

    Behrouzi, Reza; Roh, Joon Ho; Kilburn, Duncan; Briber, R.M.; Woodson, Sarah A.

    2013-04-08

    Noncoding RNAs form unique 3D structures, which perform many regulatory functions. To understand how RNAs fold uniquely despite a small number of tertiary interaction motifs, we mutated the major tertiary interactions in a group I ribozyme by single-base substitutions. The resulting perturbations to the folding energy landscape were measured using SAXS, ribozyme activity, hydroxyl radical footprinting, and native PAGE. Double- and triple-mutant cycles show that most tertiary interactions have a small effect on the stability of the native state. Instead, the formation of core and peripheral structural motifs is cooperatively linked in near-native folding intermediates, and this cooperativity depends on the native helix orientation. The emergence of a cooperative interaction network at an early stage of folding suppresses nonnative structures and guides the search for the native state. We suggest that cooperativity in noncoding RNAs arose from natural selection of architectures conducive to forming a unique, stable fold.

  10. Correlation of tertiary formations of Alaska

    USGS Publications Warehouse

    MacNeil, F.S.; Wolfe, J.A.; Miller, D.J.; Hopkins, D.M.

    1961-01-01

    Recent stratigraphic and paleontologic studies have resulted in substantial revision of the age assignments and inter-basin correlations of the Tertiary formations of Alaska as given in both an earlier compilation by P. S. Smith (1939) and a tentative chart prepared for distribution at the First International Symposium on Arctic Geology at Calgary, Alberta (Miller, MacNeil, and Wahrhaftig, 1960). Current work in Alaska by the U. S. Geological Survey and several oil companies is furnishing new information at a rapid rate and further revisions may be expected. The correlation chart (Fig. 1), the first published chart to deal exclusively with the Tertiary of Alaska, had the benefit of a considerable amount of stratigraphic data and fossil collections from some oil companies, but recent surface mapping and drilling by other oil companies in several Tertiary basins undoubtedly must have produced much more information. Nevertheless, the extent of available data justifies the publication of a revised correlation chart at this time.

  11. Protein Folding and Structure Prediction from the Ground Up: The Atomistic Associative Memory, Water Mediated, Structure and Energy Model

    PubMed Central

    Chen, Mingchen; Lin, Xingcheng; Zheng, Weihua; Onuchic, José N.; Wolynes, Peter G.

    2016-01-01

    The associative memory, water mediated, structure and energy model (AWSEM) is a coarse-grained force field with transferable tertiary interactions that incorporates local in sequence energetic biases using bioinformatically derived structural information about peptide fragments with locally similar sequence that we call memories. The memory information from the protein data bank (PDB) database guides proper protein folding. The structural information about available sequences in the database varies in quality and can sometimes lead to frustrated free energy landscapes locally. One way out of this difficulty is to construct the input fragment memory information from all-atom simulations of portions of the complete polypeptide chain. In this paper, we investigate this approach first put forward by Kwac and Wolynes in a more complete way by studying the structure prediction capabilities of this approach for six alpha-helical proteins. This scheme which we call the atomistic associative memory, water mediated, structure and energy model (AAWSEM) amounts to an ab initio protein structure prediction method that starts from the ground-up without using bioinformatic input. The free energy profiles from AAWSEM show that atomistic fragment memories are sufficient to guide the correct folding when tertiary forces are included. AAWSEM combines the efficiency of coarse-grained simulations on the full protein level with the local structural accuracy achievable from all-atom simulations of only parts of a large protein. The results suggest that a hybrid use of atomistic fragment memory and database memory in structural predictions may well be optimal for many practical applications. PMID:27148634

  12. Ab Initio Modeling of Molecular Radiation

    NASA Technical Reports Server (NTRS)

    Jaffe, Richard; Schwenke, David

    2014-01-01

    Radiative emission from excited states of atoms and molecules can comprise a significant fraction of the total heat flux experienced by spacecraft during atmospheric entry at hypersonic speeds. For spacecraft with ablating heat shields, some of this radiative flux can be absorbed by molecular constituents in the boundary layer that are formed by the ablation process. Ab initio quantum mechanical calculations are carried out to predict the strengths of these emission and absorption processes. This talk will describe the methods used in these calculations using, as examples, the 4th positive emission bands of CO and the 1g+ 1u+ absorption in C3. The results of these calculations are being used as input to NASA radiation modeling codes like NeqAir, HARA and HyperRad.

  13. Discovering chemistry with an ab initio nanoreactor

    SciTech Connect

    Wang, Lee-Ping; Titov, Alexey; McGibbon, Robert; Liu, Fang; Pande, Vijay S.; Martínez, Todd J.

    2014-11-02

    Chemical understanding is driven by the experimental discovery of new compounds and reactivity, and is supported by theory and computation that provides detailed physical insight. While theoretical and computational studies have generally focused on specific processes or mechanistic hypotheses, recent methodological and computational advances harken the advent of their principal role in discovery. Here we report the development and application of the ab initio nanoreactor – a highly accelerated, first-principles molecular dynamics simulation of chemical reactions that discovers new molecules and mechanisms without preordained reaction coordinates or elementary steps. Using the nanoreactor we show new pathways for glycine synthesis from primitive compounds proposed to exist on the early Earth, providing new insight into the classic Urey-Miller experiment. Ultimately, these results highlight the emergence of theoretical and computational chemistry as a tool for discovery in addition to its traditional role of interpreting experimental findings.

  14. Discovering chemistry with an ab initio nanoreactor

    NASA Astrophysics Data System (ADS)

    Martinez, Todd

    Traditional approaches for modeling chemical reaction networks such as those involved in combustion have focused on identifying individual reactions and using theoretical approaches to explore the underlying mechanisms. Recent advances involving graphical processing units (GPUs), commodity products developed for the videogaming industry, have made it possible to consider a distinct approach wherein one attempts to discover chemical reactions and mechanisms. We provide a brief summary of these developments and then discuss the concept behind the ``ab initio nanoreactor'' which explores the space of possible chemical reactions and molecular species for a given stoichiometry. The nanoreactor concept is exemplified with an example to the Urey-Miller reaction network which has been previously advanced as a potential model for prebiotic chemistry. We briefly discuss some of the future directions envisioned for the development of this nanoreactor concept.

  15. Ab Initio Calculation of the Hoyle State

    SciTech Connect

    Epelbaum, Evgeny; Krebs, Hermann; Lee, Dean; Meissner, Ulf-G.

    2011-05-13

    The Hoyle state plays a crucial role in the helium burning of stars heavier than our Sun and in the production of carbon and other elements necessary for life. This excited state of the carbon-12 nucleus was postulated by Hoyle as a necessary ingredient for the fusion of three alpha particles to produce carbon at stellar temperatures. Although the Hoyle state was seen experimentally more than a half century ago nuclear theorists have not yet uncovered the nature of this state from first principles. In this Letter we report the first ab initio calculation of the low-lying states of carbon-12 using supercomputer lattice simulations and a theoretical framework known as effective field theory. In addition to the ground state and excited spin-2 state, we find a resonance at -85(3) MeV with all of the properties of the Hoyle state and in agreement with the experimentally observed energy.

  16. Guiding ab initio calculations by alchemical derivatives

    NASA Astrophysics Data System (ADS)

    to Baben, M.; Achenbach, J. O.; von Lilienfeld, O. A.

    2016-03-01

    We assess the concept of alchemical transformations for predicting how a further and not-tested change in composition would change materials properties. This might help to guide ab initio calculations through multidimensional property-composition spaces. Equilibrium volumes, bulk moduli, and relative lattice stability of fcc and bcc 4d transition metals Zr, Nb, Mo, Tc, Ru, Rh, Pd, and Ag are calculated using density functional theory. Alchemical derivatives predict qualitative trends in lattice stability while equilibrium volumes and bulk moduli are predicted with less than 9% and 28% deviation, respectively. Predicted changes in equilibrium volume and bulk moduli for binary and ternary mixtures of Rh-Pd-Ag are in qualitative agreement even for predicted bulk modulus changes as large as +100% or -50%. Based on these results, it is suggested that alchemical transformations could be meaningful for enhanced sampling in the context of virtual high-throughput materials screening projects.

  17. Discovering chemistry with an ab initio nanoreactor

    PubMed Central

    Wang, Lee-Ping; Titov, Alexey; McGibbon, Robert; Liu, Fang; Pande, Vijay S.; Martínez, Todd J.

    2014-01-01

    Chemical understanding is driven by the experimental discovery of new compounds and reactivity, and is supported by theory and computation that provides detailed physical insight. While theoretical and computational studies have generally focused on specific processes or mechanistic hypotheses, recent methodological and computational advances harken the advent of their principal role in discovery. Here we report the development and application of the ab initio nanoreactor – a highly accelerated, first-principles molecular dynamics simulation of chemical reactions that discovers new molecules and mechanisms without preordained reaction coordinates or elementary steps. Using the nanoreactor we show new pathways for glycine synthesis from primitive compounds proposed to exist on the early Earth, providing new insight into the classic Urey-Miller experiment. These results highlight the emergence of theoretical and computational chemistry as a tool for discovery in addition to its traditional role of interpreting experimental findings. PMID:25411881

  18. Discovering chemistry with an ab initio nanoreactor

    DOE PAGES

    Wang, Lee-Ping; Titov, Alexey; McGibbon, Robert; ...

    2014-11-02

    Chemical understanding is driven by the experimental discovery of new compounds and reactivity, and is supported by theory and computation that provides detailed physical insight. While theoretical and computational studies have generally focused on specific processes or mechanistic hypotheses, recent methodological and computational advances harken the advent of their principal role in discovery. Here we report the development and application of the ab initio nanoreactor – a highly accelerated, first-principles molecular dynamics simulation of chemical reactions that discovers new molecules and mechanisms without preordained reaction coordinates or elementary steps. Using the nanoreactor we show new pathways for glycine synthesis frommore » primitive compounds proposed to exist on the early Earth, providing new insight into the classic Urey-Miller experiment. Ultimately, these results highlight the emergence of theoretical and computational chemistry as a tool for discovery in addition to its traditional role of interpreting experimental findings.« less

  19. Data-Based Methods for AB Initio Protein Structure Prediction

    SciTech Connect

    Dr Keith L. Frost

    2002-11-07

    OAK 270 - Per the DOE Project Officer ''Roland Hirsh'' Germantown, Md. The required final report for this award has been waived due to the fact Dr Keith Frost who was the P.I. on the research took a leave of absence at the end of March 2000, and left the university without an approval. The University adjusted their records to reflect this early termination; no further funding applied.

  20. Ab initio alpha-alpha scattering.

    PubMed

    Elhatisari, Serdar; Lee, Dean; Rupak, Gautam; Epelbaum, Evgeny; Krebs, Hermann; Lähde, Timo A; Luu, Thomas; Meißner, Ulf-G

    2015-12-03

    Processes such as the scattering of alpha particles ((4)He), the triple-alpha reaction, and alpha capture play a major role in stellar nucleosynthesis. In particular, alpha capture on carbon determines the ratio of carbon to oxygen during helium burning, and affects subsequent carbon, neon, oxygen, and silicon burning stages. It also substantially affects models of thermonuclear type Ia supernovae, owing to carbon detonation in accreting carbon-oxygen white-dwarf stars. In these reactions, the accurate calculation of the elastic scattering of alpha particles and alpha-like nuclei--nuclei with even and equal numbers of protons and neutrons--is important for understanding background and resonant scattering contributions. First-principles calculations of processes involving alpha particles and alpha-like nuclei have so far been impractical, owing to the exponential growth of the number of computational operations with the number of particles. Here we describe an ab initio calculation of alpha-alpha scattering that uses lattice Monte Carlo simulations. We use lattice effective field theory to describe the low-energy interactions of protons and neutrons, and apply a technique called the 'adiabatic projection method' to reduce the eight-body system to a two-cluster system. We take advantage of the computational efficiency and the more favourable scaling with system size of auxiliary-field Monte Carlo simulations to compute an ab initio effective Hamiltonian for the two clusters. We find promising agreement between lattice results and experimental phase shifts for s-wave and d-wave scattering. The approximately quadratic scaling of computational operations with particle number suggests that it should be possible to compute alpha scattering and capture on carbon and oxygen in the near future. The methods described here can be applied to ultracold atomic few-body systems as well as to hadronic systems using lattice quantum chromodynamics to describe the interactions of

  1. Ab initio alpha-alpha scattering

    NASA Astrophysics Data System (ADS)

    Elhatisari, Serdar; Lee, Dean; Rupak, Gautam; Epelbaum, Evgeny; Krebs, Hermann; Lähde, Timo A.; Luu, Thomas; Meißner, Ulf-G.

    2015-12-01

    Processes such as the scattering of alpha particles (4He), the triple-alpha reaction, and alpha capture play a major role in stellar nucleosynthesis. In particular, alpha capture on carbon determines the ratio of carbon to oxygen during helium burning, and affects subsequent carbon, neon, oxygen, and silicon burning stages. It also substantially affects models of thermonuclear type Ia supernovae, owing to carbon detonation in accreting carbon-oxygen white-dwarf stars. In these reactions, the accurate calculation of the elastic scattering of alpha particles and alpha-like nuclei—nuclei with even and equal numbers of protons and neutrons—is important for understanding background and resonant scattering contributions. First-principles calculations of processes involving alpha particles and alpha-like nuclei have so far been impractical, owing to the exponential growth of the number of computational operations with the number of particles. Here we describe an ab initio calculation of alpha-alpha scattering that uses lattice Monte Carlo simulations. We use lattice effective field theory to describe the low-energy interactions of protons and neutrons, and apply a technique called the ‘adiabatic projection method’ to reduce the eight-body system to a two-cluster system. We take advantage of the computational efficiency and the more favourable scaling with system size of auxiliary-field Monte Carlo simulations to compute an ab initio effective Hamiltonian for the two clusters. We find promising agreement between lattice results and experimental phase shifts for s-wave and d-wave scattering. The approximately quadratic scaling of computational operations with particle number suggests that it should be possible to compute alpha scattering and capture on carbon and oxygen in the near future. The methods described here can be applied to ultracold atomic few-body systems as well as to hadronic systems using lattice quantum chromodynamics to describe the interactions of

  2. Ab initio solution of macromolecular crystal structures without direct methods.

    PubMed

    McCoy, Airlie J; Oeffner, Robert D; Wrobel, Antoni G; Ojala, Juha R M; Tryggvason, Karl; Lohkamp, Bernhard; Read, Randy J

    2017-04-04

    The majority of macromolecular crystal structures are determined using the method of molecular replacement, in which known related structures are rotated and translated to provide an initial atomic model for the new structure. A theoretical understanding of the signal-to-noise ratio in likelihood-based molecular replacement searches has been developed to account for the influence of model quality and completeness, as well as the resolution of the diffraction data. Here we show that, contrary to current belief, molecular replacement need not be restricted to the use of models comprising a substantial fraction of the unknown structure. Instead, likelihood-based methods allow a continuum of applications depending predictably on the quality of the model and the resolution of the data. Unexpectedly, our understanding of the signal-to-noise ratio in molecular replacement leads to the finding that, with data to sufficiently high resolution, fragments as small as single atoms of elements usually found in proteins can yield ab initio solutions of macromolecular structures, including some that elude traditional direct methods.

  3. Diversification Management at Tertiary Education Level: A Review

    ERIC Educational Resources Information Center

    Takwate, Kwaji Tizhe

    2016-01-01

    This paper examines the concept of management of diversification at tertiary education level in view of the growth of national secondary education system which vested high scramble for tertiary education was made in relation to question of access and expansion. This paper examines management of diversification at tertiary education level as a…

  4. Quarterly Technical Progress Report - West Hackberry Tertiary Project

    SciTech Connect

    Bruce Cerveny; Tor Kragas; Travis Gillham

    1997-07-10

    The West Hackberry Tertiary Project is a field test of the concept that air injection can generate tertiary oil recovery through the Double Displacement Process is the gas displacement of a water invaded oil column for the purpose of recovering tertiary oil through gravity discharge. The novel aspect of this project is the use of air as the injection fluid.

  5. Quarterly Technical Progress Report - West Hackberry Tertiary Project

    SciTech Connect

    Demetrois Yannimaras; Travis Gillham

    1998-04-15

    The West Hackberry Tertiary Project is a field test of the concept that air injection can generate tertiary oil recovery through the Double Displacement Process is the gas displacement of a water invaded oil column for the purpose of recovering tertiary oil through gravity discharge. The novel aspect of this project is the use of air as the injection fluid.

  6. Understanding Australian Aboriginal Tertiary Student Needs

    ERIC Educational Resources Information Center

    Oliver, Rhonda; Rochecouste, Judith; Bennell, Debra; Anderson, Roz; Cooper, Inala; Forrest, Simon; Exell, Mike

    2013-01-01

    Drawing from a study of the experiences of Australian Aboriginal and Torres Strait Islander university students, this paper presents an overview of the specific needs of these students as they enter and progress through their tertiary education. Extracts from a set of case studies developed from both staff and student interviews and an online…

  7. Incorporating Online Tools in Tertiary Education

    ERIC Educational Resources Information Center

    Steenkamp, Leon P.; Rudman, Riaan J.

    2013-01-01

    Students currently studying at tertiary institutions have developed a set of attitudes and aptitudes as a result of growing up in an IT and media-rich environment. These attitudes and aptitudes influence how they learn and in order to be effective, lecturers must adapt to address their learning preferences and use the online teaching tools that…

  8. Tertiary Education and Training in Australia, 2009

    ERIC Educational Resources Information Center

    National Centre for Vocational Education Research (NCVER), 2011

    2011-01-01

    Sourcing data from the National VET Provider Collection and the Higher Education Statistics Collection, this publication provides a summary of participation in tertiary education and training in Australia. It covers participation in Australian Qualifications Framework certificate I qualifications through to doctorates by research, as well as…

  9. Sea-Level Changes during the Tertiary.

    ERIC Educational Resources Information Center

    Vail, Peter R.; Hardenbol, Jan

    1979-01-01

    Discussed are research procedures undertaken to determine the magnitude and timing of eustatic sea-level changes during the Tertiary Period. Data now becoming available give scientists a knowledge of conditions that may have been conducive to the formation of petroleum. (BT)

  10. Adapting Cooperative Learning in Tertiary ELT

    ERIC Educational Resources Information Center

    Ning, Huiping

    2011-01-01

    An updated guideline for tertiary ELT in China has shifted the emphasis to the development of learners' ability to communicate in English. Using group work and getting learners actively involved in the actual use of English are highlighted more than before. This article focuses on adapting cooperative learning methods for ELT with tertiary…

  11. Indigenous Students in the Tertiary Education Sector

    ERIC Educational Resources Information Center

    Bandias, Susan; Fuller, Don; Larkin, Steven

    2014-01-01

    Important recent objectives of indigenous education policy in Australia have been aimed at redressing indigenous economic and social disadvantage through increasing student retention, progression and completion rates in both compulsory and post-compulsory education. The two sectors of the tertiary education system, vocational education and…

  12. American Tertiary mollusks of the genus Clementia

    USGS Publications Warehouse

    Woodring, W.P.

    1927-01-01

    Aside from its value as an aid in determining the age of Tertiary beds, the chief interest of the genus Clementia lies in the anomalous features of its present and former distribution. An attempt is made in this paper to trace its geologic history, to point out its paleobiologic significance, and to describe all the known American Tertiary species. The fossils from Colombia used in preparing this report were collected during explorations made under the direction of Dr. 0. B. Hopkins, chief geologist of the Imperial Oil Co. (Ltd.), who kindly donated them to the United States National Museum. Dr. T. Wayland Vaughan, of the Scripps Institution of Oceanography, furnished information relating to specimens collected by him in Mexico. Dr. Bruce L. Clark, of the University of California; Dr. G. Dallas Hanna, of the California Academy of Sciences; Dr. H. A. Pilsbry, of the Philadelphia Academy of Natural Sciences; and Dr. W. D. Matthew, of the American Museum of Natural History, generously loaned type specimens and other material. Doctor Clark and Doctor Hanna also gave information concerning the Tertiary species from California. Mr. Ralph B. Stewart, of the University of California, read the manuscript, and I have taken advantage of his suggestions. I am also indebted to Mr. L. R. Cox, of the British Museum, for information relating to the fossil species from Persia, Zanzibar, and Burma, and to Dr. Axel A. Olsson, of the International Petroleum Co., for data concerning undescribed Tertiary species from Peru.

  13. Smart Utilization of Tertiary Instructional Modes

    ERIC Educational Resources Information Center

    Hamilton, John; Tee, Singwhat

    2010-01-01

    This empirical research surveys first year tertiary business students across different campuses regarding their perceived views concerning traditional, blended and flexible instructional approaches. A structural equation modeling approach shows traditional instructional modes deliver lower levels of student-perceived learning quality, learning…

  14. Collaborating in the Transition to Tertiary Writing.

    ERIC Educational Resources Information Center

    Clerehan, Rosemary; Moore, Tim; Vance, Sheila

    The Monash University (Australia) Transition to Tertiary Writing Project seeks to produce a World Wide Web-based resource for first-year students to facilitate their transition to the kinds of thinking and writing valued at the university. The background research on which this language and academic skills (LAS) project is based centers on three…

  15. Primary thrombophilia in Mexico: a single tertiary referral hospital experience.

    PubMed

    Lacayo-Leñero, Dennis; Hernández-Hernández, Darinel; Valencia-Martínez, Andrés; Barrales-Benítez, Olga; Vargas-Ruiz, Angel G

    2016-12-01

    Thrombophilia is a complex hypercoagulable state that increases the risk of thrombosis. Most reports in medical literature of the Mexican population with this disease lack statistical validity. Therefore, the aim of this study is to describe the prevalence of primary thrombophilia in a tertiary referral hospital in Mexico. This is a study of patients referred to our hospital because of a hypercoagulable state and who later on were diagnosed with primary thrombophilia. The thrombophilia workup included methylenetetrahydrofolate reductase (MTHFR) C677T, antiphospholipid antibodies, protein C, protein S, antithrombin, factor VIII, factor V Leiden, prothrombin mutation G20210A, activated protein C resistance, JAK2 V617F and homocysteine. Ninety-five individuals were tested. The MTHFR C677T polymorphism was the most frequent anomaly in 84.1% of the tested individuals. There was a relatively low prevalence of factor V Leiden (5.2%) and anticoagulant protein deficiency (8.3%). The MTHFR C677T polymorphism has a very high prevalence compared with the low prevalence of anticoagulant protein deficiency and factor V Leiden mutation in Mexicans.

  16. Ab Initio: And a New Era of Airline Pilot Training.

    ERIC Educational Resources Information Center

    Gesell, Laurence E.

    1995-01-01

    Expansion of air transportation and decreasing numbers seeking pilot training point to a shortage of qualified pilots. Ab initio training, in which candidates with no flight time are trained to air transport proficiency, could resolve the problem. (SK)

  17. Helical junctions as determinants for RNA folding: origin of tertiary structure stability of the hairpin ribozyme.

    PubMed

    Klostermeier, D; Millar, D P

    2000-10-24

    Helical junctions are ubiquitous structural elements that govern the folding and tertiary structure of RNAs. The tobacco ringspot virus hairpin ribozyme consists of two helix-loop-helix elements that lie on adjacent arms of a four-way junction. In the active form of the hairpin ribozyme, the loops are in proximity. The nature of the helical junction determines the stability of the hairpin ribozyme tertiary structure [Walter, N. G., Burke, J. M., and Millar, D. P. (1999) Nat. Struct. Biol. 6, 544-549] and thus its catalytic activity. We used two-, three-, and four-way junction hairpin ribozymes as model systems to investigate the thermodynamic basis for the different tertiary structure stabilities. The equilibrium between docked and extended conformers was analyzed as a function of temperature using time-resolved fluorescence resonance energy transfer (trFRET). As the secondary and tertiary structure transitions overlap, information from UV melting curves and trFRET had to be combined to gain insight into the thermodynamics of both structural transitions. It turned out that the higher tertiary structure stability observed in the context of a four-way junction is the result of a lower entropic cost for the docking process. In the two- and three-way junction ribozymes, a high entropic cost counteracts the favorable enthalpic term, rendering the docked conformer only marginally stable. Thus, two- and three-way junction tertiary structures are more sensitive toward regulation by ligands, whereas four-way junctions provide a stable scaffold. Altogether, RNA folding and stability appear to be governed by principles similar to those for the folding of proteins.

  18. Tertiary structure-related activity of tick defensin (persulcatusin) in the taiga tick, Ixodes persulcatus.

    PubMed

    Isogai, Emiko; Isogai, Hiroshi; Okumura, Kazuhiko; Hori, Hatsuhiro; Tsuruta, Hiroki; Kurebayashi, Yoichi

    2011-01-01

    Defensins are small cysteine-rich cationic proteins found in both vertebrates and invertebrates constituting the front line of host innate immunity. To examine the importance of the tertiary structure of tick defensin in its antimicrobial activity, we synthesized two types of the peptides with tertiary structure or primary one on basis of the information of the sequence in the defensin originated from the taiga tick, Ixodes persulcatus. Chemically synthesized peptides were used to investigate the activity spectrum against Staphylococcus aureus, Borrelia garinii and flora-associated bacteria. Both synthetic peptides showed antimicrobial activity against S. aureus in short-time killing within 1 h, but they do not show the activity against B. garinii, Stenotrophomonas maltophila and Bacillus spp., which were frequently isolated from the midgut of I. persulcatus. The teriary structure brought more potent activity to S. aureus than primary one in short-time killing. We also examined its antimicrobial activity by evaluation of growth inhibition in the presence of the synthetic peptides. Minimum inhibitory concentration (MIC) was ranged from 1.2 to 5.0 μg/ml in tertiary peptide and from 10 to 40 μg/ml in primary peptide, when 10 strains of S. aureus were used. From the curve of cumulative inhibition rates, MIC50 (MIC which half of the strains showed) to S. aureus is about 1.2 μg/ml in the peptide with tertiary structure and about 10 μg/ml in the linear one. Corynebacterium renale is 10 times or more sensitive to tertiary peptide than primary one. In conclusion, the presence of 3 disulfide bridges, which stabilize the molecule and maintain the tertiary structure, is considered to have an effect on their antimicrobial activities against Gram-positive bacteria such as S. aureus.

  19. The role of Metals in Amyloid Aggregation: A Test Case for ab initio Simulations

    SciTech Connect

    Minicozzi, V.; Rossi, G. C.; Stellato, F.; Morante, S.

    2007-12-26

    First principle ab initio molecular dynamics simulations of the Car-Parrinello type have proved to be of invaluable help in understanding the microscopic mechanisms of chemical bonding both in solid state physics and in structural biophysics. In this work we present as test cases the study of the Cu coordination mode in two especially important examples: Prion protein and {beta}-amyloids. Using medium size PC-clusters as well as larger parallel platforms, we are able to deal with systems comprising 300 to 500 atoms and 1000 to 1500 electrons for as long as 2-3 ps. We present structural results which confirm indications coming from NMR and XAS data.

  20. Ab initio molecular simulations on specific interactions between amyloid beta and monosaccharides

    NASA Astrophysics Data System (ADS)

    Nomura, Kazuya; Okamoto, Akisumi; Yano, Atsushi; Higai, Shin'ichi; Kondo, Takashi; Kamba, Seiji; Kurita, Noriyuki

    2012-09-01

    Aggregation of amyloid β (Aβ) peptides, which is a key pathogenetic event in Alzheimer's disease, can be caused by cell-surface saccharides. We here investigated stable structures of the solvated complexes of Aβ with some types of monosaccharides using molecular simulations based on protein-ligand docking and classical molecular mechanics methods. Moreover, the specific interactions between Aβ and the monosaccharides were elucidated at an electronic level by ab initio fragment molecular orbital calculations. Based on the results, we proposed which type of monosaccharide prefers to have large binding affinity to Aβ and inhibit the Aβ aggregation.

  1. Insights from modeling the tertiary structure of human BACE2.

    PubMed

    Chou, Kuo-Chen

    2004-01-01

    BACE1, or beta-secretase, is a putative prime therapeutic target for the treatment of Alzheimer's disease. Mapping to the Down syndrome critical region (chromosome 21) and identified as a homologue of BACE1, BACE2 also cleaves amyloid precursor protein at the beta-site. Thus, BACE2, named also as Asp1 or Memapsin1, represents a second beta-secretase candidate. In this paper, the tertiary structure of the protease domain of BACE2 was developed. Although the overall structural topology between BACE1 and BACE2 protease domains is quite similar, the former contains 3 disulfide bonds but the latter only two. Particularly, a subtle structural difference around the DTG/DSG active site between the two structures has been observed that is useful for the in-depth selectivity study of BACE1 and BACE2 inhibitors, stimulating new therapeutic strategies for the treatment of Alzheimer's disease and Down syndrome as well.

  2. Ab initio two-component Ehrenfest dynamics

    SciTech Connect

    Ding, Feizhi; Goings, Joshua J.; Liu, Hongbin; Lingerfelt, David B.; Li, Xiaosong

    2015-09-21

    We present an ab initio two-component Ehrenfest-based mixed quantum/classical molecular dynamics method to describe the effect of nuclear motion on the electron spin dynamics (and vice versa) in molecular systems. The two-component time-dependent non-collinear density functional theory is used for the propagation of spin-polarized electrons while the nuclei are treated classically. We use a three-time-step algorithm for the numerical integration of the coupled equations of motion, namely, the velocity Verlet for nuclear motion, the nuclear-position-dependent midpoint Fock update, and the modified midpoint and unitary transformation method for electronic propagation. As a test case, the method is applied to the dissociation of H{sub 2} and O{sub 2}. In contrast to conventional Ehrenfest dynamics, this two-component approach provides a first principles description of the dynamics of non-collinear (e.g., spin-frustrated) magnetic materials, as well as the proper description of spin-state crossover, spin-rotation, and spin-flip dynamics by relaxing the constraint on spin configuration. This method also holds potential for applications to spin transport in molecular or even nanoscale magnetic devices.

  3. Ab initio phase diagram of iridium

    NASA Astrophysics Data System (ADS)

    Burakovsky, L.; Burakovsky, N.; Cawkwell, M. J.; Preston, D. L.; Errandonea, D.; Simak, S. I.

    2016-09-01

    The phase diagram of iridium is investigated using the Z methodology. The Z methodology is a technique for phase diagram studies that combines the direct Z method for the computation of melting curves and the inverse Z method for the calculation of solid-solid phase boundaries. In the direct Z method, the solid phases along the melting curve are determined by comparing the solid-liquid equilibrium boundaries of candidate crystal structures. The inverse Z method involves quenching the liquid into the most stable solid phase at various temperatures and pressures to locate a solid-solid boundary. Although excellent agreement with the available experimental data (to ≲65 GPa) is found for the equation of state (EOS) of Ir, it is the third-order Birch-Murnaghan EOS with B0'=5 rather than the more widely accepted B0'=4 that describes our ab initio data to higher pressure (P ) . Our results suggest the existence of a random-stacking hexagonal close-packed structure of iridium at high P . We offer an explanation for the 14-layer hexagonal structure observed in experiments by Cerenius and Dubrovinsky.

  4. Ab Initio Quantum Simulations of Liquid Water

    NASA Astrophysics Data System (ADS)

    Gergely, John; Ceperley, David; Gygi, Francois

    2007-03-01

    Some recent efforts at simulating liquid water have employed ``ab initio'' molecular dynamics (AIMD) methods with forces from a version of density functional theory (DFT) and, in some cases, imaginary-time path integrals (PI) to study quantum effects of the protons. Although AIMD methods have met with many successes, errors introduced by the approximations and choices of simulation parameters are not fully understood. We report on path integral Monte Carlo (PIMC) studies of liquid water using DFT energies that provide quantitative benchmarks for PI-AIMD work. Specifically, we present convergence studies of the path integrals and address whether the Trotter number can be reduced by improving the form of the (approximate) action. Also, we assess 1) whether typical AIMD simulations are sufficiently converged in simulation time, i.e., if there is reason to suspect that nonergodic behavior in PI-AIMD methods leads to poor convergence, and 2) the relative efficiency of the methods. E. Schwegler, J.C. Grossman, F. Gygi, G. Galli, J. Chem. Phys 121, 5400 (2004).

  5. Ab initio calculations of nitramine dimers

    NASA Astrophysics Data System (ADS)

    Koh-Fallet, Sharon; Schweigert, Igor

    2015-06-01

    Elevated temperatures and pressures are typically thought to have opposing effects on the reaction channels of nitramine decomposition. These high temperatures promote reactions with loose transition structures (positive activation entropies and volumes), such as N-N bond homolysis. Elevated pressures promote reactions with tight transition structures (negative activation entropies and volumes), such as intramolecular and intermolecular H transfer. However, no quantitative data exists regarding the range of temperatures and pressures at which these effects become pronounced. We are pursuing ab initio calculations of the corresponding unimolecular and bimolecular transition structures with the objective of estimating the relevant thermochemical parameters and quantifying the effects of elevated temperature and pressures on the corresponding rate constants. Here, we present density functional theory and complete active space calculations of gas-phase molecular dimers of nitramines as an intermediate step toward modeling transition structures directly in the condensed phase. This work was supported by the Naval Research Laboratory via the American Society for Engineering and Education and by the Office of Naval Research, both directly and through the Naval Research Laboratory.

  6. Ab-initio study of hexagonal apatites

    NASA Astrophysics Data System (ADS)

    Calderin, Lazaro; Stott, Malcom J.

    2001-03-01

    A silicon stabilized mixture of calcium phosphate phases has been recognized as playing an important role in actively resorbable coatings and in ceramics as bone materials. The nature of this material is being investigated using a variety of techniques including a combination of crystallographic analysis of measured x-ray diffraction spectra, and ab initio quantum mechanics simulations. We have used all-electron, density functional based calculations to investigate a group of hexagonal apatites. The fully relaxed crystallographic structures of hydroxyapatite, and related apatites have been obtained. We will present the results and discuss the nature of the bonding in these materials. The x-ray diffraction pattern and the infra-red spectra have also been obtained and will be compared with experiment. Acknowledgments:This work is part of a collaboration with the Applied Ceramics group of M.Sayer, and with Millenium Biologix Inc. Support of the NSERC of Canada through the award of a Co-operative R & D grant to the collaboration is acknowledged.

  7. The Tertiary and Quaternary pectens of California

    USGS Publications Warehouse

    Arnold, Ralph

    1906-01-01

    This paper consists of two parts. The first is a brief outline of the different Tertiary and Pleistocene formations of California, giving the type localities, where, when, and by whom first described, their salient characters, where they and their supposed equiyalents are known to occur, the species of Pecten found in them, and their typical fauna as far as known. The second is devoted to the description and illustration of all of the known Tertiary, Pleistocene, and Recent Pectens of the western coast of North America from Alaska to and including the Gulf of California. With the description of each species is also given an account of its geologic and geographic range and, where practicable, its associated fauna.

  8. Decomposition of free chlorine with tertiary ammonium.

    PubMed

    Katano, Hajime; Uematsu, Kohei; Tatsumi, Hirosuke; Tsukatani, Toshihide

    2010-01-01

    The reaction of free chlorine with tertiary ammonium or amine compounds in aqueous solution was studied by the amperometry at a rotating Pt-disk electrode. The amperometric method can be applied to follow the concentration of free chlorine (c(Cl)) even in the presence of chloramine species. By addition of mono- and dibutylammonium to the solution containing free chlorine, the step-like decrease in c(Cl) was observed, indicating the rapid formation of the stable chloramine species. By addition of tributylammonium, the c(Cl) was decreased exponentially to nearly zero even if the free chlorine was present initially in excess. The c(Cl)-t curves can be explained by tributylammonium-species-catalyzed decomposition of free chlorine to chloride ion. The catalytic decomposition was observed also with the tertiary-ammonium-based anion-exchange resins. Furthermore, the anion-exchange resins exhibited the decomposition of not only free chlorine but also chloramines in water.

  9. Intrathyroidal parathyroid hyperplasia in tertiary hyperparathyroidism

    PubMed Central

    Kim, Byung Seup; Ryu, Han Suk; Kang, Kyung Ho; Park, Sung Jun

    2013-01-01

    We report herein a case of intrathyroidal parathyroid hyperplasia in a patient with tertiary hyperparathyroidism. The patient was recommended for parathyroidectomy due to sustained hypercalcemia after kidney transplantation. Preoperative radiologic evaluations showed a benign-looking thyroid mass and three enlarged parathyroid glands. Intraoperative intact parathyroid hormone (iPTH) level and frozen biopsy results indicated a missed parathyroid gland after immediate subtotal parathyroidectomy. Then, a secondary partial resection of thyroid including the thyroid nodule was performed. An excised intrathyroid nodule was diagnosed to be parathyroid hyperplasia by frozen biopsy, and intraoperative iPTH level abruptly decreased. A benign-looking thyroidal mass in patients with secondary or tertiary hyperparathyroidism should be carefully evaluated considering the possibility of an intrathyroidal parathyroid hyperplasia. PMID:24964443

  10. Proteins.

    ERIC Educational Resources Information Center

    Doolittle, Russell F.

    1985-01-01

    Examines proteins which give rise to structure and, by virtue of selective binding to other molecules, make genes. Binding sites, amino acids, protein evolution, and molecular paleontology are discussed. Work with encoding segments of deoxyribonucleic acid (exons) and noncoding stretches (introns) provides new information for hypotheses. (DH)

  11. Tertiary serpentinite tectonics in northern Hispaniola

    SciTech Connect

    Nagle, F.; Draper, G.

    1985-01-01

    At least 4 types of serpentinite bodies are found in N. Hispaniola, by different inclusion and Tertiary deformation styles: (1) Narrow slivers occurring on Tertiary faults, rarely containing inclusions, which occur throughout the region. (2) Massive fractured serpentinites associated with a Cretaceous volcanic plutonic and metamorphic basement, and containing rodingite dikes, occurs in the Puerto Plata region. (3) Massive, fractured, but coherent bodies containing Tertiary limestone clasts which apparently the same as nearby limestone overlying the serpentinite occur west of Puerto Plata. (4) Diapirically emplaced bodies in the Gaspar Hernandez region containing both brecciated and massive zones and containing a variety of inclusions. Type 4 bodies protrude into the clastic Upper Eocene Altamira Fm. The most common tectonic inclusions in these bodies are rounded cobbles of diorite and gabbro. Amphibolites are also common, but friable greenschists and blueschists are rare, as are blocks of clastic sediments. The authors suggest that large blocks of the Altamira Fm. were incorporated into the serpentinite during their past Eocene diapirism and that these blocks were deformed in a brittle manner into gouge zones by internal movements in the diapir. Type 4 serpentinites may therefore have incorporated inclusions at high crustal levels by brittle processes. Type 2 bodies, in contrast, may have incorporated inclusions by ductile flow of serpentinite at lower crustal levels. Type 33 bodies are the most enigmatic. They may be sedimentary, but alternatively may have incorporated limestone in a gouge (as for type 4), which has later healed to a coherent mass.

  12. Vaccinia Virus Immunomodulator A46: A Lipid and Protein-Binding Scaffold for Sequestering Host TIR-Domain Proteins

    PubMed Central

    Radakovics, Katharina; Smith, Terry K.; Bobik, Nina; Round, Adam; Djinović-Carugo, Kristina; Usón, Isabel

    2016-01-01

    Vaccinia virus interferes with early events of the activation pathway of the transcriptional factor NF-kB by binding to numerous host TIR-domain containing adaptor proteins. We have previously determined the X-ray structure of the A46 C-terminal domain; however, the structure and function of the A46 N-terminal domain and its relationship to the C-terminal domain have remained unclear. Here, we biophysically characterize residues 1–83 of the N-terminal domain of A46 and present the X-ray structure at 1.55 Å. Crystallographic phases were obtained by a recently developed ab initio method entitled ARCIMBOLDO_BORGES that employs tertiary structure libraries extracted from the Protein Data Bank; data analysis revealed an all β-sheet structure. This is the first such structure solved by this method which should be applicable to any protein composed entirely of β-sheets. The A46(1–83) structure itself is a β-sandwich containing a co-purified molecule of myristic acid inside a hydrophobic pocket and represents a previously unknown lipid-binding fold. Mass spectrometry analysis confirmed the presence of long-chain fatty acids in both N-terminal and full-length A46; mutation of the hydrophobic pocket reduced the lipid content. Using a combination of high resolution X-ray structures of the N- and C-terminal domains and SAXS analysis of full-length protein A46(1–240), we present here a structural model of A46 in a tetrameric assembly. Integrating affinity measurements and structural data, we propose how A46 simultaneously interferes with several TIR-domain containing proteins to inhibit NF-κB activation and postulate that A46 employs a bipartite binding arrangement to sequester the host immune adaptors TRAM and MyD88. PMID:27973613

  13. Three-way RNA junctions with remote tertiary contacts: A recurrent and highly versatile fold

    PubMed Central

    de la Peña, Marcos; Dufour, David; Gallego, José

    2009-01-01

    Three-way junction RNAs adopt a recurrent Y shape when two of the helices form a coaxial stack and the third helix establishes one or more tertiary contacts several base pairs away from the junction. In this review, the structure, distribution, and functional relevance of these motifs are examined. Structurally, the folds exhibit conserved junction topologies, and the distal tertiary interactions play a crucial role in determining the final shape of the structures. The junctions and remote tertiary contacts behave as flexible hinge motifs that respond to changes in the other region, providing these folds with switching mechanisms that have been shown to be functionally useful in a variety of contexts. In addition, the juxtaposition of RNA domains at the junction and at the distal tertiary complexes enables the RNA helices to adopt unusual conformations that are frequently used by proteins, RNA molecules, and antibiotics as platforms for specific binding. As a consequence of these properties, Y-shaped junctions are widely distributed in all kingdoms of life, having been observed in small naked RNAs such as riboswitches and ribozymes or embedded in complex ribonucleoprotein systems like ribosomal RNAs, RNase P, or the signal recognition particle. In all cases, the folds were found to play an essential role for the functioning or assembly of the RNA or ribonucleoprotein systems that contain them. PMID:19741022

  14. Ab initio and template-based prediction of multi-class distance maps by two-dimensional recursive neural networks

    PubMed Central

    Walsh, Ian; Baù, Davide; Martin, Alberto JM; Mooney, Catherine; Vullo, Alessandro; Pollastri, Gianluca

    2009-01-01

    Background Prediction of protein structures from their sequences is still one of the open grand challenges of computational biology. Some approaches to protein structure prediction, especially ab initio ones, rely to some extent on the prediction of residue contact maps. Residue contact map predictions have been assessed at the CASP competition for several years now. Although it has been shown that exact contact maps generally yield correct three-dimensional structures, this is true only at a relatively low resolution (3–4 Å from the native structure). Another known weakness of contact maps is that they are generally predicted ab initio, that is not exploiting information about potential homologues of known structure. Results We introduce a new class of distance restraints for protein structures: multi-class distance maps. We show that Cα trace reconstructions based on 4-class native maps are significantly better than those from residue contact maps. We then build two predictors of 4-class maps based on recursive neural networks: one ab initio, or relying on the sequence and on evolutionary information; one template-based, or in which homology information to known structures is provided as a further input. We show that virtually any level of sequence similarity to structural templates (down to less than 10%) yields more accurate 4-class maps than the ab initio predictor. We show that template-based predictions by recursive neural networks are consistently better than the best template and than a number of combinations of the best available templates. We also extract binary residue contact maps at an 8 Å threshold (as per CASP assessment) from the 4-class predictors and show that the template-based version is also more accurate than the best template and consistently better than the ab initio one, down to very low levels of sequence identity to structural templates. Furthermore, we test both ab-initio and template-based 8 Å predictions on the CASP7 targets

  15. Ab Initio Studies of Stratospheric Ozone Depletion Chemistry

    NASA Technical Reports Server (NTRS)

    Lee, Timothy J.; Head-Gordon, Martin; Langhoff, Stephen R. (Technical Monitor)

    1995-01-01

    An overview of the current understanding of ozone depletion chemistry, particularly with regards the formation of the so-called Antarctic ozone hole, will be presented together with an outline as to how ab initio quantum chemistry can be used to further our understanding of stratospheric chemistry. The ability of modern state-of-the art ab initio quantum chemical techniques to characterize reliably the gas-phase molecular structure, vibrational spectrum, electronic spectrum, and thermal stability of fluorine, chlorine, bromine and nitrogen oxide species will be demonstrated by presentation of some example studies. The ab initio results will be shown to be in excellent agreement with the available experimental data, and where the experimental data are either not known or are inconclusive, the theoretical results are shown to fill in the gaps and to resolve experimental controversies. In addition, ab initio studies in which the electronic spectra and the characterization of excited electronic states of halogen oxide species will also be presented. Again where available, the ab initio results are compared to experimental observations, and are used to aid in the interpretation of experimental studies.

  16. THERMODYNAMICS OF MATERIALS: FROM AB INITIO TO PHENOMENOLOGY

    SciTech Connect

    Turchi, P A

    2004-09-24

    Quantum mechanical-based (or ab initio) methods are used to predict the stability properties of materials although their application is limited to relatively simple systems in terms of structures and number of alloy components. However thermodynamics of complex multi-component alloys requires a more versatile approach afforded within the CALPHAD formalism. Despite its success, the lack of experimental data very often prevents the design of robust thermodynamic databases. After a brief survey of ab initio methodologies and CALPHAD, it will be shown how ab initio electronic structure methods can supplement in two ways CALPHAD for subsequent applications. The first one is rather immediate and concerns the direct input of ab initio energetics in CALPHAD databases. The other way, more involved, is the assessment of ab initio thermodynamics '{acute a} la CALPHAD'. It will be shown how these results can be used within CALPHAD to predict the equilibrium properties of multi-component alloys. Finally, comments will be made on challenges and future prospects.

  17. Skutterudites under pressure: An ab initio study

    SciTech Connect

    Ram, Swetarekha; Kanchana, V.; Valsakumar, M. C.

    2014-03-07

    Ab initio results on the band structure, density of states, and Fermi surface (FS) properties of LaRu{sub 4}X{sub 12} (X = P, As, Sb) are presented at ambient pressure as well as under compression. The analysis of density of states reveals the major contribution at the Fermi level to be mainly from the Ru-d and X-p states. We have a complicated Fermi surface with both electron and hole characters for all the three compounds which is derived mainly from the Ru-d and X-p states. There is also a simpler FS with hole character derived from the P-p{sub z} orbital for LaRu{sub 4}P{sub 12} and Ru-d{sub z{sup 2}} orbital in the case of As and Sb containing compounds. More interestingly, Fermi surface nesting feature is observed only in the case of the LaRu{sub 4}P{sub 12}. Under compression, we observe the topology of the complicated FS sheet of LaRu{sub 4}As{sub 12} to change around V/V{sub 0} = 0.85, leading to a behaviour similar to that of a multiband superconductor, and in addition, we have two more hole pockets centered around Γ at V/V{sub 0} = 0.8 for the same compound. Apart from this, we find the hole pocket to vanish at V/V{sub 0} = 0.8 in the case of LaRu{sub 4}Sb{sub 12} and the opening of the complicated FS sheet gets reduced. The de Haas van Alphen calculation shows the number of extremal orbits in the complicated sheet to change in As and Sb containing compounds under compression, where we also observe the FS topology to change.

  18. Protein

    MedlinePlus

    ... Search for: Harvard T.H. Chan School of Public Health Email People Departments Calendar Careers Give my.harvard ... Nutrition Source Harvard T.H. Chan School of Public Health > The Nutrition Source > What Should I Eat? > Protein ...

  19. Protein

    MedlinePlus

    ... Go lean with protein. • Choose lean meats and poultry. Lean beef cuts include round steaks (top loin, ... main dishes. • Use nuts to replace meat or poultry, not in addition to meat or poultry (i. ...

  20. IRIS Toxicological Review of Ethyl Tertiary Butyl Ether (Etbe) ...

    EPA Pesticide Factsheets

    EPA is conducting a peer review and public comment of the scientific basis supporting the human health hazard and dose-response assessment of ethyl tertiary butyl ether (ETBE) that when finalized will appear on the Integrated Risk Information System (IRIS) database. The draft Toxicological Review of Ethyl Tertiary Butyl Ether provides scientific support and rationale for the hazard and dose-response assessment pertaining to chronic exposure to ethyl tertiary butyl ether.

  1. Ab initio computations of photodissociation products of CFC alternatives

    SciTech Connect

    Tai, S.; Illinger, K.H.; Kenny, J.E.

    1995-12-31

    Ab initio computations, have already been used to examine the energetics of the photodissociation of stratospheric chlorofluorocarbons. Our awn research has investigated the ab initio computation of vibrational frequencies and infrared intensities of CF{sub 3}CH{sub 2}F, CF{sub 3}CF{sub 2}H, and CF{sub 3}CH{sub 3}; continuing research will attempt to expand these computations to the energetics of the photodissociation of these molecules, since sane of the most common types of chlorofluorocarbon substitutes are hydrofluoroethanes.

  2. Vibrational analysis of tertiary alkyl bromides

    NASA Astrophysics Data System (ADS)

    Crowder, G. A.; Richardson, Mary Townsends; Gross, Lorelei

    Infrared spectra have been obtained for 2-bromo-2-methylpentane and 3-bromo-3-methylpentane. Both compounds exist in THHH and TCHH conformations. Normal coordinate calculations were made for these two compounds and for 2-bromo-2-methylbutane, using the 44-parameter modified valence force field that was used for tertiary chlorides. Fifteen force constants were adjusted to fit 169 frequencies below 1500 cm-1 of six molecules (two each for the three named compounds) with an average error of 5.6 cm-1. Vibrational assignments are presented.

  3. Vibrational analysis of tertiary alkyl bromides

    NASA Astrophysics Data System (ADS)

    Crowder, G. A.; Richardson, Mary Townsends; Gross, Lorelei

    1982-11-01

    Infrared spectra have been obtained for 2-bromo-2-methylpentane and 3-bromo-3-methylpentane. Both compounds exist in THHH and TCHH conformations. Normal coordinate calculations were made for these two compounds and for 2-bromo-2-methylbutane, using the 44-parameter modified valence force field that was used for tertiary chlorides. Fifteen force constants were adjusted to fit 169 frequencies below 1500 cm -1 of six molecules (two each for the three named compounds) with an average error of 5.6 cm -1. Vibrational assignments are presented.

  4. Ab initio no core shell model

    SciTech Connect

    Barrett, Bruce R.; Navrátil, Petr; Vary, James P.

    2012-11-17

    A long-standing goal of nuclear theory is to determine the properties of atomic nuclei based on the fundamental interactions among the protons and neutrons (i.e., nucleons). By adopting nucleon-nucleon (NN), three-nucleon (NNN) and higher-nucleon interactions determined from either meson-exchange theory or QCD, with couplings fixed by few-body systems, we preserve the predictive power of nuclear theory. This foundation enables tests of nature's fundamental symmetries and offers new vistas for the full range of complex nuclear phenomena. Basic questions that drive our quest for a microscopic predictive theory of nuclear phenomena include: (1) What controls nuclear saturation; (2) How the nuclear shell model emerges from the underlying theory; (3) What are the properties of nuclei with extreme neutron/proton ratios; (4) Can we predict useful cross sections that cannot be measured; (5) Can nuclei provide precision tests of the fundamental laws of nature; and (6) Under what conditions do we need QCD to describe nuclear structure, among others. Along with other ab initio nuclear theory groups, we have pursued these questions with meson-theoretical NN interactions, such as CD-Bonn and Argonne V18, that were tuned to provide high-quality descriptions of the NN scattering phase shifts and deuteron properties. We then add meson-theoretic NNN interactions such as the Tucson-Melbourne or Urbana IX interactions. More recently, we have adopted realistic NN and NNN interactions with ties to QCD. Chiral perturbation theory within effective field theory ({chi}EFT) provides us with a promising bridge between QCD and hadronic systems. In this approach one works consistently with systems of increasing nucleon number and makes use of the explicit and spontaneous breaking of chiral symmetry to expand the strong interaction in terms of a dimensionless constant, the ratio of a generic small momentum divided by the chiral symmetry breaking scale taken to be about 1 GeV/c. The resulting NN

  5. Upregulation of BMSCs Osteogenesis by Positively-Charged Tertiary Amines on Polymeric Implants via Charge/iNOS Signaling Pathway

    NASA Astrophysics Data System (ADS)

    Zhang, Wei; Liu, Na; Shi, Haigang; Liu, Jun; Shi, Lianxin; Zhang, Bo; Wang, Huaiyu; Ji, Junhui; Chu, Paul K.

    2015-03-01

    Positively-charged surfaces on implants have a similar potential to upregulate osteogenesis of bone marrow-derived mesenchymal stem cells (BMSCs) as electromagnetic therapy approved for bone regeneration. Generally, their osteogenesis functions are generally considered to stem from the charge-induced adhesion of extracellular matrix (ECM) proteins without exploring the underlying surface charge/cell signaling molecule pathways. Herein, a positively-charged surface with controllable tertiary amines is produced on a polymer implant by plasma surface modification. In addition to inhibiting the TNF-α expression, the positively-charged surface with tertiary amines exhibits excellent cytocompatibility as well as remarkably upregulated osteogenesis-related gene/protein expressions and calcification of the contacted BMSCs. Stimulated by the charged surface, these BMSCs display high iNOS expressions among the three NOS isoforms. Meanwhile, downregulation of the iNOS by L-Can or siRNA inhibit osteogenic differentiation in the BMSCs. These findings suggest that a positively-charged surface with tertiary amines induces osteogenesis of BMSCs via the surface charge/iNOS signaling pathway in addition to elevated ECM protein adhesion. Therefore, creating a positively-charged surface with tertiary amines is a promising approach to promote osseointegration with bone tissues.

  6. Earliest known Australian Tertiary mammal fauna

    NASA Astrophysics Data System (ADS)

    Godthelp, Henk; Archer, Michael; Cifelli, Richard; Hand, Suzanne J.; Gilkeson, Coral F.

    1992-04-01

    REMAINS of Early Eocene vertebrates from freshwater clays near Murgon, southeastern Queensland, represent Australia's oldest marsupials, bats, non-volant placentals, frogs, madtsoiid snakes, trionychid turtles1and birds. Radiometric dating of illites forming part of the matrix of the mammal-bearing zone has given a minimum age estimate of 54.6 +/- 0.05 x 106 years, which is roughly twice as old as any marsupials previously known from Australia2 and well before the 38 million year (Myr) separation of Australia from Antarctica/South America3. All marsupials so far known from the Tingamarra Local Fauna are more derived (being dilambdodont) than peradectids. None of them is clearly a member of a previously known Australian family, but some could be uniquely plesiomorphic dasyuroids or perameloids. Another is autapomorphically specialized and indicative of at least partial isolation of the Australian portion of Gondwana. Here we report on the discovery of a tooth of the earliest non-volant placental known from Australia, Tingamarra porterorum gen.et sp. nov., which seems to be a condylarth-like placental mammal. The presence of non-volant placentals in the Early Tertiary of Australia challenges a common presumption that marsupials dominated Australia's therian assemblages because of failure of such placentals to reach Australia before the Late Tertiary.

  7. Tertiary structure of human {Lambda}6 light chains.

    SciTech Connect

    Pokkuluri, P. R.; Solomon, A.; Weiss, D. T.; Stevens, F. J.; Schiffer, M.; Center for Mechanistic Biology and Biotechnology; Univ. of Tennessee Medical Center /Graduate School of Medicine

    1999-01-01

    AL amyloidosis is a disease process characterized by the pathologic deposition of monoclonal light chains in tissue. To date, only limited information has been obtained on the molecular features that render such light chains amyloidogenic. Although protein products of the major human V kappa and V lambda gene families have been identified in AL deposits, one particular subgroup--lambda 6--has been found to be preferentially associated with this disease. Notably, the variable region of lambda 6 proteins (V lambda 6) has distinctive primary structural features including the presence in the third framework region (FR3) of two additional amino acid residues that distinguish members of this subgroup from other types of light chains. However, the structural consequences of these alterations have not been elucidated. To determine if lambda 6 proteins possess unique tertiary structural features, as compared to light chains of other V lambda subgroups, we have obtained x-ray diffraction data on crystals prepared from two recombinant V lambda 6 molecules. These components, isolated from a bacterial expression system, were generated from lambda 6-related cDNAs cloned from bone marrow-derived plasma cells from a patient (Wil) who had documented AL amyloidosis and another (Jto) with multiple myeloma and tubular cast nephropathy, but no evident fibrillar deposits. The x-ray crystallographic analyses revealed that the two-residue insertion located between positions 68 and 69 (not between 66 and 67 as previously surmised) extended an existing loop region that effectively increased the surface area adjacent to the first complementarity determining region (CDR1). Further, an unusual interaction between the Arg 25 and Phe 2 residues commonly found in lambda 6 molecules was noted. However, the structures of V lambda 6 Wil and Jto also differed from each other, as evidenced by the presence in the latter of certain ionic and hydrophobic interactions that we posit increased protein

  8. Multiple time step integrators in ab initio molecular dynamics

    SciTech Connect

    Luehr, Nathan; Martínez, Todd J.; Markland, Thomas E.

    2014-02-28

    Multiple time-scale algorithms exploit the natural separation of time-scales in chemical systems to greatly accelerate the efficiency of molecular dynamics simulations. Although the utility of these methods in systems where the interactions are described by empirical potentials is now well established, their application to ab initio molecular dynamics calculations has been limited by difficulties associated with splitting the ab initio potential into fast and slowly varying components. Here we present two schemes that enable efficient time-scale separation in ab initio calculations: one based on fragment decomposition and the other on range separation of the Coulomb operator in the electronic Hamiltonian. We demonstrate for both water clusters and a solvated hydroxide ion that multiple time-scale molecular dynamics allows for outer time steps of 2.5 fs, which are as large as those obtained when such schemes are applied to empirical potentials, while still allowing for bonds to be broken and reformed throughout the dynamics. This permits computational speedups of up to 4.4x, compared to standard Born-Oppenheimer ab initio molecular dynamics with a 0.5 fs time step, while maintaining the same energy conservation and accuracy.

  9. Motif based Hessian matrixfor ab initio geometry optimization ofnanostructures

    SciTech Connect

    Zhao, Zhengji; Wang, Lin-Wang; Meza, Juan

    2006-04-05

    A simple method to estimate the atomic degree Hessian matrixof a nanosystem is presented. The estimated Hessian matrix, based on themotif decomposition of the nanosystem, can be used to accelerate abinitio atomic relaxations with speedups of 2 to 4 depending on the sizeof the system. In addition, the programing implementation for using thismethod in a standard ab initio package is trivial.

  10. Towards SiC Surface Functionalization: An Ab Initio Study

    SciTech Connect

    Cicero, G; Catellani, A

    2005-01-28

    We present a microscopic model of the interaction and adsorption mechanism of simple organic molecules on SiC surfaces as obtained from ab initio molecular dynamics simulations. Our results open the way to functionalization of silicon carbide, a leading candidate material for bio-compatible devices.

  11. The application of ab initio calculations to molecular spectroscopy

    NASA Technical Reports Server (NTRS)

    Bauschlicher, Charles W., Jr.; Langhoff, Stephen R.

    1989-01-01

    The state of the art in ab initio molecular structure calculations is reviewed, with an emphasis on recent developments such as full configuration-interaction benchmark calculations and atomic natural orbital basis sets. It is shown that new developments in methodology combined with improvements in computer hardware are leading to unprecedented accuracy in solving problems in spectroscopy.

  12. The application of ab initio calculations to molecular spectroscopy

    NASA Technical Reports Server (NTRS)

    Bauschlicher, Charles W., Jr.; Langhoff, Stephen R.

    1989-01-01

    The state of the art in ab initio molecular structure calculations is reviewed with an emphasis on recent developments, such as full configuration-interaction benchmark calculations and atomic natural orbital basis sets. It is found that new developments in methodology, combined with improvements in computer hardware, are leading to unprecedented accuracy in solving problems in spectroscopy.

  13. 10 CFR 212.78 - Tertiary incentive crude oil.

    Code of Federal Regulations, 2011 CFR

    2011-01-01

    ... 10 Energy 3 2011-01-01 2011-01-01 false Tertiary incentive crude oil. 212.78 Section 212.78 Energy DEPARTMENT OF ENERGY OIL MANDATORY PETROLEUM PRICE REGULATIONS Producers of Crude Oil § 212.78 Tertiary incentive crude oil. Annual prepaid expenses report. By January 31 of each year after 1980, the...

  14. Tertiary Education Policy in Ghana. An Assessment: 1988-1998.

    ERIC Educational Resources Information Center

    Girdwood, Alison

    This study was one of several activities conducted at the end of a 5-year World Bank/Government of Ghana project, the Tertiary Education Project (TEP). This project was designed to assist the government of Ghana with the restructuring and quality enhancement of its tertiary education sector. Although the government had prepared an ambitious reform…

  15. An Exploratory Study of Collaboration in New Zealand Tertiary Libraries

    ERIC Educational Resources Information Center

    Finnerty, Colleen

    2005-01-01

    The shift in policy from market driven behaviour towards a more cooperative tertiary sector is having an effect on New Zealand academic libraries and their relationships. Despite this, there has been no investigation of collaboration specifically targeting New Zealand tertiary libraries. This research project examine the state of collaboration…

  16. Crime and Crime Management in Nigeria Tertiary Institutions

    ERIC Educational Resources Information Center

    Adebanjo, Margaret Adewunmi

    2014-01-01

    This paper examines crime and its management in Nigerian tertiary institutions. Tertiary institutions today have become arenas for crime activities such as rape, cultism, murder, theft, internet fraud, drug abuse, and examination malpractices. This paper delves into what crime is, and its causes; and the positions of the law on crime management.…

  17. Towards the 21st Century. Facilities for Tertiary Education.

    ERIC Educational Resources Information Center

    Corbett, Anne, Ed.

    This report presents observations of experts in planning, design, construction or management of tertiary educational facilities about the emerging issues and the appropriate planning and architectural solutions for higher education facilities as the new millennium approaches. Specific topics discuss the current context of tertiary education…

  18. Structural Diversity in Tertiary Education. Go8 Backgrounder 18

    ERIC Educational Resources Information Center

    Group of Eight (NJ1), 2010

    2010-01-01

    Projections of future population and tertiary education participation indicate that Australia needs soon to start planning for another surge in school leavers entering tertiary education from 2015, together with increased demand for greater skills deepening by adult workers. Hence it is necessary to find cost-effective supply solutions that…

  19. 40 CFR 721.10669 - Tertiary amine alkyl ether (generic).

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ...) TOXIC SUBSTANCES CONTROL ACT SIGNIFICANT NEW USES OF CHEMICAL SUBSTANCES Significant New Uses for Specific Chemical Substances § 721.10669 Tertiary amine alkyl ether (generic). (a) Chemical substance and significant new uses subject to reporting. (1) The chemical substance identified generically as tertiary...

  20. 10 CFR 212.78 - Tertiary incentive crude oil.

    Code of Federal Regulations, 2013 CFR

    2013-01-01

    ... 10 Energy 3 2013-01-01 2013-01-01 false Tertiary incentive crude oil. 212.78 Section 212.78 Energy DEPARTMENT OF ENERGY OIL MANDATORY PETROLEUM PRICE REGULATIONS Producers of Crude Oil § 212.78 Tertiary incentive crude oil. Annual prepaid expenses report. By January 31 of each year after 1980, the...

  1. 10 CFR 212.78 - Tertiary incentive crude oil.

    Code of Federal Regulations, 2014 CFR

    2014-01-01

    ... 10 Energy 3 2014-01-01 2014-01-01 false Tertiary incentive crude oil. 212.78 Section 212.78 Energy DEPARTMENT OF ENERGY OIL MANDATORY PETROLEUM PRICE REGULATIONS Producers of Crude Oil § 212.78 Tertiary incentive crude oil. Annual prepaid expenses report. By January 31 of each year after 1980, the...

  2. 40 CFR 721.10591 - Tertiary ammonium compound (generic).

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... 40 Protection of Environment 31 2014-07-01 2014-07-01 false Tertiary ammonium compound (generic... Specific Chemical Substances § 721.10591 Tertiary ammonium compound (generic). (a) Chemical substance and... ammonium compound (PMN P-11-110) is subject to reporting under this section for the significant new...

  3. 40 CFR 721.10591 - Tertiary ammonium compound (generic).

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... 40 Protection of Environment 32 2013-07-01 2013-07-01 false Tertiary ammonium compound (generic... Specific Chemical Substances § 721.10591 Tertiary ammonium compound (generic). (a) Chemical substance and... ammonium compound (PMN P-11-110) is subject to reporting under this section for the significant new...

  4. The Impediments Facing Community Engagement in Omani Educational Tertiary Institutions

    ERIC Educational Resources Information Center

    Issa, Jinan Hatem

    2016-01-01

    Prior to the vital role that social capital plays in accomplishing prosperity for any educational tertiary institution, it was emphasised in several countries' agendas, including the Sultanate of Oman. This study endeavours to explore the impediments facing the enhancement of the social capital in Omani educational tertiary institutions through…

  5. 10 CFR 212.78 - Tertiary incentive crude oil.

    Code of Federal Regulations, 2012 CFR

    2012-01-01

    ... 10 Energy 3 2012-01-01 2012-01-01 false Tertiary incentive crude oil. 212.78 Section 212.78 Energy DEPARTMENT OF ENERGY OIL MANDATORY PETROLEUM PRICE REGULATIONS Producers of Crude Oil § 212.78 Tertiary incentive crude oil. Annual prepaid expenses report. By January 31 of each year after 1980, the...

  6. 10 CFR 212.78 - Tertiary incentive crude oil.

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... 10 Energy 3 2010-01-01 2010-01-01 false Tertiary incentive crude oil. 212.78 Section 212.78 Energy DEPARTMENT OF ENERGY OIL MANDATORY PETROLEUM PRICE REGULATIONS Producers of Crude Oil § 212.78 Tertiary incentive crude oil. Annual prepaid expenses report. By January 31 of each year after 1980, the...

  7. High-Throughput NMR Assessment of the Tertiary Structure of Food Allergens

    PubMed Central

    Alessandri, Stefano; Sancho, Ana; Vieths, Stefan; Mills, Clare E. N.; Wal, Jean-Michel; Shewry, Peter R.; Rigby, Neil; Hoffmann-Sommergruber, Karin

    2012-01-01

    Background In vitro component-resolved diagnosis of food allergy requires purified allergens that have to meet high standards of quality. These include the authentication of their conformation, which is relevant for the recognition by specific IgE antibodies from allergic patients. Therefore, highly sensitive and reliable screening methods for the analysis of proteins/allergens are required to assess their structural integrity. In the present study one-dimensional 1H Nuclear Magnetic Resonance (1D 1H-NMR) analysis was adopted for the assessment of overall structural and dynamic properties and authentication of a set of relevant food allergens, including non-specific lipid transfer proteins from apple, peach and hazelnut, 7/8S seed storage globulins from hazelnut and peanut, 11S seed storage globulins from hazelnut and peanut, caseins from cows' and goats' milk and tropomyosin from shrimp. Methodology/Principal Findings Two sets of 1D 1H-NMR experiments, using 700 MHz and 600 MHz instruments at 298 K were carried out to determine the presence and the extent of tertiary structure. Structural similarity among members of the individual allergen families was also assessed and changes under thermal stress investigated. The nuclear magnetic resonance (NMR) results were compared with structural information available either from the literature, Protein Data Bank entries, or derived from molecular models. Conclusions/Significance 1D 1H-NMR analysis of food allergens allowed their classification into molecules with rigid, extended and ordered tertiary structures, molecules without a rigid tertiary structure and molecules which displayed both features. Differences in thermal stability were also detected. In summary, 1D 1H-NMR gives insights into molecular fold of proteins and offers an independent method for assessing structural properties of proteins. PMID:22768312

  8. 'Tertiary' nuclear burning - Neutron star deflagration?

    NASA Technical Reports Server (NTRS)

    Michel, F. Curtis

    1988-01-01

    A motivation is presented for the idea that dense nuclear matter can burn to a new class of stable particles. One of several possibilities is an 'octet' particle which is the 16 baryon extension of alpha particle, but now composed of a pair of each of the two nucleons, (3Sigma, Delta, and 2Xi). Such 'tertiary' nuclear burning (here 'primary' is H-He and 'secondary' is He-Fe) may lead to neutron star explosions rather than collapse to a black hole, analogous to some Type I supernovae models wherein accreting white dwarfs are pushed over the Chandrasekhar mass limit but explode rather than collapse to form neutron stars. Such explosions could possibly give gamma-ray bursts and power quasars, with efficient particle acceleration in the resultant relativistic shocks. The new stable particles themselves could possibly be the sought-after weakly interacting, massive particles (WIMPs) or 'dark' matter.

  9. Cretaceous-Tertiary findings, paradigms and problems

    NASA Technical Reports Server (NTRS)

    Officer, C. B.; Drake, C. L.

    1988-01-01

    The asteroid hypothesis has stimulated numerous studies of the paleontological record at Cretaceous/Tertiary time as well as of geological indicators of environmental crisis preserved in the rock record. Both extinctions and geological anomalies often occur at times that do not appear to be synchronous or instantaneous. The record includes paleontological indicators of dinosaurs, terrestrial flora, marine planktonic organisms, and shallow water marine macrofauna and geological phenomena include occurrences of iridium and other platinum metals, trace elements, clay mineralogy, shocked minerals, soot, microspherules, and isotopes of osmium, strontium and carbon. These findings are reviewed in the context of the alternate hypotheses of an exogenic cause, involving either a single asteroid impact or multiple commentary impacts, and an endogenic cause, involving intense global volcanism and major sea level regression.

  10. Aqueous flooding methods for tertiary oil recovery

    DOEpatents

    Peru, Deborah A.

    1989-01-01

    A method of aqueous flooding of subterranean oil bearing formation for tertiary oil recovery involves injecting through a well into the formation a low alkaline pH aqueous sodium bicarbonate flooding solution. The flooding solution's pH ranges from about 8.25 to 9.25 and comprises from 0.25 to 5 weight percent and preferably about 0.75 to 3.0 weight percent of sodium bicarbonate and includes a petroleum recovery surfactant of 0.05 to 1.0 weight percent and between 1 and 20 weight percent of sodium chloride. After flooding, an oil and water mixture is withdrawn from the well and the oil is separated from the oil and water mixture.

  11. LSST primary/tertiary monolithic mirror

    NASA Astrophysics Data System (ADS)

    Sebag, J.; Gressler, W.; Liang, M.; Neill, D.; Araujo-Hauck, C.; Andrew, J.; Angeli, G.; Cho, M.; Claver, C.; Daruich, F.; Gessner, C.; Hileman, E.; Krabbendam, V.; Muller, G.; Poczulp, G.; Repp, R.; Wiecha, O.; Xin, B.; Kenagy, K.; Martin, H. M.; Tuell, M. T.; West, S. C.

    2016-08-01

    At the core of the Large Synoptic Survey Telescope (LSST) three-mirror optical design is the primary/tertiary (M1M3) mirror that combines these two large mirrors onto one monolithic substrate. The M1M3 mirror was spin cast and polished at the Steward Observatory Mirror Lab at The University of Arizona (formerly SOML, now the Richard F. Caris Mirror Lab at the University of Arizona (RFCML)). Final acceptance of the mirror occurred during the year 2015 and the mirror is now in storage while the mirror cell assembly is being fabricated. The M1M3 mirror will be tested at RFCML after integration with its mirror cell before being shipped to Chile.

  12. Tertiary Lymphoid Organs in Cancer Tissues

    PubMed Central

    Hiraoka, Nobuyoshi; Ino, Yoshinori; Yamazaki-Itoh, Rie

    2016-01-01

    Tertiary lymphoid organs (TLOs) are induced postnatally in non-lymphoid tissues such as those affected by chronic infections, autoimmune diseases, and chronic allograft rejection, and also in cancer tissues. TLOs are thought to provide important lymphocytic functional environments for both cellular and humoral immunity, similar to lymph nodes or Peyer’s patches. TLOs have a structure similar to that of lymph nodes or Peyer’s patches, including T cell zones, B cell follicles, and high endothelial venules (HEV) without encapsulation. Here, we review recent advances in our knowledge of TLOs in human solid cancers, including their location, structure, methods of evaluation, and clinicopathological impact. We also discuss the formation and/or maintenance of TLOs in cancer tissues in association with the tumor immune microenvironment, cancer invasion, and the tissue structure of the cancer stroma. PMID:27446075

  13. Tertiary treatment for wastewater reuse based on the Daphnia magna filtration - comparison with conventional tertiary treatments.

    PubMed

    Serra, Teresa; Colomer, Jordi; Pau, Conxi; Marín, Maribel; Sala, Lluís

    2014-01-01

    Tertiary treatments are required to permit safe reuse of wastewater. The performance of a new biological tertiary treatment based on the filtration by a population of Daphnia magna was studied and compared with the performance of other conventional tertiary treatments such as coagulation-flocculation, settling tank, disc filtration, sand filtering and ultraviolet (UV) light. The analysis was based on the efficiency in the particle removal and Escherichia coli inactivation. The Daphnia magna treatment reduced the concentration of particles with diameters below 30 μm by 35%, depending on abiotic parameters such as water temperature and the hydraulic retention time (HRT). The Daphnia magna filtration increased with water temperature for water temperatures >20 °C, while it remained constant for water temperatures <20 °C. Lower HRTs induced the growth of the Daphnia magna population, maintaining the same water quality. Furthermore, the Daphnia magna treatment inactivated E. coli in 1.2 log units. This inactivation was six times larger than that obtained by the conventional macrofiltration systems analyzed, although lower than the inactivation attained by UV light, which ranged between 1.5 and 4 log units.

  14. Role of tertiary structures on the Root effect in fish hemoglobins.

    PubMed

    Ronda, Luca; Merlino, Antonello; Bettati, Stefano; Verde, Cinzia; Balsamo, Anna; Mazzarella, Lelio; Mozzarelli, Andrea; Vergara, Alessandro

    2013-09-01

    Many fish hemoglobins exhibit a marked dependence of oxygen affinity and cooperativity on proton concentration, called Root effect. Both tertiary and quaternary effects have been evoked to explain the allosteric regulation brought about by protons in fish hemoglobins. However, no general rules have emerged so far. We carried out a complementary crystallographic and microspectroscopic characterization of ligand binding to crystals of deoxy-hemoglobin from the Antarctic fish Trematomus bernacchii (HbTb) at pH6.2 and pH8.4. At low pH ligation has negligible structural effects, correlating with low affinity and absence of cooperativity in oxygen binding. At high pH, ligation causes significant changes at the tertiary structural level, while preserving structural markers of the T state. These changes mainly consist in a marked displacement of the position of the switch region CD corner towards an R-like position. The functional data on T-state crystals validate the relevance of the crystallographic observations, revealing that, differently from mammalian Hbs, in HbTb a significant degree of cooperativity in oxygen binding is due to tertiary conformational changes, in the absence of the T-R quaternary transition. This article is part of a Special Issue entitled: Oxygen Binding and Sensing Proteins.

  15. Error-estimation-guided rebuilding of de novo models increases the success rate of ab initio phasing.

    PubMed

    Shrestha, Rojan; Simoncini, David; Zhang, Kam Y J

    2012-11-01

    Recent advancements in computational methods for protein-structure prediction have made it possible to generate the high-quality de novo models required for ab initio phasing of crystallographic diffraction data using molecular replacement. Despite those encouraging achievements in ab initio phasing using de novo models, its success is limited only to those targets for which high-quality de novo models can be generated. In order to increase the scope of targets to which ab initio phasing with de novo models can be successfully applied, it is necessary to reduce the errors in the de novo models that are used as templates for molecular replacement. Here, an approach is introduced that can identify and rebuild the residues with larger errors, which subsequently reduces the overall C(α) root-mean-square deviation (CA-RMSD) from the native protein structure. The error in a predicted model is estimated from the average pairwise geometric distance per residue computed among selected lowest energy coarse-grained models. This score is subsequently employed to guide a rebuilding process that focuses on more error-prone residues in the coarse-grained models. This rebuilding methodology has been tested on ten protein targets that were unsuccessful using previous methods. The average CA-RMSD of the coarse-grained models was improved from 4.93 to 4.06 Å. For those models with CA-RMSD less than 3.0 Å, the average CA-RMSD was improved from 3.38 to 2.60 Å. These rebuilt coarse-grained models were then converted into all-atom models and refined to produce improved de novo models for molecular replacement. Seven diffraction data sets were successfully phased using rebuilt de novo models, indicating the improved quality of these rebuilt de novo models and the effectiveness of the rebuilding process. Software implementing this method, called MORPHEUS, can be downloaded from http://www.riken.jp/zhangiru/software.html.

  16. Predicting continuous local structure and the effect of its substitution for secondary structure in fragment-free protein structure prediction.

    PubMed

    Faraggi, Eshel; Yang, Yuedong; Zhang, Shesheng; Zhou, Yaoqi

    2009-11-11

    Local structures predicted from protein sequences are used extensively in every aspect of modeling and prediction of protein structure and function. For more than 50 years, they have been predicted at a low-resolution coarse-grained level (e.g., three-state secondary structure). Here, we combine a two-state classifier with real-value predictor to predict local structure in continuous representation by backbone torsion angles. The accuracy of the angles predicted by this approach is close to that derived from NMR chemical shifts. Their substitution for predicted secondary structure as restraints for ab initio structure prediction doubles the success rate. This result demonstrates the potential of predicted local structure for fragment-free tertiary-structure prediction. It further implies potentially significant benefits from using predicted real-valued torsion angles as a replacement for or supplement to the secondary-structure prediction tools used almost exclusively in many computational methods ranging from sequence alignment to function prediction.

  17. Assessing uncertainty in outsourcing clinical services at tertiary health centers.

    PubMed

    Billi, John E; Pai, Chih-Wen; Spahlinger, David A

    2007-01-01

    When tertiary health centers face capacity constraint, one feasible strategy to meet service demand is outsourcing clinical services to qualified community providers. Clinical outsourcing enables tertiary health centers to meet the expectations of service timeliness and provides good opportunities to collaborate with other health care providers. However, outsourcing may result in dependence and loss of control for the tertiary health centers. Other parties involved in clinical outsourcing such as local partners, patients, and payers may also encounter potential risks as well as enjoy benefits in an outsourcing arrangement. Recommendations on selecting potential outsourcing partners are given to minimize the risks associated with an outsourcing contract.

  18. Ethyl tertiary-butyl ether: a toxicological review.

    PubMed

    McGregor, Douglas

    2007-05-01

    A number of oxygenated compounds (oxygenates) are available for use in gasoline to reduce vehicle exhaust emissions, reduce the aromatic compound content, and avoid the use of organo-lead compounds, while maintaining high octane numbers. Ethyl tertiary-butyl ether (ETBE) is one such compound. The current use of ETBE in gasoline or petrol is modest but increasing, with consequently similar trends in the potential for human exposure. Inhalation is the most likely mode of exposure, with about 30% of inhaled ETBE being retained by the lungs and distributed around the body. Following cessation of exposure, the blood concentration of ETBE falls rapidly, largely as a result of its metabolism to tertiary-butyl alcohol (TBA) and acetaldehyde. TBA may be further metabolized, first to 2-methyl-1,2-propanediol and then to 2-hydroxyisobutyrate, the two dominant metabolites found in urine of volunteers and rats. The rapid oxidation of acetaldehyde suggests that its blood concentration is unlikely to rise above normal as a result of human exposure to sources of ETBE. Single-dose toxicity tests show that ETBE has low toxicity and is essentially nonirritant to eyes and skin; it did not cause sensitization in a maximization test in guinea pigs. Neurological effects have been observed only at very high exposure concentrations. There is evidence for an effect of ETBE on the kidney of rats. Increases in kidney weight were seen in both sexes, but protein droplet accumulation (with alpha(2u)-globulin involvement) and sustained increases in cell proliferation occurred only in males. In liver, centrilobular necrosis was induced in mice, but not rats, after exposure by inhalation, although this lesion was reported in some rats exposed to very high oral doses of ETBE. The proportion of liver cells engaged in S-phase DNA synthesis was increased in mice of both sexes exposed by inhalation. ETBE has no specific effects on reproduction, development, or genetic material. Carcinogenicity studies

  19. Roles of Long-Range Tertiary Interactions in Limiting Dynamics of the Tetrahymena Group I Ribozyme

    PubMed Central

    2015-01-01

    We determined the effects of mutating the long-range tertiary contacts of the Tetrahymena group I ribozyme on the dynamics of its substrate helix (referred to as P1) and on catalytic activity. Dynamics were assayed by fluorescence anisotropy of the fluorescent base analogue, 6-methyl isoxanthopterin, incorporated into the P1 helix, and fluorescence anisotropy and catalytic activity were measured for wild type and mutant ribozymes over a range of conditions. Remarkably, catalytic activity correlated with P1 anisotropy over 5 orders of magnitude of activity, with a correlation coefficient of 0.94. The functional and dynamic effects from simultaneous mutation of the two long-range contacts that weaken P1 docking are cumulative and, based on this RNA’s topology, suggest distinct underlying origins for the mutant effects. Tests of mechanistic predictions via single molecule FRET measurements of rate constants for P1 docking and undocking suggest that ablation of the P14 tertiary interaction frees P2 and thereby enhances the conformational space explored by the undocked attached P1 helix. In contrast, mutation of the metal core tertiary interaction disrupts the conserved core into which the P1 helix docks. Thus, despite following a single correlation, the two long-range tertiary contacts facilitate P1 helix docking by distinct mechanisms. These results also demonstrate that a fluorescence anisotropy probe incorporated into a specific helix within a larger RNA can report on changes in local helical motions as well as differences in more global dynamics. This ability will help uncover the physical properties and behaviors that underlie the function of RNAs and RNA/protein complexes. PMID:24738560

  20. Separable metamaterials: analytical ab-initio homogenization and chirality

    NASA Astrophysics Data System (ADS)

    Ciattoni, Alessandro; Rago, Domenico; Rizza, Carlo

    2016-11-01

    We investigate the ab-initio homogenization of separable metamaterials with factorized dielectric permittivity profiles, which can be achieved through suitable grey-scale permittivity design techniques. Separability allows such metamaterials to be physically regarded as the superposition of three fictitious 1D generating media. We prove that, in the long-wavelength limit, separable metamaterials admit a simple and analytical description of their electromagnetic bi-anisotropic response, which can be reconstructed from the properties of the 1D generating media. Our approach provides a strategy that allows the full ab-initio and flexible design of a complex bianisotropic response by using the simple and well-known properties of 1D metamaterials.

  1. High Level Ab Initio Kinetics as a Tool for Astrochemistry

    NASA Astrophysics Data System (ADS)

    Klippenstein, Stephen

    2015-05-01

    We will survey the application of ab initio theoretical kinetics to reactions of importance to astrochemistry. Illustrative examples will be taken from our calculations for (i) interstellar chemistry, (ii) Titan's atmospheric chemistry, and (iii) the chemistry of extrasolar giant planets. The accuracy of various aspects of the calculations will be summarized including (i) the underlying ab initio electronic structure calculations, (ii) the treatment of the high pressure recombination process, and (iii) the treatment of the pressure dependence of the kinetics. The applications will consider the chemistry of phosphorous on giant planets, the kinetics of water dimerization, the chemistry of nitrogen on Titan's atmosphere, as well as various reactions of interstellar chemistry interest such as the recombination of OH with H, and O(3P) reacting with C2H5, CH2, and CCS. Chemical Sciences and Engineering Division.

  2. Ab Initio Calculations Of Light-Ion Reactions

    SciTech Connect

    Navratil, P; Quaglioni, S; Roth, R; Horiuchi, W

    2012-03-12

    The exact treatment of nuclei starting from the constituent nucleons and the fundamental interactions among them has been a long-standing goal in nuclear physics. In addition to the complex nature of nuclear forces, one faces the quantum-mechanical many-nucleon problem governed by an interplay between bound and continuum states. In recent years, significant progress has been made in ab initio nuclear structure and reaction calculations based on input from QCD employing Hamiltonians constructed within chiral effective field theory. In this contribution, we present one of such promising techniques capable of describing simultaneously both bound and scattering states in light nuclei. By combining the resonating-group method (RGM) with the ab initio no-core shell model (NCSM), we complement a microscopic cluster approach with the use of realistic interactions and a microscopic and consistent description of the clusters. We discuss applications to light nuclei scattering, radiative capture and fusion reactions.

  3. Ab initio theories for light nuclei and neutron stars

    NASA Astrophysics Data System (ADS)

    Gezerlis, Alexandros

    2016-09-01

    In this talk I will touch upon several features of modern ab initio low-energy nuclear theory. I will start by discussing what ``ab initio'' means in this context. Specifically, I will spend some time going over nucleon-nucleon and three-nucleon interactions and their connections with the underlying theory of Quantum Chromodynamics. I will then show how these interactions are used to describe light nuclei using essentially exact few-body methods. I will then discuss heavier systems, especially those of astrophysical relevance, as well as the methods used to tackle them. This work was supported by the Natural Sciences and Engineering Research Council (NSERC) of Canada and the Canada Foundation for Innovation (CFI).

  4. Spin-orbit decomposition of ab initio nuclear wave functions

    NASA Astrophysics Data System (ADS)

    Johnson, Calvin W.

    2015-03-01

    Although the modern shell-model picture of atomic nuclei is built from single-particle orbits with good total angular momentum j , leading to j -j coupling, decades ago phenomenological models suggested that a simpler picture for 0 p -shell nuclides can be realized via coupling of the total spin S and total orbital angular momentum L . I revisit this idea with large-basis, no-core shell-model calculations using modern ab initio two-body interactions and dissect the resulting wave functions into their component L - and S -components. Remarkably, there is broad agreement with calculations using the phenomenological Cohen-Kurath forces, despite a gap of nearly 50 years and six orders of magnitude in basis dimensions. I suggest that L -S decomposition may be a useful tool for analyzing ab initio wave functions of light nuclei, for example, in the case of rotational bands.

  5. Ab Initio Atomistic Thermodynamics for Surfaces: A Primer

    DTIC Science & Technology

    2006-02-01

    Ab Initio Atomistic Thermodynamics for Surfaces: A Primer Jutta Rogal and Karsten Reuter Fritz - Haber -Institut der Max-Planck-Gesellschaft... Fritz - Haber -Institut der Max-Planck-Gesellschaft Faradayweg 4-6 D-14195 Berlin Germany 8. PERFORMING ORGANIZATION REPORT NUMBER 9. SPONSORING...of the Fritz - Haber -Institut, in particular Wei-Xue Li, Cathy Stampfl and Mira Todorova. Particular thanks go to Matthias Scheffler for his continued

  6. Thermochemical data for CVD modeling from ab initio calculations

    SciTech Connect

    Ho, P.; Melius, C.F.

    1993-12-31

    Ab initio electronic-structure calculations are combined with empirical bond-additivity corrections to yield thermochemical properties of gas-phase molecules. A self-consistent set of heats of formation for molecules in the Si-H, Si-H-Cl, Si-H-F, Si-N-H and Si-N-H-F systems is presented, along with preliminary values for some Si-O-C-H species.

  7. The study of molecular spectroscopy by ab initio methods

    NASA Technical Reports Server (NTRS)

    Bauschlicher, Charles W., Jr.; Langhoff, Stephen R.

    1991-01-01

    This review illustrates the potential of theory for solving spectroscopic problems. The accuracy of approximate techniques for including electron correlation have been calibrated by comparison with full configuration-interaction calculations. Examples of the application of ab initio calculations to vibrational, rotational, and electronic spectroscopy are given. It is shown that the state-averaged, complete active space self-consistent field, multireference configuration-interaction procedure provides a good approach for treating several electronic states accurately in a common molecular orbital basis.

  8. GAUSSIAN 76: An ab initio Molecular Orbital Program

    DOE R&D Accomplishments Database

    Binkley, J. S.; Whiteside, R.; Hariharan, P. C.; Seeger, R.; Hehre, W. J.; Lathan, W. A.; Newton, M. D.; Ditchfield, R.; Pople, J. A.

    1978-01-01

    Gaussian 76 is a general-purpose computer program for ab initio Hartree-Fock molecular orbital calculations. It can handle basis sets involving s, p and d-type Gaussian functions. Certain standard sets (STO-3G, 4-31G, 6-31G*, etc.) are stored internally for easy use. Closed shell (RHF) or unrestricted open shell (UHF) wave functions can be obtained. Facilities are provided for geometry optimization to potential minima and for limited potential surface scans.

  9. Ab initio calculations for industrial materials engineering: successes and challenges.

    PubMed

    Wimmer, Erich; Najafabadi, Reza; Young, George A; Ballard, Jake D; Angeliu, Thomas M; Vollmer, James; Chambers, James J; Niimi, Hiroaki; Shaw, Judy B; Freeman, Clive; Christensen, Mikael; Wolf, Walter; Saxe, Paul

    2010-09-29

    Computational materials science based on ab initio calculations has become an important partner to experiment. This is demonstrated here for the effect of impurities and alloying elements on the strength of a Zr twist grain boundary, the dissociative adsorption and diffusion of iodine on a zirconium surface, the diffusion of oxygen atoms in a Ni twist grain boundary and in bulk Ni, and the dependence of the work function of a TiN-HfO(2) junction on the replacement of N by O atoms. In all of these cases, computations provide atomic-scale understanding as well as quantitative materials property data of value to industrial research and development. There are two key challenges in applying ab initio calculations, namely a higher accuracy in the electronic energy and the efficient exploration of large parts of the configurational space. While progress in these areas is fueled by advances in computer hardware, innovative theoretical concepts combined with systematic large-scale computations will be needed to realize the full potential of ab initio calculations for industrial applications.

  10. Ab initio multiple cloning algorithm for quantum nonadiabatic molecular dynamics.

    PubMed

    Makhov, Dmitry V; Glover, William J; Martinez, Todd J; Shalashilin, Dmitrii V

    2014-08-07

    We present a new algorithm for ab initio quantum nonadiabatic molecular dynamics that combines the best features of ab initio Multiple Spawning (AIMS) and Multiconfigurational Ehrenfest (MCE) methods. In this new method, ab initio multiple cloning (AIMC), the individual trajectory basis functions (TBFs) follow Ehrenfest equations of motion (as in MCE). However, the basis set is expanded (as in AIMS) when these TBFs become sufficiently mixed, preventing prolonged evolution on an averaged potential energy surface. We refer to the expansion of the basis set as "cloning," in analogy to the "spawning" procedure in AIMS. This synthesis of AIMS and MCE allows us to leverage the benefits of mean-field evolution during periods of strong nonadiabatic coupling while simultaneously avoiding mean-field artifacts in Ehrenfest dynamics. We explore the use of time-displaced basis sets, "trains," as a means of expanding the basis set for little cost. We also introduce a new bra-ket averaged Taylor expansion (BAT) to approximate the necessary potential energy and nonadiabatic coupling matrix elements. The BAT approximation avoids the necessity of computing electronic structure information at intermediate points between TBFs, as is usually done in saddle-point approximations used in AIMS. The efficiency of AIMC is demonstrated on the nonradiative decay of the first excited state of ethylene. The AIMC method has been implemented within the AIMS-MOLPRO package, which was extended to include Ehrenfest basis functions.

  11. Ab Initio Nuclear Structure and Reaction Calculations for Rare Isotopes

    SciTech Connect

    Draayer, Jerry P.

    2014-09-28

    We have developed a novel ab initio symmetry-adapted no-core shell model (SA-NCSM), which has opened the intermediate-mass region for ab initio investigations, thereby providing an opportunity for first-principle symmetry-guided applications to nuclear structure and reactions for nuclear isotopes from the lightest p-shell systems to intermediate-mass nuclei. This includes short-lived proton-rich nuclei on the path of X-ray burst nucleosynthesis and rare neutron-rich isotopes to be produced by the Facility for Rare Isotope Beams (FRIB). We have provided ab initio descriptions of high accuracy for low-lying (including collectivity-driven) states of isotopes of Li, He, Be, C, O, Ne, Mg, Al, and Si, and studied related strong- and weak-interaction driven reactions that are important, in astrophysics, for further understanding stellar evolution, X-ray bursts and triggering of s, p, and rp processes, and in applied physics, for electron and neutrino-nucleus scattering experiments as well as for fusion ignition at the National Ignition Facility (NIF).

  12. Diffusion in liquid Germanium using ab initio molecular dynamics

    NASA Astrophysics Data System (ADS)

    Kulkarni, R. V.; Aulbur, W. G.; Stroud, D.

    1996-03-01

    We describe the results of calculations of the self-diffusion constant of liquid Ge over a range of temperatures. The calculations are carried out using an ab initio molecular dynamics scheme which combines an LDA model for the electronic structure with the Bachelet-Hamann-Schlüter norm-conserving pseudopotentials^1. The energies associated with electronic degrees of freedom are minimized using the Williams-Soler algorithm, and ionic moves are carried out using the Verlet algorithm. We use an energy cutoff of 10 Ry, which is sufficient to give results for the lattice constant and bulk modulus of crystalline Ge to within 1% and 12% of experiment. The program output includes not only the self-diffusion constant but also the structure factor, electronic density of states, and low-frequency electrical conductivity. We will compare our results with other ab initio and semi-empirical calculations, and discuss extension to impurity diffusion. ^1 We use the ab initio molecular dynamics code fhi94md, developed at 1cm the Fritz-Haber Institute, Berlin. ^2 Work supported by NASA, Grant NAG3-1437.

  13. Ab initio molecular dynamics using hybrid density functionals.

    PubMed

    Guidon, Manuel; Schiffmann, Florian; Hutter, Jürg; VandeVondele, Joost

    2008-06-07

    Ab initio molecular dynamics simulations with hybrid density functionals have so far found little application due to their computational cost. In this work, an implementation of the Hartree-Fock exchange is presented that is specifically targeted at ab initio molecular dynamics simulations of medium sized systems. We demonstrate that our implementation, which is available as part of the CP2K/Quickstep program, is robust and efficient. Several prescreening techniques lead to a linear scaling cost for integral evaluation and storage. Integral compression techniques allow for in-core calculations on systems containing several thousand basis functions. The massively parallel implementation respects integral symmetry and scales up to hundreds of CPUs using a dynamic load balancing scheme. A time-reversible multiple time step scheme, exploiting the difference in computational efficiency between hybrid and local functionals, brings further time savings. With extensive simulations of liquid water, we demonstrate the ability to perform, for several tens of picoseconds, ab initio molecular dynamics based on hybrid functionals of systems in the condensed phase containing a few thousand Gaussian basis functions.

  14. Ab initio molecular dynamics using hybrid density functionals

    NASA Astrophysics Data System (ADS)

    Guidon, Manuel; Schiffmann, Florian; Hutter, Jürg; Vandevondele, Joost

    2008-06-01

    Ab initio molecular dynamics simulations with hybrid density functionals have so far found little application due to their computational cost. In this work, an implementation of the Hartree-Fock exchange is presented that is specifically targeted at ab initio molecular dynamics simulations of medium sized systems. We demonstrate that our implementation, which is available as part of the CP2K/Quickstep program, is robust and efficient. Several prescreening techniques lead to a linear scaling cost for integral evaluation and storage. Integral compression techniques allow for in-core calculations on systems containing several thousand basis functions. The massively parallel implementation respects integral symmetry and scales up to hundreds of CPUs using a dynamic load balancing scheme. A time-reversible multiple time step scheme, exploiting the difference in computational efficiency between hybrid and local functionals, brings further time savings. With extensive simulations of liquid water, we demonstrate the ability to perform, for several tens of picoseconds, ab initio molecular dynamics based on hybrid functionals of systems in the condensed phase containing a few thousand Gaussian basis functions.

  15. A highly accurate ab initio potential energy surface for methane

    NASA Astrophysics Data System (ADS)

    Owens, Alec; Yurchenko, Sergei N.; Yachmenev, Andrey; Tennyson, Jonathan; Thiel, Walter

    2016-09-01

    A new nine-dimensional potential energy surface (PES) for methane has been generated using state-of-the-art ab initio theory. The PES is based on explicitly correlated coupled cluster calculations with extrapolation to the complete basis set limit and incorporates a range of higher-level additive energy corrections. These include core-valence electron correlation, higher-order coupled cluster terms beyond perturbative triples, scalar relativistic effects, and the diagonal Born-Oppenheimer correction. Sub-wavenumber accuracy is achieved for the majority of experimentally known vibrational energy levels with the four fundamentals of 12CH4 reproduced with a root-mean-square error of 0.70 cm-1. The computed ab initio equilibrium C-H bond length is in excellent agreement with previous values despite pure rotational energies displaying minor systematic errors as J (rotational excitation) increases. It is shown that these errors can be significantly reduced by adjusting the equilibrium geometry. The PES represents the most accurate ab initio surface to date and will serve as a good starting point for empirical refinement.

  16. Ab initio rotation-vibration spectra of HCN and HNC

    NASA Astrophysics Data System (ADS)

    Harris, Gregory J.; Polyansky, Oleg L.; Tennyson, Jonathan

    2002-03-01

    We have calculated an ab initio HCN/HNC linelist for all transitions up to J=25 and 18 000 cm -1 above the zero point energy. This linelist contains more than 200 million lines each with frequencies and transition dipoles. The linelist has been calculated using our semi-global HCN/HNC VQZANO+PES and dipole moment surface, which were reported in van Mourik et al. (J. Chem. Phys. 115 (2001) 3706). With this linelist we synthesise absorption spectra of HCN and HNC at 298 K and we present the band centre and band transition dipoles for the bands which are major features in these spectra. Several of the HCN bands and many of the HNC bands have not been previously studied. Our line intensities reproduce via fully ab initio methods the unusual intensity structure of the HCN CN stretch fundamental (00 01) for the first time and also the forbidden (02 20) HCN bending overtone. We also compare the J=1→0 pure rotational transition dipole in the HCN/HNC ground and vibrationally excited states with experimental and existing ab initio results.

  17. Ab initio multiple cloning algorithm for quantum nonadiabatic molecular dynamics

    SciTech Connect

    Makhov, Dmitry V.; Shalashilin, Dmitrii V.; Glover, William J.; Martinez, Todd J.

    2014-08-07

    We present a new algorithm for ab initio quantum nonadiabatic molecular dynamics that combines the best features of ab initio Multiple Spawning (AIMS) and Multiconfigurational Ehrenfest (MCE) methods. In this new method, ab initio multiple cloning (AIMC), the individual trajectory basis functions (TBFs) follow Ehrenfest equations of motion (as in MCE). However, the basis set is expanded (as in AIMS) when these TBFs become sufficiently mixed, preventing prolonged evolution on an averaged potential energy surface. We refer to the expansion of the basis set as “cloning,” in analogy to the “spawning” procedure in AIMS. This synthesis of AIMS and MCE allows us to leverage the benefits of mean-field evolution during periods of strong nonadiabatic coupling while simultaneously avoiding mean-field artifacts in Ehrenfest dynamics. We explore the use of time-displaced basis sets, “trains,” as a means of expanding the basis set for little cost. We also introduce a new bra-ket averaged Taylor expansion (BAT) to approximate the necessary potential energy and nonadiabatic coupling matrix elements. The BAT approximation avoids the necessity of computing electronic structure information at intermediate points between TBFs, as is usually done in saddle-point approximations used in AIMS. The efficiency of AIMC is demonstrated on the nonradiative decay of the first excited state of ethylene. The AIMC method has been implemented within the AIMS-MOLPRO package, which was extended to include Ehrenfest basis functions.

  18. Tertiary evolution of the northeastern Venezuela offshore

    NASA Astrophysics Data System (ADS)

    Ysaccis B., Raul

    1998-12-01

    On the northeastern offshore Venezuela, the pre-Tertiary basement consists of a deeply subducted accretionary complex of a Cretaceous island arc system that formed far to the west of its present location. The internal structure of this basement consists of metamorphic nappes that involve passive margin sequences, as well as oceanic (ophiolitic) elements. The Tertiary evolution of the northeastern Venezuela offshore is dominated by Paleogene (Middle Eocene-Oligocene) extension and Neogene transtension, interrupted by Oligocene to Middle Miocene inversions. The Paleogene extension is mainly an arc-normal extension associated with a retreating subduction boundary. It is limited to the La Tortuga and the La Blanquilla Basins and the southeastern Margarita and Caracolito subbasins. All of these basins are farther north of and not directly tied to the El Pilar fault system. On a reconstruction, these Paleogene extensional systems were located to the north of the present day Maracaibo Basin. By early Miocene the leading edge of the now overall transpressional system had migrated to a position to the north of the Ensenada de Barcelona. This relative to South America eastward migration is responsible for the Margarita strike-slip fault and the major inversions that began during the Oligocene and lasted into the Middle Miocene. The Bocono-El Pilar-Casanay-Warm Springs and the La Tortuga-Coche-North Coast fault systems are exclusively Neogene with major transtension occurring during the Late Miocene to Recent and act independently from the earlier Paleogene extensional system. They are responsible for the large Neogene transtensional basins of the area: the Cariaco trough, the Northern Tuy-Cariaco and the Paria sub-basins, and the Gulf of Paria Basin. This latest phase is characterized by strain-partitioning into strike slip faults, a transtensional northern domain and a transpressional southern domain that is responsible for the decollement tectonics and/or inversions of the

  19. DIRECT SYNTHESIS OF TERTIARY AMINES IN WATER USING MICROWAVES

    EPA Science Inventory

    A direct synthesis of tertiary amines is presented that proceeds expeditiously via N-alkylation of amines using alkyl halides in alkaline aqueous medium. This environmentally benign reaction is accelerated upon exposure to microwave irradiation resulting in shortened reaction tim...

  20. Information and redundancy in the burial folding code of globular proteins within a wide range of shapes and sizes.

    PubMed

    Ferreira, Diogo C; van der Linden, Marx G; de Oliveira, Leandro C; Onuchic, José N; de Araújo, Antônio F Pereira

    2016-04-01

    Recent ab initio folding simulations for a limited number of small proteins have corroborated a previous suggestion that atomic burial information obtainable from sequence could be sufficient for tertiary structure determination when combined to sequence-independent geometrical constraints. Here, we use simulations parameterized by native burials to investigate the required amount of information in a diverse set of globular proteins comprising different structural classes and a wide size range. Burial information is provided by a potential term pushing each atom towards one among a small number L of equiprobable concentric layers. An upper bound for the required information is provided by the minimal number of layers L(min) still compatible with correct folding behavior. We obtain L(min) between 3 and 5 for seven small to medium proteins with 50 ≤ Nr ≤ 110 residues while for a larger protein with Nr = 141 we find that L ≥ 6 is required to maintain native stability. We additionally estimate the usable redundancy for a given L ≥ L(min) from the burial entropy associated to the largest folding-compatible fraction of "superfluous" atoms, for which the burial term can be turned off or target layers can be chosen randomly. The estimated redundancy for small proteins with L = 4 is close to 0.8. Our results are consistent with the above-average quality of burial predictions used in previous simulations and indicate that the fraction of approachable proteins could increase significantly with even a mild, plausible, improvement on sequence-dependent burial prediction or on sequence-independent constraints that augment the detectable redundancy during simulations.

  1. Predicting loop-helix tertiary structural contacts in RNA pseudoknots.

    PubMed

    Cao, Song; Giedroc, David P; Chen, Shi-Jie

    2010-03-01

    Tertiary interactions between loops and helical stems play critical roles in the biological function of many RNA pseudoknots. However, quantitative predictions for RNA tertiary interactions remain elusive. Here we report a statistical mechanical model for the prediction of noncanonical loop-stem base-pairing interactions in RNA pseudoknots. Central to the model is the evaluation of the conformational entropy for the pseudoknotted folds with defined loop-stem tertiary structural contacts. We develop an RNA virtual bond-based conformational model (Vfold model), which permits a rigorous computation of the conformational entropy for a given fold that contains loop-stem tertiary contacts. With the entropy parameters predicted from the Vfold model and the energy parameters for the tertiary contacts as inserted parameters, we can then predict the RNA folding thermodynamics, from which we can extract the tertiary contact thermodynamic parameters from theory-experimental comparisons. These comparisons reveal a contact enthalpy (DeltaH) of -14 kcal/mol and a contact entropy (DeltaS) of -38 cal/mol/K for a protonated C(+)*(G-C) base triple at pH 7.0, and (DeltaH = -7 kcal/mol, DeltaS = -19 cal/mol/K) for an unprotonated base triple. Tests of the model for a series of pseudoknots show good theory-experiment agreement. Based on the extracted energy parameters for the tertiary structural contacts, the model enables predictions for the structure, stability, and folding pathways for RNA pseudoknots with known or postulated loop-stem tertiary contacts from the nucleotide sequence alone.

  2. Aqueous flooding methods for tertiary oil recovery

    SciTech Connect

    Peru, D.A.

    1989-04-04

    A method is described for flooding of a subterranean petroleum bearing formation for tertiary oil recovery, comprising the steps of providing at least one production well having at least one inlet within the subterranean petroleum bearing formation, and at least one injection well having at least one outlet within the subterranean petroleum bearing formation, injecting into the petroleum bearing formation through the injection well, a low alkaline pH aqueous sodium bicarbonate flooding solution having a pH in the range of from about 8.25 to about 9.25 comprising from about 0.25 to about 5 weight percent of sodium bicarbonate, from about 0.05 to about 1.0 weight percent of petroleum recovery surfactant, and from about 1 to about 20 weight percent of sodium chloride, based on the total weight of the aqueous flooding solution, withdrawing through at least one inlet of the production wells, an oil and water mixture comprising petroleum from the subterranean petroleum bearing formation and at least a portion of the low alkaline pH sodium bicarbonate aqueous flooding solution, and separating the oil from the aqueous oil and water mixture.

  3. The Tertiary tectonics of the southeast Asia

    SciTech Connect

    Honza, Eiichi )

    1990-06-01

    Most of the terranes in eastern Asia appear to be relics of arcs, oceanic islands, and subduction complexes. They have collided and accreted from the inner (northwestern) side in China since the Silurian. They are characterized by three stages of Pacific and Tethys evolution. The first collision is related to the Pacific domain in the Permian in which these movements are not clearly reconstructed. The second collision is related to the closure of the Paleo-Tethys in the Late Triassic to Early Jurassic. The third is related to closure of the Neo-Tethys and the subsequent collision of India in the Tertiary. Southeast Asia is in one of the most enigmatic plate boundaries in the world, forming many small plates, collisions, and consumptions. This complication is also suggested to be a result of the northward movement of Australia since its break-up from Gondwanaland in the Cretaceous. During their evolution, most of them have associated with arcs. These arcs also have formed superimpositions on the older exotic blocks of terranes. They are reconstructed on the base of the regular duration on the formation of arcs and backarc basins, which can be seen in the Western Pacific Arc Chain.

  4. Tertiary tectonic in the Tehuantepec Isthmus, Mexico

    SciTech Connect

    Lopez, F.A.

    1993-02-01

    A microplate model in the basement was proposed according to photointerpretation of satellite imagery and supported with microtectonic studies in the Tehuantepec's Isthmus. The microplate is located in the northwestern part of the [open quotes]Sierra de Chiapas,[close quotes] and structurally has lineaments that correspond with sinestral wrench faults oriented northeast-southwest and dextral faults oriented northwest-southeast. In the front of the microplate, these faults are joined in an arc form. The microplate began its movement forward to the north in the middle Tertiary. This movement originated in a regional compressional stress that was younger to the north. The stress changed the orientation of the anticline axis from northwest-southeast to west-east. In its western limit, the stress produces a sinestral shear stress that built a rotational deformation in the [open quotes]Sierra Atravesada,[close quotes] and represents a superimposed tectonic block over an ancient (laramide) orogeny. This system has also produced other secondary transtensional effects oriented northwest-southeast, represented along the [open quotes]Depression Central del Istmo.[close quotes] The microplate has formed a tensional system opening the [open quotes]Superior, Inferior, and Mar Muerto[close quotes] lagoons. The microplate is strongly related with the relief, seismic activity, and the tectonics of the salt of the Tehuantepec's Isthmus.

  5. Assembly of transmembrane helices of simple polytopic membrane proteins from sequence conservation patterns.

    PubMed

    Park, Yungki; Helms, Volkhard

    2006-09-01

    The transmembrane (TM) domains of most membrane proteins consist of helix bundles. The seemingly simple task of TM helix bundle assembly has turned out to be extremely difficult. This is true even for simple TM helix bundle proteins, i.e., those that have the simple form of compact TM helix bundles. Herein, we present a computational method that is capable of generating native-like structural models for simple TM helix bundle proteins having modest numbers of TM helices based on sequence conservation patterns. Thus, the only requirement for our method is the presence of more than 30 homologous sequences for an accurate extraction of sequence conservation patterns. The prediction method first computes a number of representative well-packed conformations for each pair of contacting TM helices, and then a library of tertiary folds is generated by overlaying overlapping TM helices of the representative conformations. This library is scored using sequence conservation patterns, and a subsequent clustering analysis yields five final models. Assuming that neighboring TM helices in the sequence contact each other (but not that TM helices A and G contact each other), the method produced structural models of Calpha atom root-mean-square deviation (CA RMSD) of 3-5 A from corresponding crystal structures for bacteriorhodopsin, halorhodopsin, sensory rhodopsin II, and rhodopsin. In blind predictions, this type of contact knowledge is not available. Mimicking this, predictions were made for the rotor of the V-type Na(+)-adenosine triphosphatase without such knowledge. The CA RMSD between the best model and its crystal structure is only 3.4 A, and its contact accuracy reaches 55%. Furthermore, the model correctly identifies the binding pocket for sodium ion. These results demonstrate that the method can be readily applied to ab initio structure prediction of simple TM helix bundle proteins having modest numbers of TM helices.

  6. Death of Metaphors in Life Science?--A Study of Upper Secondary and Tertiary Students' Use of Metaphors in Their Meaning-Making of Scientific Content

    ERIC Educational Resources Information Center

    Rundgren, Carl-Johan; Hirsch, Richard; Tibell, Lena A. E.

    2009-01-01

    The study reported in this article investigated the use of metaphors by upper secondary and tertiary students while learning a specific content area in molecular life science, protein function. Terms and expressions in science can be used in such precise and general senses that they are totally dissociated from their metaphoric origins. Beginners…

  7. Geriatric Prescription in a Nigerian Tertiary Hospital

    PubMed Central

    Osemeke, Nwani Paul; Hart, Onwukwe Chikezie; Cosmas, Nwosu Maduaburochukwu; Ohumagho, Isah Ambrose

    2016-01-01

    Objectives: To assess the medications prescribed for elderly inpatients on specific days during hospital admission with a view to detecting areas of irrational prescription. Methods: It was a prospective study of all patients aged 65 years and above admitted to the medical wards of a Nigerian tertiary hospital over a 12-month period. The World Health Organization/International Network of Rational Use of Drugs (WHO/INRUD) drug use indicators were used to assess drug prescriptions on various days of admission. Results: A total of 1513 patient encounters involving 345 patients aged between 65 and 92 years were assessed on hospital days 1, 3, 5, 7, 14, and 28. The average number of medicines per encounter ranged from 6.1 ± 2.5 on hospital day 1 to 7.8 ± 2.4 on hospital day 28. This difference was statistically significant (F = 14.42; P < 0.05). The percentage of encounters with an antibiotic prescribed ranged from 50.4% on hospital day 1 to 62.9% on hospital day 28 while the percentage of encounters with an injection prescribed decreased from 72.8% on hospital day 1 to 50.0% on day 28. Conclusions: This study suggests some degree of irrational prescribing as evident by the high average number of medicine per encounter and the high percentages of encounters with an antibiotic or injection prescribed. However, there is a need to develop standard values for the WHO/INRUD indicators based on the recently published national treatment guidelines for common elderly diseases which will serve as yardsticks to assess elderly inpatients prescriptions using WHO/INRUD core indicators in future studies. PMID:28104970

  8. Ab initio molecular simulations with numeric atom-centered orbitals

    NASA Astrophysics Data System (ADS)

    Blum, Volker; Gehrke, Ralf; Hanke, Felix; Havu, Paula; Havu, Ville; Ren, Xinguo; Reuter, Karsten; Scheffler, Matthias

    2009-11-01

    We describe a complete set of algorithms for ab initio molecular simulations based on numerically tabulated atom-centered orbitals (NAOs) to capture a wide range of molecular and materials properties from quantum-mechanical first principles. The full algorithmic framework described here is embodied in the Fritz Haber Institute "ab initio molecular simulations" (FHI-aims) computer program package. Its comprehensive description should be relevant to any other first-principles implementation based on NAOs. The focus here is on density-functional theory (DFT) in the local and semilocal (generalized gradient) approximations, but an extension to hybrid functionals, Hartree-Fock theory, and MP2/GW electron self-energies for total energies and excited states is possible within the same underlying algorithms. An all-electron/full-potential treatment that is both computationally efficient and accurate is achieved for periodic and cluster geometries on equal footing, including relaxation and ab initio molecular dynamics. We demonstrate the construction of transferable, hierarchical basis sets, allowing the calculation to range from qualitative tight-binding like accuracy to meV-level total energy convergence with the basis set. Since all basis functions are strictly localized, the otherwise computationally dominant grid-based operations scale as O(N) with system size N. Together with a scalar-relativistic treatment, the basis sets provide access to all elements from light to heavy. Both low-communication parallelization of all real-space grid based algorithms and a ScaLapack-based, customized handling of the linear algebra for all matrix operations are possible, guaranteeing efficient scaling (CPU time and memory) up to massively parallel computer systems with thousands of CPUs.

  9. Ab initio Study of He Stability in hcp-Ti

    SciTech Connect

    Dai, Yunya; Yang, Li; Peng, SM; Long, XG; Gao, Fei; Zu, Xiaotao T.

    2010-12-20

    The stability of He in hcp-Ti was studied using ab initio method based on density functional theory. The results indicate that a single He atom prefers to occupy the tetrahedral site rather than the octahedral site. The interaction of He defects with Ti atoms has been used to explain the relative stabilities of He point defects in hcp-Ti. The relative stability of He defects in hcp-Ti is useful for He clustering and bubble nucleation in metal tritides, which provides the basis for development of improved atomistic models.

  10. Ab Initio Study of Phase Equilibria in TiCx

    NASA Astrophysics Data System (ADS)

    Korzhavyi, P. A.; Pourovskii, L. V.; Hugosson, H. W.; Ruban, A. V.; Johansson, B.

    2002-01-01

    The phase diagram for the vacancy-ordered structures in the substoichiometric TiCx ( x = 0.5-1.0) has been established from Monte Carlo simulations with the long-range pair and multisite effective interactions obtained from ab initio calculations. Three ordered superstructures of vacancies ( Ti2C, Ti3C2, and Ti6C5) are found to be ground state configurations. Their stability has been verified by full-potential total energy calculations of the fully relaxed structures.

  11. Pseudorotation motion in tetrahydrofuran: an ab initio study.

    PubMed

    Rayón, Víctor M; Sordo, Jose A

    2005-05-22

    The use of different models based on experimental information about the observed level splitings, rotational constants, and far-infrared transition frequencies leads to different predictions on the equilibrium geometry for tetrahydrofuran. High-level ab initio calculations [coupled cluster singles, doubles (triples)/complete basis set (second order Moller-Plesset triple, quadrupole, quintuple)+zero-point energy(anharmonic)] suggest that the equilibrium conformation of tetrahydrofuran is an envelope C(s) structure. The theoretical geometrical parameters might be helpful to plan further microwave spectroscopic studies in order to get a physical interpretation of the measurements.

  12. Accelerating ab initio molecular dynamics simulations by linear prediction methods

    NASA Astrophysics Data System (ADS)

    Herr, Jonathan D.; Steele, Ryan P.

    2016-09-01

    Acceleration of ab initio molecular dynamics (AIMD) simulations can be reliably achieved by extrapolation of electronic data from previous timesteps. Existing techniques utilize polynomial least-squares regression to fit previous steps' Fock or density matrix elements. In this work, the recursive Burg 'linear prediction' technique is shown to be a viable alternative to polynomial regression, and the extrapolation-predicted Fock matrix elements were three orders of magnitude closer to converged elements. Accelerations of 1.8-3.4× were observed in test systems, and in all cases, linear prediction outperformed polynomial extrapolation. Importantly, these accelerations were achieved without reducing the MD integration timestep.

  13. Morphing ab initio potential energy curve of beryllium monohydride

    NASA Astrophysics Data System (ADS)

    Špirko, Vladimír

    2016-12-01

    Effective (mass-dependent) potential energy curves of the ground electronic states of 9BeH, 9BeD, and 9BeT are constructed by morphing a very accurate MR-ACPF ab initio potential of Koput (2011) within the framework of the reduced potential energy curve approach of Jenč (1983). The morphing is performed by fitting the RPC parameters to available experimental ro-vibrational data. The resulting potential energy curves provide a fairly quantitative reproduction of the fitted data. This allows for a reliable prediction of the so-far unobserved molecular states in terms of only a small number of fitting parameters.

  14. Ab initio evidence for nonthermal characteristics in ultrafast laser melting

    NASA Astrophysics Data System (ADS)

    Lian, Chao; Zhang, S. B.; Meng, Sheng

    2016-11-01

    Laser melting of semiconductors has been observed for almost 40 years; surprisingly, it is not well understood where most theoretical simulations show a laser-induced thermal process. Ab initio nonadiabatic simulations based on real-time time-dependent density functional theory reveal intrinsic nonthermal melting of silicon, at a temperature far below the thermal melting temperature of 1680 K. Both excitation threshold and time evolution of diffraction intensity agree well with experiment. Nonthermal melting is attributed to excitation-induced drastic changes in bonding electron density, and the subsequent decrease in the melting barrier, rather than lattice heating as previously assumed in the two-temperature models.

  15. Communication: Ab initio Joule-Thomson inversion data for argon

    NASA Astrophysics Data System (ADS)

    Wiebke, Jonas; Senn, Florian; Pahl, Elke; Schwerdtfeger, Peter

    2013-02-01

    The Joule-Thomson coefficient μH(P, T) is computed from the virial equation of state up to seventh-order for argon obtained from accurate ab initio data. Higher-order corrections become increasingly more important to fit the low-temperature and low-pressure regime and to avoid the early onset of divergence in the Joule-Thomson inversion curve. Good agreement with experiment is obtained for temperatures T > 250 K. The results also illustrate the limitations of the virial equation in regions close to the critical temperature.

  16. Ab initio quantum chemical study of electron transfer in carboranes

    NASA Astrophysics Data System (ADS)

    Pati, Ranjit; Pineda, Andrew C.; Pandey, Ravindra; Karna, Shashi P.

    2005-05-01

    The electron transfer (ET) properties of 10- and 12-vertex carboranes are investigated by the ab initio Hartree-Fock method within the Marcus-Hush (MH) two-state model and the Koopman theorem (KT) approach. The calculated value of the ET coupling matrix element, VAB, is consistently higher in the KT approach than in the MH two-state model. For the carborane molecules functionalized by -CH 2 groups at C-vertices, VAB strongly depends on the relative orientation of the planes containing the terminal -CH 2 groups. The predicted conformation dependence of VAB offers a molecular mechanism to control ET between two active centers in molecular systems.

  17. Ab-Initio Shell Model with a Core

    SciTech Connect

    Lisetskiy, A F; Barrett, B R; Kruse, M; Navratil, P; Stetcu, I; Vary, J P

    2008-06-04

    We construct effective 2- and 3-body Hamiltonians for the p-shell by performing 12{h_bar}{Omega} ab initio no-core shell model (NCSM) calculations for A=6 and 7 nuclei and explicitly projecting the many-body Hamiltonians onto the 0{h_bar}{Omega} space. We then separate these effective Hamiltonians into 0-, 1- and 2-body contributions (also 3-body for A=7) and analyze the systematic behavior of these different parts as a function of the mass number A and size of the NCSM basis space. The role of effective 3- and higher-body interactions for A > 6 is investigated and discussed.

  18. Ab Initio and Ab Exitu No-Core Shell Model

    SciTech Connect

    Vary, J P; Navratil, P; Gueorguiev, V G; Ormand, W E; Nogga, A; Maris, P; Shirokov, A

    2007-10-02

    We outline two complementary approaches based on the no core shell model (NCSM) and present recent results. In the ab initio approach, nuclear properties are evaluated with two-nucleon (NN) and three-nucleon interactions (TNI) derived within effective field theory (EFT) based on chiral perturbation theory (ChPT). Fitting two available parameters of the TNI generates good descriptions of light nuclei. In a second effort, an ab exitu approach, results are obtained with a realistic NN interaction derived by inverse scattering theory with off-shell properties tuned to fit light nuclei. Both approaches produce good results for observables sensitive to spin-orbit properties.

  19. Ab-initio study of transition metal hydrides

    SciTech Connect

    Sharma, Ramesh; Shukla, Seema Dwivedi, Shalini Sharma, Yamini

    2014-04-24

    We have performed ab initio self consistent calculations based on Full potential linearized augmented plane wave (FP-LAPW) method to investigate the optical and thermal properties of yttrium hydrides. From the band structure and density of states, the optical absorption spectra and specific heats have been calculated. The band structure of Yttrium metal changes dramatically due to hybridization of Y sp orbitals with H s orbitals and there is a net charge transfer from metal to hydrogen site. The electrical resistivity and specific heats of yttrium hydrides are lowered but the thermal conductivity is slightly enhanced due to increase in scattering from hydrogen sites.

  20. Ab Initio Calculations Applied to Problems in Metal Ion Chemistry

    NASA Technical Reports Server (NTRS)

    Bauschlicher, Charles W., Jr.; Langhoff, Stephen R.; Partridge, Harry; Arnold, James O. (Technical Monitor)

    1994-01-01

    Electronic structure calculations can provide accurate spectroscopic data (such as molecular structures) vibrational frequencies, binding energies, etc.) that have been very useful in explaining trends in experimental data and in identifying incorrect experimental measurements. In addition, ab initio calculations. have given considerable insight into the many interactions that make the chemistry of transition metal systems so diverse. In this review we focus on cases where calculations and experiment have been used to solve interesting chemical problems involving metal ions. The examples include cases where theory was used to differentiate between disparate experimental values and cases where theory was used to explain unexpected experimental results.

  1. Electric field response in bilayer graphene: Ab initio investigation

    NASA Astrophysics Data System (ADS)

    Mori, Yutaro; Minamitani, Emi; Ando, Yasunobu; Kasamatsu, Shusuke; Watanabe, Satoshi

    2016-11-01

    Stimulated by quantum capacitance measurements, we have investigated the electric properties of bilayer graphene (BLG) with carrier doping under an external electric field using ab initio calculations. We found that the relative permittivity of BLG depends weakly on the applied electric field, and that the BLG can be regarded as a dielectric material rather than a pair of metallic films. We also found that carrier doping affects the band gap of BLG under electric fields, although carrier doping has a much smaller effect on the band gap and density of states than the application of electric fields.

  2. Communication: Ab initio Joule-Thomson inversion data for argon.

    PubMed

    Wiebke, Jonas; Senn, Florian; Pahl, Elke; Schwerdtfeger, Peter

    2013-02-21

    The Joule-Thomson coefficient μ(H)(P, T) is computed from the virial equation of state up to seventh-order for argon obtained from accurate ab initio data. Higher-order corrections become increasingly more important to fit the low-temperature and low-pressure regime and to avoid the early onset of divergence in the Joule-Thomson inversion curve. Good agreement with experiment is obtained for temperatures T > 250 K. The results also illustrate the limitations of the virial equation in regions close to the critical temperature.

  3. Surface Segregation Energies of BCC Binaries from Ab Initio and Quantum Approximate Calculations

    NASA Technical Reports Server (NTRS)

    Good, Brian S.

    2003-01-01

    We compare dilute-limit segregation energies for selected BCC transition metal binaries computed using ab initio and quantum approximate energy method. Ab initio calculations are carried out using the CASTEP plane-wave pseudopotential computer code, while quantum approximate results are computed using the Bozzolo-Ferrante-Smith (BFS) method with the most recent parameterization. Quantum approximate segregation energies are computed with and without atomistic relaxation. The ab initio calculations are performed without relaxation for the most part, but predicted relaxations from quantum approximate calculations are used in selected cases to compute approximate relaxed ab initio segregation energies. Results are discussed within the context of segregation models driven by strain and bond-breaking effects. We compare our results with other quantum approximate and ab initio theoretical work, and available experimental results.

  4. Ab initio centroid path integral molecular dynamics: Application to vibrational dynamics of diatomic molecular systems

    NASA Astrophysics Data System (ADS)

    Ohta, Yasuhito; Ohta, Koji; Kinugawa, Kenichi

    2004-01-01

    An ab initio centroid molecular dynamics (CMD) method is developed by combining the CMD method with the ab initio molecular orbital method. The ab initio CMD method is applied to vibrational dynamics of diatomic molecules, H2 and HF. For the H2 molecule, the temperature dependence of the peak frequency of the vibrational spectral density is investigated. The results are compared with those obtained by the ab initio classical molecular dynamics method and exact quantum mechanical treatment. It is shown that the vibrational frequency obtained from the ab initio CMD approaches the exact first excitation frequency as the temperature lowers. For the HF molecule, the position autocorrelation function is also analyzed in detail. The present CMD method is shown to well reproduce the exact quantum result for the information on the vibrational properties of the system.

  5. Generation, structure and reactivity of tertiary organolithium reagents.

    PubMed

    Perry, Matthew A; Rychnovsky, Scott D

    2015-04-01

    Tertiary alkyllithium reagents are very useful intermediates in synthesis. Alkyllithium reagents with adjacent heteroatoms may be formed stereoselectively or may react stereoselectively, and have been used in the synthesis of alkaloids, C-glycosides and spirocycles. An overview of the generation, reactivity and stereochemistry of tertiary alkyllithium reagents will be presented, as well as examples of their use in organic synthesis. The discussion will be focused on a conceptual understanding of the generation and reactivity of these intermediates. The reactions described herein generate fully substituted carbon atoms, and the forces driving stereoselectivity will be discussed in detail. Where appropriate, computational results will be introduced to provide a better understanding for the structure and reactivity of tertiary alkyllithium reagents.

  6. Three-dimensional tertiary structure of yeast phenylalanine transfer RNA

    NASA Technical Reports Server (NTRS)

    Kim, S. H.; Sussman, J. L.; Suddath, F. L.; Quigley, G. J.; Mcpherson, A.; Wang, A. H. J.; Seeman, N. C.; Rich, A.

    1974-01-01

    Results of an analysis and interpretation of a 3-A electron density map of yeast phenylalanine transfer RNA. Some earlier detailed assignments of nucleotide residues to electron density peaks are found to be in error, even though the overall tracing of the backbone conformation of yeast phenylalanine transfer RNA was generally correct. A new, more comprehensive interpretation is made which makes it possible to define the tertiary interactions in the molecule. The new interpretation makes it possible to visualize a number of tertiary interactions which not only explain the structural role of most of the bases which are constant in transfer RNAs, but also makes it possible to understand in a direct and simple fashion the chemical modification data on transfer RNA. In addition, this pattern of tertiary interactions provides a basis for understanding the general three-dimensional folding of all transfer RNA molecules.

  7. The equity imperative in tertiary education: Promoting fairness and efficiency

    NASA Astrophysics Data System (ADS)

    Salmi, Jamil; Bassett, Roberta Malee

    2014-06-01

    While the share of the tertiary education age cohort (19-25) which is being given the opportunity to study has increased worldwide over the past two decades, this does not in fact translate into reduced inequality. For many young people, especially in the developing world, major obstacles such as disparities in terms of gender, minority population membership or disabilities as well as academic and financial barriers are still standing in their way. The authors of this article propose a conceptual framework to analyse equity issues in tertiary education and document the scope, significance and consequences of disparities in tertiary education opportunities. They throw some light on the main determinants of these inequalities and offer suggestions about effective equity promotion policies directed towards widening participation and improving the chances of success of underprivileged youths in order to create societies which uphold humanistic values.

  8. Three-cluster dynamics within an ab initio framework

    DOE PAGES

    Quaglioni, Sofia; Romero-Redondo, Carolina; Navratil, Petr

    2013-09-26

    In this study, we introduce a fully antisymmetrized treatment of three-cluster dynamics within the ab initio framework of the no-core shell model/resonating-group method. Energy-independent nonlocal interactions among the three nuclear fragments are obtained from realistic nucleon-nucleon interactions and consistent ab initio many-body wave functions of the clusters. The three-cluster Schrödinger equation is solved with bound-state boundary conditions by means of the hyperspherical-harmonic method on a Lagrange mesh. We discuss the formalism in detail and give algebraic expressions for systems of two single nucleons plus a nucleus. Using a soft similarity-renormalization-group evolved chiral nucleon-nucleon potential, we apply the method to amore » 4He+n+n description of 6He and compare the results to experiment and to a six-body diagonalization of the Hamiltonian performed within the harmonic-oscillator expansions of the no-core shell model. Differences between the two calculations provide a measure of core (4He) polarization effects.« less

  9. An Ab Initio Study of Alkali-C60 Complexes

    NASA Astrophysics Data System (ADS)

    Frick, Nathan; Hira, A. S.; Ray, A. K.

    2003-03-01

    We extend our previous work on fullerene-alkali complexes1-2 by presenting the results of an ab initio theoretical study of the alkali LiC60+, LiC60, NaC60+, NaC60, KC60+, and KC60 complexes. In the endohedral complexes for Li and Na, there is displacement of the adatom from the center. Of the ions, exohedral Li+ will sit closest to the cage, and among the neutrals, exohedral K remains closest. Bond lengths are consistently longer for the fivefold and threefold approaches. Adsorbates inside the fullerene donate negative charge to the carbons, but ions outside obtain a small amount, resulting in a polarization of the molecule. In the ion complexes, there is lowering of the orbital energy levels by 3 to 4 eV, resulting in an increase in the number of bound, but unoccupied, electronic orbitals. The HOMO-LUMO gap, of interest in superconductivity studies, is reduced by about 50 1. A.S. Hira and A.K. Ray, Phys. Rev. A 52, 141(1995); A 54, 2205(1996). 2. Ajit Hira and A. K. Ray, "An Initio Modeling of the Endohedral and Exohedral Complexes of C60Na2+ Complexes", Bull. Am. Phys. Soc. 47 (March 2002).

  10. Ab initio study of hot electrons in GaAs.

    PubMed

    Bernardi, Marco; Vigil-Fowler, Derek; Ong, Chin Shen; Neaton, Jeffrey B; Louie, Steven G

    2015-04-28

    Hot carrier dynamics critically impacts the performance of electronic, optoelectronic, photovoltaic, and plasmonic devices. Hot carriers lose energy over nanometer lengths and picosecond timescales and thus are challenging to study experimentally, whereas calculations of hot carrier dynamics are cumbersome and dominated by empirical approaches. In this work, we present ab initio calculations of hot electrons in gallium arsenide (GaAs) using density functional theory and many-body perturbation theory. Our computed electron-phonon relaxation times at the onset of the Γ, L, and X valleys are in excellent agreement with ultrafast optical experiments and show that the ultrafast (tens of femtoseconds) hot electron decay times observed experimentally arise from electron-phonon scattering. This result is an important advance to resolve a controversy on hot electron cooling in GaAs. We further find that, contrary to common notions, all optical and acoustic modes contribute substantially to electron-phonon scattering, with a dominant contribution from transverse acoustic modes. This work provides definitive microscopic insight into hot electrons in GaAs and enables accurate ab initio computation of hot carriers in advanced materials.

  11. Emission Spectroscopy and Ab Initio Calculations for TaN

    NASA Astrophysics Data System (ADS)

    Ram, R. S.; Liévin, J.; Bernath, P. F.

    2002-10-01

    The emission spectra of TaN have been investigated in the region 3000-35 000 cm -1 using a Fourier transform spectrometer. The spectra were observed in a tantalum hollow-cathode lamp by discharging a mixture of 1.5 Torr of Ne and about 6 mTorr of N 2. In addition to previously known bands, numerous additional bands were observed and assigned to a number of new transitions. The spectroscopic properties of the low-lying electronic states of TaN were also predicted by ab initio calculations. A 1Σ + state, with equilibrium constants of Be=0.457 852 1(48) cm -1, α e=0.002 235 9(67) cm -1, and Re=1.683 099 9(88) Å, has been identified as the ground state of TaN based on our experimental observations supported by the ab initio results. The first excited state has been identified as the a3Δ 1 spin component at 2827 cm -1 above the ground state. To higher energies, the states become difficult to assign because of their Hund's case (c) behavior and extensive interactions between the spin components of the electronic terms.

  12. Ab initio dynamics of the cytochrome P450 hydroxylation reaction

    PubMed Central

    Elenewski, Justin E.; Hackett, John C

    2015-01-01

    The iron(IV)-oxo porphyrin π-cation radical known as Compound I is the primary oxidant within the cytochromes P450, allowing these enzymes to affect the substrate hydroxylation. In the course of this reaction, a hydrogen atom is abstracted from the substrate to generate hydroxyiron(IV) porphyrin and a substrate-centered radical. The hydroxy radical then rebounds from the iron to the substrate, yielding the hydroxylated product. While Compound I has succumbed to theoretical and spectroscopic characterization, the associated hydroxyiron species is elusive as a consequence of its very short lifetime, for which there are no quantitative estimates. To ascertain the physical mechanism underlying substrate hydroxylation and probe this timescale, ab initio molecular dynamics simulations and free energy calculations are performed for a model of Compound I catalysis. Semiclassical estimates based on these calculations reveal the hydrogen atom abstraction step to be extremely fast, kinetically comparable to enzymes such as carbonic anhydrase. Using an ensemble of ab initio simulations, the resultant hydroxyiron species is found to have a similarly short lifetime, ranging between 300 fs and 3600 fs, putatively depending on the enzyme active site architecture. The addition of tunneling corrections to these rates suggests a strong contribution from nuclear quantum effects, which should accelerate every step of substrate hydroxylation by an order of magnitude. These observations have strong implications for the detection of individual hydroxylation intermediates during P450 catalysis. PMID:25681906

  13. Ab initio thermodynamic model for magnesium carbonates and hydrates.

    PubMed

    Chaka, Anne M; Felmy, Andrew R

    2014-09-04

    An ab initio thermodynamic framework for predicting properties of hydrated magnesium carbonate minerals has been developed using density-functional theory linked to macroscopic thermodynamics through the experimental chemical potentials for MgO, water, and CO2. Including semiempirical dispersion via the Grimme method and small corrections to the generalized gradient approximation of Perdew, Burke, and Ernzerhof for the heat of formation yields a model with quantitative agreement for the benchmark minerals brucite, magnesite, nesquehonite, and hydromagnesite. The model shows how small differences in experimental conditions determine whether nesquehonite, hydromagnesite, or magnesite is the result of laboratory synthesis from carbonation of brucite, and what transformations are expected to occur on geological time scales. Because of the reliance on parameter-free first-principles methods, the model is reliably extensible to experimental conditions not readily accessible to experiment and to any mineral composition for which the structure is known or can be hypothesized, including structures containing defects, substitutions, or transitional structures during solid state transformations induced by temperature changes or processes such as water, CO2, or O2 diffusion. Demonstrated applications of the ab initio thermodynamic framework include an independent means to evaluate differences in thermodynamic data for lansfordite, predicting the properties of Mg analogues of Ca-based hydrated carbonates monohydrocalcite and ikaite, which have not been observed in nature, and an estimation of the thermodynamics of barringtonite from the stoichiometry and a single experimental observation.

  14. Unified ab initio approaches to nuclear structure and reactions

    DOE PAGES

    Navratil, Petr; Quaglioni, Sofia; Hupin, Guillaume; ...

    2016-04-13

    The description of nuclei starting from the constituent nucleons and the realistic interactions among them has been a long-standing goal in nuclear physics. In addition to the complex nature of the nuclear forces, with two-, three- and possibly higher many-nucleon components, one faces the quantum-mechanical many-nucleon problem governed by an interplay between bound and continuum states. In recent years, significant progress has been made in ab initio nuclear structure and reaction calculations based on input from QCD-employing Hamiltonians constructed within chiral effective field theory. After a brief overview of the field, we focus on ab initio many-body approaches—built upon the no-core shell model—that are capable of simultaneously describing both bound and scattering nuclear states, and present results for resonances in light nuclei, reactions important for astrophysics and fusion research. In particular, we review recent calculations of resonances in the 6He halo nucleus, of five- and six-nucleon scattering, and an investigation of the role of chiral three-nucleon interactions in the structure of 9Be. Further, we discuss applications to the 7Bemore » $${({\\rm{p}},\\gamma )}^{8}{\\rm{B}}$$ radiative capture. Lastly, we highlight our efforts to describe transfer reactions including the 3H$${({\\rm{d}},{\\rm{n}})}^{4}$$He fusion.« less

  15. Implementation of renormalized excitonic method at ab initio level.

    PubMed

    Zhang, Hongjiang; Malrieu, Jean-Paul; Ma, Haibo; Ma, Jing

    2012-01-05

    The renormalized excitonic method [Hajj et al., Phys Rev B 2005, 72, 224412], in which the excited state of the whole system may be described as a linear combination of local excitations, has been implemented at ab initio level. Its performance is tested on the ionization potential and the energy gap between singlet ground state and lowest triplet for linear molecular hydrogen chains and more realistic systems, such as polyenes and polysilenes, using full configuration interaction (FCI) wave functions with a minimal basis set. The influence of different block sizes and the extent of interblock interactions are investigated. It has been demonstrated that satisfactory results can be obtained if the near degeneracies between the model space and the outer space are avoided and if interactions between the next-nearest neighbor blocks are considered. The method can be used with larger basis sets and other accurate enough ab initio evaluations (instead of FCI) of local excited states, from blocks, or from dimers or trimers of blocks. It provides a new possibility to accurately and economically describe the low-lying delocalized excited states of large systems, even inhomogeneous ones.

  16. AB INITIO SIMULATIONS FOR MATERIAL PROPERTIES ALONG THE JUPITER ADIABAT

    SciTech Connect

    French, Martin; Becker, Andreas; Lorenzen, Winfried; Nettelmann, Nadine; Bethkenhagen, Mandy; Redmer, Ronald; Wicht, Johannes

    2012-09-15

    We determine basic thermodynamic and transport properties of hydrogen-helium-water mixtures for the extreme conditions along Jupiter's adiabat via ab initio simulations, which are compiled in an accurate and consistent data set. In particular, we calculate the electrical and thermal conductivity, the shear and longitudinal viscosity, and diffusion coefficients of the nuclei. We present results for associated quantities like the magnetic and thermal diffusivity and the kinematic shear viscosity along an adiabat that is taken from a state-of-the-art interior structure model. Furthermore, the heat capacities, the thermal expansion coefficient, the isothermal compressibility, the Grueneisen parameter, and the speed of sound are calculated. We find that the onset of dissociation and ionization of hydrogen at about 0.9 Jupiter radii marks a region where the material properties change drastically. In the deep interior, where the electrons are degenerate, many of the material properties remain relatively constant. Our ab initio data will serve as a robust foundation for applications that require accurate knowledge of the material properties in Jupiter's interior, e.g., models for the dynamo generation.

  17. Ab initio study of hot electrons in GaAs

    PubMed Central

    Bernardi, Marco; Vigil-Fowler, Derek; Ong, Chin Shen; Neaton, Jeffrey B.; Louie, Steven G.

    2015-01-01

    Hot carrier dynamics critically impacts the performance of electronic, optoelectronic, photovoltaic, and plasmonic devices. Hot carriers lose energy over nanometer lengths and picosecond timescales and thus are challenging to study experimentally, whereas calculations of hot carrier dynamics are cumbersome and dominated by empirical approaches. In this work, we present ab initio calculations of hot electrons in gallium arsenide (GaAs) using density functional theory and many-body perturbation theory. Our computed electron–phonon relaxation times at the onset of the Γ, L, and X valleys are in excellent agreement with ultrafast optical experiments and show that the ultrafast (tens of femtoseconds) hot electron decay times observed experimentally arise from electron–phonon scattering. This result is an important advance to resolve a controversy on hot electron cooling in GaAs. We further find that, contrary to common notions, all optical and acoustic modes contribute substantially to electron–phonon scattering, with a dominant contribution from transverse acoustic modes. This work provides definitive microscopic insight into hot electrons in GaAs and enables accurate ab initio computation of hot carriers in advanced materials. PMID:25870287

  18. Ab initio dynamics of the cytochrome P450 hydroxylation reaction

    SciTech Connect

    Elenewski, Justin E.; Hackett, John C

    2015-02-14

    The iron(IV)-oxo porphyrin π-cation radical known as Compound I is the primary oxidant within the cytochromes P450, allowing these enzymes to affect the substrate hydroxylation. In the course of this reaction, a hydrogen atom is abstracted from the substrate to generate hydroxyiron(IV) porphyrin and a substrate-centered radical. The hydroxy radical then rebounds from the iron to the substrate, yielding the hydroxylated product. While Compound I has succumbed to theoretical and spectroscopic characterization, the associated hydroxyiron species is elusive as a consequence of its very short lifetime, for which there are no quantitative estimates. To ascertain the physical mechanism underlying substrate hydroxylation and probe this timescale, ab initio molecular dynamics simulations and free energy calculations are performed for a model of Compound I catalysis. Semiclassical estimates based on these calculations reveal the hydrogen atom abstraction step to be extremely fast, kinetically comparable to enzymes such as carbonic anhydrase. Using an ensemble of ab initio simulations, the resultant hydroxyiron species is found to have a similarly short lifetime, ranging between 300 fs and 3600 fs, putatively depending on the enzyme active site architecture. The addition of tunneling corrections to these rates suggests a strong contribution from nuclear quantum effects, which should accelerate every step of substrate hydroxylation by an order of magnitude. These observations have strong implications for the detection of individual hydroxylation intermediates during P450 catalysis.

  19. Ab Initio Thermodynamic Model for Magnesium Carbonates and Hydrates

    SciTech Connect

    Chaka, Anne M.; Felmy, Andrew R.

    2014-03-28

    An ab initio thermodynamic framework for predicting properties of hydrated magnesium carbonate minerals has been developed using density-functional theory linked to macroscopic thermodynamics through the experimental chemical potentials for MgO, water, and CO2. Including semiempirical dispersion via the Grimme method and small corrections to the generalized gradient approximation of Perdew, Burke, and Ernzerhof for the heat of formation yields a model with quantitative agreement for the benchmark minerals brucite, magnesite, nesquehonite, and hydromagnesite. The model shows how small differences in experimental conditions determine whether nesquehonite, hydromagnesite, or magnesite is the result of laboratory synthesis from carbonation of brucite, and what transformations are expected to occur on geological time scales. Because of the reliance on parameter-free first principles methods, the model is reliably extensible to experimental conditions not readily accessible to experiment and to any mineral composition for which the structure is known or can be hypothesized, including structures containing defects, substitutions, or transitional structures during solid state transformations induced by temperature changes or processes such as water, CO2, or O2 diffusion. Demonstrated applications of the ab initio thermodynamic framework include an independent means to evaluate differences in thermodynamic data for lansfordite, predicting the properties of Mg analogs of Ca-based hydrated carbonates monohydrocalcite and ikaite which have not been observed in nature, and an estimation of the thermodynamics of barringtonite from the stoichiometry and a single experimental observation.

  20. Structure-Function Relationships of a Tertiary Amine-Based Polycarboxybetaine.

    PubMed

    Lee, Chen-Jung; Wu, Haiyan; Tang, Qiong; Cao, Bin; Wang, Huifeng; Cong, Hongbo; Zhe, Jiang; Xu, Fujian; Cheng, Gang

    2015-09-15

    Zwitterionic polycarboxybetaine (PCB) materials have attracted noticeable interest for biomedical applications, such as wound healing/tissue engineering, medical implants, and biosensors, due to their excellent antifouling properties and design flexibility. Antifouling materials with buffering capability are particularly useful for many biomedical applications. In this work, an integrated zwitterionic polymeric material, poly(2-((2-hydroxyethyl)(2-methacrylamidoethyl)ammonio)acetate) (PCBMAA-1T), was synthesized to carry desired properties (antifouling, switchability and buffering capability). A tertiary amine was used to replace quaternary ammonium as the cation to endow the materials with buffering capability under neutral pH. Through this study, a better understanding on the structure-property relationship of zwitterionic materials was obtained. The tertiary amine cation does not compromise antifouling properties of zwitterionic materials. The amount of adsorbed proteins on PCBMAA-1T polymer brushes is less than 0.8 ng/cm(2) for fibrinogen and 0.3 ng/cm(2) (detection limit of the surface plasmon resonance sensor) for both undiluted blood plasma and serum. It is found that the tertiary amine is favorable to obtain good lactone ring stability in switchable PCB materials. Titration study showed that PCBMAA-1T could resist pH changes under both acidic (pH 1-3) and neutral/basic (pH 7-9) conditions. To the best of our knowledge, such an all-in-one material has not been reported. We believe this material might be potentially used for a variety of applications, including tissue engineering, chronic wound healing and medical device coating.

  1. Discovery of Tertiary Sulfonamides as Potent Liver X Receptor Antagonists

    SciTech Connect

    Zuercher, William J.; Buckholz†, Richard G.; Campobasso, Nino; Collins, Jon L.; Galardi, Cristin M.; Gampe, Robert T.; Hyatt, Stephen M.; Merrihew, Susan L.; Moore, John T.; Oplinger, Jeffrey A.; Reid, Paul R.; Spearing, Paul K.; Stanley, Thomas B.; Stewart, Eugene L.; Willson, Timothy M.

    2010-08-12

    Tertiary sulfonamides were identified in a HTS as dual liver X receptor (LXR, NR1H2, and NR1H3) ligands, and the binding affinity of the series was increased through iterative analogue synthesis. A ligand-bound cocrystal structure was determined which elucidated key interactions for high binding affinity. Further characterization of the tertiary sulfonamide series led to the identification of high affinity LXR antagonists. GSK2033 (17) is the first potent cell-active LXR antagonist described to date. 17 may be a useful chemical probe to explore the cell biology of this orphan nuclear receptor.

  2. Fluid migration, HC concentration in South Louisiana Tertiary sands

    SciTech Connect

    Leach, W.G.

    1993-03-15

    This is the second part of a three part series about the distribution of hydrocarbons in the Tertiary sands of South Louisiana. Most commercial hydrocarbons have disappeared at a pressure gradient of 0.85 psi/ft and a temperature of 350 F. in the South Louisiana Tertiary. The reason is quite simple. The bulk of all hydrocarbons is concentrated near the onset of abnormal pressure and between 140 and 260 F. Very little production is found beyond this pressure/temperature environment. The article attempts to explain why hydrocarbons do not occur outside this temperature/pressure region. It discusses vertical fluid migration and probable gas and oil sources.

  3. IRIS Toxicological Review of Ethyl Tertiary Butyl Ether (ETBE) ...

    EPA Pesticide Factsheets

    The IRIS Toxicological Review of Ethyl Tertiary Butyl Ether (ETBE) was released for external peer review in April 2017. EPA’s Science Advisory Board’s (SAB) Chemical Assessment Advisory Committee (CAAC) will conduct a peer review of the scientific basis supporting the ETBE assessment and release a final report of their review. Information regarding the peer review can be found on the SAB website. EPA is conducting an Integrated Risk Information System (IRIS) health assessment for Ethyl Tertiary Butyl Ether (ETBE). The outcome of this project is a Toxicological Review and IRIS Summary for ETBE that will be entered into the IRIS database.

  4. Crystallization of viruses and virus proteins

    NASA Astrophysics Data System (ADS)

    Sehnke, Paul C.; Harrington, Melissa; Hosur, M. V.; Li, Yunge; Usha, R.; Craig Tucker, R.; Bomu, Wu; Stauffacher, Cynthia V.; Johnson, John E.

    1988-07-01

    Methods for crystallizing six isometric plant and insect viruses are presented. Procedures developed for modifying, purifying and crystallizing coat protein subunits isolated from a virus forming asymmetric, spheroidal particles, stabilized almost exclusively by protein-RNA interactions, are also discussed. The tertiary and quaternary structures of small RNA viruses are compared.

  5. Conserved tertiary couplings stabilize elements in the PDZ fold, leading to characteristic patterns of domain conformational flexibility.

    PubMed

    Ho, Bosco K; Agard, David A

    2010-03-01

    Single-domain allostery has been postulated to occur through intramolecular pathways of signaling within a protein structure. We had previously investigated these pathways by introducing a local thermal perturbation and analyzed the anisotropic propagation of structural changes throughout the protein. Here, we develop an improved approach, the Rotamerically Induced Perturbation (RIP), that identifies strong couplings between residues by analyzing the pathways of heat-flow resulting from thermal excitation of rotameric rotations at individual residues. To explore the nature of these couplings, we calculate the complete coupling maps of 5 different PDZ domains. Although the PDZ domain is a well conserved structural fold that serves as a scaffold in many protein-protein complexes, different PDZ domains display unique patterns of conformational flexibility in response to ligand binding: some show a significant shift in a set of alpha-helices, while others do not. Analysis of the coupling maps suggests a simple relationship between the computed couplings and observed conformational flexibility. In domains where the alpha-helices are rigid, we find couplings of the alpha-helices to the body of the protein, whereas in domains having ligand-responsive alpha-helices, no couplings are found. This leads to a model where the alpha-helices are intrinsically dynamic but can be damped if sidechains interact at key tertiary contacts. These tertiary contacts correlate to high covariation contacts as identified by the statistical coupling analysis method. As these dynamic modules are exploited by various allosteric mechanisms, these tertiary contacts have been conserved by evolution.

  6. Ab initio phasing by molecular averaging in real space with new criteria: application to structure determination of a betanodavirus

    PubMed Central

    Yoshimura, Masato; Chen, Nai-Chi; Guan, Hong-Hsiang; Chuankhayan, Phimonphan; Lin, Chien-Chih; Nakagawa, Atsushi; Chen, Chun-Jung

    2016-01-01

    Molecular averaging, including noncrystallographic symmetry (NCS) averaging, is a powerful method for ab initio phase determination and phase improvement. Applications of the cross-crystal averaging (CCA) method have been shown to be effective for phase improvement after initial phasing by molecular replacement, isomorphous replacement, anomalous dispersion or combinations of these methods. Here, a two-step process for phase determination in the X-ray structural analysis of a new coat protein from a betanodavirus, Grouper nervous necrosis virus, is described in detail. The first step is ab initio structure determination of the T = 3 icosahedral virus-like particle using NCS averaging (NCSA). The second step involves structure determination of the protrusion domain of the viral molecule using cross-crystal averaging. In this method, molecular averaging and solvent flattening constrain the electron density in real space. To quantify these constraints, a new, simple and general indicator, free fraction (ff), is introduced, where ff is defined as the ratio of the volume of the electron density that is freely changed to the total volume of the crystal unit cell. This indicator is useful and effective to evaluate the strengths of both NCSA and CCA. Under the condition that a mask (envelope) covers the target molecule well, an ff value of less than 0.1, as a new rule of thumb, gives sufficient phasing power for the successful construction of new structures. PMID:27377380

  7. 40 CFR 721.10090 - Tertiary amine salt of glycol succinate (generic).

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 40 Protection of Environment 30 2010-07-01 2010-07-01 false Tertiary amine salt of glycol... Specific Chemical Substances § 721.10090 Tertiary amine salt of glycol succinate (generic). (a) Chemical... as tertiary amine salt of glycol succinate (PMN P-01-595) is subject to reporting under this...

  8. 40 CFR 721.10090 - Tertiary amine salt of glycol succinate (generic).

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... 40 Protection of Environment 31 2011-07-01 2011-07-01 false Tertiary amine salt of glycol... Specific Chemical Substances § 721.10090 Tertiary amine salt of glycol succinate (generic). (a) Chemical... as tertiary amine salt of glycol succinate (PMN P-01-595) is subject to reporting under this...

  9. A New Synthesis of Tertiary Alkyl N-Arylcarbamates from Isocyanates.

    ERIC Educational Resources Information Center

    Bailey, William J.; Griffith, James R.

    1978-01-01

    The method involves the dissolution of a small piece of metallic lithium in a small quantity of tertiary alcohol followed by addition to a mixture of the isocyanate and the tertiary alcohol in ether. This should be useful in organic chemistry laboratory courses for the identification of tertiary alcohols. (Author/BB)

  10. Analysis of Management Practices in Lagos State Tertiary Institutions through Total Quality Management Structural Framework

    ERIC Educational Resources Information Center

    AbdulAzeez, Abbas Tunde

    2016-01-01

    This research investigated total quality management practices and quality teacher education in public tertiary institutions in Lagos State. The study was therefore designed to analyse management practices in Lagos state tertiary institutions through total quality management structural framework. The selected public tertiary institutions in Lagos…

  11. Policy Innovation and Tertiary Education Graduation Rates: A Cross-Country Analysis

    ERIC Educational Resources Information Center

    Delaney, Jennifer A.; Yu, Patricia

    2013-01-01

    This study extends Trow's theory of higher education development to examine changes in national-level tertiary education graduation rates. Applying Trow's framework we arrive at three stages: (1) elite systems with gross tertiary graduation rates less than 15%, (2) massified systems with gross tertiary graduation rates between 15% and 50%, and (3)…

  12. The Policy Determinants of Investment in Tertiary Education. OECD Economics Department Working Papers, No. 576

    ERIC Educational Resources Information Center

    Martins, Joaquim Oliveira; Boarini, Romina; Strauss, Hubert; de la Maisonneuve, Christine; Saadi, Clarice

    2007-01-01

    This paper assesses how policies and institutions affect private returns to invest in tertiary human capital, the ability of individuals to finance this investment and the institutional characteristics of tertiary education systems. Focusing on core tertiary education services, the paper presents new measures of private returns to tertiary…

  13. 40 CFR 721.10090 - Tertiary amine salt of glycol succinate (generic).

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... 40 Protection of Environment 31 2014-07-01 2014-07-01 false Tertiary amine salt of glycol... Specific Chemical Substances § 721.10090 Tertiary amine salt of glycol succinate (generic). (a) Chemical... as tertiary amine salt of glycol succinate (PMN P-01-595) is subject to reporting under this...

  14. 40 CFR 721.10090 - Tertiary amine salt of glycol succinate (generic).

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... 40 Protection of Environment 32 2012-07-01 2012-07-01 false Tertiary amine salt of glycol... Specific Chemical Substances § 721.10090 Tertiary amine salt of glycol succinate (generic). (a) Chemical... as tertiary amine salt of glycol succinate (PMN P-01-595) is subject to reporting under this...

  15. 40 CFR 721.10090 - Tertiary amine salt of glycol succinate (generic).

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... 40 Protection of Environment 32 2013-07-01 2013-07-01 false Tertiary amine salt of glycol... Specific Chemical Substances § 721.10090 Tertiary amine salt of glycol succinate (generic). (a) Chemical... as tertiary amine salt of glycol succinate (PMN P-01-595) is subject to reporting under this...

  16. The Equity Imperative in Tertiary Education: Promoting Fairness and Efficiency

    ERIC Educational Resources Information Center

    Salmi, Jamil; Bassett, Roberta Malee

    2014-01-01

    While the share of the tertiary education age cohort (19-25) which is being given the opportunity to study has increased worldwide over the past two decades, this does not in fact translate into reduced inequality. For many young people, especially in the developing world, major obstacles such as disparities in terms of gender, minority population…

  17. Breast Self Examination Practice among Female Students of Tertiary Institutions

    ERIC Educational Resources Information Center

    Agbonifoh, Julia Adesua

    2016-01-01

    Against the background of the dangers posed by breast cancer world-wide, and the importance of its early detection and therefore breast self examination (BSE), this study investigated the practice of BSE among female students in tertiary institutions in Edo state. A sample of 723 participants selected through a combination of multi-stage,…

  18. On the significance of an RNA tertiary structure prediction

    PubMed Central

    Hajdin, Christine E.; Ding, Feng; Dokholyan, Nikolay V.; Weeks, Kevin M.

    2010-01-01

    Tertiary structure prediction is important for understanding structure–function relationships for RNAs whose structures are unknown and for characterizing RNA states recalcitrant to direct analysis. However, it is unknown what root-mean-square deviation (RMSD) corresponds to a statistically significant RNA tertiary structure prediction. We use discrete molecular dynamics to generate RNA-like folds for structures up to 161 nucleotides (nt) that have complex tertiary interactions and then determine the RMSD distribution between these decoys. These distributions are Gaussian-like. The mean RMSD increases with RNA length and is smaller if secondary structure constraints are imposed while generating decoys. The compactness of RNA molecules with true tertiary folds is intermediate between closely packed spheres and a freely jointed chain. We use this scaling relationship to define an expression relating RMSD with the confidence that a structure prediction is better than that expected by chance. This is the prediction significance, and corresponds to a P-value. For a 100-nt RNA, the RMSD of predicted structures should be within 25 Å of the accepted structure to reach the P ≤ 0.01 level if the secondary structure is predicted de novo and within 14 Å if secondary structure information is used as a constraint. This significance approach should be useful for evaluating diverse RNA structure prediction and molecular modeling algorithms. PMID:20498460

  19. The Place of VET in the Tertiary Sector. Conference Paper

    ERIC Educational Resources Information Center

    Beddie, Francesca

    2010-01-01

    The utilitarian spirit of Australian education has meant that since the nineteenth century the notion of tertiary education has embraced all post-school learning, delivered in sandstone universities or working men's institutes or on the job. This is not the definition the peak bodies TAFE (Technical and Further Education) Directors Australia (TDA)…

  20. Reflections on the Tertiary Education Sector in Australia. Conference Paper

    ERIC Educational Resources Information Center

    Karmel, Tom

    2009-01-01

    The split between higher education and vocational education and training (VET) in Australia is not clean. This paper discusses a number of aspects of this tertiary education sector: the Australian Qualifications Framework (AQF), which describes the qualifications offered by the three education sectors: schools, higher education and VET; student…

  1. Omalizumab use during pregnancy for CIU: a tertiary care experience.

    PubMed

    Cuervo-Pardo, L; Barcena-Blanch, M; Radojicic, C

    2016-07-01

    The treatment of antihistamine and steroid resistant Chronic Idiopathic Urticaria (CIU) during pregnancy poses a challenge due to teratogenicity of immunosuppressants. Omalizumab is a recently FDA approved therapy for CIU and is classified as pregnancy category B. We present an initial series of subjects treated at a tertiary care center for antihistamine and steroid resistant CIU with omalizumab who became pregnant during therapy.

  2. Tertiary age for upper Nubian sandstone formation, central Sudan

    SciTech Connect

    Prasad, G.; Lejal-Nicol, A.; Vaudois-Mieja, N.

    1986-02-01

    In central and northern Sudan, oil exploration is now active in the basins containing sediments of the Nubian Sandstone Formation. On the evidence of planned pipeline construction, significant volumes of oil appear to have been discovered in southwestern Sudan. A newly discovered flora from the upper Nubian Sandstone Formation near Khartoum in central Sudan is Tertiary in age. The flora is well preserved, and comprises leaves, flowers, and fruits, many not yet described. At the generic level, they are comparable to forms that are known fro the Eocene to Miocene. Aquatic plants indicate a lacustrine paleoenvironment; humid tropical forests thrived on the lakeshores. The Nubian Sandstone Formation of Sudan had been considered to be entirely of Cretaceous age; this new flora shifts the upper boundary into the Tertiary. The Tertiary Hudi Chert, found in scattered outcrops in the region of Atbara, was considered to overlie the Nubian Sandstone Formation. The authors suggest that the Hudi Chert is partly age equivalent to the Tertiary upper Nubian Sandstone at Jebel Mudaha.

  3. Tertiary Institutions, Entrepreneurship Education and Youth Empowerment in Nigeria

    ERIC Educational Resources Information Center

    Olasunkanmi, Abari Ayodeji; Olufunke, Oyetola Idowu; Adetayo, Okunuga Adedapo

    2013-01-01

    Entrepreneurship Education has recently become a global phenomenon in the development of world youths for self employment and self-reliance. The Nigerian nation cannot afford to be left out and left behind in this new trend in education both at the secondary and tertiary levels. However, while the Universal Basic Education (UBE) curriculum has…

  4. Introductory Statistics Course Tertiary Students' Understanding of P-Values

    ERIC Educational Resources Information Center

    Reaburn, Robyn

    2014-01-01

    This study aimed to gain knowledge of students' beliefs and difficulties in understanding p-values, and to use this knowledge to develop improved teaching programs. This study took place over four consecutive teaching semesters of a one-semester tertiary statistics unit. The study was cyclical, in that the results of each semester were used to…

  5. Pedagogical Practices of Reflection in Tertiary Dance Education

    ERIC Educational Resources Information Center

    Leijen, Ali; Lam, Ineke; Simons, P. Robert-Jan; Wildschut, Liesbeth

    2008-01-01

    The three different perspectives on reflection in education are embedded in the philosophical traditions of pragmatism, critical social theory and Kant. We aimed to describe the pedagogical practices of reflection, and to develop a descriptive model of the practices of reflection in tertiary dance education which can be used by dance educators to…

  6. Counselling for Sustainable Peace in Tertiary Institutions in Nigeria

    ERIC Educational Resources Information Center

    Nduka-Ozo, Stella Ngozi

    2016-01-01

    This study reviewed the nature of peace in Tertiary Institutions in Nigeria using Ebonyi State University as a case study. The purpose of the study was to review the various factors responsible for lack of peace. The sample was drawn from the three hundred level students of the Faculty of Education. Thirty students were selected from each of the…

  7. Competency Discourses: An Analysis of Secondary and Tertiary Assessments

    ERIC Educational Resources Information Center

    McNaughton, Susan M.

    2013-01-01

    Analysis of a sample of assessment tasks used in New Zealand first-year clinical and final-year secondary school Biology and Chemistry National Certificate of Educational Achievement summative assessments was conducted to assess whether similarities and differences existed in secondary and tertiary competency discourses. Findings suggested…

  8. A Conceptual Approach for Blended Leadership for Tertiary Education Institutions

    ERIC Educational Resources Information Center

    Jones, Sandra; Harvey, Marina; Lefoe, Geraldine

    2014-01-01

    Over the last 20 years, the tertiary education sector has adopted new administrative management approaches, with the aim of improving accountable and strategic focus. Over the same period, the question of how to build leadership capacity to improve learning and teaching and research outcomes has led to discussion on what constitutes academic…

  9. Self-Assessment in Professional Programmes within Tertiary Institutions

    ERIC Educational Resources Information Center

    Bourke, Roseanna

    2014-01-01

    Self-assessment at tertiary level is a critical pedagogical and assessment tool to support students in their transition to professional careers where on-going learning and assessment is required. Beyond the safety-net of course content, external assessment and pre-determined criteria, novice professionals need to find ways to self-assess their…

  10. Food Insecurity: Is It an Issue among Tertiary Students?

    ERIC Educational Resources Information Center

    Gallegos, Danielle; Ramsey, Rebecca; Ong, Kai Wen

    2014-01-01

    Insufficient access to food is known to compromise tertiary studies. Students often belong to groups known to have poor food security such as those renting or relying on government payments. The present study administered a cross-sectional survey incorporating the USDA food security survey module (FSSM) to 810 students at a metropolitan university…

  11. Tertiary Educational Institutions for Teaching, Research and Development

    ERIC Educational Resources Information Center

    Amoo, Sikiru A.

    2014-01-01

    This paper examines the quality of teaching and research in developing human resources to facilitate the development of tertiary education in the nation. It discusses the challenges and the roles of research in higher education. The author argues that the combination of content and pedagogical knowledge could help to develop human resources for…

  12. Secret Cults in Tertiary Institutions in Nigeria: An Appraisal

    ERIC Educational Resources Information Center

    Aluede, Raymond O. A.; Oniyama, Hope O.

    2009-01-01

    Cultism has remained a problem for tertiary institutions in Nigeria and the Larger Nigerian society since the first decade of the existence of university education in Nigeria. It has been worrisome to have children on campuses and several measures had been adopted to curb cultism some of such measures were the expulsion of the cultists caught and…

  13. The Introduction of New Technology in Tertiary Institutions.

    ERIC Educational Resources Information Center

    Schroder, M.

    1979-01-01

    New information-processing technologies are seen as solutions to problems for tertiary educational administrators. Two case studies are recounted. The introduction of word processing (stand-alone micro computer based) and computer output microfilm cataloging in the library of Armidale College of Advanced Education are described. (MLW)

  14. Accountability of Tertiary Education at the National Level: A Chimera?

    ERIC Educational Resources Information Center

    Lindsay, Alan; O'Byrne, Garry

    1979-01-01

    The concept of accountability and its application to Australian higher education are discussed. It is suggested that due to political, financial, and educational characteristics of tertiary education at the national system level there are fundamental and insoluble problems associated with achieving accountability. (SF)

  15. The Impact of Cooperative Learning on Tertiary EFL Learners' Motivation

    ERIC Educational Resources Information Center

    Ning, Huiping; Hornby, Garry

    2014-01-01

    This study was aimed at investigating the impact of cooperative learning on the motivation of tertiary English learners. Participants were from two randomly assigned classes at a university in the north of China. A pre-test-post-test control group design was employed to compare the impact of the cooperative learning approach with that of…

  16. Ruthenium-catalyzed tertiary amine formation from nitroarenes and alcohols.

    PubMed

    Feng, Chao; Liu, Yong; Peng, Shengming; Shuai, Qi; Deng, Guojun; Li, Chao-Jun

    2010-11-05

    A highly selective ruthenium-catalyzed C-N bond formation was developed by using the hydrogen-borrowing strategy. Various tertiary amines were obtained efficiently from nitroarenes and primary alcohols. The reaction tolerates a wide range of functionalities. A tentative mechanism was proposed for this direct amination reaction of alcohols with nitroarenes.

  17. Synthesis of unsymmetric tertiary amines via alcohol amination.

    PubMed

    Pang, Shaofeng; Deng, Youquan; Shi, Feng

    2015-06-11

    The first one-pot selective synthesis of unsymmetric tertiary amines is reported by the amination of two types of alcohols with primary amines via the development of a simple CuAlOx-HT catalyst and enables the synthesis of unsymmetric amines in a wide variety of primary amines and alcohols.

  18. Tertiary architecture of the Oceanobacillus iheyensis group II intron

    SciTech Connect

    Toor, Navtej; Keating, Kevin S.; Fedorova, Olga; Rajashankar, Kanagalaghatta; Wang, Jimin; Pyle, Anna Marie

    2010-05-03

    Group II introns are large ribozymes that act as self-splicing and retrotransposable RNA molecules. They are of great interest because of their potential evolutionary relationship to the eukaryotic spliceosome, their continued influence on the organization of many genomes in bacteria and eukaryotes, and their potential utility as tools for gene therapy and biotechnology. One of the most interesting features of group II introns is their relative lack of nucleobase conservation and covariation, which has long suggested that group II intron structures are stabilized by numerous unusual tertiary interactions and backbone-mediated contacts. Here, we provide a detailed description of the tertiary interaction networks within the Oceanobacillus iheyensis group IIC intron, for which a crystal structure was recently solved to 3.1 {angstrom} resolution. The structure can be described as a set of several intricately constructed tertiary interaction nodes, each of which contains a core of extended stacking networks and elaborate motifs. Many of these nodes are surrounded by a web of ribose zippers, which appear to further stabilize local structure. As predicted from biochemical and genetic studies, the group II intron provides a wealth of new information on strategies for RNA folding and tertiary structural organization.

  19. Microstructural Characterization of Alloy 617 Crept into the Tertiary Regime

    SciTech Connect

    Lillo, Thomas Martin; Wright, Richard Neil

    2015-07-01

    The microstructure of Alloy 617 was characterized following creep tests interrupted at total creep strains ranging from 2-20%. A range of creep temperatures (750-1000oC) and initial creep stresses (10-145 MPa) produced creep test durations ranging from 1 to 5800 hours. Image analysis of optical photomicrographs on longitudinal sections of the gage length was used to document the fraction of creep porosity as a function of creep parameters. Creep porosity was negligible below tertiary creep strains of 10% and increased with tertiary creep strain, thereafter. For a given temperature and total creep strain, creep porosity increased with decreasing creep stress. Creep porosity increased linearly with duration of the creep experiment. TEM performed on the gage sections did not reveal significant creep cavity formation on grain boundaries at the sub-micron level. It was concluded that the onset of tertiary creep did not result from creep cavitation and more likely arose due to the formation of low energy dislocation substructures with increasing tertiary strain.

  20. Interatomic Coulombic decay widths of helium trimer: Ab initio calculations

    SciTech Connect

    Kolorenč, Přemysl; Sisourat, Nicolas

    2015-12-14

    We report on an extensive study of interatomic Coulombic decay (ICD) widths in helium trimer computed using a fully ab initio method based on the Fano theory of resonances. Algebraic diagrammatic construction for one-particle Green’s function is utilized for the solution of the many-electron problem. An advanced and universal approach to partitioning of the configuration space into discrete states and continuum subspaces is described and employed. Total decay widths are presented for all ICD-active states of the trimer characterized by one-site ionization and additional excitation of an electron into the second shell. Selected partial decay widths are analyzed in detail, showing how three-body effects can qualitatively change the character of certain relaxation transitions. Previously unreported type of three-electron decay processes is identified in one class of the metastable states.

  1. Ab initio electronic and lattice dynamical properties of cerium dihydride

    NASA Astrophysics Data System (ADS)

    Gurel, Tanju; Eryigit, Resul

    2007-03-01

    The rare-earth metal hydrides are interesting systems because of the dramatic structural and electronic changes due to the hydrogen absorption and desorption. Among them, cerium dihydride (CeH2) is one of the less studied rare-earth metal-hydride. To have a better understanding, we have performed an ab initio study of electronic and lattice dynamical properties of CeH2 by using pseudopotential density functional theory within local density approximation (LDA) and a plane-wave basis. Electronic band structure of CeH2 have been obtained within LDA and as well as GW approximation. Lattice dynamical properties are calculated using density functional perturbation theory. The phonon spectrum is found to contain a set of high-frequency (˜ 850-1000 cm-1) optical bands, mostly hydrogen related, and low frequency cerium related acoustic modes climbing to 160 cm^ -1 at the zone boundary.

  2. Approximate ab initio calculations of electronic structure of amorphous silicon

    NASA Astrophysics Data System (ADS)

    Durandurdu, M.; Drabold, D. A.; Mousseau, N.

    2000-12-01

    We report on ab initio calculations of electronic states of two large and realistic models of amorphous silicon generated using a modified version of the Wooten-Winer-Weaire algorithm and relaxed, in both cases, with a Keating and a modified Stillinger-Weber potentials. The models have no coordination defects and a very narrow bond-angle distribution. We compute the electronic density-of-states and pay particular attention to the nature of the band-tail states around the electronic gap. All models show a large and perfectly clean optical gap and realistic Urbach tails. Based on these results and the extended quasi-one-dimensional stringlike structures observed for certain eigenvalues in the band tails, we postulate that the generation of model a-Si without localized states might be achievable under certain circumstances.

  3. The ab-initio density matrix renormalization group in practice

    SciTech Connect

    Olivares-Amaya, Roberto; Hu, Weifeng; Sharma, Sandeep; Yang, Jun; Chan, Garnet Kin-Lic; Nakatani, Naoki

    2015-01-21

    The ab-initio density matrix renormalization group (DMRG) is a tool that can be applied to a wide variety of interesting problems in quantum chemistry. Here, we examine the density matrix renormalization group from the vantage point of the quantum chemistry user. What kinds of problems is the DMRG well-suited to? What are the largest systems that can be treated at practical cost? What sort of accuracies can be obtained, and how do we reason about the computational difficulty in different molecules? By examining a diverse benchmark set of molecules: π-electron systems, benchmark main-group and transition metal dimers, and the Mn-oxo-salen and Fe-porphine organometallic compounds, we provide some answers to these questions, and show how the density matrix renormalization group is used in practice.

  4. Ab initio engineering of materials with stacked hexagonal tin frameworks

    PubMed Central

    Shao, Junping; Beaufils, Clément; Kolmogorov, Aleksey N.

    2016-01-01

    The group-IV tin has been hypothesized to possess intriguing electronic properties in an atom-thick hexagonal form. An attractive pathway of producing sizable 2D crystallites of tin is based on deintercalation of bulk compounds with suitable tin frameworks. Here, we have identified a new synthesizable metal distannide, NaSn2, with a 3D stacking of flat hexagonal layers and examined a known compound, BaSn2, with buckled hexagonal layers. Our ab initio results illustrate that despite being an exception to the 8-electron rule, NaSn2 should form under pressures easily achievable in multi-anvil cells and remain (meta)stable under ambient conditions. Based on calculated Z2 invariants, the predicted NaSn2 may display topologically non-trivial behavior and the known BaSn2 could be a strong topological insulator. PMID:27387140

  5. Efficient Ab initio Modeling of Random Multicomponent Alloys.

    PubMed

    Jiang, Chao; Uberuaga, Blas P

    2016-03-11

    We present in this Letter a novel small set of ordered structures (SSOS) method that allows extremely efficient ab initio modeling of random multicomponent alloys. Using inverse II-III spinel oxides and equiatomic quinary bcc (so-called high entropy) alloys as examples, we demonstrate that a SSOS can achieve the same accuracy as a large supercell or a well-converged cluster expansion, but with significantly reduced computational cost. In particular, because of this efficiency, a large number of quinary alloy compositions can be quickly screened, leading to the identification of several new possible high-entropy alloy chemistries. The SSOS method developed here can be broadly useful for the rapid computational design of multicomponent materials, especially those with a large number of alloying elements, a challenging problem for other approaches.

  6. Quantum plasmonics: from jellium models to ab initio calculations

    NASA Astrophysics Data System (ADS)

    Varas, Alejandro; García-González, Pablo; Feist, Johannes; García-Vidal, F. J.; Rubio, Angel

    2016-08-01

    Light-matter interaction in plasmonic nanostructures is often treated within the realm of classical optics. However, recent experimental findings show the need to go beyond the classical models to explain and predict the plasmonic response at the nanoscale. A prototypical system is a nanoparticle dimer, extensively studied using both classical and quantum prescriptions. However, only very recently, fully ab initio time-dependent density functional theory (TDDFT) calculations of the optical response of these dimers have been carried out. Here, we review the recent work on the impact of the atomic structure on the optical properties of such systems. We show that TDDFT can be an invaluable tool to simulate the time evolution of plasmonic modes, providing fundamental understanding into the underlying microscopical mechanisms.

  7. Ab initio electronic stopping power of protons in bulk materials

    NASA Astrophysics Data System (ADS)

    Shukri, Abdullah Atef; Bruneval, Fabien; Reining, Lucia

    2016-01-01

    The electronic stopping power is a crucial quantity for ion irradiation: it governs the deposited heat, the damage profile, and the implantation depth. Whereas experimental data are readily available for elemental solids, the data are much more scarce for compounds. Here we develop a fully ab initio computational scheme based on linear response time-dependent density-functional theory to predict the random electronic stopping power (RESP) of materials without any empirical fitting. We show that the calculated RESP compares well with experimental data, when at full convergence, with the inclusion of the core states and of the exchange correlation. We evaluate the unexpectedly limited magnitude of the nonlinear terms in the RESP by comparing with other approaches based on the time propagation of time-dependent density-functional theory. Finally, we check the validity of a few empirical rules of thumbs that are commonly used to estimate the electronic stopping power.

  8. Ab initio study of II-(VI)2 dichalcogenides

    NASA Astrophysics Data System (ADS)

    Olsson, P.; Vidal, J.; Lincot, D.

    2011-10-01

    The structural stabilities of the (Zn,Cd)(S,Se,Te)2 dichalcogenides have been determined ab initio. These compounds are shown to be stable in the pyrite phase, in agreement with available experiments. Structural parameters for the ZnTe2 pyrite semiconductor compound proposed here are presented. The opto-electronic properties of these dichalcogenide compounds have been calculated using quasiparticle GW theory. Bandgaps, band structures and effective masses are proposed as well as absorption coefficients and refraction indices. The compounds are all indirect semiconductors with very flat conduction band dispersion and high absorption coefficients. The work functions and surface properties are predicted. The Te and Se based compounds could be of interest as absorber materials in photovoltaic applications.

  9. Reactive Monte Carlo sampling with an ab initio potential

    DOE PAGES

    Leiding, Jeff; Coe, Joshua D.

    2016-05-04

    Here, we present the first application of reactive Monte Carlo in a first-principles context. The algorithm samples in a modified NVT ensemble in which the volume, temperature, and total number of atoms of a given type are held fixed, but molecular composition is allowed to evolve through stochastic variation of chemical connectivity. We also discuss general features of the method, as well as techniques needed to enhance the efficiency of Boltzmann sampling. Finally, we compare the results of simulation of NH3 to those of ab initio molecular dynamics (AIMD). Furthermore, we find that there are regions of state space formore » which RxMC sampling is much more efficient than AIMD due to the “rare-event” character of chemical reactions.« less

  10. Ab initio engineering of materials with stacked hexagonal tin frameworks

    NASA Astrophysics Data System (ADS)

    Shao, Junping; Beaufils, Clément; Kolmogorov, Aleksey N.

    2016-07-01

    The group-IV tin has been hypothesized to possess intriguing electronic properties in an atom-thick hexagonal form. An attractive pathway of producing sizable 2D crystallites of tin is based on deintercalation of bulk compounds with suitable tin frameworks. Here, we have identified a new synthesizable metal distannide, NaSn2, with a 3D stacking of flat hexagonal layers and examined a known compound, BaSn2, with buckled hexagonal layers. Our ab initio results illustrate that despite being an exception to the 8-electron rule, NaSn2 should form under pressures easily achievable in multi-anvil cells and remain (meta)stable under ambient conditions. Based on calculated Z2 invariants, the predicted NaSn2 may display topologically non-trivial behavior and the known BaSn2 could be a strong topological insulator.

  11. Ab initio water pair potential with flexible monomers.

    PubMed

    Jankowski, Piotr; Murdachaew, Garold; Bukowski, Robert; Akin-Ojo, Omololu; Leforestier, Claude; Szalewicz, Krzysztof

    2015-03-26

    A potential energy surface for the water dimer with explicit dependence on monomer coordinates is presented. The surface was fitted to a set of previously published interaction energies computed on a grid of over a quarter million points in the 12-dimensional configurational space using symmetry-adapted perturbation theory and coupled-cluster methods. The present fit removes small errors in published fits, and its accuracy is critically evaluated. The minimum and saddle-point structures of the potential surface were found to be very close to predictions from direct ab initio optimizations. The computed second virial coefficients agreed well with experimental values. At low temperatures, the effects of monomer flexibility in the virial coefficients were found to be much smaller than the quantum effects.

  12. Ab initio study of helium behavior in titanium tritides

    SciTech Connect

    Liang, J. H.; Dai, Yunya; Yang, Li; Peng, SM; Fan, K. M.; Long, XG; Zhou, X. S.; Zu, Xiaotao; Gao, Fei

    2013-03-01

    Ab initio calculations based on density functional theory have been performed to investigate the relative stability of titanium tritides and the helium behavior in stable titanium tritides. The results show that the β-phase TiT1.5 without two tritium along the [100] direction (TiT1.5[100]) is more stable than other possible structures. The stability of titanium tritides decrease with the increased generation of helium in TiT1.5[100]. In addition, helium generated by tritium decay prefers locating at a tetrahedral site, and favorably migrates between two neighbor vacant tetrahedral sites through an intermediate octahedral site in titanium tritides, with a migration energy of 0.23 eV. Furthermore, helium is easily accumulated on a (100) plane in β-phase TiT1.5[100].

  13. Ab initio electron propagator theory of molecular wires. I. Formalism.

    PubMed

    Dahnovsky, Yu; Zakrzewski, V G; Kletsov, A; Ortiz, J V

    2005-11-08

    Ab initio electron propagator methodology may be applied to the calculation of electrical current through a molecular wire. A new theoretical approach is developed for the calculation of the retarded and advanced Green functions in terms of the electron propagator matrix for the bridge molecule. The calculation of the current requires integration in a complex half plane for a trace that involves terminal and Green's-function matrices. Because the Green's-function matrices have complex poles represented by matrices, a special scheme is developed to express these "matrix poles" in terms of ordinary poles. An expression for the current is derived for a terminal matrix of arbitrary rank. For a single terminal orbital, the analytical expression for the current is given in terms of pole strengths, poles, and terminal matrix elements of the electron propagator. It is shown that Dyson orbitals with high pole strengths and overlaps with terminal orbitals are most responsible for the conduction of electrical current.

  14. Ab initio simulations of liquid carbon monoxide at high pressure

    NASA Astrophysics Data System (ADS)

    Leonhardi, Tanis C.; Militzer, Burkhard

    2017-03-01

    Carbon monoxide occurs as a volatile species in the interiors of terrestrial planets, and as a disequilibrium atmospheric constituent in the giant planets. It plays an important role during the accretionary stages of planet formation reacting with gases to form compounds such as CH4 and H2O. The structure of carbon monoxide is unknown over the majority of the temperature and pressure regime in giant planet interiors. Here we perform ab initio molecular dynamics simulations to characterize CO to 140 GPa and 5,000 K. We find that CO is stable as a molecular liquid at lower P-T conditions, as a polymeric liquid at higher P-T conditions found in ice giant interiors, and as a plasma at high-T.

  15. Ab initio Potential Energy Surface for H-H2

    NASA Technical Reports Server (NTRS)

    Partridge, Harry; Bauschlicher, Charles W., Jr.; Stallcop, James R.; Levin, Eugene

    1993-01-01

    Ab initio calculations employing large basis sets are performed to determine an accurate potential energy surface for H-H2 interactions for a broad range of separation distances. At large distances, the spherically averaged potential determined from the calculated energies agrees well with the corresponding results determined from dispersion coefficients; the van der Waals well depth is predicted to be 75 +/- (mu)E(sub h). Large basis sets have also been applied to reexamine the accuracy of theoretical repulsive potential energy surfaces. Multipolar expansions of the computed H-H2 potential energy surface are reported for four internuclear separation distances (1.2, 1.401, 1.449, and 1.7a(sub 0) of the hydrogen molecule. The differential elastic scattering cross section calculated from the present results is compared with the measurements from a crossed beam experiment.

  16. An ab initio study on anionic aerogen bonds

    NASA Astrophysics Data System (ADS)

    Esrafili, Mehdi D.; Mohammadian-Sabet, Fariba

    2017-01-01

    An ab initio study is carried out to investigate the anionic aerogen bonds in complexes of KrO3, XeO3 and XeOF2 with F-, Cl-, Br-, CN-, NC-, N3-, SH-, SCN-, NCS-, OH- and OCH3- anions. All of the anionic aerogen bonds analyzed here have a partial covalent character. Charge transfer from the anion to the Kr-O or Xe-O σ∗ orbital stabilizes these complexes and leads to a sizable redshift in the corresponding stretching frequencies. The J(Kr-O) or J(Xe-O) spin-spin coupling constants can be regarded as a useful tool for the characterization of strength of the anionic aerogen-bonded complexes.

  17. Ab Initio Study of KCl and NaCl Clusters

    NASA Astrophysics Data System (ADS)

    Brownrigg, Clifton; Hira, Ajit; Pacheco, Jose; Salazar, Justin

    2013-03-01

    We continue our interest in the theoretical study of molecular clusters to examine the chemical properties of small KnCln and NanCln clusters (n = 2 - 15). The potentially important role of these molecular species in biochemical and medicinal processes is well known. This work applies the hybrid ab initio methods of quantum chemistry to derive the different alkali-halide (MnHn) geometries. Of particular interest is the competition between hexagonal ring geometries and rock salt structures. Electronic energies, rotational constants, dipole moments, and vibrational frequencies for these geometries are calculated. Magic numbers for cluster stability are identified and are related to the property of cluster compactness. Mapping of the singlet, triplet, and quintet, potential energy surfaces is performed. Calculations have been performed to examine the interactions of these clusters with some atoms and molecules of biological interest, including O, O2, and Fe. The potential for design of new medicinal drugs is explored.

  18. Simple calculation of ab initio melting curves: Application to aluminum

    NASA Astrophysics Data System (ADS)

    Robert, Grégory; Legrand, Philippe; Arnault, Philippe; Desbiens, Nicolas; Clérouin, Jean

    2015-03-01

    We present a simple, fast, and promising method to compute the melting curves of materials with ab initio molecular dynamics. It is based on the two-phase thermodynamic model of Lin et al [J. Chem. Phys. 119, 11792 (2003), 10.1063/1.1624057] and its improved version given by Desjarlais [Phys. Rev. E 88, 062145 (2013), 10.1103/PhysRevE.88.062145]. In this model, the velocity autocorrelation function is utilized to calculate the contribution of the nuclei motion to the entropy of the solid and liquid phases. It is then possible to find the thermodynamic conditions of equal Gibbs free energy between these phases, defining the melting curve. The first benchmark on the face-centered cubic melting curve of aluminum from 0 to 300 GPa demonstrates how to obtain an accuracy of 5%-10%, comparable to the most sophisticated methods, for a much lower computational cost.

  19. Ab initio quantum transport in atomic carbon chains

    NASA Astrophysics Data System (ADS)

    Botello-Méndez, Andrés R.; Charlier, Jean-Christophe; Banhart, Florian; NAPS Team; Carbyne Collaboration

    2015-03-01

    Carbyne, the sp-hybridized phase of carbon, is still a missing link in the family of carbon allotropes. Recently, detailed electrical measurements and first-principles electronic transport calculations have been performed on monoatomic carbon chains. When the 1D system is under strain, the current-voltage curves exhibit a semiconducting behavior, which corresponds to the polyyne structure of the atomic chain with alternating single and triple bonds. Conversely, when the chain is unstrained, the ohmic behavior is observed in agreement with the metallic cumulene structure with double bonds, confirming recent theoretical predictions, namely that a metal-insulator transition can be induced by adjusting the strain. The key role of the contacting leads is also scrutinized by ab initio quantum conductance calculations, explaining the rectifying behavior measured in monoatomic carbon chains in a non-symmetric contact configuration.

  20. High-throughput ab-initio dilute solute diffusion database

    NASA Astrophysics Data System (ADS)

    Wu, Henry; Mayeshiba, Tam; Morgan, Dane

    2016-07-01

    We demonstrate automated generation of diffusion databases from high-throughput density functional theory (DFT) calculations. A total of more than 230 dilute solute diffusion systems in Mg, Al, Cu, Ni, Pd, and Pt host lattices have been determined using multi-frequency diffusion models. We apply a correction method for solute diffusion in alloys using experimental and simulated values of host self-diffusivity. We find good agreement with experimental solute diffusion data, obtaining a weighted activation barrier RMS error of 0.176 eV when excluding magnetic solutes in non-magnetic alloys. The compiled database is the largest collection of consistently calculated ab-initio solute diffusion data in the world.

  1. Ab-initio theory of spin fluctuations in magnets

    NASA Astrophysics Data System (ADS)

    Antropov, Vladimir; Ke, Liqin; van Schilfgaarde, Mark; Katsnelson, Mikhael

    2011-03-01

    We propose a framework for a true ab initio theory of magnetism, based on many-body perturbation theory (MPBT). It fits in naturally with methods based MPBT such as the GW approximation; but the approach can be implemented as an extension to any existing static method for electronic structure such as the local spin density approximation to density functional theory, to include spin fluctuations. Initially we calculated the spin fluctuation contributions using random phase approximation. The self consistency procedure similar to the one used in Moryia-Kawabata theory can be naturally implemented. The fluctuation dissipation theorem is used to calculate the reduction of the mean field magnetic moment in itinerant magnets. The applications of the technique includes traditional 3d ferromagnetic metals, their alloys and compounds and 5f systems.

  2. Heats of Segregation of BCC Binaries from ab Initio and Quantum Approximate Calculations

    NASA Technical Reports Server (NTRS)

    Good, Brian S.

    2004-01-01

    We compare dilute-limit heats of segregation for selected BCC transition metal binaries computed using ab initio and quantum approximate energy methods. Ab initio calculations are carried out using the CASTEP plane-wave pseudopotential computer code, while quantum approximate results are computed using the Bozzolo-Ferrante-Smith (BFS) method with the most recent LMTO-based parameters. Quantum approximate segregation energies are computed with and without atomistic relaxation, while the ab initio calculations are performed without relaxation. Results are discussed within the context of a segregation model driven by strain and bond-breaking effects. We compare our results with full-potential quantum calculations and with available experimental results.

  3. Ab initio calculations of the melting temperatures of refractory bcc metals.

    PubMed

    Wang, L G; van de Walle, A

    2012-01-28

    We present ab initio calculations of the melting temperatures for bcc metals Nb, Ta and W. The calculations combine phase coexistence molecular dynamics (MD) simulations using classical embedded-atom method potentials and ab initio density functional theory free energy corrections. The calculated melting temperatures for Nb, Ta and W are, respectively, within 3%, 4%, and 7% of the experimental values. We compare the melting temperatures to those obtained from direct ab initio molecular dynamics simulations and see if they are in excellent agreement with each other. The small remaining discrepancies with experiment are thus likely due to inherent limitations associated with exchange-correlation energy approximations within density-functional theory.

  4. Ab initio path integral ring polymer molecular dynamics: Vibrational spectra of molecules

    NASA Astrophysics Data System (ADS)

    Shiga, Motoyuki; Nakayama, Akira

    2008-01-01

    The path integral ring polymer molecular dynamics method is combined with 'on-the-fly' ab initio electronic structure calculations and applied to vibrational spectra of small molecules, LiH and H 2O, at the room temperature. The results are compared with those of the numerically exact solution and ab initio path integral centroid molecular dynamics calculation. The peak positions in the calculated spectra are found to be reasonable, showing the red-shift due to potential anharmonicity. This unification enables the investigation of real-time quantum dynamics of chemically complex molecular systems on the ab initio Born-Oppenheimer potential energy surface.

  5. Ab initio MCDHF calculations of electron-nucleus interactions

    NASA Astrophysics Data System (ADS)

    Bieroń, Jacek; Froese Fischer, Charlotte; Fritzsche, Stephan; Gaigalas, Gediminas; Grant, Ian P.; Indelicato, Paul; Jönsson, Per; Pyykkö, Pekka

    2015-05-01

    We present recent advances in the development of atomic ab initio multiconfiguration Dirac-Hartree-Fock theory, implemented in the GRASP relativistic atomic structure code. For neutral atoms, the deviations of properties calculated within the Dirac-Hartree-Fock (DHF) method (based on independent particle model of an atomic cloud) are usually dominated by electron correlation effects, i.e. the non-central interactions of individual electrons. We present the recent advances in accurate calculations of electron correlation effects in small, medium, and heavy neutral atoms. We describe methods of systematic development of multiconfiguration expansions leading to systematic, controlled improvement of the accuracy of the ab initio calculations. These methods originate from the concept of the complete active space (CAS) model within the DHF theory, which, at least in principle, permits fully relativistic calculations with full account of electron correlation effects. The calculations within the CAS model on currently available computer systems are feasible only for very light systems. For heavier atoms or ions with more than a few electrons, restrictions have to be imposed on the multiconfiguration expansions. We present methods and tools, which are designed to extend the numerical calculations in a controlled manner, where multiconfiguration expansions account for all leading electron correlation effects. We show examples of applications of the GRASP code to calculations of hyperfine structure constants, but the code may be used for calculations of arbitrary bound-state atomic properties. In recent years it has been applied to calculations of atomic and ionic spectra (transition energies and rates), to determinations of nuclear electromagnetic moments, as well as to calculations related to interactions of bound electrons with nuclear electromagnetic moments leading to violations of discrete symmetries.

  6. Targeted drug delivery through the traceless release of tertiary and heteroaryl amines from antibody-drug conjugates.

    PubMed

    Staben, Leanna R; Koenig, Stefan G; Lehar, Sophie M; Vandlen, Richard; Zhang, Donglu; Chuh, Josefa; Yu, Shang-Fan; Ng, Carl; Guo, Jun; Liu, Yanzhou; Fourie-O'Donohue, Aimee; Go, MaryAnn; Linghu, Xin; Segraves, Nathaniel L; Wang, Tao; Chen, Jinhua; Wei, BinQing; Phillips, Gail D Lewis; Xu, Keyang; Kozak, Katherine R; Mariathasan, Sanjeev; Flygare, John A; Pillow, Thomas H

    2016-12-01

    The reversible attachment of a small-molecule drug to a carrier for targeted delivery can improve pharmacokinetics and the therapeutic index. Previous studies have reported the delivery of molecules that contain primary and secondary amines via an amide or carbamate bond; however, the ability to employ tertiary-amine-containing bioactive molecules has been elusive. Here we describe a bioreversible linkage based on a quaternary ammonium that can be used to connect a broad array of tertiary and heteroaryl amines to a carrier protein. Using a concise, protecting-group-free synthesis we demonstrate the chemoselective modification of 12 complex molecules that contain a range of reactive functional groups. We also show the utility of this connection with both protease-cleavable and reductively cleavable antibody-drug conjugates that were effective and stable in vitro and in vivo. Studies with a tertiary-amine-containing antibiotic show that the resulting antibody-antibiotic conjugate provided appropriate stability and release characteristics and led to an unexpected improvement in activity over the conjugates previously connected via a carbamate.

  7. Robustness and optimal use of design principles of arthropod exoskeletons studied by ab initio-based multiscale simulations.

    PubMed

    Nikolov, S; Fabritius, H; Petrov, M; Friák, M; Lymperakis, L; Sachs, C; Raabe, D; Neugebauer, J

    2011-02-01

    Recently, we proposed a hierarchical model for the elastic properties of mineralized lobster cuticle using (i) ab initio calculations for the chitin properties and (ii) hierarchical homogenization performed in a bottom-up order through all length scales. It has been found that the cuticle possesses nearly extremal, excellent mechanical properties in terms of stiffness that strongly depend on the overall mineral content and the specific microstructure of the mineral-protein matrix. In this study, we investigated how the overall cuticle properties changed when there are significant variations in the properties of the constituents (chitin, amorphous calcium carbonate (ACC), proteins), and the volume fractions of key structural elements such as chitin-protein fibers. It was found that the cuticle performance is very robust with respect to variations in the elastic properties of chitin and fiber proteins at a lower hierarchy level. At higher structural levels, variations of design parameters such as the volume fraction of the chitin-protein fibers have a significant influence on the cuticle performance. Furthermore, we observed that among the possible variations in the cuticle ingredients and volume fractions, the experimental data reflect an optimal use of the structural variations regarding the best possible performance for a given composition due to the smart hierarchical organization of the cuticle design.

  8. Ab Initio Studies of Halogen and Nitrogen Oxide Species of Interest in Stratospheric Chemistry

    NASA Technical Reports Server (NTRS)

    Lee, Timothy J.; Langhoff, Stephen R. (Technical Monitor)

    1995-01-01

    The ability of modern state-of-the art ab initio quantum chemical techniques to characterize reliably the gas-phase molecular structure, vibrational spectrum, electronic spectrum, and thermal stability of fluorine, chlorine, bromine and nitrogen oxide species will be demonstrated by presentation of some example studies. The ab initio results are shown to be in excellent agreement with the available experimental data, and where the experimental data are either not known or are inconclusive, the theoretical results are shown to fill in the gaps and to resolve experimental controversies. In addition, ab initio studies in which the electronic spectra and the characterization of excited electronic states of halogen oxide species will also be presented. Again where available, the ab initio results are compared to experimental observations, and are used to aid in the interpretation of experimental studies.

  9. Characteristics of the tertiary egg membrane of cuttlefish Sepiella maindroni de Rochebrune

    NASA Astrophysics Data System (ADS)

    Wang, Chunlin; Fan, Xiaoxu; Jiang, Xiamin; Song, Weiwei; Xu, Yongjian

    2010-11-01

    We separated tertiary egg membrane (TGM) from 2- and 25-day-old eggs of cuttlefish Sepiella maindroni de Rochebrune, and revealed its ultrastructure, physical (solubility, barrier property) and biochemical (histology, histochemistry, nutritional components, bacteriostasis) characteristics. The results show that TGM could not be dissolved with natural seawater, alcohol, ether or hydrochloric acid (HCl), but it could be dissolved with 2-chloroethanol, diethylamine, and sodium hydroxide (NaOH). The black TGM was more effective in blocking off mud particulates, microorganisms ( Chlorella vulgaris, Vibrio alginolyticus) and lighter than the white TGM. The elasticity of black and white TGMs was 1.8 N and 1.5 N, respectively. There were some ink particulates and rod-shaped bacteria in the black TGM. The nutritional components were different between black and white TGMs: Lipid content was lower and protein content was higher in the black TGM. TGM could also inhibit the growth of Vibrio alginolyticus.

  10. Transmembrane segments form tertiary hairpins in the folding vestibule of the ribosome.

    PubMed

    Tu, Liwei; Khanna, Pooja; Deutsch, Carol

    2014-01-09

    Folding of membrane proteins begins in the ribosome as the peptide is elongated. During this process, the nascent peptide navigates along 100Å of tunnel from the peptidyltransferase center to the exit port. Proximal to the exit port is a "folding vestibule" that permits the nascent peptide to compact and explore conformational space for potential tertiary folding partners. The latter occurs for cytosolic subdomains but has not yet been shown for transmembrane segments. We now demonstrate, using an accessibility assay and an improved intramolecular crosslinking assay, that the helical transmembrane S3b-S4 hairpin ("paddle") of a voltage-gated potassium (Kv) channel, a critical region of the Kv voltage sensor, forms in the vestibule. S3-S4 hairpin interactions are detected at an early stage of Kv biogenesis. Moreover, this vestibule hairpin is consistent with a closed-state conformation of the Kv channel in the plasma membrane.

  11. A replica exchange Monte Carlo algorithm for protein folding in the HP model

    PubMed Central

    Thachuk, Chris; Shmygelska, Alena; Hoos, Holger H

    2007-01-01

    Background The ab initio protein folding problem consists of predicting protein tertiary structure from a given amino acid sequence by minimizing an energy function; it is one of the most important and challenging problems in biochemistry, molecular biology and biophysics. The ab initio protein folding problem is computationally challenging and has been shown to be NP MathType@MTEF@5@5@+=feaafiart1ev1aaatCvAUfKttLearuWrP9MDH5MBPbIqV92AaeXatLxBI9gBaebbnrfifHhDYfgasaacH8akY=wiFfYdH8Gipec8Eeeu0xXdbba9frFj0=OqFfea0dXdd9vqai=hGuQ8kuc9pgc9s8qqaq=dirpe0xb9q8qiLsFr0=vr0=vr0dc8meaabaqaciaacaGaaeqabaqabeGadaaakeaat0uy0HwzTfgDPnwy1egaryqtHrhAL1wy0L2yHvdaiqaacqWFneVtcqqGqbauaaa@3961@-hard even when conformations are restricted to a lattice. In this work, we implement and evaluate the replica exchange Monte Carlo (REMC) method, which has already been applied very successfully to more complex protein models and other optimization problems with complex energy landscapes, in combination with the highly effective pull move neighbourhood in two widely studied Hydrophobic Polar (HP) lattice models. Results We demonstrate that REMC is highly effective for solving instances of the square (2D) and cubic (3D) HP protein folding problem. When using the pull move neighbourhood, REMC outperforms current state-of-the-art algorithms for most benchmark instances. Additionally, we show that this new algorithm provides a larger ensemble of ground-state structures than the existing state-of-the-art methods. Furthermore, it scales well with sequence length, and it finds significantly better conformations on long biological sequences and sequences with a provably unique ground-state structure, which is believed to be a characteristic of real proteins. We also present evidence that our REMC algorithm can fold sequences which exhibit significant interaction between termini in the hydrophobic core relatively easily. Conclusion We demonstrate that REMC utilizing the pull move neighbourhood

  12. Ab initio Quantum Chemical Reaction Kinetics: Recent Applications in Combustion Chemistry (Briefing Charts)

    DTIC Science & Technology

    2015-06-28

    Charts 3. DATES COVERED (From - To) June 2015-June 2015 4. TITLE AND SUBTITLE AB INITIO QUANTUM CHEMICAL REACTION KINETICS: RECENT APPLICATIONS IN...Unlimited. 13. SUPPLEMENTARY NOTES Briefing Charts presented at 9th Int. Conf. Chemical Kinetics; Ghent, Belgium; 28 Jun 2015. PA#15351. 14. ABSTRACT...ghanshyam.vaghjiani@us.af.mil Ab initio Quantum Chemical Reaction Kinetics: Recent Applications in Combustion Chemistry Ghanshyam L. Vaghjiani* DISTRIBUTION A

  13. Experimental and ab initio study of the mechanical properties of hydroxyapatite

    NASA Astrophysics Data System (ADS)

    Snyders, R.; Music, D.; Sigumonrong, D.; Schelnberger, B.; Jensen, J.; Schneider, J. M.

    2007-05-01

    The authors have studied the elastic properties of radio frequency sputtered phase pure, stoichiometric, and dense hydroxyapatite films by nanoindentation. The measured elastic modulus values have been compared to ab initio calculated data. The calculation technique was based on the determination of all elastic constants. The calculated and measured elastic modulus values differ by ˜10%. The good agreement indicates that the elasticity of hydroxyapatite can be described using ab initio calculations, establishing the elastic modulus thereof.

  14. Split-and-pool Synthesis and Characterization of Peptide Tertiary Amide Library

    PubMed Central

    Gao, Yu; Kodadek, Thomas

    2014-01-01

    Peptidomimetics are great sources of protein ligands. The oligomeric nature of these compounds enables us to access large synthetic libraries on solid phase by using combinatorial chemistry. One of the most well studied classes of peptidomimetics is peptoids. Peptoids are easy to synthesize and have been shown to be proteolysis-resistant and cell-permeable. Over the past decade, many useful protein ligands have been identified through screening of peptoid libraries. However, most of the ligands identified from peptoid libraries do not display high affinity, with rare exceptions. This may be due, in part, to the lack of chiral centers and conformational constraints in peptoid molecules. Recently, we described a new synthetic route to access peptide tertiary amides (PTAs). PTAs are a superfamily of peptidomimetics that include but are not limited to peptides, peptoids and N-methylated peptides. With side chains on both α-carbon and main chain nitrogen atoms, the conformation of these molecules are greatly constrained by sterical hindrance and allylic 1,3 strain. (Figure 1) Our study suggests that these PTA molecules are highly structured in solution and can be used to identify protein ligands. We believe that these molecules can be a future source of high-affinity protein ligands. Here we describe the synthetic method combining the power of both split-and-pool and sub-monomer strategies to synthesize a sample one-bead one-compound (OBOC) library of PTAs. PMID:24998250

  15. Ab initio calculation of the potential bubble nucleus 34Si

    NASA Astrophysics Data System (ADS)

    Duguet, T.; Somà, V.; Lecluse, S.; Barbieri, C.; Navrátil, P.

    2017-03-01

    Background: The possibility that an unconventional depletion (referred to as a "bubble") occurs in the center of the charge density distribution of certain nuclei due to a purely quantum mechanical effect has attracted theoretical and experimental attention in recent years. Based on a mean-field rationale, a correlation between the occurrence of such a semibubble and an anomalously weak splitting between low angular-momentum spin-orbit partners has been further conjectured. Energy density functional and valence-space shell model calculations have been performed to identify and characterize the best candidates, among which 34Si appears as a particularly interesting case. While the experimental determination of the charge density distribution of the unstable 34Si is currently out of reach, (d ,p ) experiments on this nucleus have been performed recently to test the correlation between the presence of a bubble and an anomalously weak 1 /2--3 /2- splitting in the spectrum of 35Si as compared to 37S. Purpose: We study the potential bubble structure of 34Si on the basis of the state-of-the-art ab initio self-consistent Green's function many-body method. Methods: We perform the first ab initio calculations of 34Si and 36S. In addition to binding energies, the first observables of interest are the charge density distribution and the charge root-mean-square radius for which experimental data exist in 36S. The next observable of interest is the low-lying spectroscopy of 35Si and 37S obtained from (d ,p ) experiments along with the spectroscopy of 33Al and 35P obtained from knock-out experiments. The interpretation in terms of the evolution of the underlying shell structure is also provided. The study is repeated using several chiral effective field theory Hamiltonians as a way to test the robustness of the results with respect to input internucleon interactions. The convergence of the results with respect to the truncation of the many-body expansion, i.e., with respect to

  16. Tertiary and Quaternary Research with Remote Sensing Methods

    NASA Technical Reports Server (NTRS)

    Conel, J. E.

    1985-01-01

    Problems encountered in mapping the Quaternary section of the Wind River Region using remote sensing methods are discussed. Analysis of the stratigraphic section is a fundamental aspect of the geologic study of sedimentary basins. Stratigraphic analysis of post-Cretaceous rocks in the Wind River Basin encounters problems of a distinctly different character from those involved in studying the pre-Cretaceous section. The interior of the basin is predominantly covered by Tertiary and Quaternary sediments. These rocks, except on the basin margin to the north, are mostly flat lying or gently dipping. The Tertiary section consists of sandstones, siltstones, and tuffaceous sediments, some variegated, but in general poorly bedded and of great lithologic similarity. The Quaternary sediments consist of terrace, fan, and debris tongue deposits, unconsolidated alluvium occupying the bottoms of modern watercourses, deposits of eolian origin and tufa. Terrace and fan deposits are compositionally diverse and reflect the lithologic diversity of the source terranes.

  17. Nucleobases Undergo Dynamic Rearrangements during RNA Tertiary Folding.

    PubMed

    Welty, Robb; Hall, Kathleen B

    2016-11-06

    The tertiary structure of the GTPase center (GAC) of 23S ribosomal RNA (rRNA) as seen in cocrystals is extremely compact. It is stabilized by long-range hydrogen bonds and nucleobase stacking and by a triloop that forms within its three-way junction. Its folding pathway from secondary structure to tertiary structure has not been previously observed, but it was shown to require Mg(2+) ions in equilibrium experiments. The fluorescent nucleotide 2-aminopurine was substituted at selected sites within the 60-nt GAC. Fluorescence intensity changes upon addition of MgCl2 were monitored over a time-course from 1ms to 100s as the RNA folds. The folding pathway is revealed here to be hierarchical through several intermediates. Observation of the nucleobases during folding provides a new perspective on the process and the pathway, revealing the dynamics of nucleobase conformational exchange during the folding transitions.

  18. The role of palynology in paleoecological analyses of Tertiary coals

    USGS Publications Warehouse

    Nichols, D.J.

    1995-01-01

    Among the most important factors controlling the petrographic composition and facies characteristics of coal deposits are the types and relative abundances of plants that composed the peat. At present, wetland environments in which peat accumulates (mires) range from marshes and bogs to forested swamps; each is inhabited by distinctive plant communities. These plant communities are associated with varied conditions of climate, water depth, chemistry, and nutrient supply, and the floras can be indicative of these conditions. In the Tertiary Period, plant communities of mires were also highly diverse and specialized (especially as compared with those of the Carboniferous). The dominant species in some Paleocene mire floras were gymnosperms, but angiosperms became increasingly prominent through the Tertiary. The diverse angiosperm-dominated mire floras produced coals that vary significantly in facies and hence in quality. -from Author

  19. Cretaceous and Tertiary extension throughout the Ross Sea, Antarctica

    USGS Publications Warehouse

    Decesari, Robert C.; Wilson, Douglas C.; Luyendyk, Bruce P.; Faulkner, Michael

    2007-01-01

    Marine geophysical data from the deep sea adjacent to the Ross Sea, Antarctica suggest that 70 km of extension occurred between East and West Antarctica from 46 to 2 Ma. The Northern and Victoria Land Basins in the western Ross Sea adjacent to the Transantarctic Mountains accommodated 95 km of this extension. Several kilometers of Oligocene sediments are found in the Central Trough and Eastern Basin in the eastern Ross Sea. Subsidence modeling accounts for these accumulations with about 40 km of extension in each basin centered on 35 Ma; therefore Ross Sea-wide Tertiary extension was comparable to extension in the deep-sea system. The early Tertiary geometry was of one oceanic rift that branched into at least three rifts in the continental lithosphere. This pattern is likely due to the contrast of physical properties and thermal state between the two different lithospheres at the continent-ocean boundary.

  20. Aqueous Cation-Amide Binding: Free Energies and IR Spectral Signatures by Ab Initio Molecular Dynamics

    SciTech Connect

    Pluharova, Eva; Baer, Marcel D.; Mundy, Christopher J.; Schmidt, Burkhard; Jungwirth, Pavel

    2014-07-03

    Understanding specific ion effects on proteins remains a considerable challenge. N-methylacetamide serves as a useful proxy for the protein backbone that can be well characterized both experimentally and theoretically. The spectroscopic signatures in the amide I band reflecting the strength of the interaction of alkali cations and alkali earth dications with the carbonyl group remain difficult to assign and controversial to interpret. Herein, we directly compute the IR shifts corresponding to the binding of either sodium or calcium to aqueous N-methylacetamide using ab initio molecular dynamics simulations. We show that the two cations interact with aqueous N-methylacetamide with different affinities and in different geometries. Since sodium exhibits a weak interaction with the carbonyl group, the resulting amide I band is similar to an unperturbed carbonyl group undergoing aqueous solvation. In contrast, the stronger calcium binding results in a clear IR shift with respect to N-methylacetamide in pure water. Support from the Czech Ministry of Education (grant LH12001) is gratefully acknowledged. EP thanks the International Max-Planck Research School for support and the Alternative Sponsored Fellowship program at Pacific Northwest National Laboratory (PNNL). PJ acknowledges the Praemium Academie award from the Academy of Sciences. Calculations of the free energy profiles were made possible through generous allocation of computer time from the North-German Supercomputing Alliance (HLRN). Calculations of vibrational spectra were performed in part using the computational resources in the National Energy Research Supercomputing Center (NERSC) at Lawrence Berkeley National Laboratory. This work was supported by National Science Foundation grant CHE-0431312. CJM is supported by the U.S. Department of Energy`s (DOE) Office of Basic Energy Sciences, Division of Chemical Sciences, Geosciences and Biosciences. PNNL is operated for the Department of Energy by Battelle. MDB is

  1. SCRATCH: a protein structure and structural feature prediction server

    PubMed Central

    Cheng, J.; Randall, A. Z.; Sweredoski, M. J.; Baldi, P.

    2005-01-01

    SCRATCH is a server for predicting protein tertiary structure and structural features. The SCRATCH software suite includes predictors for secondary structure, relative solvent accessibility, disordered regions, domains, disulfide bridges, single mutation stability, residue contacts versus average, individual residue contacts and tertiary structure. The user simply provides an amino acid sequence and selects the desired predictions, then submits to the server. Results are emailed to the user. The server is available at . PMID:15980571

  2. Is the sword moss (Bryoxiphium) a preglacial Tertiary relict?

    PubMed

    Patiño, Jairo; Goffinet, Bernard; Sim-Sim, Manuela; Vanderpoorten, Alain

    2016-03-01

    The disjunction of floras between East Asia, Southeast North America, West North America, and Southwest Eurasia has been interpreted in terms of the fragmentation of a once continuous mixed mesophytic forest that occurred throughout the Northern Hemisphere due to the climatic and geological changes during the late Tertiary. The sword moss, Bryoxiphium, exhibits a distribution that strikingly resembles that of the mesophytic forest elements such as Liriodendron and is considered as the only living member of an early Tertiary flora in Iceland. These hypotheses are tested here using molecular dating analyses and ancestral area estimations. The results suggest that the extant range of Bryoxiphium results from the fragmentation of a formerly wider range encompassing North America and Southeast Asia about 10 million years ago. The split of continental ancestral populations is too recent to match with a continental drift scenario but is spatially and temporally remarkably congruent with that observed in Tertiary angiosperm relict species. The timing of the colonization of Iceland from Macaronesian ancestors, about two million years ago, is, however, incompatible with the hypothesis that Bryoxiphium is the only living member of an early Tertiary flora of the island. Alaska was recurrently colonized from East Asia. The ability of Bryoxiphium to overcome large oceanic barriers is further evidenced by its occurrence on remote oceanic archipelagos. In particular, Madeira was colonized twice independently from American and East Asian ancestors, respectively. The striking range disjunction of Bryoxiphium is interpreted in terms of its mating system, as the taxon exhibits a very singular pattern of spatial segregation of the sexes.

  3. Major wildfires at the Cretaceous-Tertiary boundary

    NASA Technical Reports Server (NTRS)

    Anders, Edward; Wolbach, Wendy S.; Gilmour, Iain

    1991-01-01

    The current status of the reconstruction of major biomass fire events at the Cretaceous-Tertiary boundary is discussed. Attention is given to the sources of charcoal and soot, the identification of biomass and fossil carbon, and such ignition-related problems as delated fires, high atmospheric O2 content, ignition mechanisms, and the greenhouse-effect consequences of fire on the scale envisioned. Consequences of these factors for species extinction patterns are noted.

  4. Tertiary Containment in a Multi-Room Tritium Facility

    SciTech Connect

    Kent, L. R.

    1985-04-01

    An experimental system to provide tertiary containment at Mound has been upgraded to support a new multi-room tritium handling facility. This system is used to remove tritium from room air in the event of primary (process) and secondary (glovebox) containment failure. The upgraded system includes a faster response time, piping and valves that are more leaktight, and a new control panel that better indicates the system status and operating conditions.

  5. Early Tertiary Anaconda metamorphic core complex, southwestern Montana

    USGS Publications Warehouse

    O'Neill, J. M.; Lonn, J.D.; Lageson, D.R.; Kunk, M.J.

    2004-01-01

    A sinuous zone of gently southeast-dipping low-angle Tertiary normal faults is exposed for 100 km along the eastern margins of the Anaconda and Flint Creek ranges in southwest Montana. Faults in the zone variously place Mesoproterozoic through Paleozoic sedimentary rocks on younger Tertiary granitic rocks or on sedimentary rocks older than the overlying detached rocks. Lower plate rocks are lineated and mylonitic at the main fault and, below the mylonitic front, are cut by mylonitic mesoscopic to microscopic shear zones. The upper plate consists of an imbricate stack of younger-on-older sedimentary rocks that are locally mylonitic at the main, lowermost detachment fault but are characteristically strongly brecciated or broken. Kinematic indicators in the lineated mylonite indicate tectonic transport to the east-southeast. Syntectonic sedimentary breccia and coarse conglomerate derived solely from upper plate rocks were deposited locally on top of hanging-wall rocks in low-lying areas between fault blocks and breccia zones. Muscovite occurs locally as mica fish in mylonitic quartzites at or near the main detachment. The 40Ar/39Ar age spectrum obtained from muscovite in one mylonitic quartzite yielded an age of 47.2 + 0.14 Ma, interpreted to be the age of mylonitization. The fault zone is interpreted as a detachment fault that bounds a metamorphic core complex, here termed the Anaconda metamorphic core complex, similar in age and character to the Bitterroot mylonite that bounds the Bitterroot metamorphic core complex along the Idaho-Montana state line 100 km to the west. The Bitterroot and Anaconda core complexes are likely components of a continuous, tectonically integrated system. Recognition of this core complex expands the region of known early Tertiary brittle-ductile crustal extension eastward into areas of profound Late Cretaceous contractile deformation characterized by complex structural interactions between the overthrust belt and Laramide basement uplifts

  6. Rapid Access to 3-Aminoindazoles from Tertiary Amides.

    PubMed

    Cyr, Patrick; Régnier, Sophie; Bechara, William S; Charette, André B

    2015-07-17

    A two-step synthesis of structurally diverse 3-aminoindazoles from readily available starting materials was developed. This sequence includes a one-pot synthesis of aminohydrazones through chemoselective Tf2O-mediated activation of tertiary amides and subsequent addition of nucleophilic hydrazides. These precursors then participate in an intramolecular ligand-free Pd-catalyzed C-H amination reaction. The azaheterocycles synthesized via this approach were further diversified through subsequent deprotection/functionalization reactions.

  7. Protons in polar media: An ab initio molecular dynamics study

    NASA Astrophysics Data System (ADS)

    von Rosenvinge, Tycho

    1998-10-01

    The hydrates of hydrogen chloride are ionic crystals that contain hydronium (H3O+). The hydronium in the monohydrate has been reported to be statistically disordered between two possible sites related by inversion symmetry. Ab initio molecular dynamics calculations are presented for the monohydrate, as well as the di-, and tri-hydrates, of hydrogen chloride using the density functional based Car-Parrinello technique. The simulations were carried out with the goal of investigating proton disorder in these crystals. The possible role of nuclear quantum effects has been explored via path integral molecular dynamic simulations. The present results suggest that the proposed disordered sites in the monohydrate are dynamically unstable and therefore unlikely to be responsible for the reported disorder. No useful information was obtained for the dihydrate because the large unit cell leads to difficulties in carrying out the simulations. Nuclear quantum effects are shown to be important for characterizing the proton distributions in the trihydrate. The structure and dynamical behavior of liquid HF with dissolved KF have been investigated using the Car- Parrinello ab initio molecular dynamics scheme. Specifically, a system with stoichiometry KFċ2HF was studied at temperatures of 400K and 1000K. This system, which was started from a phase separated mixture, rapidly formed into solvated potassium ions and HnFn+1/sp- polyfluoride anions with n = 1, 2, 3, and 4. The resulting polyfluoride anions were classified, and their structures and dynamical behavior were compared with the known structures and spectra of crystalline compounds KF/cdot xHF and with theoretical predictions of isolated gas phase species. The present study reveals dramatic frequency shifts in the H atom vibrational modes with variation in the HF coordination number of the polyfluoride anion. In particular the FH wagging motion red shifts while the FH stretch blue shifts as n increases. The present calculations

  8. Late tertiary structure and stratigraphy of north Sinai continental margin

    SciTech Connect

    Ben-Avraham, Z.; Mart, Y.

    1981-06-01

    New seismic data provide information on the structural development and late Tertiary stratigraphy of the continental slope and rise off northern Sinai. The upper continental slope is characterized by a marginal plateau composed of a series of platforms or steps. The lower continental slope is smooth, except for a low ridge paralleling the western part. Numerous diapiric structures along the continental margin north of the Sinai Peninsula emerge from an evaporitic layer of late Tertiary age. The diapirs usually are aligned along west-northwest-trending faults. A salt ridge 90 km long produces a submarine ridge in the lower continental rise. Two main fault trends have been mapped. In the western part of the continental margin they trend west-northwest and, in the eastern part, northeast. These trends parallel the continental slopes of northern Sinai and southern Israel, respectively. The structural grain of the Sinai margin appears to be controlled by two main tectonic elements: (1) rejuvenated basement faults of the continent-ocean transition zone; and (2) salt diapirism due to loading of Messinian evaporites with Nile-derived upper Tertiary clastics.

  9. General allylic C-H alkylation with tertiary nucleophiles.

    PubMed

    Howell, Jennifer M; Liu, Wei; Young, Andrew J; White, M Christina

    2014-04-16

    A general method for intermolecular allylic C-H alkylation of terminal olefins with tertiary nucleophiles has been accomplished employing palladium(II)/bis(sulfoxide) catalysis. Allylic C-H alkylation furnishes products in good yields (avg. 64%) with excellent regio- and stereoselectivity (>20:1 linear:branched, >20:1 E:Z). For the first time, the olefin scope encompasses unactivated aliphatic olefins as well as activated aromatic/heteroaromatic olefins and 1,4-dienes. The ease of appending allyl moieties onto complex scaffolds is leveraged to enable this mild and selective allylic C-H alkylation to rapidly diversify phenolic natural products. The tertiary nucleophile scope is broad and includes latent functionality for further elaboration (e.g., aliphatic alcohols, α,β-unsaturated esters). The opportunities to effect synthetic streamlining with such general C-H reactivity are illustrated in an allylic C-H alkylation/Diels-Alder reaction cascade: a reactive diene is generated via intermolecular allylic C-H alkylation and approximated to a dienophile contained within the tertiary nucleophile to furnish a common tricyclic core found in the class I galbulimima alkaloids.

  10. IRIS Toxicological Review of Ethyl Tertiary Butyl Ether (Etbe) ...

    EPA Pesticide Factsheets

    In September 2016, EPA released the draft IRIS Toxicological Review of Ethyl Tertiary Butyl Ether (ETBE) for public comment and discussion. The draft assessment was reviewed internally by EPA and by other federal agencies and White House Offices before public release. Consistent with the May 2009 IRIS assessment development process, all written comments on IRIS assessments submitted by other federal agencies and White House Offices are made publicly available. Accordingly, interagency comments and the interagency science consultation materials provided to other agencies, including interagency review drafts of the IRIS Toxicological Review of Ethyl Tertiary Butyl Ether are posted on this site. EPA is undertaking an new health assessment for ethyl tertiary butyl ether (ETBE) for the Integrated Risk Information System (IRIS). The outcome of this project will be a Toxicological Review and IRIS Summary of ETBE that will be entered on the IRIS database. IRIS is an EPA database containing Agency scientific positions on potential adverse human health effects that may result from chronic (or lifetime) exposure to chemicals in the environment. IRIS contains chemical-specific summaries of qualitative and quantitative health information in support of two steps of the risk assessment process, i.e., hazard identification and dose-response evaluation. IRIS assessments are used nationally and internationally in combination with specific situational exposure assessment infor

  11. Source rock evaluation of Cretaceous and Tertiary series in Tunisia

    SciTech Connect

    Oudin, J. )

    1988-08-01

    Tunisia represents a mature hydrocarbon province with a long exploration history. In the Sfax-Kerkennah and Gabes Gulf areas, the hydrocarbon accumulations are located in series of Cretaceous and Tertiary age. To estimate the petroleum potential of this region, an evaluation of the source rock quality of the Cretaceous and Tertiary series was undertaken. In the Sfax-Kerkennak area, most of the wells studied indicate that, in the Tertiary, Ypresian and lower Lutetian show good organic content but, taking into account the potential productivity, only the Ypresian can be considered as a potential source rock. In the Cretaceous, mainly studies in the offshore area of the Gabes Gulf, the amount of organic matter is fair and it is chiefly located in Albian and Cenomanian. The Vraconian with its quite good potential is a valuable source rock. Due to the difference in the environment of deposition for these two possible source rocks - the Ypresian with its lagoon facies being carbonate and the Vraconian shaly - variations in the type of organic matter can be noted, although both are of marine origin. The hydrocarbons generated from these source rocks reflect these variations and permit them to correlate the different crude oils found in this area with their original source beds.

  12. Cryptosporidium and Giardia removal by secondary and tertiary wastewater treatment.

    PubMed

    Taran-Benshoshan, Marina; Ofer, Naomi; Dalit, Vaizel-Ohayon; Aharoni, Avi; Revhun, Menahem; Nitzan, Yeshayahu; Nasser, Abidelfatah M

    2015-01-01

    Wastewater disposal may be a source of environmental contamination by Cryptosporidium and Giardia. This study was conducted to evaluate the prevalence of Cryptosporidium oocysts and Giardia cysts in raw and treated wastewater effluents. A prevalence of 100% was demonstrated for Giardia cysts in raw wastewater, at a concentration range of 10 to 12,225 cysts L(-1), whereas the concentration of Cryptosporidium oocysts in raw wastewater was 4 to 125 oocysts L(-1). The removal of Giardia cysts by secondary and tertiary treatment processes was greater than those observed for Cryptosporidium oocysts and turbidity. Cryptosporidium and Giardia were present in 68.5% and 76% of the tertiary effluent samples, respectively, at an average concentration of 0.93 cysts L(-1) and 9.94 oocysts L(-1). A higher detection limit of Cryptosporidium oocysts in wastewater was observed for nested PCR as compared to immune fluorescent assay (IFA). C. hominis was found to be the dominant genotype in wastewater effluents followed by C. parvum and C. andersoni or C. muris. Giardia was more prevalent than Cryptosporidium in the studied community and treatment processes were more efficient for the removal of Giardia than Cryptosporidium. Zoonotic genotypes of Cryptosporidium were also present in the human community. To assess the public health significance of Cryptosporidium oocysts present in tertiary effluent, viability (infectivity) needs to be assessed.

  13. Phase retrieval in protein crystallography.

    PubMed

    Liu, Zhong Chuan; Xu, Rui; Dong, Yu Hui

    2012-03-01

    Solution of the phase problem is central to crystallographic structure determination. An oversampling method is proposed, based on the hybrid input-output algorithm (HIO) [Fienup (1982). Appl. Opt. 21, 2758-2769], to retrieve the phases of reflections in crystallography. This method can extend low-resolution structures to higher resolution for structure determination of proteins without additional sample preparation. The method requires an envelope of the protein which divides a unit cell into the density region where the proteins are located and the non-density region occupied by solvents. After a few hundred to a few thousand iterations, the correct phases and density maps are recovered. The method has been used successfully in several cases to retrieve the phases from the experimental X-ray diffraction data and the envelopes of proteins constructed from structure files downloaded from the Protein Data Bank. It is hoped that this method will greatly facilitate the ab initio structure determination of proteins.

  14. HIGH LEVELS OF MONOAROMATIC COMPOUNDS LIMIT THE USE OF SOLID-PHASE MICROEXTRACTION OF METHYL TERTIARY BUTYL ETHER AND TERTIARY BUTYL ALCOHOL

    EPA Science Inventory

    Recently, two papers reported the use of solid-phase microextraction (SPME) with polydimethylsiloxane(PDMS)/Carboxen fibers to determine trace levels of methyl tertiary butyl ether (MTBE) and tertiary butyl alcohol (tBA) in water. Attempts were made to apply this technique to th...

  15. Ab initio study of MoS2 nanotube bundles

    NASA Astrophysics Data System (ADS)

    Verstraete, Matthieu; Charlier, Jean-Christophe

    2003-07-01

    Recently, the synthesis of a new phase of MoS2I1/3 stoichiometry was reported [M. Remskar, A. Mrzel, Z. Skraba, A. Jesih, M. Ceh, J. Demšar, P. Stadelmann, F. Lévy, and D. Mihailovic, Science 292, 479 (2001)]. Electron microscope images and diffraction data were interpreted to indicate bundles of sub-nanometer-diameter single-wall MoS2 nanotubes. After experimental characterization, the structure was attributed to an assembly of “armchair” nanotubes with interstitial iodine. Using first-principles total-energy calculations, bundles of MoS2 nanotubes with different topologies and stoichiometries are investigated. All of the systems are strongly metallic. Configurations with “zigzag” structures are found to be more stable energetically than the “armchair” ones, though all of the structures have similar stabilities. After relaxation, there remain several candidates which give a lattice parameter in relative agreement with experiment. Further, spin-polarized calculations indicate that a structure with armchair tubes iodine atoms in their center acquires a very large spontaneous magnetic moment of 12μB, while the other structures are nonmagnetic. Our ab initio calculations show that in most of the other structures, the tubes are very strongly bound together, and that the compounds should be considered as a crystal, rather than as a bundle of tubes in the habitual sense.

  16. Ab initio electronic structure and optical conductivity of bismuth tellurohalides

    NASA Astrophysics Data System (ADS)

    Schwalbe, Sebastian; Wirnata, René; Starke, Ronald; Schober, Giulio A. H.; Kortus, Jens

    2016-11-01

    We investigate the electronic structure, dielectric, and optical properties of bismuth tellurohalides BiTe X (X =I , Cl, Br) by means of all-electron density functional theory. In particular, we present the ab initio conductivities and dielectric tensors calculated over a wide frequency range, and compare our results with the recent measurements by Akrap et al. [Phys. Rev. B 90, 035201 (2014), 10.1103/PhysRevB.90.035201], Makhnev et al. [Opt. Spectrosc. 117, 764 (2014), 10.1134/S0030400X14110125], and Rusinov et al. [JETP Lett. 101, 507 (2015), 10.1134/S0021364015080147]. We show how the low-frequency branch of the optical conductivity can be used to identify characteristic intra- and interband transitions between the Rashba spin-split bands in all three bismuth tellurohalides. We further calculate the refractive indices and dielectric constants, which in turn are systematically compared to previous predictions and measurements. We expect that our quantitative analysis will contribute to the general assessment of bulk Rashba materials for their potential use in spintronics devices.

  17. Ab initio simulations of pseudomorphic silicene and germanene bidimensional heterostructures

    NASA Astrophysics Data System (ADS)

    Debernardi, Alberto; Marchetti, Luigi

    2016-06-01

    Among the novel two-dimensional (2D) materials, silicene and germanene, which are two honeycomb crystal structures composed of a monolayer of Si and Ge, respectively, have attracted the attention of material scientists because they combine the advantages of the new 2D ultimate-scaled electronics with their compatibility with industrial processes presently based on Si and Ge. We envisage pseudomorphic lateral heterostructures based on ribbons of silicene and germanene, which are the 2D analogs of conventional 3D Si/Ge superlattices and quantum wells. In spite of the considerable lattice mismatch (˜4 % ) between free-standing silicene and germanene, our ab initio simulations predict that, considering striped 2D lateral heterostructures made by alternating silicene and germanene ribbons of constant width, the silicene/germanene junction remains pseudomorphic—i.e., it maintains lattice-matched edges—up to critical ribbon widths that can reach some tens of nanometers. Such critical widths are one order of magnitude larger than the critical thickness measured in 3D pseudomorphic Si/Ge heterostructures and the resolution of state-of-the-art lithography, thus enabling the possibility of lithography patterned silicene/germanene junctions. We computed how the strain produced by the pseudomorphic growth modifies the crystal structure and electronic bands of the ribbons, providing a mechanism for band-structure engineering. Our results pave the way for lithography patterned lateral heterostructures that can serve as the building blocks of novel 2D electronics.

  18. Lead-Chalcogenides Under Pressure: Ab-Initio Study

    NASA Astrophysics Data System (ADS)

    Gupta, Dinesh C.; Hamid, Idris

    ab-initio calculations using fully relativistic pseudo-potential have been performed to investigate the high pressure phase transition, elastic and electronic properties of lead-chalcogenides including the less known lead polonium. The calculated ground state parameters, for the rock-salt structure show good agreement with the experimental data. The enthalpy calculations show that these materials undergo a first-order phase transition from rock-salt to CsCl structure at 19.4, 15.5, 11.5 and 7.3 GPa for PbS, PbSe, PbTe and PbPo, respectively. Present calculations successfully predicted the location of the band gap at L-point of Brillouin zone as well as the value of the band gap in every case at ambient pressure. It is observed that unlike other lead-chalcogenides, PbPo is semi-metal at ambient pressure. The pressure variation of the energy gap indicates that these materials metalized under high pressures. For this purpose, the electronic structure of these materials has also been computed in parent as well as in high pressure phase.

  19. Melting curves of metals by ab initio calculations

    NASA Astrophysics Data System (ADS)

    Minakov, Dmitry; Levashov, Pavel

    2015-06-01

    In this work we used several ab initio approaches to reproduce melting curves and discussed their abilities, advantages and drawbacks. We used quasiharmonic appoximation and Lindemann criterion to build melting curves in wide region of pressures. This approach allows to calculate the total free energy of electrons and phonons, so it is possible to obtain all thermodynamic properties in the crystalline state. We also used quantum molecular dynamics simulations to investigate melting at various pressures. We explored the size-effect of the heat until it melts (HUM) method in detail. Special attention was paid to resolve the boundaries of the melting region on density. All calculations were performed for aluminum, copper and gold. Results were in good agreement with available experimental data. Also we studied the influence of electronic temperature on melting curves. It turned out that the melting temperature increased with the rise of electron temperature at normal density and had non-monotonic behavior at higher densities. This work is supported by the Ministry of Education and Science of the Russian Federation (Project No. 3.522.2014/K).

  20. Challenges for large scale ab initio Quantum Monte Carlo

    NASA Astrophysics Data System (ADS)

    Kent, Paul

    2015-03-01

    Ab initio Quantum Monte Carlo is an electronic structure method that is highly accurate, well suited to large scale computation, and potentially systematically improvable in accuracy. Due to increases in computer power, the method has been applied to systems where established electronic structure methods have difficulty reaching the accuracies desired to inform experiment without empiricism, a necessary step in the design of materials and a helpful step in the improvement of cheaper and less accurate methods. Recent applications include accurate phase diagrams of simple materials through to phenomena in transition metal oxides. Nevertheless there remain significant challenges to achieving a methodology that is robust and systematically improvable in practice, as well as capable of exploiting the latest generation of high-performance computers. In this talk I will describe the current state of the art, recent applications, and several significant challenges for continued improvement. Supported through the Predictive Theory and Modeling for Materials and Chemical Science program by the Office of Basic Energy Sciences (BES), Department of Energy (DOE).

  1. Ab-Initio Study of Incongruent Melting in Silicates

    NASA Astrophysics Data System (ADS)

    Pinilla, C.; Stixrude, L. P.

    2014-12-01

    Knowledge of the multi-component thermodynamics and phase equilibria of silicate melts at Earth's interior conditions are key to understand the chemical and thermal evolution of the planet. Yet they remain poorly constrained with a wide uncertainty on the eutectic composition and temperature. In this work we present results from ab-initio molecular dynamics in combination with the two-phase coexistance method to study properties of a system of MgSiO3 liquid coexisting with crystalline MgO at conditions of the deep lower mantle. During incongruent melting the crystal may either grow via partial freezing of the liquid or shrink via partial melting at a given temperature and pressure. The melting process can be studied using the two-phases method where liquid and solid are in contact at a given temperature and pressure and so under thermodynamic equilibrium. We characterise the composition and densities of the resultant solid and liquid phases, provide chemical potentials of the liquid phase and study the structural and dynamical properties of the melt. In addition, we discuss the performance of alternative computational methods applied to the study of incongruent melting in silicate systems where long simulation times and a large number of atoms are usually needed. Finally, we discuss the implication of our findings for the evolution of the Earth's interior.

  2. Ab initio description of the exotic unbound 7He nucleus

    DOE PAGES

    Baroni, Simone; Navratil, Petr; Quaglioni, Sofia

    2013-01-11

    In this study, the neutron-rich unbound 7He nucleus has been the subject of many experimental investigations. While the ground-state 3/2– resonance is well established, there is a controversy concerning the excited 1/2– resonance reported in some experiments as low lying and narrow (ER~1 MeV, Γ≤1 MeV) while in others as very broad and located at a higher energy. This issue cannot be addressed by ab initio theoretical calculations based on traditional bound-state methods. We introduce a new unified approach to nuclear bound and continuum states based on the coupling of the no-core shell model, a bound-state technique, with the no-coremore » shell model combined with the resonating-group method, a nuclear scattering technique. Our calculations describe the ground-state resonance in agreement with experiment and, at the same time, predict a broad 1/2– resonance above 2 MeV.« less

  3. Volumic omit maps in ab initio dual-space phasing.

    PubMed

    Oszlányi, Gábor; Sütő, András

    2016-07-01

    Alternating-projection-type dual-space algorithms have a clear construction, but are susceptible to stagnation and, thus, inefficient for solving the phase problem ab initio. To improve this behaviour new omit maps are introduced, which are real-space perturbations applied periodically during the iteration process. The omit maps are called volumic, because they delete some predetermined subvolume of the unit cell without searching for atomic regions or analysing the electron density in any other way. The basic algorithms of positivity, histogram matching and low-density elimination are tested by their solution statistics. It is concluded that, while all these algorithms based on weak constraints are practically useless in their pure forms, appropriate volumic omit maps can transform them to practically useful methods. In addition, the efficiency of the already useful reflector-type charge-flipping algorithm can be further improved. It is important that these results are obtained by using non-sharpened structure factors and without any weighting scheme or reciprocal-space perturbation. The mathematical background of volumic omit maps and their expected applications are also discussed.

  4. Ab Initio Study of Covalently Functionalized Graphene and Carbon Nanotubes

    NASA Astrophysics Data System (ADS)

    Jha, Sanjiv; Hammouri, Mahmoud; Vasiliev, Igor; Magedov, Igor; Frolova, Liliya; Kalugin, Nikolai

    2014-03-01

    The electronic and structural properties of carbon nanomaterials can be affected by chemical functionalization. We apply ab initio computational methods based on density functional theory to study the properties of graphene and single-walled carbon nanotubes functionalized with benzyne. Our calculations are carried out using the SIESTA electronic structure code combined with the generalized gradient approximation for the exchange correlation functional. The calculated binding energies, densities of states, and band structures of functionalized graphene and carbon nanotubes are analyzed in comparison with the available experimental data. The surfaces of carbon nanotubes are found to be significantly more reactive toward benzyne molecules than the surface of graphene. The strength of interaction between benzyne and carbon nanotubes is affected by the curvature of the nanotube sidewall. The binding energies of benzyne molecules attached to both semiconducting zigzag and metallic armchair nanotubes increase with decreasing the nanotube diameter. Supported by NSF CHE-1112388, NMSU GREG Award, NSF ECCS-0925988, NIH-5P20RR016480-12, and NIH- P20 GM103451.

  5. Accurate ab initio vibrational energies of methyl chloride

    SciTech Connect

    Owens, Alec; Yurchenko, Sergei N.; Yachmenev, Andrey; Tennyson, Jonathan; Thiel, Walter

    2015-06-28

    Two new nine-dimensional potential energy surfaces (PESs) have been generated using high-level ab initio theory for the two main isotopologues of methyl chloride, CH{sub 3}{sup 35}Cl and CH{sub 3}{sup 37}Cl. The respective PESs, CBS-35{sup  HL}, and CBS-37{sup  HL}, are based on explicitly correlated coupled cluster calculations with extrapolation to the complete basis set (CBS) limit, and incorporate a range of higher-level (HL) additive energy corrections to account for core-valence electron correlation, higher-order coupled cluster terms, scalar relativistic effects, and diagonal Born-Oppenheimer corrections. Variational calculations of the vibrational energy levels were performed using the computer program TROVE, whose functionality has been extended to handle molecules of the form XY {sub 3}Z. Fully converged energies were obtained by means of a complete vibrational basis set extrapolation. The CBS-35{sup  HL} and CBS-37{sup  HL} PESs reproduce the fundamental term values with root-mean-square errors of 0.75 and 1.00 cm{sup −1}, respectively. An analysis of the combined effect of the HL corrections and CBS extrapolation on the vibrational wavenumbers indicates that both are needed to compute accurate theoretical results for methyl chloride. We believe that it would be extremely challenging to go beyond the accuracy currently achieved for CH{sub 3}Cl without empirical refinement of the respective PESs.

  6. Ab initio liquid water from PBE0 hybrid functional simulations

    NASA Astrophysics Data System (ADS)

    Li, Zhaofeng; Wu, Xifan; Car, Roberto

    2010-03-01

    For reasons of computational efficiency, so far most ab initio molecular dynamics simulations of liquid water have been based on semi-local density functional approximations, such as PBE and BLYP. These approaches yield a liquid structure that, albeit qualitatively correct, is overstructured compared to experiment, even after nuclear quantum effects have been taken into account.footnotetextJ. A. Morrone and R. Car, Phys. Rev. Lett. 101, 017801(2008) A major cause of this inaccuracy is the delocalization error associated to semi-local density functional approximations, which, as a consequence, overestimate slightly the hydrogen bond strength in the liquid. In this work we adopt the PBE0 hybrid functional approximation, which, by mixing a fraction of exact (Hartree-Fock) exchange, reduces significantly the delocalization error of semi-local functionals. Our approach is based on a numerically efficient order-N implementation of exact exchange.footnotetextX. Wu, A. Selloni, and R. Car, Phys. Rev. B 79, 085102(2009) We find that PBE0 systematically improves the agreement of the simulated liquid with experiment. Our conclusion is substantiated by the calculated radial distribution functions, H-bond statistics, and molecular dipole distribution.

  7. Ab initio predictions of the symmetry energy and recent constraints

    NASA Astrophysics Data System (ADS)

    Sammarruca, Francesca

    2017-01-01

    The symmetry energy plays a crucial role in the structure and the dynamics of neutron-rich systems, including the formation of neutron skins, the location of neutron drip lines, as well as intriguing correlations with the structure of compact stars. With experimental efforts in progress or being planned to shed light on the less known aspects of the nuclear chart, microscopic predictions based on ab initio approaches are very important. In recent years, chiral effective field theory has become popular because of its firm connection with quantum chromodynamics and its systematic approach to the development of nuclear forces. Predictions of the symmetry energy obtained from modern chiral interactions will be discussed in the light of recent empirical constraints extracted from heavy ion collisions at 400 MeV per nucleon at GSI. Applications of our equations of state to neutron-rich systems will also be discussed, with particular emphasis on neutron skins, which are sensitive to the density dependence of the symmetry energy.

  8. An efficient approach to ab initio Monte Carlo simulation.

    PubMed

    Leiding, Jeff; Coe, Joshua D

    2014-01-21

    We present a Nested Markov chain Monte Carlo (NMC) scheme for building equilibrium averages based on accurate potentials such as density functional theory. Metropolis sampling of a reference system, defined by an inexpensive but approximate potential, was used to substantially decorrelate configurations at which the potential of interest was evaluated, thereby dramatically reducing the number needed to build ensemble averages at a given level of precision. The efficiency of this procedure was maximized on-the-fly through variation of the reference system thermodynamic state (characterized here by its inverse temperature β(0)), which was otherwise unconstrained. Local density approximation results are presented for shocked states of argon at pressures from 4 to 60 GPa, where-depending on the quality of the reference system potential-acceptance probabilities were enhanced by factors of 1.2-28 relative to unoptimized NMC. The optimization procedure compensated strongly for reference potential shortcomings, as evidenced by significantly higher speedups when using a reference potential of lower quality. The efficiency of optimized NMC is shown to be competitive with that of standard ab initio molecular dynamics in the canonical ensemble.

  9. Ab initio studies of phosphorene island single electron transistor

    NASA Astrophysics Data System (ADS)

    Ray, S. J.; Venkata Kamalakar, M.; Chowdhury, R.

    2016-05-01

    Phosphorene is a newly unveiled two-dimensional crystal with immense potential for nanoelectronic and optoelectronic applications. Its unique electronic structure and two dimensionality also present opportunities for single electron devices. Here we report the behaviour of a single electron transistor (SET) made of a phosphorene island, explored for the first time using ab initio calculations. We find that the band gap and the charging energy decrease monotonically with increasing layer numbers due to weak quantum confinement. When compared to two other novel 2D crystals such as graphene and MoS2, our investigation reveals larger adsorption energies of gas molecules on phosphorene, which indicates better a sensing ability. The calculated charge stability diagrams show distinct changes in the presence of an individual molecule which can be applied to detect the presence of different molecules with sensitivity at a single molecular level. The higher charging energies of the molecules within the SET display operational viability at room temperature, which is promising for possible ultra sensitive detection applications.

  10. Predicting lattice thermal conductivity with help from ab initio methods

    NASA Astrophysics Data System (ADS)

    Broido, David

    2015-03-01

    The lattice thermal conductivity is a fundamental transport parameter that determines the utility a material for specific thermal management applications. Materials with low thermal conductivity find applicability in thermoelectric cooling and energy harvesting. High thermal conductivity materials are urgently needed to help address the ever-growing heat dissipation problem in microelectronic devices. Predictive computational approaches can provide critical guidance in the search and development of new materials for such applications. Ab initio methods for calculating lattice thermal conductivity have demonstrated predictive capability, but while they are becoming increasingly efficient, they are still computationally expensive particularly for complex crystals with large unit cells . In this talk, I will review our work on first principles phonon transport for which the intrinsic lattice thermal conductivity is limited only by phonon-phonon scattering arising from anharmonicity. I will examine use of the phase space for anharmonic phonon scattering and the Grüneisen parameters as measures of the thermal conductivities for a range of materials and compare these to the widely used guidelines stemming from the theory of Liebfried and Schölmann. This research was supported primarily by the NSF under Grant CBET-1402949, and by the S3TEC, an Energy Frontier Research Center funded by the US DOE, office of Basic Energy Sciences under Award No. DE-SC0001299.

  11. Ab-Initio Molecular Dynamics Simulation of Graphene Sheet

    NASA Astrophysics Data System (ADS)

    Kolev, S.; Balchev, I.; Cvetkov, K.; Tinchev, S.; Milenov, T.

    2017-01-01

    The study of graphene is important because it is a promising material for a variety of applications in the electronic industry. In the present work, the properties of а 2D periodic graphene sheet are studied with the use of ab initio molecular dynamics. DFT in the generalized gradient approximation is used in order to carry out the dynamical simulations. The PBE functional and DZVP-MOLOPT basis set are implemented in the CP2K/Quickstep package. A periodic box, consisting of 288 carbon atoms is chosen for the simulations. After geometry optimization it has dimensions 2964 x 2964 x 1500 pm and form angles of 90, 90, 60 degrees. The dynamical simulation is run for 1 ps in the NPT ensemble, at temperature T = 298.15 K. The radial distribution function shows a first peak at 142 pm, marking the bond length between carbon atoms. The density of states for the periodic systems is simulated as occupied orbitals represent the valence band and unoccupied ones the conduction band. The calculated bandgap, as expected is close to 0 eV.

  12. Ab initio Raman spectroscopy of water under extreme conditions

    NASA Astrophysics Data System (ADS)

    Rozsa, Viktor; Pan, Ding; Wan, Quan; Galli, Giulia

    Water exhibits one of the most complex phase diagrams of any binary compound. Despite extensive studies, the melting lines of high-pressure ice phases remain very controversial, with reports differing by hundreds of Kelvin. The boundary between ice VII and liquid phase is particularly disputed, with recent work exploring plasticity and amorphization mediating the transition. Raman measurements are often used to fingerprint melting, yet their interpretation is difficult without atomistic modeling. Here, we report a study of high P/T water where we computed Raman spectra using a method combining ab initio molecular dynamics and density functional perturbation theory, as implemented in the Qbox code. Spectra were computed for the liquid at 10 and 20 GPa, both at 1000 K, and for solid ice VII (20 GPa, 500 K). Decomposing the spectra into inter and intra molecular contributions provided insight into the dynamics of the hydrogen-bonded network at extreme conditions. The relevance of our simulation results for models of water in Earth, Uranus, and Neptune will be discussed, and an interpretation of existing experiments at high pressure will be presented.

  13. Ab initio studies of niobium defects in uranium

    SciTech Connect

    Xiang, S; Huang, H; Hsiung, L

    2007-06-01

    Uranium (U), with the addition of small amount of niobium (Nb), is stainless. The Nb is fully miscible with the high temperature phase of U and tends to segregate upon cooling below 647 C. The starting point of segregation is the configuration of Nb substitutional or interstitial defects. Using density-functional-theory based ab initio calculations, the authors find that the formation energy of a single vacancy is 1.08 eV, that of Nb substitution is 0.59 eV, that of Nb interstitial at octahedral site is 1.58 eV, and that of Nb interstitial at tetrahedral site is 2.35 eV; all with reference to a reservoir of {gamma} phase U and pure Nb. The formation energy of Nb defects correlates with the local perturbation of electron distribution; higher formation energy to larger perturbation. Based on this study, Nb atoms thermodynamically prefer to occupy substitutional sites in {gamma} phase U, and they prefer to be in individual substitutional defects than clusters.

  14. Perovskite transparent conducting oxides: an ab initio study.

    PubMed

    Dabaghmanesh, S; Saniz, R; Amini, M N; Lamoen, D; Partoens, B

    2013-10-16

    We present an ab initio study of the electronic structure and of the formation energies of various point defects in BaSnO3 and SrGeO3. We show that La and Y impurities substituting Ba or Sr are shallow donors with a preferred 1 + charge state. These defects have a low formation energy within all the suitable equilibrium growth conditions considered. Oxygen vacancies behave as shallow donors as well, preferring the 2 + charge state. Their formation energies, however, are higher in most growth conditions, indicating a limited contribution to conductivity. The calculated electron effective mass in BaSnO3, with a value of 0.21 m(e), and the very high mobility reported recently in La-doped BaSnO3 single-crystals, suggest that remarkably low scattering rates can be achieved in the latter. In the case of SrGeO3, our results point to carrier density and mobility values in the low range for typical polycrystalline TCOs, in line with experiment.

  15. Ab initio calculations of nuclear reactions important for astrophysics

    NASA Astrophysics Data System (ADS)

    Navratil, Petr; Dohet-Eraly, Jeremy; Calci, Angelo; Horiuchi, Wataru; Hupin, Guillaume; Quaglioni, Sofia

    2016-09-01

    In recent years, significant progress has been made in ab initio nuclear structure and reaction calculations based on input from QCD employing Hamiltonians constructed within chiral effective field theory. One of the newly developed approaches is the No-Core Shell Model with Continuum (NCSMC), capable of describing both bound and scattering states in light nuclei simultaneously. We will present NCSMC results for reactions important for astrophysics that are difficult to measure at relevant low energies, such as 3He(α,γ)7Be and 3H(α,γ)7Li and 11C(p,γ)12N radiative capture, as well as the 3H(d,n)4He fusion. We will also address prospects of calculating the 2H(α,γ)6Li capture reaction within the NCSMC formalism. Prepared in part by LLNL under Contract DE-AC52-07NA27344. Supported by the U.S. DOE, OS, NP, under Work Proposal No. SCW1158, and by the NSERC Grant No. SAPIN-2016-00033. TRIUMF receives funding from the NRC Canada.

  16. Ab Initio Potential Energy Surface for H-H2

    NASA Technical Reports Server (NTRS)

    Patridge, Harry; Bauschlicher, Charles W., Jr.; Stallcop, James R.; Levin, Eugene

    1993-01-01

    Ab initio calculations employing large basis sets are performed to determine an accurate potential energy surface for H-H2 interactions for a broad range of separation distances. At large distances, the spherically averaged potential determined from the calculated energies agrees well with the corresponding results determined from dispersion coefficients; the van der Waals well depth is predicted to be 75 +/- 3 micro E(h). Large basis sets have also been applied to reexamine the accuracy of theoretical repulsive potential energy surfaces (25-70 kcal/mol above the H-H2 asymptote) at small interatomic separations; the Boothroyd, Keogh, Martin, and Peterson (BKMP) potential energy surface is found to agree with results of the present calculations within the expected uncertainty (+/- 1 kcal/mol) of the fit. Multipolar expansions of the computed H-H2 potential energy surface are reported for four internuclear separation distances (1.2, 1.401, 1.449, and 1.7a(0)) of the hydrogen molecule. The differential elastic scattering cross section calculated from the present results is compared with the measurements from a crossed beam experiment.

  17. An Ab Initio Based Potential Energy Surface for Water

    NASA Technical Reports Server (NTRS)

    Partridge, Harry; Schwenke, David W.; Langhoff, Stephen R. (Technical Monitor)

    1996-01-01

    We report a new determination of the water potential energy surface. A high quality ab initio potential energy surface (PES) and dipole moment function of water have been computed. This PES is empirically adjusted to improve the agreement between the computed line positions and those from the HITRAN 92 data base. The adjustment is small, nonetheless including an estimate of core (oxygen 1s) electron correlation greatly improves the agreement with experiment. Of the 27,245 assigned transitions in the HITRAN 92 data base for H2(O-16), the overall root mean square (rms) deviation between the computed and observed line positions is 0.125/cm. However the deviations do not correspond to a normal distribution: 69% of the lines have errors less than 0.05/cm. Overall, the agreement between the line intensities computed in the present work and those contained in the data base is quite good, however there are a significant number of line strengths which differ greatly.

  18. Electronic structure and conductivity of ferroelectric hexaferrite: Ab initio calculations

    NASA Astrophysics Data System (ADS)

    Knížek, K.; Novák, P.; Küpferling, M.

    2006-04-01

    Ba0.5Sr1.5Zn2Fe12O22 is a promising multiferroic compound in which the electric polarization is intimately connected to the magnetic state. In principle, ferroelectrity might exist above the room temperature, but the electrical conductivity that increases with increasing temperature limits it to temperatures below ≈130K . We present results of an ab initio electronic structure calculation of the (BaSr)Zn2Fe12O22 system. To improve the description of strongly correlated 3d electrons of iron, the GGA+U method is used. The results show that the electrical conductivity strongly depends on relative fractions of iron and zinc in the tetrahedral sublattice that belongs to the spinel block of the hexaferrite structure. If this sublattice is fully occupied by zinc, the system is an insulator with a gap of ≈1.5eV . If it is occupied equally by Fe and Zn the gap decreases by a factor of 2, and the system is metallic when this sublattice is filled by iron only.

  19. Exploring the free energy surface using ab initio molecular dynamics

    NASA Astrophysics Data System (ADS)

    Samanta, Amit; Morales, Miguel A.; Schwegler, Eric

    2016-04-01

    Efficient exploration of configuration space and identification of metastable structures in condensed phase systems are challenging from both computational and algorithmic perspectives. In this regard, schemes that utilize a set of pre-defined order parameters to sample the relevant parts of the configuration space [L. Maragliano and E. Vanden-Eijnden, Chem. Phys. Lett. 426, 168 (2006); J. B. Abrams and M. E. Tuckerman, J. Phys. Chem. B 112, 15742 (2008)] have proved useful. Here, we demonstrate how these order-parameter aided temperature accelerated sampling schemes can be used within the Born-Oppenheimer and the Car-Parrinello frameworks of ab initio molecular dynamics to efficiently and systematically explore free energy surfaces, and search for metastable states and reaction pathways. We have used these methods to identify the metastable structures and reaction pathways in SiO2 and Ti. In addition, we have used the string method [W. E, W. Ren, and E. Vanden-Eijnden, Phys. Rev. B 66, 052301 (2002); L. Maragliano et al., J. Chem. Phys. 125, 024106 (2006)] within the density functional theory to study the melting pathways in the high pressure cotunnite phase of SiO2 and the hexagonal closed packed to face centered cubic phase transition in Ti.

  20. Ab initio modeling of decomposition in iron based alloys

    NASA Astrophysics Data System (ADS)

    Gorbatov, O. I.; Gornostyrev, Yu. N.; Korzhavyi, P. A.; Ruban, A. V.

    2016-12-01

    This paper reviews recent progress in the field of ab initio based simulations of structure and properties of Fe-based alloys. We focus on thermodynamics of these alloys, their decomposition kinetics, and microstructure formation taking into account disorder of magnetic moments with temperature. We review modern theoretical tools which allow a consistent description of the electronic structure and energetics of random alloys with local magnetic moments that become totally or partially disordered when temperature increases. This approach gives a basis for an accurate finite-temperature description of alloys by calculating all the relevant contributions to the Gibbs energy from first-principles, including a configurational part as well as terms due to electronic, vibrational, and magnetic excitations. Applications of these theoretical approaches to the calculations of thermodynamics parameters at elevated temperatures (solution energies and effective interatomic interactions) are discussed including atomistic modeling of decomposition/clustering in Fe-based alloys. It provides a solid basis for understanding experimental data and for developing new steels for modern applications. The precipitation in Fe-Cu based alloys, the decomposition in Fe-Cr, and the short-range order formation in iron alloys with s-p elements are considered as examples.

  1. Ab initio calculation of infrared intensities for hydrogen peroxide

    NASA Technical Reports Server (NTRS)

    Rogers, J. D.; Hillman, J. J.

    1982-01-01

    Results of an ab initio SCF quantum mechanical study are used to derive estimates for the infrared intensities of the fundamental vibrations of hydrogen peroxide. Atomic polar tensors (APTs) were calculated on the basis of a 4-31G basis set, and used to derive absolute intensities for the vibrational transitions. Comparison of the APTs calculated for H2O2 with those previously obtained for H2O and CH3OH, and of the absolute intensities derived from the H2O2 APTs with those derived from APTs transferred from H2O and CH3OH, reveals the sets of values to differ by no more than a factor of two, supporting the validity of the theoretical calculation. Values of the infrared intensities obtained correspond to A1 = 14.5 km/mol, A2 = 0.91 km/mol, A3 = 0.058 km/mol, A4 = 123 km/mol, A5 = 46.2 km/mol, and A6 = 101 km/mol. Charge, charge flux and overlap contributions to the dipole moment derivatives are also computed.

  2. Ab initio calculations of correlated electron dynamics in ultrashort pulses

    NASA Astrophysics Data System (ADS)

    Feist, Johannes

    2010-03-01

    The availability of ultrashort and intense light pulses on the femtosecond and attosecond timescale promises to allow to directly probe and control electron dynamics on their natural timescale. A crucial ingredient to understanding the dynamics in many-electron systems is the influence of electron correlation, induced by the interelectronic repulsion. In order to study electron correlation in ultrafast processes, we have implemented an ab initio simulation of the two-electron dynamics in helium atoms. We solve the time-dependent Schr"odinger equation in its full dimensionality, with one temporal and five spatial degrees of freedom in linearly polarized laser fields. In our computational approach, the wave function is represented through a combination of time-dependent close coupling with the finite element discrete variable representation, while time propagation is performed using an Arnoldi-Lanczos approximation with adaptive step size. This approach is optimized to allow for efficient parallelization of the program and has been shown to scale linearly using up to 1800 processor cores for typical problem sizes. This has allowed us to perform highly accurate and well- converged computations for the interaction of ultrashort laser pulses with He. I will present some recent results on using attosecond and femtosecond pulses to probe and control the temporal structure of the ionization process. This work was performed in collaboration with Stefan Nagele, Renate Pazourek, Andreas Kaltenb"ack, Emil Persson, Barry I. Schneider, Lee A. Collins, and Joachim Burgd"orfer.

  3. Ab initio molecular dynamics calculations of ion hydration free energies.

    PubMed

    Leung, Kevin; Rempe, Susan B; von Lilienfeld, O Anatole

    2009-05-28

    We apply ab initio molecular dynamics (AIMD) methods in conjunction with the thermodynamic integration or "lambda-path" technique to compute the intrinsic hydration free energies of Li(+), Cl(-), and Ag(+) ions. Using the Perdew-Burke-Ernzerhof functional, adapting methods developed for classical force field applications, and with consistent assumptions about surface potential (phi) contributions, we obtain absolute AIMD hydration free energies (DeltaG(hyd)) within a few kcal/mol, or better than 4%, of Tissandier et al.'s [J. Phys. Chem. A 102, 7787 (1998)] experimental values augmented with the SPC/E water model phi predictions. The sums of Li(+)/Cl(-) and Ag(+)/Cl(-) AIMD DeltaG(hyd), which are not affected by surface potentials, are within 2.6% and 1.2 % of experimental values, respectively. We also report the free energy changes associated with the transition metal ion redox reaction Ag(+)+Ni(+)-->Ag+Ni(2+) in water. The predictions for this reaction suggest that existing estimates of DeltaG(hyd) for unstable radiolysis intermediates such as Ni(+) may need to be extensively revised.

  4. Methods for Using Ab Initio Potential Energy Surfaces in Studies of Gas-Phase Reactions of Energetic Molecules

    DTIC Science & Technology

    2014-08-20

    Ab Initio Potential Energy Surfaces in Studies of Gas-Phase Reactions of Energetic Molecules The focus of this research was to apply efficient...methods for using ab initio potential energy surfaces (PESs) computed with high levels of quantum chemistry theory to predict chemical reaction properties...in non peer-reviewed journals: Methods for Using Ab Initio Potential Energy Surfaces in Studies of Gas-Phase Reactions of Energetic Molecules Report

  5. Ab initio Kinetics of Methylamine Radical Thermal Decomposition and H-abstraction from Monomethylhydrazine by H Atom

    DTIC Science & Technology

    2014-08-01

    Technical Paper 3. DATES COVERED (From - To) December 2013- August 2014 4. TITLE AND SUBTITLE Ab initio Kinetics of Methylamine Radical Thermal...phase kinetics of H-abstraction reactions from CH3NHNH2 by H atoms was further investigated by ab initio second-order multireference perturbation...distribution unlimited Ab initio Kinetics of Methylamine Radical Thermal Decomposition and H-abstraction from Monomethylhydrazine by H Atom

  6. An investigation of ab initio shell-model interactions derived by no-core shell model

    NASA Astrophysics Data System (ADS)

    Wang, XiaoBao; Dong, GuoXiang; Li, QingFeng; Shen, CaiWan; Yu, ShaoYing

    2016-09-01

    The microscopic shell-model effective interactions are mainly based on the many-body perturbation theory (MBPT), the first work of which can be traced to Brown and Kuo's first attempt in 1966, derived from the Hamada-Johnston nucleon-nucleon potential. However, the convergence of the MBPT is still unclear. On the other hand, ab initio theories, such as Green's function Monte Carlo (GFMC), no-core shell model (NCSM), and coupled-cluster theory with single and double excitations (CCSD), have made many progress in recent years. However, due to the increasing demanding of computing resources, these ab initio applications are usually limited to nuclei with mass up to A = 16. Recently, people have realized the ab initio construction of valence-space effective interactions, which is obtained through a second-time renormalization, or to be more exactly, projecting the full-manybody Hamiltonian into core, one-body, and two-body cluster parts. In this paper, we present the investigation of such ab initio shell-model interactions, by the recent derived sd-shell effective interactions based on effective J-matrix Inverse Scattering Potential (JISP) and chiral effective-field theory (EFT) through NCSM. In this work, we have seen the similarity between the ab initio shellmodel interactions and the interactions obtained by MBPT or by empirical fitting. Without the inclusion of three-body (3-bd) force, the ab initio shell-model interactions still share similar defects with the microscopic interactions by MBPT, i.e., T = 1 channel is more attractive while T = 0 channel is more repulsive than empirical interactions. The progress to include more many-body correlations and 3-bd force is still badly needed, to see whether such efforts of ab initio shell-model interactions can reach similar precision as the interactions fitted to experimental data.

  7. Molecular interactions between proteins and synthetic membrane polymer films

    SciTech Connect

    Pincet, F.; Perez, E.; Belfort, G.

    1995-04-01

    To help understand the effects of protein adsorption on membrane filtration performance, we have measured the molecular interactions between cellulose acetate films and two proteins with different properties (ribonuclease A and human serum albumin) with a surface force apparatus. Comparison of forces between two protein layers with those between a protein layer and a cellulose acetate (CA) film shows that, at high pH, both proteins retained their native conformation on interacting with the CA film while at the isoelectric point (pI) or below the tertiary structure of proteins was disturbed. These measurements provide the first molecular evidence that disruption of protein tertiary structure could be responsible for the reduced permeation flows observed during membrane filtration of protein solutions and suggest that operating at high pH values away from the pI of proteins will reduce such fouling. 60 refs., 9 figs., 5 tabs.

  8. Kinetic and thermodynamic framework for P4-P6 RNA reveals tertiary motif modularity and modulation of the folding preferred pathway

    PubMed Central

    Bisaria, Namita; Greenfeld, Max; Limouse, Charles; Pavlichin, Dmitri S.; Mabuchi, Hideo; Herschlag, Daniel

    2016-01-01

    The past decade has seen a wealth of 3D structural information about complex structured RNAs and identification of functional intermediates. Nevertheless, developing a complete and predictive understanding of the folding and function of these RNAs in biology will require connection of individual rate and equilibrium constants to structural changes that occur in individual folding steps and further relating these steps to the properties and behavior of isolated, simplified systems. To accomplish these goals we used the considerable structural knowledge of the folded, unfolded, and intermediate states of P4-P6 RNA. We enumerated structural states and possible folding transitions and determined rate and equilibrium constants for the transitions between these states using single-molecule FRET with a series of mutant P4-P6 variants. Comparisons with simplified constructs containing an isolated tertiary contact suggest that a given tertiary interaction has a stereotyped rate for breaking that may help identify structural transitions within complex RNAs and simplify the prediction of folding kinetics and thermodynamics for structured RNAs from their parts. The preferred folding pathway involves initial formation of the proximal tertiary contact. However, this preference was only ∼10 fold and could be reversed by a single point mutation, indicating that a model akin to a protein-folding contact order model will not suffice to describe RNA folding. Instead, our results suggest a strong analogy with a modified RNA diffusion-collision model in which tertiary elements within preformed secondary structures collide, with the success of these collisions dependent on whether the tertiary elements are in their rare binding-competent conformations. PMID:27493222

  9. The Bohr effect of hemoglobin intermediates and the role of salt bridges in the tertiary/quaternary transitions.

    PubMed

    Russo, R; Benazzi, L; Perrella, M

    2001-04-27

    Understanding mechanisms in cooperative proteins requires the analysis of the intermediate ligation states. The release of hydrogen ions at the intermediate states of native and chemically modified hemoglobin, known as the Bohr effect, is an indicator of the protein tertiary/quaternary transitions, useful for testing models of cooperativity. The Bohr effects due to ligation of one subunit of a dimer and two subunits across the dimer interface are not additive. The reductions of the Bohr effect due to the chemical modification of a Bohr group of one and two alpha or beta subunits are additive. The Bohr effects of monoliganded chemically modified hemoglobins indicate the additivity of the effects of ligation and chemical modification with the possible exception of ligation and chemical modification of the alpha subunits. These observations suggest that ligation of a subunit brings about a tertiary structure change of hemoglobin in the T quaternary structure, which breaks some salt bridges, releases hydrogen ions, and is signaled across the dimer interface in such a way that ligation of a second subunit in the adjacent dimer promotes the switch from the T to the R quaternary structure. The rupture of the salt bridges per se does not drive the transition.

  10. Ionic strength affects tertiary structure and aggregation propensity of a monoclonal antibody adsorbed to silicone oil-water interfaces.

    PubMed

    Gerhardt, Alana; Bonam, Kurt; Bee, Jared S; Carpenter, John F; Randolph, Theodore W

    2013-02-01

    Therapeutic proteins formulated in prefilled syringes lubricated with silicone oil come in contact with silicone oil-water interfaces for their entire shelf lives. Thus, the interactions between protein and silicone oil were studied to determine the effect of silicone oil on a monoclonal antibody's stability, both at the interface and in the bulk solution. The influence of ionic strength on these interactions was also investigated through the addition of various monovalent and divalent salts to sample formulations. The tertiary structure of the antibody was perturbed when it adsorbed to the silicone oil-water interface in solutions at low ionic strength. However, the tertiary structure of the antibody at the interface was not perturbed when the ionic strength of the formulation was increased. Even at low ionic strength, the secondary structure of the antibody adsorbed to the silicone oil-water interface was retained, suggesting that at low ionic strength, the adsorbed antibody assumes a molten globule-like conformation. This partially unfolded species was aggregation-prone, especially during agitation. Silicone oil-induced aggregation of the antibody was inhibited at higher ionic strength.

  11. Cosmic-Ray Modulation: an Ab Initio Approach

    NASA Astrophysics Data System (ADS)

    Engelbrecht, N. E.; Burger, R. A.

    2014-10-01

    A better understanding of cosmic-ray modulation in the heliosphere can only be gained through a proper understanding of the effects of turbulence on the diffusion and drift of cosmic rays. We present an ab initio model for cosmic-ray modulation, incorporating for the first time the results yielded by a two-component turbulence transport model. This model is solved for periods of minimum solar activity, utilizing boundary values chosen so that model results are in fair to good agreement with spacecraft observations of turbulence quantities, not only in the solar ecliptic plane but also along the out-of-ecliptic trajectory of the Ulysses spacecraft. These results are employed as inputs for modelled slab and 2D turbulence energy spectra. The latter spectrum is chosen based on physical considerations, with a drop-off at the very lowest wavenumbers commencing at the 2D outerscale. There currently exist no models or observations for this quantity, and it is the only free parameter in this study. The modelled turbulence spectra are used as inputs for parallel mean free path expressions based on those derived from quasi-linear theory and perpendicular mean free paths from extended nonlinear guiding center theory. Furthermore, the effects of turbulence on cosmic-ray drifts are modelled in a self-consistent way, employing a recently developed model for drift along the wavy current sheet. The resulting diffusion coefficients and drift expressions are applied to the study of galactic cosmic-ray protons and antiprotons using a three-dimensional, steady-state cosmic-ray modulation code, and sample solutions in fair agreement with multiple spacecraft observations are presented.

  12. The hydration structure of carbon monoxide by ab initio methods

    NASA Astrophysics Data System (ADS)

    Awoonor-Williams, Ernest; Rowley, Christopher N.

    2017-01-01

    The solvation of carbon monoxide (CO) in liquid water is important for understanding its toxicological effects and biochemical roles. In this paper, we use ab initio molecular dynamics (AIMD) and CCSD(T)-F12 calculations to assess the accuracy of the Straub and Karplus molecular mechanical (MM) model for CO(aq). The CCSD(T)-F12 CO-H2O potential energy surfaces show that the most stable structure corresponds to water donating a hydrogen bond to the C center. The MM-calculated surface incorrectly predicts that the O atom is a stronger hydrogen bond acceptor than the C atom. The AIMD simulations indicate that CO is solvated like a hydrophobic solute, with very limited hydrogen bonding with water. The MM model tends to overestimate the degree of hydrogen bonding and overestimates the atomic radius of the C atom. The calculated Gibbs energy of hydration using the TIP3P water model is in good agreement with the experiment (9.3 kJ mol-1 expt. vs 10.7 kJ mol-1 calc.). The calculated diffusivity of CO (aq) in TIP3P-model water was 5.1 ×10-5 cm2/s calc., more than double the experimental value of 2.3 ×10-5 cm2/s. The hydration energy calculated using the TIP4P-FB water model is in poorer agreement with the experiment (ΔG = 6.8 kJ/mol) but the diffusivity is in better agreement (D =2.5 ±0.1 ×10-5 cm2/s).

  13. Ab initio molecular dynamics of liquid hydrogen chloride

    NASA Astrophysics Data System (ADS)

    Dubois, Vincent; Pasquarello, Alfredo

    2005-03-01

    We carried out an ab initio molecular dynamics simulation of liquid hydrogen chloride (ℓ-HCl) at a temperature of 313 K. Comparison with inelastic neutron scattering data shows that the simulation achieves an overall good description of the structural correlations, improving significantly upon a description based on classical interaction potentials. Despite some minor differences between theory and experiment in the H-H partial structure factor, the simulation gives a description of the hydrogen bonding in impressive agreement with experiment, for both the amount and the bond-length distribution of the bonds. In the simulation, 40% of the molecules are nonbonded, while the hydrogen-bonded chains are short, principally consisting of dimers (25%) and trimers (15%). Neighboring molecules in the simulation are found to form L-shaped arrangements, like in the isolated (HCl)2 dimer and in crystalline phases of HCl. The time correlation of the molecular-axis orientation is found to be characterized by a very short decay time (0.13 ps), consistent with the short length of the hydrogen-bonded chains. Other dynamical properties investigated in this work include the diffusion coefficient and the vibrational density of states. We evaluated the molecular dipole of the HCl molecule in the liquid using a definition based on the coupling of rotational modes to an external electric field. The average dipole moment (1.53 D) derived in this way is found to be considerably larger than for the isolated molecule (1.11 D). Our results show that the dipole moment in ℓ-HCl undergoes large fluctuations, both in orientation and in modulus. Upon the onset of an external field, such dipole fluctuations concur to reduce the fluctuations of the dielectric response.

  14. Ab initio valence-space theory for exotic nuclei

    NASA Astrophysics Data System (ADS)

    Holt, Jason

    2015-10-01

    Recent advances in ab initio nuclear structure theory have led to groundbreaking predictions in the exotic medium-mass region, from the location of the neutron dripline to the emergence of new magic numbers far from stability. Playing a key role in this progress has been the development of sophisticated many-body techniques and chiral effective field theory, which provides a systematic basis for consistent many-nucleon forces and electroweak currents. Within the context of valence-space Hamiltonians derived from the nonperturbative in-medium similarity renormalization group (IM-SRG) approach, I will discuss the importance of 3N forces in understanding and making new discoveries in the exotic sd -shell region. Beginning in oxygen, we find that the effects of 3N forces are decisive in explaining why 24O is the last bound oxygen isotope, validating first predictions of this phenomenon from several years ago. Furthermore, 3N forces play a key role in reproducing spectroscopy, including signatures of doubly magic 22,24O, and physics beyond the dripline. Similar improvements are obtained in new spectroscopic predictions for exotic fluorine and neon isotopes, where agreement with recent experimental data is competitive with state-of-the-art phenomenology. Finally, I will discuss first applications of the IM-SRG to effective valence-space operators, such as radii and E 0 transitions, as well as extensions to general operators crucial for our future understanding of electroweak processes, such as neutrinoless double-beta decay. This work was supported by NSERC and the NRC Canada.

  15. Resonance and aromaticity: an ab initio valence bond approach.

    PubMed

    Rashid, Zahid; van Lenthe, Joop H; Havenith, Remco W A

    2012-05-17

    Resonance energy is one of the criteria to measure aromaticity. The effect of the use of different orbital models is investigated in the calculated resonance energies of cyclic conjugated hydrocarbons within the framework of the ab initio Valence Bond Self-Consistent Field (VBSCF) method. The VB wave function for each system was constructed using a linear combination of the VB structures (spin functions), which closely resemble the Kekulé valence structures, and two types of orbitals, that is, strictly atomic (local) and delocalized atomic (delocal) p-orbitals, were used to describe the π-system. It is found that the Pauling-Wheland's resonance energy with nonorthogonal structures decreases, while the same with orthogonalized structures and the total mean resonance energy (the sum of the weighted off-diagonal contributions in the Hamiltonian matrix of orthogonalized structures) increase when delocal orbitals are used as compared to local p-orbitals. Analysis of the interactions between the different structures of a system shows that the resonance in the 6π electrons conjugated circuits have the largest contributions to the resonance energy. The VBSCF calculations also show that the extra stability of phenanthrene, a kinked benzenoid, as compared to its linear counterpart, anthracene, is a consequence of the resonance in the π-system rather than the H-H interaction in the bay region as suggested previously. Finally, the empirical parameters for the resonance interactions between different 4n+2 or 4n π electrons conjugated circuits, used in Randić's conjugated circuits theory or Herdon's semi-emprical VB approach, are quantified. These parameters have to be scaled by the structure coefficients (weights) of the contributing structures.

  16. AN AB INITIO MODEL FOR COSMIC-RAY MODULATION

    SciTech Connect

    Engelbrecht, N. E.; Burger, R. A.

    2013-07-20

    A proper understanding of the effects of turbulence on the diffusion and drift of cosmic rays (CRs) is of vital importance for a better understanding of CR modulation in the heliosphere. This study presents an ab initio model for CR modulation, incorporating for the first time the results yielded by a two-component turbulence transport model. This model is solved for solar minimum heliospheric conditions, utilizing boundary values chosen so that model results are in reasonable agreement with spacecraft observations of turbulence quantities in the solar ecliptic plane and along the out-of-ecliptic trajectory of the Ulysses spacecraft. These results are employed as inputs for modeled slab and two-dimensional (2D) turbulence energy spectra. The modeled 2D spectrum is chosen based on physical considerations, with a drop-off at the very lowest wavenumbers. There currently exist no models or observations for the wavenumber where this drop-off occurs, and it is considered to be the only free parameter in this study. The modeled spectra are used as inputs for parallel mean free path expressions based on those derived from quasi-linear theory and perpendicular mean free paths from extended nonlinear guiding center theory. Furthermore, the effects of turbulence on CR drifts are modeled in a self-consistent way, also employing a recently developed model for wavy current sheet drift. The resulting diffusion and drift coefficients are applied to the study of galactic CR protons and antiprotons using a 3D, steady-state CR modulation code, and sample solutions in fair to good agreement with multiple spacecraft observations are presented.

  17. Uniaxial phase transition in Si: Ab initio calculations

    NASA Astrophysics Data System (ADS)

    Cheng, C.

    2003-04-01

    Based on a previously proposed thermodynamic analysis, [C. Cheng, W. H. Huang, and H. J. Li, Phys. Rev. B 63, 153202 (2001)] we study the relative stabilities of five Si phases under uniaxial compression using ab initio methods. The five phases are diamond, βSn, simple-hexagonal (sh), simple-cubic, and hexagonal closed-packed structures. The possible phase-transition patterns were investigated by considering the phase transitions between any two chosen phases of the five phases. By analyzing the different contributions to the relative phase stability, we identified the most important factors in reducing the phase-transition pressures at uniaxial compression. We also show that it is possible to have phase transitions occur only when the phases are under uniaxial compression, in spite of no phase transition when under hydrostatic compression. Taking all five phases into consideration, the phase diagram at uniaxial compression was constructed for pressures up to 20 GPa. The stable phases were found to be diamond, βSn, and sh structures, i.e., the same as those when under hydrostatic condition. According to the phase diagram, direct phase transition from the diamond to the sh phase is possible if the applied uniaxial pressures, on increasing, satisfy the condition Px>Pz. Similarly, the sh-to-βSn transition on increasing pressures is also possible if the applied uniaxial pressures are varied from the condition of Px>Pz, on which the phase of sh is stable to the condition Px

  18. The Tertiary Arc Chain in the Western Pacific

    NASA Astrophysics Data System (ADS)

    Honza, E.

    1991-02-01

    The arcs bordering the Pacific Plate on the Western and Southwestern Pacific rim are reconstructed since their initiation in the Eocene and Oligocene. They occur in a zone forming an arc chain from the Western Pacific tropics to the eastern margin of Australia. They are the Bonin, Mariana, Yap, Palau, Halmahera, North New Guinea-West Melanesia, Solomon, Vanuatu, and Tonga-Kermadec Arcs, designated here the Tertiary Arc Chain. They are associated with the formation and consumption of backarc basins. Reversals of arc polarity and episodic subduction has occurred in some of them. The Tertiary Arc Chain is characterized by four major stages in its evolution which can be seen characteristically in some of the arcs. The first stage is the occurrence of the arc chain from the middle Eocene to earliest Oligocene. The second stage is the formation of the backarc basins from the early to late Oligocene. The third stage is the occurrence of double arcs on the inner side of the arc chain in the early to middle Miocene and the fourth stage is the reversal of arc polarities due to collisions since the late Miocene. The backarc basins associated with the arcs of the Tertiary Arc Chain have fixed limits of duration in their evolution. The backarc basins initially form 15 million years after the initiation of the volcanic arc. Several to 10 million years after the initial opening, backarc spreading terminates. Approximately 20 million years after the cessation of the backarc spreading, a second phase of opening occurs in the backarc region. In the case of arc collision, reversal of the arc polarity occurs if there is oceanic crust on the backarc side, and opening of a backarc basin occurs within several million years. These occurrences and durations have a variation of ca. 3-5 million years.

  19. [Meningeal tertiary lymphoid organs: Major actors in intrathecal autoimmunity].

    PubMed

    Bonnan, M

    2015-01-01

    Multiple sclerosis (MS) is characterized by an intrathecal synthesis of immunoglobulins synthesized by B-cell clones and by a brain infiltrate of clonal T-cells. The clonal maturation of these lymphocytes takes place in tertiary lymphoid organs (TLO) developed in the intrathecal compartment. TLO are acquired lymphoid organs able to develop in the vicinity of the inflammatory sites, where they mount a complete antigen-driven immune response. We here review TLO pathophysiology in animal models of MS and human MS. Several pieces of evidence suggest that intrathecal TLO may play a major role in the clinical impairment. Potential therapeutic applications are examined.

  20. Ignition of global wildfires at the Cretaceous/Tertiary boundary

    NASA Technical Reports Server (NTRS)

    Melosh, H. J.; Schneider, N. M.; Zahnle, K. J.; Latham, D.

    1990-01-01

    The recent discovery of an apparently global soot layer at the Cretaceous/Tertiary boundary indicates that global wildfires were somehow ignited by the impact of a comet or asteroid. It is shown here that the thermal radiation produced by the ballistic reentry of ejecta condensed from the vapor plume of the impact could have increased the global radiation flux by factors of 50 to 150 times the solar input for periods ranging from one to several hours. This great increase in thermal radiation may have been responsible for the ignition of global wildfires, as well as having deleterious effects on unprotected animal life.

  1. Automated motif extraction and classification in RNA tertiary structures

    PubMed Central

    Djelloul, Mahassine; Denise, Alain

    2008-01-01

    We used a novel graph-based approach to extract RNA tertiary motifs. We cataloged them all and clustered them using an innovative graph similarity measure. We applied our method to three widely studied structures: Haloarcula marismortui 50S (H.m 50S), Escherichia coli 50S (E. coli 50S), and Thermus thermophilus 16S (T.th 16S) RNAs. We identified 10 known motifs without any prior knowledge of their shapes or positions. We additionally identified four putative new motifs. PMID:18957493

  2. An exploration of gender differences in tertiary mathematics

    NASA Astrophysics Data System (ADS)

    Watson, Jane M.

    1989-02-01

    Data from 400 students in a tertiary mathematics course were analysed to explore gender differences on a number of variables associated with learning mathematics. It was concluded that while differences did occur on variables associated with confidence, self-concept, test anxiety and quantitative ability indicating a detrimental effect for women, compensating behaviour by women, including increased assignment work and tutorial attendance, resulted in comparable final course performance for women and men. These findings are discussed in light of participation rates of women in mathematics.

  3. Protein Repeats from First Principles.

    PubMed

    Turjanski, Pablo; Parra, R Gonzalo; Espada, Rocío; Becher, Verónica; Ferreiro, Diego U

    2016-04-05

    Some natural proteins display recurrent structural patterns. Despite being highly similar at the tertiary structure level, repeating patterns within a single repeat protein can be extremely variable at the sequence level. We use a mathematical definition of a repetition and investigate the occurrences of these in sequences of different protein families. We found that long stretches of perfect repetitions are infrequent in individual natural proteins, even for those which are known to fold into structures of recurrent structural motifs. We found that natural repeat proteins are indeed repetitive in their families, exhibiting abundant stretches of 6 amino acids or longer that are perfect repetitions in the reference family. We provide a systematic quantification for this repetitiveness. We show that this form of repetitiveness is not exclusive of repeat proteins, but also occurs in globular domains. A by-product of this work is a fast quantification of the likelihood of a protein to belong to a family.

  4. Protein Repeats from First Principles

    PubMed Central

    Turjanski, Pablo; Parra, R. Gonzalo; Espada, Rocío; Becher, Verónica; Ferreiro, Diego U.

    2016-01-01

    Some natural proteins display recurrent structural patterns. Despite being highly similar at the tertiary structure level, repeating patterns within a single repeat protein can be extremely variable at the sequence level. We use a mathematical definition of a repetition and investigate the occurrences of these in sequences of different protein families. We found that long stretches of perfect repetitions are infrequent in individual natural proteins, even for those which are known to fold into structures of recurrent structural motifs. We found that natural repeat proteins are indeed repetitive in their families, exhibiting abundant stretches of 6 amino acids or longer that are perfect repetitions in the reference family. We provide a systematic quantification for this repetitiveness. We show that this form of repetitiveness is not exclusive of repeat proteins, but also occurs in globular domains. A by-product of this work is a fast quantification of the likelihood of a protein to belong to a family. PMID:27044676

  5. An ab initio-based Er–He interatomic potential in hcp Er

    SciTech Connect

    Yang, Li; ye, Yeting; Fan, K. M.; Shen, Huahai; Peng, Shuming; Long, XG; Zhou, X. S.; Zu, Xiaotao; Gao, Fei

    2014-09-01

    We have developed an empirical erbium-helium (Er-He) potential by fitting to the results calculated from ab initio method. Based on the electronic hybridization between Er and He atoms, an s-band model, along with a repulsive pair potential, has been derived to describe the Er-He interaction. The atomic configurations and the formation energies of single He defects, small He interstitial clusters (Hen) and He-vacancy (HenV ) clusters obtained by ab initio calculations are used as the fitting database. The binding energies and relative stabilities of the HnVm clusters are studied by the present potential and compared with the ab initio calculations. The Er-He potential is also applied to study the migration of He in hcp-Er at different temperatures, and He clustering is found to occur at 600 K in hcp Er crystal, which may be due to the anisotropic migration behavior of He interstitials.

  6. Electron Transport through Polyene Junctions in between Carbon Nanotubes: an Ab Initio Realization

    NASA Astrophysics Data System (ADS)

    Chen, Yiing-Rei; Chen, Kai-Yu; Dou, Kun-Peng; Tai, Jung-Shen; Lee, Hsin-Han; Kaun, Chao-Cheng

    With both ab initio and tight-binding model calculations, we study a system of polyene bridged armchair carbon nanotube electrodes, considering one-polyene and two-polyene cases, to address aspects of quantum transport through junctions with multiple conjugated molecules. The ab initio results of the two-polyene cases not only show the interference effect in transmission, but also the sensitive dependence of such effect on the combination of relative contact sites, which agrees nicely with the tight-binding model. Moreover, we show that the discrepancy mainly brought by ab initio relaxation provides an insight into the influence upon transmission spectra, from the junction's geometry, bonding and effective potential. This work was supported by the Ministry of Science and Technology of the Republic of China under Grant Nos. 99-2112-M-003-012-MY2 and 103-2622-E-002-031, and the National Center for Theoretical Sciences of Taiwan.

  7. Ab initio calculation of (hyper)polarizabilities using a sum-over-states formalism.

    NASA Astrophysics Data System (ADS)

    Taylor, Caroline M.; Chaudhuri, Rajat K.; Potts, Davin M.; Freed, Karl F.

    2001-03-01

    Hyperpolarizabilities are relevant to a wide range of non-linear optical properties. Ab initio computations often require a high level of correlation for accurate determination of β and γ , and especially of thier frequency dependence. While sum-over-states methods are widely used within semi-empirical frameworks, they have not been employed with high level ab initio methods because of the computational costs associated with calculating a sufficient number of states. The effective valence shell Hamiltonian method (H^v) is a highly correlated, size-extensive, ab initio, multireference, perturbative (``perturb-then-diagonalize'') method. A single H^v calculation yields a large number of states, making it ideal for use with the sum-over-states fomalism for determination of molecular properties. The method has been used to calculate the (hyper)polarizabilities of small polyene systems.

  8. Classical and ab-initio molecular dynamic simulation of an amorphous silica surface

    NASA Astrophysics Data System (ADS)

    Mischler, C.; Kob, W.; Binder, K.

    2002-08-01

    We present the results of a classical molecular dynamic simulation as well as of an ab-initio molecular dynamic simulation of an amorphous silica surface. In the case of the classical simulation we use the potential proposed by van Beest et al. (BKS) whereas the ab-initio simulation is done with a Car-Parrinello method (CPMD). We find that the surfaces generated by BKS have a higher concentration of defects (e.g., concentration of two-membered rings) than those generated with CPMD. In addition also the distribution functions of the angles and of the distances are different for the short rings. Hence we conclude that whereas the BKS potential is able to correctly reproduce the surface on the length scale beyond ≈5 Å, it is necessary to use an ab-initio method to reliably predict the structure at small scales.

  9. Global exploration of the energy landscape of solids on the ab initio level.

    PubMed

    Doll, K; Schön, J C; Jansen, M

    2007-12-14

    Predicting which crystalline modifications can be present in a chemical system requires the global exploration of its energy landscape. Due to the large computational effort involved, in the past this search for sufficiently stable minima has been performed employing a variety of empirical potentials and cost functions followed by a local optimization on the ab initio level. However, this entails the risk of overlooking important modifications that are not modeled accurately using empirical potentials. In order to overcome this critical limitation, we develop an approach to employ ab initio energy functions during the global optimization phase of the structure prediction. As an example, we perform a global exploration of the landscape of LiF on the ab initio level and show that the relevant crystalline modifications are found during the search.

  10. Density-matrix based determination of low-energy model Hamiltonians from ab initio wavefunctions.

    PubMed

    Changlani, Hitesh J; Zheng, Huihuo; Wagner, Lucas K

    2015-09-14

    We propose a way of obtaining effective low energy Hubbard-like model Hamiltonians from ab initio quantum Monte Carlo calculations for molecular and extended systems. The Hamiltonian parameters are fit to best match the ab initio two-body density matrices and energies of the ground and excited states, and thus we refer to the method as ab initio density matrix based downfolding. For benzene (a finite system), we find good agreement with experimentally available energy gaps without using any experimental inputs. For graphene, a two dimensional solid (extended system) with periodic boundary conditions, we find the effective on-site Hubbard U(∗)/t to be 1.3 ± 0.2, comparable to a recent estimate based on the constrained random phase approximation. For molecules, such parameterizations enable calculation of excited states that are usually not accessible within ground state approaches. For solids, the effective Hamiltonian enables large-scale calculations using techniques designed for lattice models.

  11. Physiologically based pharmacokinetic model for ethyl tertiary-butyl ether and tertiary-butyl alcohol in rats: Contribution of binding to α2u-globulin in male rats and high-exposure nonlinear kinetics to toxicity and cancer outcomes.

    PubMed

    Borghoff, Susan J; Ring, Caroline; Banton, Marcy I; Leavens, Teresa L

    2017-05-01

    In cancer bioassays, inhalation, but not drinking water exposure to ethyl tertiary-butyl ether (ETBE), caused liver tumors in male rats, while tertiary-butyl alcohol (TBA), an ETBE metabolite, caused kidney tumors in male rats following exposure via drinking water. To understand the contribution of ETBE and TBA kinetics under varying exposure scenarios to these tumor responses, a physiologically based pharmacokinetic model was developed based on a previously published model for methyl tertiary-butyl ether, a structurally similar chemical, and verified against the literature and study report data. The model included ETBE and TBA binding to the male rat-specific protein α2u-globulin, which plays a role in the ETBE and TBA kidney response observed in male rats. Metabolism of ETBE and TBA was described as a single, saturable pathway in the liver. The model predicted similar kidney AUC0-∞ for TBA for various exposure scenarios from ETBE and TBA cancer bioassays, supporting a male-rat-specific mode of action for TBA-induced kidney tumors. The model also predicted nonlinear kinetics at ETBE inhalation exposure concentrations above ~2000 ppm, based on blood AUC0-∞ for ETBE and TBA. The shift from linear to nonlinear kinetics at exposure concentrations below the concentration associated with liver tumors in rats (5000 ppm) suggests the mode of action for liver tumors operates under nonlinear kinetics following chronic exposure and is not relevant for assessing human risk. Copyright © 2016 The Authors Journal of Applied Toxicology Published by John Wiley & Sons Ltd.

  12. Regional prospectivity of Mesozoic and Tertiary in the eastern Adriatic and adjacent area

    SciTech Connect

    Scott, J.; Dolan, P.; Lunn, G. )

    1988-08-01

    Post-Hercynian deposits in the eastern Adriatic and the adjacent external zones of the Dinarides and Albanian Hellenides may be subdivided into four facies groups. (1) Permian-Lower Triassic clastics and carbonates with some evaporites, (2) Middle Triassic-lower Tertiary carbonate platform facies with associated continental margin deeper marine sequences, (3) Upper Cretaceous-lower Tertiary flysch, and (4) middle Tertiary molasse and postorogenic Neogene sediments. The Permian to lower Tertiary section was deposited during the complex Alpine cycle, while the upper Tertiary section is the product of post-Alpine deposition. This depositional history during markedly different tectonic regimes creates two groups of petroleum plays in the eastern Adriatic: (1) Alpine cycle plays in the Permian to lower Tertiary in the thrust-faulted and folded foreland of Adria and (2) post-Alpine plays in upper Tertiary postorogenic or late synorogenic basins. Around the Adriatic, the post-Alpine plays have so far proved the most successful. Major production occurs in the onshore Po basin and its extension beneath the Adriatic. Some of this production is from deep Alpine-cycle reservoirs, but the bulk is from the upper Tertiary-Quaternary. Similar horizons produce onshore and offshore the central-southern Adriatic coast of Italy. Major Tertiary production also occurs to the northeast in the Pannonian basin of Yugoslavia and Hungary from Miocene and younger sequences. Onshore Albania produces significant quantities of hydrocarbons; although data are scarce, much of this production is presumably from upper Tertiary molasse or lower Tertiary flysch.

  13. Interaction Energies in Complexes of Zn and Amino Acids: A Comparison of Ab Initio and Force Field Based Calculations.

    PubMed

    Ahlstrand, Emma; Hermansson, Kersti; Friedman, Ran

    2017-03-24

    Zinc plays important roles in structural stabilization of proteins, enzyme catalysis, and signal transduction. Many Zn binding sites are located at the interface between the protein and the cellular fluid. In aqueous solutions, Zn ions adopt an octahedral coordination, while in proteins zinc can have different coordinations, with a tetrahedral conformation found most frequently. The dynamics of Zn binding to proteins and the formation of complexes that involve Zn are dictated by interactions between Zn and its binding partners. We calculated the interaction energies between Zn and its ligands in complexes that mimic protein binding sites and in Zn complexes of water and one or two amino acid moieties, using quantum mechanics (QM) and molecular mechanics (MM). It was found that MM calculations that neglect or only approximate polarizability did not reproduce even the relative order of the QM interaction energies in these complexes. Interaction energies calculated with the CHARMM-Drude polarizable force field agreed better with the ab initio results, although the deviations between QM and MM were still rather large (40-96 kcal/mol). In order to gain further insight into Zn-ligand interactions, the free energies of interaction were estimated by QM calculations with continuum solvent representation, and we performed energy decomposition analysis calculations to examine the characteristics of the different complexes. The ligand-types were found to have high impact on the relative strength of polarization and electrostatic interactions. Interestingly, ligand-ligand interactions did not play a significant role in the binding of Zn. Finally, analysis of ligand exchange energies suggests that carboxylates could be exchanged with water molecules, which explains the flexibility in Zn binding dynamics. An exchange between carboxylate (Asp/Glu) and imidazole (His) is less likely.

  14. Positive selection sites in tertiary structure of Leguminosae chalcone isomerase 1.

    PubMed

    Wang, R K; Zhan, S F; Zhao, T J; Zhou, X L; Wang, C E

    2015-03-20

    Isoflavonoids and the related synthesis enzyme, chalcone isomerase 1 (CHI1), are unique in the Leguminosae, with diverse biological functions. Among the Leguminosae, the soybean is an important oil, protein crop, and model plant. In this study, we aimed to detect the generation pattern of Leguminosae CHI1. Genome-wide sequence analysis of CHI in 3 Leguminosae and 3 other closely related model plants was performed; the expression levels of soybean chalcone isomerases were also analyzed. By comparing positively selected sites and their protein structures, we retrieved the evolution patterns for Leguminosae CHI1. A total of 28 CHI and 7 FAP3 (CHI4) genes were identified and separated into 4 clades: CHI1, CHI2, CHI3, and FAP3. Soybean genes belonging to the same chalcone isomerase subfamily had similar expression patterns. CHI1, the unique chalcone isomerase subfamily in Leguminosae, showed signs of significant positive selection as well as special expression characteristics, indicating an accelerated evolution throughout its divergence. Eight sites were identified as undergoing positive selection with high confidence. When mapped onto the tertiary structure of CHI1, these 8 sites were observed surrounding the enzyme substrate only; some of them connected to the catalytic core of CHI. Thus, we inferred that the generation of Leguminosae CHI1 is dependent on the positively selected amino acids surrounding its catalytic substrate. In other words, the evolution of CHI1 was driven by specific selection or processing conditions within the substrate.

  15. Novel stereospecificity of the L-arabinose-binding protein

    NASA Astrophysics Data System (ADS)

    Quiocho, Florante A.; Vyas, Nand K.

    1984-08-01

    Tertiary structure refinement at 1.7 Å resolution of the liganded form of L-arabinose-binding protein from Escherichia coli has revealed a novel binding site geometry which accommodates both α- and β-anomers of L-arabinose. This detailed structure analysis provides new understanding of protein-sugar interaction, the process by which the binding protein minimizes the difference in the stability of the two bound sugar anomers, and the roles of periplasmic binding proteins in active transport

  16. Early Tertiary subsidence and sedimentary facies - northern Sirte Basin, Libya

    SciTech Connect

    Gumati, Y.D.; Kanes, W.H.

    1985-01-01

    The subsidence curves and subsidence rate curves for the Sirte basin, constructed from the stratigraphic record, show that subsidence was continuous throughout Late Cretaceous and Tertiary times, reaching a maximum during the Paleocene and Eocene, when a major reactivation of faults occurred. Shales and carbonates were deposited during all of the Late Cretaceous and Tertiary. Abrupt lateral facies changes occur from the platform areas toward the deeper troughs along with steep downdip thickening. These conditions were probably assisted by contemporaneous faulting along structurally weak hinge lines where the dominant structural elements are normal step faults. The absence of upper Paleozoic and lower Mesozoic sediments suggests that the area was domed, faulted, and eroded during the late Mesozoic. As a result of crustal extension during the Paleocene, a marked lithologic and structural change occurred. The Heira Shale succeeded the Kalash Limestone in the Marada trough. Reactivation of the earlier faults, accompanied by an increase in the sediment supply from the south, caused these lower Paleocene shales to cover the entire area, with the exception of the old highs where carbonate deposition continued. An intercalation of shales and carbonates provides a sensitive indicator of change of depth and sediment type.

  17. Early Tertiary subsidence and sedimentary facies - Northern Sirte Basin, Libya

    SciTech Connect

    Gumati, Y.D.; Kanes, W.H.

    1985-12-01

    The subsidence curves and subsidence rate curves for the Sirte basin, constructed from the stratigraphic record, show that subsidence was continuous throughout Late Cretaceous and Tertiary times, reaching a maximum during the Paleocene and Eocene, when a major reactivation of faults occurred. Shales and carbonates were deposited during all of the Late Cretaceous and Tertiary. Abrupt lateral facies changes occur from the platform areas toward the deeper troughs along with steep downdip thickening. The absence of upper Paleozoic and lower Mesozoic sediments suggests that the area was domed, faulted, and eroded during the late Mesozoic. As a result of crustal extension during the Paleocene, a marked lithologic and structural change occurred. The Heira Shale succeeded the Kalash Limestone in the Marada trough. Reactivation of the earlier faults, accompanied by an increase in the sediment supply from the south, caused these lower Paleocene shales to cover the entire area, with the exception of the old highs where carbonate deposition continued. An intercalation of shales and carbonates provides a sensitive indicator of change of depth and sediment type. 14 figures.

  18. Vertebrate extinctions and survival across the Cretaceous-Tertiary boundary

    NASA Astrophysics Data System (ADS)

    Buffetaut, Eric

    1990-01-01

    A critical analysis of the fossil vertebrate record across the Cretaceous-Tertiary boundary shows that the available evidence is far less accurate than that concerning invertebrates and microfossils. Far-reaching conclusions have been drawn from generalisations about vertebrate extinctions in the continental realm based on the local record from western North America, but little is known about patterns of terminal Cretaceous vertebrate extinctions in other parts of the world, and even the western North American record is ambiguous. Despite this unsatisfactory record, it clearly appears that terminal Cretaceous vertebrate extinctions were highly selective, with some groups (e.g. dinosaurs) becoming completely extinct, whereas others seem to be virtually unaffected. This argues against devastating catastrophes of the kind postulated by some recent impact scenarios. However, the survival of groups known to be sensitive to climatic deterioration (such as crocodilians and other non-dinosaurian reptiles) indicates that alternative hypotheses involving gradual but fairly important climatic changes on a world-wide scale are not convincing either. The pattern of extinction and survival among vertebrates across the Cretaceous-Tertiary boundary may be explained as a consequence of the disruption of some food chains following a crisis in the plant kingdom, which itself may have been the result of the atmospheric consequences of unusual extraterrestrial or internal events.

  19. Tertiary phase diagram of cellulose, ionic liquid and organic solvent

    NASA Astrophysics Data System (ADS)

    Zhang, Xin; Henderson, Doug; Tyagi, Madhusudan; Mao, Yimin; Briber, Robert M.; Wang, Howard

    Cellulose is the most abundant natural polymer on earth, and widely used in products from clothing to paper. Fundamental understanding of molecular solutions of cellulose is the key to realize advanced technologies beyond cellulose fibers. It has been reported that certain ionic liquid/organic solvent mixtures dissolve cellulose. In this study, the tertiary phase diagram of microcrystalline cellulose, 1-Ethyl-3-methylimidazolium acetate (EMIMAc), and dimethylformamide (DMF) mixtures has been determined using optical cloud point method and small angle neutron scattering (SANS). Data indicate that a molar ratio of EMIMAc to cellulose repeating unit equal or greater than 3 is necessary but not sufficient in forming one-phase homogeneous solutions. A miscibility gap exists in the dilute regime, where a minimum of 5 mol% of EMIM Ac in DMF is needed to form homogenous solutions. SANS show that cellulose chains adopt Gaussian-like conformation in homogenous solutions. The solutions exhibit the characteristics of upper critical solution temperature. Clustering of cellulose chains occurs at low EMIMAc/DMF or EMIMAc/cellulose ratio, or at low temperatures. The mechanism of cellulose dissolution in tertiary mixture is discussed.

  20. IRIS Toxicological Review of Ethyl Tertiary Butyl Ether (Etbe) ...

    EPA Pesticide Factsheets

    In August 2013, EPA released the draft literature searches and associated search strategies, evidence tables, and exposure response arrays for ETBE to obtain input from stakeholders and the public prior to developing the draft IRIS assessment. Specifically, EPA was interested in comments on the following: Draft literature search strategies The approach for identifying studies The screening process for selecting pertinent studies The resulting list of pertinent studies Preliminary evidence tables The process for selecting studies to include in evidence tables The quality of the studies in the evidence tables The literature search strategy, which describes the processes for identifying scientific literature, contains the studies that EPA considered and selected to include in the evidence tables. The preliminary evidence tables and exposure-response arrays present the key study data in a standardized format. The evidence tables summarize the available critical scientific literature. The exposure-response figures provide a graphical representation of the responses at different levels of exposure for each study in the evidence table. The draft Toxicological Review of Ethyl Tertiary Butyl Ether provides scientific support and rationale for the hazard and dose-response assessment pertaining to chronic exposure to ethyl tertiary butyl ether.

  1. Extraterrestrial cause for the cretaceous-tertiary extinction.

    PubMed

    Alvarez, L W; Alvarez, W; Asaro, F; Michel, H V

    1980-06-06

    Platinum metals are depleted in the earth's crust relative to their cosmic abundance; concentrations of these elements in deep-sea sediments may thus indicate influxes of extraterrestrial material. Deep-sea limestones exposed in Italy, Denmark, and New Zealand show iridium increases of about 30, 160, and 20 times, respectively, above the background level at precisely the time of the Cretaceous-Tertiary extinctions, 65 million years ago. Reasons are given to indicate that this iridium is of extraterrestrial origin, but did not come from a nearby supernova. A hypothesis is suggested which accounts for the extinctions and the iridium observations. Impact of a large earth-crossing asteroid would inject about 60 times the object's mass into the atmosphere as pulverized rock; a fraction of this dust would stay in the stratosphere for several years and be distributed worldwide. The resulting darkness would suppress photosynthesis, and the expected biological consequences match quite closely the extinctions observed in the paleontological record. One prediction of this hypothesis has been verified: the chemical composition of the boundary clay, which is thought to come from the stratospheric dust, is markedly different from that of clay mixed with the Cretaceous and Tertiary limestones, which are chemically similar to each other. Four different independent estimates of the diameter of the asteroid give values that lie in the range 10 +/- 4 kilometers.

  2. In situ reactive oxygen species production for tertiary wastewater treatment.

    PubMed

    Guitaya, Léa; Drogui, Patrick; Blais, Jean François

    2015-05-01

    The goal of this research was to develop a new approach for tertiary water treatment, particularly disinfection and removal of refractory organic compounds, without adding any chemical. Hydrogen peroxide can indeed be produced from dissolved oxygen owing to electrochemical processes. Using various current intensities (1.0 to 4.0 A), it was possible to in situ produce relatively high concentration of H2O2 with a specific production rate of 0.05 × 10(-5) M/min/A. Likewise, by using ultraviolet-visible absorption spectroscopy method, it was shown that other reactive oxygen species (ROS) including HO(*) radical and O3 could be simultaneously formed during electrolysis. The ROS concentration passed from 0.45 × 10(-5) M after 20 min of electrolysis to a concentration of 2.87 × 10(-5) M after 100 min of electrolysis. The disinfection and the organic matter removal were relatively high during the tertiary treatment of municipal and domestic wastewaters. More than 90 % of organic compounds (chemical oxygen demand) can be removed, whereas 99 % of faecal coliform abatement can be reached. Likewise, the process was also effective in removing turbidity (more than 90 % of turbidity was removed) so that the effluent became more and more transparent.

  3. Heats of Segregation of BCC Binaries from Ab Initio and Quantum Approximate Calculations

    NASA Technical Reports Server (NTRS)

    Good, Brian S.

    2003-01-01

    We compare dilute-limit segregation energies for selected BCC transition metal binaries computed using ab initio and quantum approximate energy methods. Ab initio calculations are carried out using the CASTEP plane-wave pseudopotential computer code, while quantum approximate results are computed using the Bozzolo-Ferrante-Smith (BFS) method with the most recent parameters. Quantum approximate segregation energies are computed with and without atomistic relaxation. Results are discussed within the context of segregation models driven by strain and bond-breaking effects. We compare our results with full-potential quantum calculations and with available experimental results.

  4. Ab initio study of collective excitations in a disparate mass molten salt.

    PubMed

    Bryk, Taras; Klevets, Ivan

    2012-12-14

    Ab initio molecular dynamics simulations and the approach of generalized collective modes are applied for calculations of spectra of longitudinal and transverse collective excitations in molten LiBr. Dispersion and damping of low- and high-frequency branches of collective excitations as well as wave-number dependent relaxing modes were calculated. The main mode contributions to partial, total, and concentration dynamic structure factors were estimated in a wide region of wave numbers. A role of polarization effects is discussed from comparison of mode contributions to concentration dynamic structure factors calculated for molten LiBr from ab initio and classical rigid ion simulations.

  5. Microscopic properties of liquid water from combined ab initio molecular dynamics and energy decomposition studies.

    PubMed

    Khaliullin, Rustam Z; Kühne, Thomas D

    2013-10-14

    The application of newly developed first-principle modeling techniques to liquid water deepens our understanding of the microscopic origins of its unusual macroscopic properties and behaviour. Here, we review two novel ab initio computational methods: second-generation Car-Parrinello molecular dynamics and decomposition analysis based on absolutely localized molecular orbitals. We show that these two methods in combination not only enable ab initio molecular dynamics simulations on previously inaccessible time and length scales, but also provide unprecedented insights into the nature of hydrogen bonding between water molecules. We discuss recent applications of these methods to water clusters and bulk water.

  6. A density functional and ab initio investigation of the p-aminobenzoic acid molecule

    NASA Astrophysics Data System (ADS)

    Lago, A. F.; Dávalos, J. Z.; de Brito, A. Naves

    2007-08-01

    The p-aminobenzoic acid (C 7H 7NO 2) molecule has been investigated at different levels of theory. DFT methods (B3LYP and PBE1PBE), second order Møller-Plesset perturbation theory (MP2) and composite ab initio methods (G3MP2 and CBS) have been employed, in conjunction with large basis sets. Important informations on the electronic structure and thermochemistry of this molecule have been extracted, and the performance of the density functional and ab initio methods has been evaluated, based on the comparison of the calculated and the available experimental data.

  7. Ab initio approach to the development of interatomic potentials for the shell model of silica polymorphs

    NASA Astrophysics Data System (ADS)

    de Boer, K.; Jansen, A. P. J.; van Santen, R. A.

    1994-06-01

    We have developed a new method for deriving parameters for the shell model of silica polymorphs. All parameters for the shell model are derived in a self-consistent way from ab initio energy surfaces, polarizabilities and dipole moments of small clusters. This yields an ab initio partial charge shell model potential. The predictive power of our potential is demonstrated by presenting predictions for the structure of α-quartz, α-cristobalite, coesite, stishovite and the IR spectrum of α-quartz which are compared with experiment and predictions of the widely used potentials of Jackson and Catlow, and Kramer, Farragher, van Beest and van Santen.

  8. Haemostatic Profile in Patients of Myeloproliferative Neoplasms-A Tertiary Care Centre Experience

    PubMed Central

    Parashar, Yatendra; Kumar, Ashutosh; Agarwal, Kamal; Singh, U.S; Jain, Mili; Verma, S.P; Tripathi, A.K

    2016-01-01

    Introduction Patients of MPN commonly present with abnormalities in laboratory coagulation tests that are consistent with hypercoagulable state. Some individuals with MPN exhibit a pattern of exclusive bleeding or thrombotic events; many others have both bleeding and thrombosis during the course of the disease. Aim This study was undertaken to assess the haemostatic defects and platelet functions in patients of MPN. Materials and Methods One year prospective study was conducted at a tertiary care centre in North India in Department of Pathology in collaboration with Department of Clinical Haematology. All recently diagnosed cases of MPN along with 30 age and sex matched controls were included. Patients on antiplatelet drugs, antimyeloproliferative treatment, vitamin K agonists or antagonists, OCPs, Platelet count <1,00,000/μl, high grade fever, liver disease, pregnancy were excluded from this study. All the patients underwent screening investigations like CBC, peripheral smear evaluation, BT, PT, aPTT, Protein C and S measurement (clot based assay) and aggregation studies with ADP (5μM) (Optical Aggregometry with AGGRO/LINK 8 software and CHRONOLOG 700 aggregometer). Results In present study, 50 cases were included. There was an occult prothrombotic state, suggested by significantly (p<0.001) reduced levels of Protein C and Protein S, but no patient presented with frank thrombosis while 8 out of 50 patients had haemorrhagic manifestations ranging from subdural haematoma to pin point petechial haemorrhages. Patients of CML-CP, ET, PV, PMF, MPN-NOS showed significantly reduced maximal aggregation with ADP (5μM) when compared to control (p<0.001). MPV also showed a statistically significant increase in these patients. Conclusion Thrombohaemorrhagic complications significantly affect the morbidity and mortality of MPN patients. This can be assessed by the use of platelet aggregation studies, Protein C and S activities and other coagulation studies. Timely diagnosis

  9. Ab initio study of the optical properties of carbon nanotubes

    NASA Astrophysics Data System (ADS)

    Chang, Eric

    2006-03-01

    We present an ab initio study of the optical properties of carbon nanotubes. We use state-of-the-art electronic structure methods based on many-body perturbation theory to compute the optical absorption and resonance Raman spectra of large tubes which have up to 200 atoms [1,2]. Our symmetry-based method makes the study of large tubes feasible within the many- body framework and also allows us to understand the symmetry properties of the excitons and selection rules. We include a study of the so-called dark excitons which are crucial for understanding luminescence efficiency in carbon nanotubes. The mechanism that explains the dark-bright splitting can be understood within our symmetry-based approach. Finally, we present an analysis of the two-photon spectra for several carbon nanotubes, a theoretical analysis which, in conjunction with combined one- and two-photon experiments, allows one to measure the binding energy of excitons. We find in all cases that the excitonic binding energy is large, ranging from 0.5 to 0.9 eV depending on the diameter of the tube, and that the excitonic wavefunction is Wannier-like and extended over many atoms. Our studies for the one- and two-photon absorption and resonance Raman spectra have been fruitful for understanding the corresponding experiments. In particular, our theoretical results are in good agreement with one- and two-photon absorption experiments [3-5]. The results for resonance Raman show that such a spectroscopic technique is a good alternative to optical absorption since it allows for the selection of tubes of a given diameter while probing the same excited states. 1. E.K. Chang, G. Bussi, A. Ruini, and E. Molinari, Phys. Rev. Lett. 92, 196401 (2004). 2. E.K. Chang, G. Bussi, A. Ruini, and E. Molinari, Phys. Rev. B 72, 195423 (2005). 3. M. Y. Sfeir et al., Science 306, 1540 (2004). 4. J. Maultzsch et al., to be published in Phys. Rev. B, see also cond-mat/0505150. 5. Z. M. Li et. al., Phys. Rev. Lett. 87, 127401 (2001).

  10. Ab initio computational applications to complex biomolecular systems

    NASA Astrophysics Data System (ADS)

    Liang, Lei

    A series of biomaterial related systems---including water and DNA molecules---have been studied using ab initio (first-principles) methods. By investigating the properties of water as the preliminary step, the hydrogen bond (HB) interactions, which play important roles in biomolecules, were better understood from the quantum mechanical viewpoint. The calculated K-edge x-ray absorption near edge structure (XANES) spectra of all 340 oxygen atoms in the model have been accumulated to reproduce the experimental one. The spectra were shown to be very sensitive to the HB configurations of O atoms, which could be used to elucidate the subtle structural variations in complex biomolecules. The simulation of single-molecule DNA overstretching experiments under torsionally constrained condition has been carried out afterwards. The initial DNA models were stretched stepwisely and eventually gained an extension of 1.5-fold (150% x the original length). The variation of total energy, atomic configuration, and the electronic structure during this process were analyzed in details. At the extension of ˜1.3-fold, the ring opening reactions occurred in the backbones. The backbone nicks appeared at elongations of ˜1.40-fold. The whole process was accompanied by HB breaking and charge transfers. We have proposed an overstretched structure named O-DNA (Opened-DNA) to clarify the confusion in understanding the behavior of DNA under high force load. With more experiences gained, a comprehensive methodology revealing the underlying principles of bioprocesses from the quantum mechanical viewpoint eventually come up. For the purpose of better computational accuracy, the scheme of implementing the generalized gradient approximation (GGA) exchange-correlation functionals into the Orthogonalized Linear Combination of Atomic Orbitals (OLCAO) program suite has been discussed, and the computational efficiency has been analyzed correspondingly. Moreover, the parallel strategy for performing

  11. ab initio MD simulations of geomaterials with ~1000 atoms

    NASA Astrophysics Data System (ADS)

    Martin, G. B.; Kirtman, B.; Spera, F. J.

    2009-12-01

    In the last two decades, ab initio studies of materials using Density Functional Theory (DFT) have increased exponentially in popularity. DFT codes are now used routinely to simulate properties of geomaterials--mainly silicates and geochemically important metals such as Fe. These materials are ubiquitous in the Earth’s mantle and core and in terrestrial exoplanets. Because of computational limitations, most First Principles Molecular Dynamics (FPMD) calculations are done on systems of only ~100 atoms for a few picoseconds. While this approach can be useful for calculating physical quantities related to crystal structure, vibrational frequency, and other lattice-scale properties (especially in crystals), it is statistically marginal for duplicating physical properties of the liquid state like transport and structure. In MD simulations in the NEV ensemble, temperature (T), and pressure (P) fluctuations scale as N-1/2; small particle number (N) systems are therefore characterized by greater statistical state point location uncertainty than large N systems. Previous studies have used codes such as VASP where CPU time increases with N2, making calculations with N much greater than 100 impractical. SIESTA (Soler, et al. 2002) is a DFT code that enables electronic structure and MD computations on larger systems (N~103) by making some approximations, such as localized numerical orbitals, that would be useful in modeling some properties of geomaterials. Here we test the applicability of SIESTA to simulate geosilicates, both hydrous and anhydrous, in the solid and liquid state. We have used SIESTA for lattice calculations of brucite, Mg(OH)2, that compare very well to experiment and calculations using CRYSTAL, another DFT code. Good agreement between more classical DFT calculations and SIESTA is needed to justify study of geosilicates using SIESTA across a range of pressures and temperatures relevant to the Earth’s interior. Thus, it is useful to adjust parameters in

  12. Thermal hysteresis proteins.

    PubMed

    Barrett, J

    2001-02-01

    Extreme environments present a wealth of biochemical adaptations. Thermal hysteresis proteins (THPs) have been found in vertebrates, invertebrates, plants, bacteria and fungi and are able to depress the freezing point of water (in the presence of ice crystals) in a non-colligative manner by binding to the surface of nascent ice crystals. The THPs comprise a disparate group of proteins with a variety of tertiary structures and often no common sequence similarities or structural motifs. Different THPs bind to different faces of the ice crystal, and no single mechanism has been proposed to account for THP ice binding affinity and specificity. Experimentally THPs have been used in the cryopreservation of tissues and cells and to induce cold tolerance in freeze susceptible organisms. THPs represent a remarkable example of parallel and convergent evolution with different proteins being adapted for an anti-freeze role.

  13. Standardization or Localization: A Study of Online Learning Programmes by Tertiary Institutions in Ghana

    ERIC Educational Resources Information Center

    Djan, Josephine; George, Babu

    2016-01-01

    Many universities in Ghana have had a desire to ensure equitable access to formal tertiary education for the growing number of the working public who have sought to improve or better their educational status in tertiary institutions. For many of these working public or individuals, it is almost impossible to stay off work to enrol in these…

  14. Synchronous Communication and Higher-Order Thinking in a Tertiary Course in Occupational Therapy

    ERIC Educational Resources Information Center

    Penman, Merrolee; Lai, Kwok-Wing

    2003-01-01

    The use of the Internet to deliver courses at tertiary level is growing steadily, with the Internet being seen as the ideal solution to a range of issues facing educators in the 21st century. However, little is known as how best to use synchronous communication to support students' learning. This paper documents a New Zealand tertiary course…

  15. Entrepreneurship Education in Delta State Tertiary Institution as a Means of Achieving National Growth and Development

    ERIC Educational Resources Information Center

    Osakwe, Regina N.

    2015-01-01

    This study examined entrepreneurship education in Delta Sate tertiary institutions as a means of national growth and development. Two research questions were asked to guide the study. The population comprised all the 1,898 academic staff in eight tertiary institutions in the state. A sample of 800 lecturers was drawn through the multi stage and…

  16. Willing and Enabled: The Academic Outcomes of a Tertiary Enabling Program in Regional Australia

    ERIC Educational Resources Information Center

    Andrewartha, Lisa; Harvey, Andrew

    2014-01-01

    This paper examines the achievement levels of students undertaking the Tertiary Enabling Program (TEP) at La Trobe University. The TEP is an alternative pathway program that traverses multiple institutions, campuses, and disciplinary areas, and is designed to prepare a diverse student cohort for tertiary study. The Program integrates several…

  17. On Progress of Mass Tertiary Education: Case of Lebanon, Kenya and Oman

    ERIC Educational Resources Information Center

    Liu, Zhimin; Mutinda, Gladys

    2016-01-01

    Mass higher education is a huge force to be reckoned with and its existence, already in the expansion of tertiary institutions is undeniable. This study will focus on three countries: Lebanon, Kenya and Oman. The purpose of this study is to evaluate mass tertiary education progress in these countries. It will synthesize data results of gross…

  18. Inside the Collaborative Inter-Arts Improvisatory Process: Tertiary Music Students' Perspectives

    ERIC Educational Resources Information Center

    Blom, Diana

    2012-01-01

    While research has explored aspects of inter-arts collaboration at professional and primary level, there is little on inter-arts collaboration in the tertiary environment. This article explores aspects of the learning of tertiary music students undertaking a short-term collaborative inter-arts improvisation project with dance and theater peers,…

  19. Problem-Based Learning in Tertiary Education: Teaching Old "Dogs" New Tricks?

    ERIC Educational Resources Information Center

    Yeo, Roland K.

    2005-01-01

    Purpose--The paper sets out to explore the challenges of problem-based learning (PBL) in tertiary education and to propose a framework with implications for practice and learning. Design/Methodology/Approach--A total of 18 tertiary students divided into three groups participated in the focus group discussions. A quantitative instrument was used as…

  20. Is It Ever Too Late to Study? The Economic Returns on Late Tertiary Degrees in Sweden

    ERIC Educational Resources Information Center

    Hallsten, Martin

    2012-01-01

    This paper addresses the economic returns on tertiary degrees obtained in ages above 30 for individuals with upper-secondary schooling in light of current ideas on lifelong learning. Sweden is a case in point: Swedish tertiary education is open to older students, and labor market legislation supports employees who take a leave to study. The…

  1. A Study of People-Run Tertiary Education in South and West China

    ERIC Educational Resources Information Center

    Wang, Yongyang; Secombe, Margaret

    2004-01-01

    Chinese People-Run tertiary education institutions have grown dramatically in recent years. This paper aims to discuss the government deregulation policy and its impact on private tertiary education in China since the 1980s, particularly on south and west China, Gui Zhou province. Three colleges have been selected respectively from economically…

  2. A Comparison of Teacher and Lecturer Perspectives on the Transition from Secondary to Tertiary Mathematics Education

    ERIC Educational Resources Information Center

    Hong, Ye Yoon; Kerr, Suzanne; Klymchuk, Sergiy; McHardy, Johanna; Murphy, Priscilla; Spencer, Sue; Thomas, Michael O. J.; Watson, Peter

    2009-01-01

    The transition from school to tertiary study of mathematics comes under increasing scrutiny in research. This article reports on some findings from a project analysing the transition from secondary to tertiary education in mathematics. One key variable in this transition is the teacher or lecturer. This article deals with a small part of the data…

  3. The Singapore Global Schoolhouse: An Analysis of the Development of the Tertiary Education Landscape in Singapore

    ERIC Educational Resources Information Center

    Ng, Pak Tee; Tan, Charlene

    2010-01-01

    Purpose: This paper seeks to analyse the Singapore government's recent attempt to make Singapore a "Global Schoolhouse" by transforming its tertiary education sector. It aims to examine the government's attempt to promote greater diversity and autonomy in the tertiary education landscape; it also aims to examine the government's systems…

  4. Framework of Assessment for the Evaluation of Thinking Skills of Tertiary Level Students

    ERIC Educational Resources Information Center

    Heng, Chan Swee; Ziguang, Yan

    2015-01-01

    In the 21st century, students are required to master thinking skills in order to deal with many situations that arise in the tertiary environment which later would translate into the workplace. Nowadays, thinking skills play a vital role in tertiary education. To provide an approach for teachers, this paper identifies a 4-step model that can be…

  5. Assessment of Social Media Utilization and Study Habit of Students of Tertiary Institutions in Katsina State

    ERIC Educational Resources Information Center

    Olutola, Adekunle Thomas; Olatoye, Olufunke Omotoke; Olatoye, Rafiu Ademola

    2016-01-01

    This study investigated assessment of social media utilization and study habits of students of tertiary institutions in Katsina State. The descriptive survey design was adopted for this study. Three hundred and eighty-one (381) students' of tertiary institutions in Katsina State were randomly selected for the study. Researchers'-designed…

  6. Emotional Intelligence and the Conflict Resolution Repertoire of Couples in Tertiary Institutions in Imo State

    ERIC Educational Resources Information Center

    Nnodum, B. I.; Ugwuegbulam, C. N.; Agbaenyi, I. G.

    2016-01-01

    This study is a descriptive survey that investigated the relationship between emotional intelligence and conflict resolution repertoire of couples in tertiary institutions. A sample of 250 married people were drawn from the population of couples in tertiary institutions in Imo State. Two researcher made and validated instruments were used in…

  7. The Petasis Reaction: Microscale Synthesis of a Tertiary Amine Antifungal Analog

    ERIC Educational Resources Information Center

    Koroluk, Katherine J.; Jackson, Derek A.; Dicks, Andrew P.

    2012-01-01

    Students prepare a tertiary amine antifungal analog in an upper-level undergraduate organic laboratory. A microscale Petasis reaction is performed to generate a liquid compound readily characterized via IR and proton NMR spectroscopy. The biological relevance of the product is highlighted, with the tertiary amine scaffold being an important…

  8. Attitudes of Tertiary Students towards a Group Project in a Science Unit

    ERIC Educational Resources Information Center

    Bartle, Emma K.; Dook, Jan; Mocerino, Mauro

    2011-01-01

    This study focused on the attitude of tertiary students, in a science discipline, towards completing collaborative learning tasks. Two samples of students, enrolled in different units across different tertiary institutions, were considered. Students in sample 1 were required to work in small groups to produce an information poster on an allocated…

  9. The Teaching of English in Tasmania: Building Links between Senior Secondary and Tertiary Teachers

    ERIC Educational Resources Information Center

    Fletcher, Lisa; Clarke, Robert; Crane, Ralph; Gaby, Rosemary; Milthorpe, Naomi; Stark, Hannah

    2016-01-01

    This article tells the story of two projects initiated by the University of Tasmania's English program, which were designed to investigate and improve the pathway from pre-tertiary to tertiary English studies in the state: the First Year English Survey (2012-2014) and the Teaching of English in Tasmania Community of Practice (TETCoP). The authors…

  10. Who Has to Pay for Their Education? Evidence from European Tertiary Education

    ERIC Educational Resources Information Center

    Lim, Gieyoung; Kim, Chong-Uk

    2013-01-01

    In this article, we investigate a positive tertiary education externality in 18 European countries. Using a simple Cobb-Douglas-type production function with constant returns to scale, we find that there are positive spillover effects from tertiary education in European countries. According to our model prediction, on average, 72,000 new employed…

  11. Student Expectations of Tertiary Institutions: A Case Study of the Fiji National University (FNU)

    ERIC Educational Resources Information Center

    Khan, Shana Nigar

    2012-01-01

    Education is a human right and Fiji's tertiary education board recently declared that all tertiary institutions in Fiji must abide by the framework in order to meet student-customers' needs. The Fiji National University's (FNU's) destiny to be Fiji's leading higher education provider could be a reality if students and staff's expectations are…

  12. Tertiary Educators' Voices in Australia and South Africa: Experiencing and Engaging in African Music and Culture

    ERIC Educational Resources Information Center

    Joseph, Dawn

    2015-01-01

    Music tertiary educators can foster positive experiences that promote diversity, enhance intercultural and cross-cultural understanding through our teaching. Through findings of interview data of tertiary music educators' understandings of multicultural music practice at two South African universities and at an Australia university, I used…

  13. Transition from Senior Secondary to Tertiary Languages Study: Student Attitudes in Three Sydney Schools

    ERIC Educational Resources Information Center

    Moloney, Robyn; Harbon, Lesley

    2014-01-01

    This paper reports on a small study of attitudes to tertiary language study amongst senior secondary language learners in three independent New South Wales schools. The study examines what elements of preparedness may be the most effective in supporting transition to tertiary study for this sample of languages students. An analysis of survey data…

  14. Understanding and Enhancing Learning Communities in Tertiary Education in Science and Engineering

    ERIC Educational Resources Information Center

    Forret, Michael; Eames, Chris; Coll, Richard

    2007-01-01

    This research aims to build upon current research in the area of teaching and learning at tertiary level and explore the nature of learning communities in tertiary science and engineering. This study uses a sociocultural approach to address the following question: "What are teachers' and learners' perceptions of the nature of the learning…

  15. Benchmarking Australian and New Zealand University Meta-Policy in an Increasingly Regulated Tertiary Environment

    ERIC Educational Resources Information Center

    Freeman, Brigid

    2014-01-01

    The agencies responsible for tertiary education quality assurance in Australia and New Zealand have established regulatory regimes that increasingly intersect with tertiary institution policy management. An examination of university meta-policies identified good practices guiding university policy and policy management. Most Australian and half of…

  16. Why Do Tertiary Education Graduates Regret Their Study Program? A Comparison between Spain and the Netherlands

    ERIC Educational Resources Information Center

    Kucel, Aleksander; Vilalta-Bufi, Montserrat

    2013-01-01

    In this paper we investigate the determinants of regret of study program for tertiary education graduates in Spain and the Netherlands. These two countries differ in their educational system in terms of the tracking structure in their secondary education and the strength of their education-labor market linkages in tertiary education. Therefore, by…

  17. The Performance in Context Model: A 21st Century Tertiary Dance Teaching Pedagogy

    ERIC Educational Resources Information Center

    Stevens, Kym; Huddy, Avril

    2016-01-01

    Despite tertiary institutions acknowledging that reflective practice is an essential component of undergraduate dance teacher training, there is often a disparity between the tertiary students' reflective skills and the more sophisticated reflective ability needed to navigate the twenty-first-century workforce. This paper charts the evolution of a…

  18. Must a Developed Democratic State Fully Resource Any Tertiary Education for Its Citizens?

    ERIC Educational Resources Information Center

    Scholes, Vanessa

    2014-01-01

    This article takes a parsimonious conception of a developed State operating under a minimalist conception of democracy and asks whether such a State must fully resource any tertiary (post-compulsory) education for its citizens A key public policy barrier to arguing an absolute obligation for the State to resource any tertiary education is…

  19. A New Vision of Professional Development for Tertiary Teachers in Pakistan

    ERIC Educational Resources Information Center

    Chaudary, Imran Anjum

    2011-01-01

    Professional development for tertiary teachers in Pakistan is problematic. In most cases, it does not exist; and if it does, it is very brief, sporadic and traditional, and is conveyed off-site through top-down teacher training strategies. The Pakistani tertiary education sector is predominantly public in nature and consists of two main wings: the…

  20. Modelling of carbohydrate-aromatic interactions: ab initio energetics and force field performance

    NASA Astrophysics Data System (ADS)

    Spiwok, Vojtěch; Lipovová, Petra; Skálová, Tereza; Vondráčková, Eva; Dohnálek, Jan; Hašek, Jindřich; Králová, Blanka

    2005-12-01

    Aromatic amino acid residues are often present in carbohydrate-binding sites of proteins. These binding sites are characterized by a placement of a carbohydrate moiety in a stacking orientation to an aromatic ring. This arrangement is an example of CH/π interactions. Ab initio interaction energies for 20 carbohydrate-aromatic complexes taken from 6 selected ultra-high resolution X-ray structures of glycosidases and carbohydrate-binding proteins were calculated. All interaction energies of a pyranose moiety with a side chain of an aromatic residue were calculated as attractive with interaction energy ranging from -2.8 to -12.3 kcal/mol as calculated at the MP2/6-311+G(d) level. Strong attractive interactions were observed for a wide range of orientations of carbohydrate and aromatic ring as present in selected X-ray structures. The most attractive interaction was associated with apparent combination of CH/π interactions and classical H-bonds. The failure of Hartree-Fock method (interaction energies from +1.0 to -6.9 kcal/mol) can be explained by a dispersion nature of a majority of the studied complexes. We also present a comparison of interaction energies calculated at the MP2 level with those calculated using molecular mechanics force fields (OPLS, GROMOS, CSFF/CHARMM, CHEAT/CHARMM, Glycam/AMBER, MM2 and MM3). For a majority of force fields there was a strong correlation with MP2 values. RMSD between MP2 and force field values were 1.0 for CSFF/CHARMM, 1.2 for Glycam/AMBER, 1.2 for GROMOS, 1.3 for MM3, 1.4 for MM2, 1.5 for OPLS and to 2.3 for CHEAT/CHARMM (in kcal/mol). These results show that molecular mechanics approximates interaction energies very well and support an application of molecular mechanics methods in the area of glycochemistry and glycobiology.

  1. Protonation of trimethylamine N-oxide (TMAO) is required for stabilization of RNA tertiary structure.

    PubMed

    Denning, Elizabeth J; Thirumalai, D; MacKerell, Alexander D

    2013-12-31

    The osmolyte trimethylamine N-oxide (TMAO) stabilizes the tertiary but not the secondary structures of RNA. However, molecular dynamics simulations performed on the PreQ1 riboswitch showed that TMAO destabilizes the tertiary riboswitch structure, leading us to hypothesize that the presence of RNA could result in enhanced population of the protonated form, TMAOP. Constant pH replica exchange simulations showed that a percentage of TMAO is indeed protonated, thus contributing to the stability of the tertiary but not the secondary structure of PreQ1. TMAOP results in an unfavorable dehydration of phosphodiester backbone, which is compensated by electrostatic attraction between TMAOP and the phosphate groups. In addition, TMAOP interacts with specific sites in the tertiary RNA structure, mimicking the behavior of positively charged ions and of the PreQ1 ligand in stabilizing RNA. Finally, we predict that TMAO-induced stabilization of RNA tertiary structures should be strongly pH dependent.

  2. Protonation of Trimethylamine N-Oxide (TMAO) is required for stabilization of RNA tertiary structure

    PubMed Central

    Denning, Elizabeth J.; Thirumalai, D.; MacKerell, Alexander D.

    2013-01-01

    The osmolyte trimethylamine N-oxide (TMAO) stabilizes the tertiary but not the secondary structures of RNA. However, molecular dynamics simulations performed on the PreQl riboswitch showed that TMAO destabilizes the tertiary riboswitch structure, leading us to hypothesize that the presence of RNA could result in enhanced population of the protonated form, TMAOP. Constant pH replica exchange simulations showed that a percentage of TMAO is indeed protonated, thus contributing to the stability of the tertiary but not the secondary structure of PreQl. TMAOP results in an unfavorable dehydration of phosphodiester backbone, which is compensated by electrostatic attraction between TMAOP and the phosphate groups. In addition, TMAOP interacts with specific sites in the tertiary RNA structure, mimicking the behavior of positively charged ions and of the PreQl ligand in stabilizing RNA. Finally, we predict that TMAO-induced stabilization of RNA tertiary structures should be strongly pH dependent. PMID:24012912

  3. A protein structure data and analysis system.

    PubMed

    Tian, Hao; Sunderraman, Rajshekhar; Weber, Irene; Wang, Haibin; Yang, Hong

    2005-01-01

    In this paper, we present the design and implementation of a protein structure data and analysis system that is only used in the lab for analyzing the proprietary data. It is capable of storing public protein data, such as the data in Protein Data Bank (PDB) [1], and life scientists' proprietary data. This toolkit is targeted at life scientists who want to maintain proprietary protein structure data (may be incomplete), to search and query publicly known protein structures and to compare their structure data with others. The comparison functions can be used to find structure differences between two proteins at atom level, especially in mutant versions of proteins. The system can also be used as a tool of choosing better protein structure template in new protein's tertiary structure prediction. The system is developed in Java and the protein data is stored in a relational database (Oracle 9i).

  4. Tertiary care availability and adolescent pregnancy characteristics in Saudi Arabia

    PubMed Central

    Al-Kadri, Hanan M; Madkhali, Azza; Al-Kadi, Mohammed T; Bakhsh, Hanadi; Alruwaili, Nourah N; Tamim, Hani M

    2014-01-01

    Background In this study, we aimed to assess the rate of adolescent delivery in a Saudi tertiary health care center and to investigate the association between maternal age and fetal, neonatal, and maternal complications where a professional tertiary medical care service is provided. Methods A cross-sectional study was performed between 2005 and 2010 at King Abdulaziz Medical City, Riyadh, Saudi Arabia. All primigravid Saudi women ≥24 weeks gestation, carrying a singleton pregnancy, aged <35 years, and with no chronic medical problems were eligible. Women were divided into three groups based on their age, ie, group 1 (G1) <16 years, group 2 (G2) ≥16 up to 19 years, and group 3 (G3) ≥19 up to 35 years. Data were collected from maternal and neonatal medical records. We calculated the association between the different age groups and maternal characteristics, as well as events and complications during the antenatal period, labor, and delivery. Results The rates of adolescent delivery were 20.0 and 16.3 per 1,000 births in 2009 and 2010, respectively. Compared with G1 and G2 women, G3 women tended to have a higher body mass index, a longer first and second stage of labor, more blood loss at delivery, and a longer hospital stay. Compared with G1 and G2 women, respectively, G3 women had a 42% and a 67% increased risk of cesarean section, and had a 52% increased risk of instrumental delivery. G3 women were more likely to develop gestational diabetes or anemia, G2 women had a three-fold increased risk of premature delivery (odds ratio 2.81), and G3 neonates had a 50% increased overall risk of neonatal complications (odds ratio 0.51). Conclusion The adolescent birth rate appears to be low in central Saudi Arabia compared with other parts of the world. Excluding preterm delivery, adolescent delivery cared for in a tertiary health care center is not associated with a significantly increased medical risk to the mother, fetus, or neonate. The psychosocial effect of

  5. Tertiary facies architecture in the Kutai Basin, Kalimantan, Indonesia

    NASA Astrophysics Data System (ADS)

    Moss, Steve J.; Chambers, John L. C.

    1999-04-01

    The Kutai Basin occupies an area of extensive accommodation generated by Tertiary extension of an economic basement of mixed continental/oceanic affinity. The underlying crust to the basin is proposed here to be Jurassic and Cretaceous in age and is composed of ophiolitic units overlain by a younger Cretaceous turbidite fan, sourced from Indochina. A near complete Tertiary sedimentary section from Eocene to Recent is present within the Kutai Basin; much of it is exposed at the surface as a result of the Miocene and younger tectonic processes. Integration of geological and geophysical surface and subsurface data-sets has resulted in re-interpretation of the original facies distributions, relationships and arrangement of Tertiary sediments in the Kutai Basin. Although much lithostratigraphic terminology exists for the area, existing formation names can be reconciled with a simple model explaining the progressive tectonic evolution of the basin and illustrating the resulting depositional environments and their arrangements within the basin. The basin was initiated in the Middle Eocene in conjunction with rifting and likely sea floor spreading in the Makassar Straits. This produced a series of discrete fault-bounded depocentres in some parts of the basin, followed by sag phase sedimentation in response to thermal relaxation. Discrete Eocene depocentres have highly variable sedimentary fills depending upon position with respect to sediment source and palaeo water depths and geometries of the half-graben. This contrasts strongly with the more regionally uniform sedimentary styles that followed in the latter part of the Eocene and the Oligocene. Tectonic uplift documented along the southern and northern basin margins and related subsidence of the Lower Kutai Basin occurred during the Late Oligocene. This subsidence is associated with significant volumes of high-level andesitic-dacitic intrusive and associated volcanic rocks. Volcanism and uplift of the basin margins

  6. Is Tertiary Education Expansion Observable in Private Returns to Education? (Evidence for Middle and Eastern European Countries)

    ERIC Educational Resources Information Center

    Štefánik, Miroslav; Horvát, Peter

    2015-01-01

    This article provides evidence about differences in the recent tertiary education expansion in Austria, Germany, the Czech Republic, Poland and Slovakia. Focusing on these differences, we have examined private returns to tertiary education acquired before and after the tertiary education expansion. We compare these returns as follows: Austria with…

  7. An efficient method for electron-atom scattering using ab-initio calculations

    NASA Astrophysics Data System (ADS)

    Xu, Yuan; Yang, Yonggang; Xiao, Liantuan; Jia, Suotang

    2017-02-01

    We present an efficient method based on ab-initio calculations to investigate electron-atom scatterings. Those calculations profit from methods implemented in standard quantum chemistry programs. The new approach is applied to electron-helium scattering. The results are compared with experimental and other theoretical references to demonstrate the efficiency of our method.

  8. Ab Initio Studies of Chlorine Oxide and Nitrogen Oxide Species of Interest in Stratospheric Chemistry

    NASA Technical Reports Server (NTRS)

    Lee, Timothy J.; Langhoff, Stephen R. (Technical Monitor)

    1995-01-01

    The ability of modern state-of-the art ab initio quantum chemical techniques to characterize reliably the gas-phase molecular structure, vibrational spectrum, electronic spectrum, and thermal stability of chlorine oxide and nitrogen oxide species will be demonstrated by presentation of some example studies. In particular the geometrical structures, vibrational spectra, and heats of formation Of ClNO2, CisClONO, and trans-ClONO are shown to be in excellent agreement with the available experimental data, and where the experimental data are either not known or are inconclusive, the ab initio results are shown to fill in the gaps and to resolve the experimental controversy. In addition, ab initio studies in which the electronic spectra and the characterization of excited electronic states of ClONO2, HONO2, ClOOC17 ClOOH, and HOOH will also be presented. Again where available, the ab initio results are compared to experimental observations, and are used to aid in the interpretation of the experimental studies.

  9. Ab initio molecular dynamics simulations of a binary system of ionic liquids.

    PubMed

    Brüssel, Marc; Brehm, Martin; Voigt, Thomas; Kirchner, Barbara

    2011-08-14

    This work presents first insights into the structural properties of a binary mixture of ionic liquids from the perspective of ab initio molecular dynamics simulations. Simulations were carried out for a one-to-one mixture of 1-ethyl-3-methyl-imidazolium thiocyanate and 1-ethyl-3-methyl-imidazolium chloride and compared to pure 1-ethyl-3-methyl-imidazolium thiocyanate.

  10. Computer simulation of acetonitrile and methanol with ab initio-based pair potentials

    NASA Astrophysics Data System (ADS)

    Hloucha, M.; Sum, A. K.; Sandler, S. I.

    2000-10-01

    This study address the adequacy of ab initio pair interaction energy potentials for the prediction of macroscopic properties. Recently, Bukowski et al. [J. Phys. Chem. A 103, 7322 (1999)] performed a comprehensive study of the potential energy surfaces for several pairs of molecules using symmetry-adapted perturbation theory. These ab initio energies were then fit to an appropriate site-site potential form. In an attempt to bridge the gap between ab initio interaction energy information and macroscopic properties prediction, we performed Gibbs ensemble Monte Carlo (GEMC) simulations using their developed pair potentials for acetonitrile and methanol. The simulations results show that the phase behavior of acetonitrile is well described by just the pair interaction potential. For methanol, on the other hand, pair interactions are insufficient to properly predict its vapor-liquid phase behavior, and its saturated liquid density. We also explored simplified forms for representing the ab initio interaction energies by refitting a selected range of the data to a site-site Lennard-Jones and to a modified Buckingham (exponential-6) potentials plus Coulombic interactions. These were also used in GEMC simulations in order to evaluate the quality and computational efficiency of these different potential forms. It was found that the phase behavior prediction for acetonitrile and methanol are highly dependent on the details of the interaction potentials developed.

  11. Ab initio prediction of vacancy properties in concentrated alloys: The case of fcc Cu-Ni

    NASA Astrophysics Data System (ADS)

    Zhang, Xi; Sluiter, Marcel H. F.

    2015-05-01

    Vacancy properties in concentrated alloys continue to be of great interest because nowadays ab initio supercell simulations reach a scale where even defect properties in disordered alloys appear to be within reach. We show that vacancy properties cannot generally be extracted from supercell total energies in a consistent manner without a statistical model. Essential features of such a model are knowledge of the chemical potential and imposition of invariants. In the present work, we derive the simplest model that satisfies these requirements and we compare it with models in the literature. As illustration we compute ab initio vacancy properties of fcc Cu-Ni alloys as a function of composition and temperature. Ab initio density functional calculations were performed for SQS supercells at various compositions with and without vacancies. Various methods of extracting alloy vacancy properties were examined. A ternary cluster expansion yielded effective cluster interactions (ECIs) for the Cu-Ni-Vac system. Composition and temperature dependent alloy vacancy concentrations were obtained using statistical thermodynamic models with the ab initio ECIs. An Arrhenius analysis showed that the heat of vacancy formation was well represented by a linear function of temperature. The positive slope of the temperature dependence implies a negative configurational entropy contribution to the vacancy formation free energy in the alloy. These findings can be understood by considering local coordination effects.

  12. Matrix product operators, matrix product states, and ab initio density matrix renormalization group algorithms.

    PubMed

    Chan, Garnet Kin-Lic; Keselman, Anna; Nakatani, Naoki; Li, Zhendong; White, Steven R

    2016-07-07

    Current descriptions of the ab initio density matrix renormalization group (DMRG) algorithm use two superficially different languages: an older language of the renormalization group and renormalized operators, and a more recent language of matrix product states and matrix product operators. The same algorithm can appear dramatically different when written in the two different vocabularies. In this work, we carefully describe the translation between the two languages in several contexts. First, we describe how to efficiently implement the ab initio DMRG sweep using a matrix product operator based code, and the equivalence to the original renormalized operator implementation. Next we describe how to implement the general matrix product operator/matrix product state algebra within a pure renormalized operator-based DMRG code. Finally, we discuss two improvements of the ab initio DMRG sweep algorithm motivated by matrix product operator language: Hamiltonian compression, and a sum over operators representation that allows for perfect computational parallelism. The connections and correspondences described here serve to link the future developments with the past and are important in the efficient implementation of continuing advances in ab initio DMRG and related algorithms.

  13. Ab initio calculations on the inclusion complexation of cyclobis(paraquat- p-phenylene)

    NASA Astrophysics Data System (ADS)

    Zhang, Ke-Chun; Liu, Lei; Mu, Ting-Wei; Guo, Qing-Xiang

    2001-01-01

    Semiempirical PM3, ab initio HF/3-21g ∗, and DFT B3LYP/6-31g ∗ calculations in vacuum and in solution were performed on the inclusion complexation of cyclobis(paraquat- p-phenylene) with nine symmetric aromatic substrates. A good correlation was found between the theoretical stabilization energies and experimental free energy changes upon complexation.

  14. Dispersion Interactions between Rare Gas Atoms: Testing the London Equation Using ab Initio Methods

    ERIC Educational Resources Information Center

    Halpern, Arthur M.

    2011-01-01

    A computational chemistry experiment is described in which students can use advanced ab initio quantum mechanical methods to test the ability of the London equation to account quantitatively for the attractive (dispersion) interactions between rare gas atoms. Using readily available electronic structure applications, students can calculate the…

  15. Matrix product operators, matrix product states, and ab initio density matrix renormalization group algorithms

    NASA Astrophysics Data System (ADS)

    Chan, Garnet Kin-Lic; Keselman, Anna; Nakatani, Naoki; Li, Zhendong; White, Steven R.

    2016-07-01

    Current descriptions of the ab initio density matrix renormalization group (DMRG) algorithm use two superficially different languages: an older language of the renormalization group and renormalized operators, and a more recent language of matrix product states and matrix product operators. The same algorithm can appear dramatically different when written in the two different vocabularies. In this work, we carefully describe the translation between the two languages in several contexts. First, we describe how to efficiently implement the ab initio DMRG sweep using a matrix product operator based code, and the equivalence to the original renormalized operator implementation. Next we describe how to implement the general matrix product operator/matrix product state algebra within a pure renormalized operator-based DMRG code. Finally, we discuss two improvements of the ab initio DMRG sweep algorithm motivated by matrix product operator language: Hamiltonian compression, and a sum over operators representation that allows for perfect computational parallelism. The connections and correspondences described here serve to link the future developments with the past and are important in the efficient implementation of continuing advances in ab initio DMRG and related algorithms.

  16. An efficient and accurate molecular alignment and docking technique using ab initio quality scoring

    PubMed Central

    Füsti-Molnár, László; Merz, Kenneth M.

    2008-01-01

    An accurate and efficient molecular alignment technique is presented based on first principle electronic structure calculations. This new scheme maximizes quantum similarity matrices in the relative orientation of the molecules and uses Fourier transform techniques for two purposes. First, building up the numerical representation of true ab initio electronic densities and their Coulomb potentials is accelerated by the previously described Fourier transform Coulomb method. Second, the Fourier convolution technique is applied for accelerating optimizations in the translational coordinates. In order to avoid any interpolation error, the necessary analytical formulas are derived for the transformation of the ab initio wavefunctions in rotational coordinates. The results of our first implementation for a small test set are analyzed in detail and compared with published results of the literature. A new way of refinement of existing shape based alignments is also proposed by using Fourier convolutions of ab initio or other approximate electron densities. This new alignment technique is generally applicable for overlap, Coulomb, kinetic energy, etc., quantum similarity measures and can be extended to a genuine docking solution with ab initio scoring. PMID:18624561

  17. Mid-tertiary ash flow tuff cauldrons, southwestern New Mexico

    NASA Technical Reports Server (NTRS)

    Elston, W. E.

    1984-01-01

    Characteristics of 28 known or suspected mid-Tertiary ash-flow tuff cauldrons in New Mexico are described. The largest region is 40 km in diameter, and erosional and block faulting processes have exposed levels as far down as the plutonic roots. The study supports a five-stage process: precursor, caldera collapse, early post-collapse, volcanism, major ring-fracture volcanism, and hydrothermal activity. The stages can repeat or the process can stop at any stage. Post-collapse lavas fell into two categories: cauldron lavas, derived from shallow defluidized residues of caldera-forming ash flow tuff eruption, and framework lavas, evolved from a siliceous pluton below the cauldron complex. The youngest caldera was shallow and formed from asymmetric subsidence and collapse of the caldera walls.

  18. New exploration enhancements in S. Louisiana Tertiary sediments

    SciTech Connect

    Leach, W.G.

    1993-03-01

    The bulk of all oil and gas reserves in the South Louisiana Tertiary sands is concentrated near the top of abnormal pressure. Most hydrocarbons have pulsated up from older source beds by way of ruptured reservoirs. Vertical fluid migration has resulted in pressure-temperature crossovers or hot spots. Location of the hydrocarbons at the top of abnormal pressure is related to formation fracture strength. This relationship, distance from abnormal pressure, can be determined through a production distribution plot or maximum hydrocarbon window (MHW) technique. The MHW technique can be used in conjunction with an abnormal pressure map to determine the most optimum hydrocarbon environment or drilling depth. Identification of hot spots helps to further upgrade the prospect.

  19. Depositional relations of cretaceous and Lower Tertiary Rocks, Northeastern Alaska

    SciTech Connect

    Molenaar, C.M.

    1983-07-01

    Analysis of depositional environments, new paleontologic data, and analogy with depositional patterns observed in areas to the west all indicate the need for revision of Cretaceous and lower Tertiary stratigraphy in northeastern Alaska. In the Sadlerochit Mountains area of the Arctic National Wildlife Refuge, the northernderived (Ellesmerian), late Neocomian Kemik Sandstone Member and organic-rich pebble shale member of the Kongakut Formation unconformably overlie Jurassic and Triassic rocks. The unconformity, which is of midNeocomian age, is present throughout northernmost Alaska and passes southward into a conformable shelf sequence. After pebble shale deposition, the depositional pattern is simply one of progradational basin filling from a southern (Brookian) provenance. This pattern is represented in vertical sequence initially by deep-marine basinal deposits succeeded by prodelta slope shales, and ultimately by deltaic deposits that prograded to the east or northeast in a predictable fashion over most of the area.

  20. IRIS Toxicological Review of Ethyl Tertiary Butyl Ether (Etbe) ...

    EPA Pesticide Factsheets

    In September 2016, the U.S. Environmental Protection Agency's (USEPA) released the draft Integrated Risk Information System (IRIS) Toxicological Review of Ethyl Tertiary Butyl Ether (ETBE). Consistent with the 2013 IRIS Enhancements, draft IRIS assessments are released prior to external peer review for a 60-day public comment period and discussed at an upcoming public science meeting. Accordingly, the toxicological review, supplementary information, and other materials pertaining to this draft assessment are posted on this site. This material is being released for public viewing and comment prior to a public meeting, providing an opportunity for the IRIS Program to engage in early discussions with stakeholders and the public on data that may be used to identify adverse health effects and characterize exposure-response relationships.