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Sample records for initio protein tertiary

  1. AB Initio Protein Tertiary Structure Prediction: Comparative-Genetic Algorithm with Graph Theoretical Methods

    SciTech Connect

    Gregurick, S. K.

    2001-04-20

    During the period from September 1, 1998 until September 1, 2000 I was awarded a Sloan/DOE postdoctoral fellowship to work in collaboration with Professor John Moult at the Center for Advanced Research in Biotechnology (CARB). Our research project, ''Ab Initio Protein Tertiary Structure Prediction and a Comparative Genetic algorithm'', yielded promising initial results. In short, the project is designed to predict the native fold, or native tertiary structure, of a given protein by inputting only the primary sequence of the protein (one or three letter code). The algorithm is based on a general learning, or evolutionary algorithm and is called Genetic Algorithm (GAS). In our particular application of GAS, we search for native folds, or lowest energy structures, using two different descriptions for the interactions of the atoms and residues in a given protein sequence. One potential energy function is based on a free energy description, while the other function is a threading potential derived by Moult and Samudrala. This modified genetic algorithm was loosely termed a Comparative Genetic Algorithm and was designed to search for native folded structures on both potential energy surfaces, simultaneously. We tested the algorithm on a series of peptides ranging from 11 to 15 residues in length, which are thought to be independent folding units and thereby will fold to native structures independent of the larger protein environment. Our initial results indicated a modest increase in accuracy, as compared to a standard Genetic Algorithm. We are now in the process of improving the algorithm to increase the sensitivity to other inputs, such as secondary structure requirements. The project did not involve additional students and as of yet, the work has not been published.

  2. Macromolecular ab initio phasing enforcing secondary and tertiary structure.

    PubMed

    Millán, Claudia; Sammito, Massimo; Usón, Isabel

    2015-01-01

    Ab initio phasing of macromolecular structures, from the native intensities alone with no experimental phase information or previous particular structural knowledge, has been the object of a long quest, limited by two main barriers: structure size and resolution of the data. Current approaches to extend the scope of ab initio phasing include use of the Patterson function, density modification and data extrapolation. The authors' approach relies on the combination of locating model fragments such as polyalanine α-helices with the program PHASER and density modification with the program SHELXE. Given the difficulties in discriminating correct small substructures, many putative groups of fragments have to be tested in parallel; thus calculations are performed in a grid or supercomputer. The method has been named after the Italian painter Arcimboldo, who used to compose portraits out of fruit and vegetables. With ARCIMBOLDO, most collections of fragments remain a 'still-life', but some are correct enough for density modification and main-chain tracing to reveal the protein's true portrait. Beyond α-helices, other fragments can be exploited in an analogous way: libraries of helices with modelled side chains, β-strands, predictable fragments such as DNA-binding folds or fragments selected from distant homologues up to libraries of small local folds that are used to enforce nonspecific tertiary structure; thus restoring the ab initio nature of the method. Using these methods, a number of unknown macromolecules with a few thousand atoms and resolutions around 2 Å have been solved. In the 2014 release, use of the program has been simplified. The software mediates the use of massive computing to automate the grid access required in difficult cases but may also run on a single multicore workstation (http://chango.ibmb.csic.es/ARCIMBOLDO_LITE) to solve straightforward cases.

  3. Macromolecular ab initio phasing enforcing secondary and tertiary structure.

    PubMed

    Millán, Claudia; Sammito, Massimo; Usón, Isabel

    2015-01-01

    Ab initio phasing of macromolecular structures, from the native intensities alone with no experimental phase information or previous particular structural knowledge, has been the object of a long quest, limited by two main barriers: structure size and resolution of the data. Current approaches to extend the scope of ab initio phasing include use of the Patterson function, density modification and data extrapolation. The authors' approach relies on the combination of locating model fragments such as polyalanine α-helices with the program PHASER and density modification with the program SHELXE. Given the difficulties in discriminating correct small substructures, many putative groups of fragments have to be tested in parallel; thus calculations are performed in a grid or supercomputer. The method has been named after the Italian painter Arcimboldo, who used to compose portraits out of fruit and vegetables. With ARCIMBOLDO, most collections of fragments remain a 'still-life', but some are correct enough for density modification and main-chain tracing to reveal the protein's true portrait. Beyond α-helices, other fragments can be exploited in an analogous way: libraries of helices with modelled side chains, β-strands, predictable fragments such as DNA-binding folds or fragments selected from distant homologues up to libraries of small local folds that are used to enforce nonspecific tertiary structure; thus restoring the ab initio nature of the method. Using these methods, a number of unknown macromolecules with a few thousand atoms and resolutions around 2 Å have been solved. In the 2014 release, use of the program has been simplified. The software mediates the use of massive computing to automate the grid access required in difficult cases but may also run on a single multicore workstation (http://chango.ibmb.csic.es/ARCIMBOLDO_LITE) to solve straightforward cases. PMID:25610631

  4. Macromolecular ab initio phasing enforcing secondary and tertiary structure

    PubMed Central

    Millán, Claudia; Sammito, Massimo; Usón, Isabel

    2015-01-01

    Ab initio phasing of macromolecular structures, from the native intensities alone with no experimental phase information or previous particular structural knowledge, has been the object of a long quest, limited by two main barriers: structure size and resolution of the data. Current approaches to extend the scope of ab initio phasing include use of the Patterson function, density modification and data extrapolation. The authors’ approach relies on the combination of locating model fragments such as polyalanine α-helices with the program PHASER and density modification with the program SHELXE. Given the difficulties in discriminating correct small substructures, many putative groups of fragments have to be tested in parallel; thus calculations are performed in a grid or supercomputer. The method has been named after the Italian painter Arcimboldo, who used to compose portraits out of fruit and vegetables. With ARCIMBOLDO, most collections of fragments remain a ‘still-life’, but some are correct enough for density modification and main-chain tracing to reveal the protein’s true portrait. Beyond α-helices, other fragments can be exploited in an analogous way: libraries of helices with modelled side chains, β-strands, predictable fragments such as DNA-binding folds or fragments selected from distant homologues up to libraries of small local folds that are used to enforce nonspecific tertiary structure; thus restoring the ab initio nature of the method. Using these methods, a number of unknown macromolecules with a few thousand atoms and resolutions around 2 Å have been solved. In the 2014 release, use of the program has been simplified. The software mediates the use of massive computing to automate the grid access required in difficult cases but may also run on a single multicore workstation (http://chango.ibmb.csic.es/ARCIMBOLDO_LITE) to solve straightforward cases. PMID:25610631

  5. 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.

  6. The MULTICOM protein tertiary structure prediction system.

    PubMed

    Li, Jilong; Bhattacharya, Debswapna; Cao, Renzhi; Adhikari, Badri; Deng, Xin; Eickholt, Jesse; Cheng, Jianlin

    2014-01-01

    With the expansion of genomics and proteomics data aided by the rapid progress of next-generation sequencing technologies, computational prediction of protein three-dimensional structure is an essential part of modern structural genomics initiatives. Prediction of protein structure through understanding of the theories behind protein sequence-structure relationship, however, remains one of the most challenging problems in contemporary life sciences. Here, we describe MULTICOM, a multi-level combination technique, intended to predict moderate- to high-resolution structure of a protein through a novel approach of combining multiple sources of complementary information derived from the experimentally solved protein structures in the Protein Data Bank. The MULTICOM web server is freely available at http://sysbio.rnet.missouri.edu/multicom_toolbox/.

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

    PubMed Central

    Spencer, Matt; Eickholt, Jesse; Cheng, Jianlin

    2014-01-01

    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% 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 data set of 198 proteins, achieving a Q3 accuracy of 80.7% and a Sov accuracy of 74.2%. PMID:25750595

  8. 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.

  9. From Ramachandran Maps to Tertiary Structures of Proteins.

    PubMed

    DasGupta, Debarati; Kaushik, Rahul; Jayaram, B

    2015-08-27

    Sequence to structure of proteins is an unsolved problem. A possible coarse grained resolution to this entails specification of all the torsional (Φ, Ψ) angles along the backbone of the polypeptide chain. The Ramachandran map quite elegantly depicts the allowed conformational (Φ, Ψ) space of proteins which is still very large for the purposes of accurate structure generation. We have divided the allowed (Φ, Ψ) space in Ramachandran maps into 27 distinct conformations sufficient to regenerate a structure to within 5 Å from the native, at least for small proteins, thus reducing the structure prediction problem to a specification of an alphanumeric string, i.e., the amino acid sequence together with one of the 27 conformations preferred by each amino acid residue. This still theoretically results in 27(n) conformations for a protein comprising "n" amino acids. We then investigated the spatial correlations at the two-residue (dipeptide) and three-residue (tripeptide) levels in what may be described as higher order Ramachandran maps, with the premise that the allowed conformational space starts to shrink as we introduce neighborhood effects. We found, for instance, for a tripeptide which potentially can exist in any of the 27(3) "allowed" conformations, three-fourths of these conformations are redundant to the 95% confidence level, suggesting sequence context dependent preferred conformations. We then created a look-up table of preferred conformations at the tripeptide level and correlated them with energetically favorable conformations. We found in particular that Boltzmann probabilities calculated from van der Waals energies for each conformation of tripeptides correlate well with the observed populations in the structural database (the average correlation coefficient is ∼0.8). An alpha-numeric string and hence the tertiary structure can be generated for any sequence from the look-up table within minutes on a single processor and to a higher level of accuracy

  10. 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.

  11. 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

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

    SciTech Connect

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

    2015-02-01

    Two ab initio modelling programs solve complementary sets of targets, enhancing the success of AMPLE with small proteins. 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.

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

    PubMed Central

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

    2015-01-01

    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. PMID:25664744

  14. 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.

  15. Assessment of Immunologically Relevant Dynamic Tertiary Structural Features of the HIV-1 V3 Loop Crown R2 Sequence by ab initio Folding

    PubMed Central

    Almond, David; Cardozo, Timothy

    2010-01-01

    The antigenic diversity of HIV-1 has long been an obstacle to vaccine design, and this variability is especially pronounced in the V3 loop of the virus' surface envelope glycoprotein. We previously proposed that the crown of the V3 loop, although dynamic and sequence variable, is constrained throughout the population of HIV-1 viruses to an immunologically relevant β-hairpin tertiary structure. Importantly, there are thousands of different V3 loop crown sequences in circulating HIV-1 viruses, making 3D structural characterization of trends across the diversity of viruses difficult or impossible by crystallography or NMR. Our previous successful studies with folding of the V3 crown1, 2 used the ab initio algorithm 3 accessible in the ICM-Pro molecular modeling software package (Molsoft LLC, La Jolla, CA) and suggested that the crown of the V3 loop, specifically from positions 10 to 22, benefits sufficiently from the flexibility and length of its flanking stems to behave to a large degree as if it were an unconstrained peptide freely folding in solution. As such, rapid ab initio folding of just this portion of the V3 loop of any individual strain of the 60,000+ circulating HIV-1 strains can be informative. Here, we folded the V3 loop of the R2 strain to gain insight into the structural basis of its unique properties. R2 bears a rare V3 loop sequence thought to be responsible for the exquisite sensitivity of this strain to neutralization by patient sera and monoclonal antibodies4, 5. The strain mediates CD4-independent infection and appears to elicit broadly neutralizing antibodies. We demonstrate how evaluation of the results of the folding can be informative for associating observed structures in the folding with the immunological activities observed for R2. PMID:20864931

  16. 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.

  17. Incorporating Ab Initio energy into threading approaches for protein structure prediction

    PubMed Central

    2011-01-01

    Background Native structures of proteins are formed essentially due to the combining effects of local and distant (in the sense of sequence) interactions among residues. These interaction information are, explicitly or implicitly, encoded into the scoring function in protein structure prediction approaches—threading approaches usually measure an alignment in the sense that how well a sequence adopts an existing structure; while the energy functions in Ab Initio methods are designed to measure how likely a conformation is near-native. Encouraging progress has been observed in structure refinement where knowledge-based or physics-based potentials are designed to capture distant interactions. Thus, it is interesting to investigate whether distant interaction information captured by the Ab Initio energy function can be used to improve threading, especially for the weakly/distant homologous templates. Results In this paper, we investigate the possibility to improve alignment-generating through incorporating distant interaction information into the alignment scoring function in a nontrivial approach. Specifically, the distant interaction information is introduced through employing an Ab Initio energy function to evaluate the “partial” decoy built from an alignment. Subsequently, a local search algorithm is utilized to optimize the scoring function. Experimental results demonstrate that with distant interaction items, the quality of generated alignments are improved on 68 out of 127 query-template pairs in Prosup benchmark. In addition, compared with state-to-art threading methods, our method performs better on alignment accuracy comparison. Conclusions Incorporating Ab Initio energy functions into threading can greatly improve alignment accuracy. PMID:21342587

  18. 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.

  19. 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

  20. Sucrose prevents protein fibrillation through compaction of the tertiary structure but hardly affects the secondary structure.

    PubMed

    Estrela, Nídia; Franquelim, Henri G; Lopes, Carlos; Tavares, Evandro; Macedo, Joana A; Christiansen, Gunna; Otzen, Daniel E; Melo, Eduardo P

    2015-11-01

    Amyloid fibers, implicated in a wide range of diseases, are formed when proteins misfold and stick together in long rope-like structures. As a natural mechanism, osmolytes can be used to modulate protein aggregation pathways with no interference with other cellular functions. The osmolyte sucrose delays fibrillation of the ribosomal protein S6 leading to softer and less shaped-defined fibrils. The molecular mechanism used by sucrose to delay S6 fibrillation was studied based on the two-state unfolding kinetics of the secondary and tertiary structures. It was concluded that the delay in S6 fibrillation results from stabilization and compaction of the slightly expanded tertiary native structure formed under fibrillation conditions. Interestingly, this compaction extends to almost all S6 tertiary structure but hardly affects its secondary structure. The part of the S6 tertiary structure that suffered more compaction by sucrose is known to be the first part to unfold, indicating that the native S6 has entered the unfolding pathway under fibrillation conditions.

  1. Ab Initio Protein Structure Assembly Using Continuous Structure Fragments and Optimized Knowledge-based Force Field

    PubMed Central

    Xu, Dong; Zhang, Yang

    2012-01-01

    Ab initio protein folding is one of the major unsolved problems in computational biology due 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 non-homologous proteins. Although no global templates are used and all fragments from experimental structures with template modeling score (TM-score) >0.5 are excluded, QUARK can successfully construct 3D models of correct folds in 1/3 cases of short proteins up to 100 residues. In the ninth community-wide Critical Assessment of protein Structure Prediction (CASP9) 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 (GDT-TS) scores in the free modeling (FM) category. Although ab initio protein folding remains a significant challenge, these data demonstrate new progress towards the solution of the most important problem in the field. PMID:22411565

  2. 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.

  3. 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.

  4. Rapid search for tertiary fragments reveals protein sequence–structure relationships

    PubMed Central

    Zhou, Jianfu; Grigoryan, Gevorg

    2015-01-01

    Finding backbone substructures from the Protein Data Bank that match an arbitrary query structural motif, composed of multiple disjoint segments, is a problem of growing relevance in structure prediction and protein design. Although numerous protein structure search approaches have been proposed, methods that address this specific task without additional restrictions and on practical time scales are generally lacking. Here, we propose a solution, dubbed MASTER, that is both rapid, enabling searches over the Protein Data Bank in a matter of seconds, and provably correct, finding all matches below a user-specified root-mean-square deviation cutoff. We show that despite the potentially exponential time complexity of the problem, running times in practice are modest even for queries with many segments. The ability to explore naturally plausible structural and sequence variations around a given motif has the potential to synthesize its design principles in an automated manner; so we go on to illustrate the utility of MASTER to protein structural biology. We demonstrate its capacity to rapidly establish structure–sequence relationships, uncover the native designability landscapes of tertiary structural motifs, identify structural signatures of binding, and automatically rewire protein topologies. Given the broad utility of protein tertiary fragment searches, we hope that providing MASTER in an open-source format will enable novel advances in understanding, predicting, and designing protein structure. PMID:25420575

  5. 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.

  6. 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.

  7. Ab initio MO studies of interaction mechanisms of Protein Kinase C with cell membranes

    NASA Astrophysics Data System (ADS)

    Tsuda, Ken-ichiro; Kaneko, Hiroki; Shimada, Jiro; Takada, Toshikazu

    2001-12-01

    Protein Kinase C (PKC) is a family of regulatory enzymes. It is considered that binding with phorbol ester which are PKC activators, increases affinity of PKC for the membranes and consequently induces its conformation change. Electrostatic interactions between PKC and the membrane is assumed to be important, and performed ab initio MO calculations of one domain of PKC consisting of 50 amino acids and its complex with the ester is performed to investigate how the electrostatic potential of PKC changes through docking with the substrate. From the calculation, it is shown that the electrostatic potential of PKC near the binding site is dramatically affected through the binding, suggesting attractive interactions with the cell membrane.

  8. Ab initio molecular-replacement phasing for symmetric helical membrane proteins

    PubMed Central

    Strop, Pavel; Brzustowicz, Michael R.; Brunger, Axel T.

    2007-01-01

    Obtaining phases for X-ray diffraction data can be a rate-limiting step in structure determination. Taking advantage of constraints specific to membrane proteins, an ab initio molecular-replacement method has been developed for phasing X-ray diffraction data for symmetric helical membrane proteins without prior knowledge of their structure or heavy-atom derivatives. The described method is based on generating all possible orientations of idealized transmembrane helices and using each model in a molecular-replacement search. The number of models is significantly reduced by taking advantage of geometrical and structural restraints specific to membrane proteins. The top molecular-replacement results are evaluated based on noncrystallographic symmetry (NCS) map correlation, OMIT map correlation and R free value after refinement of a polyalanine model. The feasibility of this approach is illustrated by phasing the mechanosensitive channel of large conductance (MscL) with only 4 Å diffraction data. No prior structural knowledge was used other than the number of transmembrane helices. The search produced the correct spatial organization and the position in the asymmetric unit of all transmembrane helices of MscL. The resulting electron-density maps were of sufficient quality to automatically build all helical segments of MscL including the cytoplasmic domain. The method does not require high-resolution diffraction data and can be used to obtain phases for symmetrical helical membrane proteins with one or two helices per monomer. PMID:17242512

  9. 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.

  10. 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

  11. 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.

  12. A Parallel Framework for Multipoint Spiral Search in ab Initio Protein Structure Prediction

    PubMed Central

    Rashid, Mahmood A.; Newton, M. A. Hakim; Hoque, Md Tamjidul; Sattar, Abdul

    2014-01-01

    Protein structure prediction is computationally a very challenging problem. A large number of existing search algorithms attempt to solve the problem by exploring possible structures and finding the one with the minimum free energy. However, these algorithms perform poorly on large sized proteins due to an astronomically wide search space. In this paper, we present a multipoint spiral search framework that uses parallel processing techniques to expedite exploration by starting from different points. In our approach, a set of random initial solutions are generated and distributed to different threads. We allow each thread to run for a predefined period of time. The improved solutions are stored threadwise. When the threads finish, the solutions are merged together and the duplicates are removed. A selected distinct set of solutions are then split to different threads again. In our ab initio protein structure prediction method, we use the three-dimensional face-centred-cubic lattice for structure-backbone mapping. We use both the low resolution hydrophobic-polar energy model and the high-resolution 20 × 20 energy model for search guiding. The experimental results show that our new parallel framework significantly improves the results obtained by the state-of-the-art single-point search approaches for both energy models on three-dimensional face-centred-cubic lattice. We also experimentally show the effectiveness of mixing energy models within parallel threads. PMID:24744779

  13. 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

  14. Structural difficulty index: a reliable measure for modelability of protein tertiary structures.

    PubMed

    Kaushik, Rahul; Jayaram, B

    2016-09-01

    The success in protein tertiary-structure prediction is considered to be a function of coverage and similarity/identity of their sequences with suitable templates in the structural databases. However, this measure of modelability of a protein sequence into its structure may be misleading. Addressing this limitation, we propose here a 'structural difficulty (SD)' index, which is derived from secondary structures, homology and physicochemical features of protein sequences. The SD index reflects the capability of predicting accurate structures and helps to assess the potential for developing proteome level structural databases for various organisms with some of the best methodologies available currently. For instance, the plausibility of populating the structural database of human proteome with reliable quality structures under 3 Å root mean square deviation from the corresponding natives is found to be ∼37% of a total of 11 084 manually curated soluble proteins and ∼64% for all annotated and reviewed unique soluble protein (344 661 sequences) of UniProtKB. Also for 77 human pathogenic viruses comprising 2365 globular viral proteins out of which only 162 structures are solved experimentally, SD index scores 1336 proteins in the modelable zone. Availability of reliable protein structures may prove a crucial aid in developing species-wise structural proteomic databases for accelerating function annotation and for drug development endeavors.

  15. Ab initio structure determination and refinement of a scorpion protein toxin.

    PubMed

    Smith, G D; Blessing, R H; Ealick, S E; Fontecilla-Camps, J C; Hauptman, H A; Housset, D; Langs, D A; Miller, R

    1997-09-01

    The structure of toxin II from the scorpion Androctonus australis Hector has been determined ab initio by direct methods using SnB at 0.96 A resolution. For the purpose of this structure redetermination, undertaken as a test of the minimal function and the SnB program, the identity and sequence of the protein was withheld from part of the research team. A single solution obtained from 1 619 random atom trials was clearly revealed by the bimodal distribution of the final value of the minimal function associated with each individual trial. Five peptide fragments were identified from a conservative analysis of the initial E-map, and following several refinement cycles with X-PLOR, a model was built of the complete structure. At the end of the X-PLOR refinement, the sequence was compared with the published sequence and 57 of the 64 residues had been correctly identified. Two errors in sequence resulted from side chains with similar size while the rest of the errors were a result of severe disorder or high thermal motion in the side chains. Given the amino-acid sequence, it is estimated that the initial E-map could have produced a model containing 99% of all main-chain and 81% of side-chain atoms. The structure refinement was completed with PROFFT, including the contributions of protein H atoms, and converged at a residual of 0.158 for 30 609 data with F >or= 2sigma(F) in the resolution range 8.0-0.964 A. The final model consisted of 518 non-H protein atoms (36 disordered), 407 H atoms, and 129 water molecules (43 with occupancies less than unity). This total of 647 non-H atoms represents the largest light-atom structure solved to date.

  16. 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).

  17. 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

    2014-04-01

    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.

  18. ANS Fluorescence Detects Widespread Perturbations of Protein Tertiary Structure in Ice

    PubMed Central

    Gabellieri, Edi; Strambini, Giovanni B.

    2006-01-01

    Freeze-induced perturbations of the protein native fold are poorly understood owing to the difficulty of monitoring their structure in ice. Here, we report that binding of the fluorescence probe 1-anilino-8-naphthalene sulfonate (ANS) to proteins in ice can provide a general monitor of ice-induced alterations of their tertiary structure. Experiments conducted with copper-free azurin from Pseudomonas aeruginosa and mutants I7S, F110S, and C3A/C26A correlate the magnitude of the ice-induced perturbation, as inferred from the extent of ANS binding, to the plasticity of the globular fold, increasing with less stable globular folds as well as when the flexibility of the macromolecule is enhanced. The distortion of the native structure inferred from ANS binding was found to draw a parallel with the extent of irreversible denaturation by freeze-thawing, suggesting that these altered conformations play a direct role on freeze damage. ANS binding experiments, extended to a set of proteins including serum albumin, α-amylase, β-galactosidase, alcohol dehydrogenase from horse liver, alcohol dehydrogenase from yeast, lactic dehydrogenase, and aldolase, confirmed that a stressed condition of the native fold in the frozen state appears to be general to most proteins and pointed out that oligomers tend to be more labile than monomers presumably because the globular fold can be further destabilized by subunit dissociation. The results of this study suggest that the ANS binding method may find practical utility in testing the effectiveness of various additives employed in protein formulations as well as to devise safer freeze-drying protocols of pharmaceutical proteins. PMID:16461396

  19. MEGADOCK: an all-to-all protein-protein interaction prediction system using tertiary structure data.

    PubMed

    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

  20. Predictions of Tertiary Structures of α-Helical Membrane Proteins by Replica-Exchange Method with Consideration of Helix Deformations

    NASA Astrophysics Data System (ADS)

    Urano, Ryo; Kokubo, Hironori; Okamoto, Yuko

    2015-08-01

    We propose an improved prediction method of the tertiary structures of α-helical membrane proteins based on the replica-exchange method by taking into account helix deformations. Our method has wide applications because transmembrane helices of native membrane proteins are often distorted. In order to test the effectiveness of the present method, we applied it to the structure predictions of glycophorin A and phospholamban. The results were in good agreement with experiments.

  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. 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).

  3. Tertiary Dentin Formation after Indirect Pulp Capping Using Protein CPNE7.

    PubMed

    Choung, H W; Lee, D S; Lee, Ji-Hyun; Shon, W J; Lee, Jong-Ho; Ku, Y; Park, J C

    2016-07-01

    If there is a partial loss of dentin, the exposed dentinal surface should be protected by an indirect pulp capping (IPC) procedure to preserve pulp vitality and prevent symptoms of dentin hypersensitivity. In our previous study, copine7 (CPNE7) induced odontoblast differentiation in vitro and promoted dentin formation in vivo. The aim of this study was to investigate the possibility of IPC therapy using the CPNE7 protein at the exposed dentinal surface and the resulting effects on tertiary dentin formation in a beagle model. CPNE7 promoted mineralization of odontoblasts and had high calcium ion-binding capacity. The in vivo IPC model with canine teeth showed that regeneration of physiologic reactionary dentin with dentinal tubule structures was clearly observed beneath the remaining dentin in the CPNE7 group, whereas irregular features of reparative dentin were generated in the mineral trioxide aggregate (MTA) group. The CPNE7+MTA group also showed typical reactionary dentin without reparative dentin, showing synergistic effects of CPNE7 with MTA. A scanning electron microscopy analysis showed that dentinal tubules beneath the original dentin were occluded by the deposition of peritubular dentin in the CPNE7 and CPNE7+MTA groups, whereas those in the control group were opened. Therefore, CPNE7 may be able to serve as a novel IPC material and improve symptoms of dentin hypersensitivity. PMID:27013639

  4. Beyond BLASTing: Tertiary and Quaternary Structure Analysis Helps Identify Major Vault Proteins

    PubMed Central

    Daly, Toni K.; Sutherland-Smith, Andrew J.; Penny, David

    2013-01-01

    We examine the advantages of going beyond sequence similarity and use both protein three-dimensional (3D) structure prediction and then quaternary structure (docking) of inferred 3D structures to help evaluate whether comparable sequences can fold into homologous structures with sufficient lateral associations for quaternary structure formation. Our test case is the major vault protein (MVP) that oligomerizes in multiple copies to form barrel-like vault particles and is relatively widespread among eukaryotes. We used the iterative threading assembly refinement server (I-TASSER) to predict whether putative MVP sequences identified by BLASTp and PSI Basic Local Alignment Search Tool are structurally similar to the experimentally determined rodent MVP tertiary structures. Then two identical predicted quaternary structures from I-TASSER are analyzed by RosettaDock to test whether a pair-wise association occurs, and hence whether the oligomeric vault complex is likely to form for a given MVP sequence. Positive controls for the method are the experimentally determined rat (Rattus norvegicus) vault X-ray crystal structure and the purple sea urchin (Strongylocentrotus purpuratus) MVP sequence that forms experimentally observed vaults. These and two kinetoplast MVP structural homologs were predicted with high confidence value, and RosettaDock predicted that these MVP sequences would dock laterally and therefore could form oligomeric vaults. As the negative control, I-TASSER did not predict an MVP-like structure from a randomized rat MVP sequence, even when constrained to the rat MVP crystal structure (PDB:2ZUO), thus further validating the method. The protocol identified six putative homologous MVP sequences in the heterobolosean Naegleria gruberi within the excavate kingdom. Two of these sequences are predicted to be structurally similar to rat MVP, despite being in excess of 300 residues shorter. The method can be used generally to help test predictions of homology via

  5. Correction of erroneously packed protein's side chains in the NMR structure based on ab initio chemical shift calculations.

    PubMed

    Zhu, Tong; Zhang, John Z H; He, Xiao

    2014-09-14

    In this work, protein side chain (1)H chemical shifts are used as probes to detect and correct side-chain packing errors in protein's NMR structures through structural refinement. By applying the automated fragmentation quantum mechanics/molecular mechanics (AF-QM/MM) method for ab initio calculation of chemical shifts, incorrect side chain packing was detected in the NMR structures of the Pin1 WW domain. The NMR structure is then refined by using molecular dynamics simulation and the polarized protein-specific charge (PPC) model. The computationally refined structure of the Pin1 WW domain is in excellent agreement with the corresponding X-ray structure. In particular, the use of the PPC model yields a more accurate structure than that using the standard (nonpolarizable) force field. For comparison, some of the widely used empirical models for chemical shift calculations are unable to correctly describe the relationship between the particular proton chemical shift and protein structures. The AF-QM/MM method can be used as a powerful tool for protein NMR structure validation and structural flaw detection.

  6. 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

  7. 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

    2014-01-01

    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.

  8. Specific interactions between lactose repressor protein and DNA affected by ligand binding: ab initio molecular orbital calculations.

    PubMed

    Ohyama, Tatsuya; Hayakawa, Masato; Nishikawa, Shin; Kurita, Noriyuki

    2011-06-01

    Transcription mechanisms of gene information from DNA to mRNA are essentially controlled by regulatory proteins such as a lactose repressor (LacR) protein and ligand molecules. Biochemical experiments elucidated that a ligand binding to LacR drastically changes the mechanism controlled by LacR, although the effect of ligand binding has not been clarified at atomic and electronic levels. We here investigated the effect of ligand binding on the specific interactions between LacR and operator DNA by the molecular simulations combined with classical molecular mechanics and ab initio fragment molecular orbital methods. The results indicate that the binding of anti-inducer ligand strengthens the interaction between LacR and DNA, which is consistent with the fact that the binding of anti-inducer enhances the repression of gene transcription by LacR. It was also elucidated that hydrating water molecules existing between LacR and DNA contribute to the specific interactions between LacR and DNA. PMID:21328406

  9. 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

  10. Ab Initio Computation of Spin Orbit Coupling Effects on Magnetic Properties of Iron-Containing Complexes and Proteins

    NASA Astrophysics Data System (ADS)

    Aquino, Fredy; Rodriguez, Jorge H.

    2007-03-01

    Zero-Field Splittings (ZFS) in metalloproteins and other metal complexes arise from the combined action of crystalline fields acting on the metal valence electrons and spin-orbit coupling (SOC), a relativistic effect. The ab-initio calculation of ZFS parameters of metal-containing (bio)molecules is a challenging computational problem of practical relevance to metalloenzyme biochemistry, inorganic chemistry, and molecular-based bio- nanotechnology. We have implemented a methodology which treats the nonrelativistic electronic structure of magnetic (bio) molecules within the framework of spin density functional theory (SDFT) and adds the relativistic effects of SOC via perturbation theory (PT). This combined SDFT-PT approach allowed us to compute the ZFS parameters of iron-containing complexes and non-heme iron proteins with a good degree of accuracy. We also developed a semiquantitative approach to elucidate the physico-chemical origin of the magnitudes of ZFS parameters. We present results for biochemically relevant iron complexes and for nitric oxide-containing non-heme iron proteins, such as isopenicillin N synthase, which have unusually large ZFS. The computed ZFS parameters are in good agreement with experiment. Supported by NSF CAREER Award CHE- 0349189 (JHR).

  11. 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

  12. 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. PMID:27437113

  13. A comparative study of the reported performance of ab initio protein structure prediction algorithms.

    PubMed

    Helles, Glennie

    2008-04-01

    Protein structure prediction is one of the major challenges in bioinformatics today. Throughout the past five decades, many different algorithmic approaches have been attempted, and although progress has been made the problem remains unsolvable even for many small proteins. While the general objective is to predict the three-dimensional structure from primary sequence, our current knowledge and computational power are simply insufficient to solve a problem of such high complexity. Some prediction algorithms do, however, appear to perform better than others, although it is not always obvious which ones they are and it is perhaps even less obvious why that is. In this review, the reported performance results from 18 different recently published prediction algorithms are compared. Furthermore, the general algorithmic settings most likely responsible for the difference in the reported performance are identified, and the specific settings of each of the 18 prediction algorithms are also compared. The average normalized r.m.s.d. scores reported range from 11.17 to 3.48. With a performance measure including both r.m.s.d. scores and CPU time, the currently best-performing prediction algorithm is identified to be the I-TASSER algorithm. Two of the algorithmic settings--protein representation and fragment assembly--were found to have definite positive influence on the running time and the predicted structures, respectively. There thus appears to be a clear benefit from incorporating this knowledge in the design of new prediction algorithms.

  14. Unexpectedly strong energy stabilization inside the hydrophobic core of small protein rubredoxin mediated by aromatic residues: correlated ab initio quantum chemical calculations.

    PubMed

    Vondrásek, Jirí; Bendová, Lada; Klusák, Vojtech; Hobza, Pavel

    2005-03-01

    The formation of a hydrophobic core of globular proteins is believed to be the consequence of exterior hydrophobic forces of entropic nature. This, together with the low occurrence of hydrogen bonds in the protein core, leads to the opinion that the energy contribution of core formation to protein folding and stability is negligible. We show that stabilization inside the hydrophobic core of a small protein, rubredoxin, determined by means of high-level correlated ab initio calculations (complete basis set limit of MP2 stabilization energy + CCSD(T) correction term), amounted to approximately 50 kcal/mol. These results clearly demonstrate strong attraction inside a hydrophobic core. This finding may lead to substantial changes in the current view of protein folding. We also point out the inability of the DFT/B3LYP method to describe a strong attraction between studied amino acids.

  15. ASTRO-FOLD: A Combinatorial and Global Optimization Framework for Ab Initio Prediction of Three-Dimensional Structures of Proteins from the Amino Acid Sequence

    PubMed Central

    Klepeis, J. L.; Floudas, C. A.

    2003-01-01

    The field of computational biology has been revolutionized by recent advances in genomics. The completion of a number of genome projects, including that of the human genome, has paved the way toward a variety of challenges and opportunities in bioinformatics and biological systems engineering. One of the first challenges has been the determination of the structures of proteins encoded by the individual genes. This problem, which represents the progression from sequence to structure (genomics to structural genomics), has been widely known as the structure-prediction-in-protein-folding problem. We present the development and application of ASTRO-FOLD, a novel and complete approach for the ab initio prediction of protein structures given only the amino acid sequences of the proteins. The approach exhibits many novel components and the merits of its application are examined for a suite of protein systems, including a number of targets from several critical-assessment-of-structure-prediction experiments. PMID:14507680

  16. 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

  17. 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.

  18. SWISS-MODEL: modelling protein tertiary and quaternary structure using evolutionary information.

    PubMed

    Biasini, Marco; Bienert, Stefan; Waterhouse, Andrew; Arnold, Konstantin; Studer, Gabriel; Schmidt, Tobias; Kiefer, Florian; Gallo Cassarino, Tiziano; Bertoni, Martino; Bordoli, Lorenza; Schwede, Torsten

    2014-07-01

    Protein structure homology modelling has become a routine technique to generate 3D models for proteins when experimental structures are not available. Fully automated servers such as SWISS-MODEL with user-friendly web interfaces generate reliable models without the need for complex software packages or downloading large databases. Here, we describe the latest version of the SWISS-MODEL expert system for protein structure modelling. The SWISS-MODEL template library provides annotation of quaternary structure and essential ligands and co-factors to allow for building of complete structural models, including their oligomeric structure. The improved SWISS-MODEL pipeline makes extensive use of model quality estimation for selection of the most suitable templates and provides estimates of the expected accuracy of the resulting models. The accuracy of the models generated by SWISS-MODEL is continuously evaluated by the CAMEO system. The new web site allows users to interactively search for templates, cluster them by sequence similarity, structurally compare alternative templates and select the ones to be used for model building. In cases where multiple alternative template structures are available for a protein of interest, a user-guided template selection step allows building models in different functional states. SWISS-MODEL is available at http://swissmodel.expasy.org/.

  19. SWISS-MODEL: modelling protein tertiary and quaternary structure using evolutionary information

    PubMed Central

    Biasini, Marco; Bienert, Stefan; Waterhouse, Andrew; Arnold, Konstantin; Studer, Gabriel; Schmidt, Tobias; Kiefer, Florian; Cassarino, Tiziano Gallo; Bertoni, Martino; Bordoli, Lorenza; Schwede, Torsten

    2014-01-01

    Protein structure homology modelling has become a routine technique to generate 3D models for proteins when experimental structures are not available. Fully automated servers such as SWISS-MODEL with user-friendly web interfaces generate reliable models without the need for complex software packages or downloading large databases. Here, we describe the latest version of the SWISS-MODEL expert system for protein structure modelling. The SWISS-MODEL template library provides annotation of quaternary structure and essential ligands and co-factors to allow for building of complete structural models, including their oligomeric structure. The improved SWISS-MODEL pipeline makes extensive use of model quality estimation for selection of the most suitable templates and provides estimates of the expected accuracy of the resulting models. The accuracy of the models generated by SWISS-MODEL is continuously evaluated by the CAMEO system. The new web site allows users to interactively search for templates, cluster them by sequence similarity, structurally compare alternative templates and select the ones to be used for model building. In cases where multiple alternative template structures are available for a protein of interest, a user-guided template selection step allows building models in different functional states. SWISS-MODEL is available at http://swissmodel.expasy.org/. PMID:24782522

  20. Manifestations of food protein induced gastrointestinal allergies presenting to a single tertiary paediatric gastroenterology unit

    PubMed Central

    2013-01-01

    Background Food protein induced gastrointestinal allergies are difficult to characterise due to the delayed nature of this allergy and absence of simple diagnostic tests. Diagnosis is based on an allergy focused history which can be challenging and often yields ambiguous results. We therefore set out to describe a group of children with this delayed type allergy, to provide an overview on typical profile, symptoms and management strategies. Methods This retrospective analysis was performed at Great Ormond Street Children’s Hospital. Medical notes were included from 2002 – 2009 where a documented medical diagnosis of food protein induced gastrointestinal allergies was confirmed by an elimination diet with resolution of symptoms, followed by reintroduction with reoccurrence of symptoms. Age of onset of symptoms, diagnosis, current elimination diets and food elimination at time of diagnosis and co-morbidities were collected and parents were phoned again at the time of data collection to ascertain current allergy status. Results Data from 437 children were analysis. The majority (67.7%) of children had an atopic family history and 41.5% had atopic dermatitis at an early age. The most common diagnosis included, non-IgE mediated gastrointestinal food allergy (n = 189) and allergic enterocolitis (n = 154) with symptoms of: vomiting (57.8%), back-arching and screaming (50%), constipation (44.6%), diarrhoea (81%), abdominal pain (89.9%), abdominal bloating (73.9%) and rectal bleeding (38.5%). The majority of patients were initially managed with a milk, soy, egg and wheat free diet (41.7%). At a median age of 8 years, 24.7% of children still required to eliminate some of the food allergens. Conclusions This large retrospective study on children with food induced gastrointestinal allergies highlights the variety of symptoms and treatment modalities used in these children. However, further prospective studies are required in this area of food allergy. PMID:23919257

  1. An Alternative Approach to Protein Folding

    PubMed Central

    Kang, Yeona; Fortmann, Charles M.

    2013-01-01

    A diffusion theory-based, all-physical ab initio protein folding simulation is described and applied. The model is based upon the drift and diffusion of protein substructures relative to one another in the multiple energy fields present. Without templates or statistical inputs, the simulations were run at physiologic and ambient temperatures (including pH). Around 100 protein secondary structures were surveyed, and twenty tertiary structures were determined. Greater than 70% of the secondary core structures with over 80% alpha helices were correctly identified on protein ranging from 30 to 200 amino-acid sequence. The drift-diffusion model predicted tertiary structures with RMSD values in the 3–5 Angstroms range for proteins ranging 30 to 150 amino acids. These predictions are among the best for an all ab initio protein simulation. Simulations could be run entirely on a desktop computer in minutes; however, more accurate tertiary structures were obtained using molecular dynamic energy relaxation. The drift-diffusion model generated realistic energy versus time traces. Rapid secondary structures followed by a slow compacting towards lower energy tertiary structures occurred after an initial incubation period in agreement with observations. PMID:24078920

  2. 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.

  3. Ab Initio Structural Modeling of and Experimental Validation for Chlamydia trachomatis Protein CT296 Reveal Structural Similarity to Fe(II) 2-Oxoglutarate-Dependent Enzymes▿

    PubMed Central

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

    2011-01-01

    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-Å Cα root mean square deviation [RMSD]) the high-resolution (1.8-Å) 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. PMID:21965559

  4. Whether proton transition to the triphosphate tail of ATP occurs at protein kinase environment: A Car-Parrinello ab initio molecular dynamics study

    NASA Astrophysics Data System (ADS)

    Yang, Sheng-Yong; Zou, Jun; Xiang, Ming-Li; Xie, Guo-Bin; Shi, Bing; Wei, Yu-Quan

    Protonation state of the triphosphate tail of ATP (adenosine triphosphate) in protein environment is a fundamental issue, which has significant impact on the mechanism investigation of biochemical processes with ATP involved. Proton transition from surroundings (water molecule coordinating to magnesium, HW; amino group of Lys, HL) to the ATP tail in the catalytic core of protein kinase found recently disproved the commonly accepted deprotonation state of ATP tail. In this account, Car-Parrinello ab initio molecular dynamics (CP-AIMD) method has been employed to examine whether the proton transition occurs. To provide a comparison basis for the dynamics simulations, static quantum mechanics (QM), and combined quantum mechanics and molecular mechanics (QM/MM) calculations have also been carried out. Consistent results have been obtained that complete transition of hydrogen from the surroundings to the triphosphate tail of ATP is not allowed. The most dominant conformations correspond to the ones with HW bonding to O(W) and H-bonding to O(ATP), [O(W)-HW···O(ATP)], HL bonding to N(Lys) and H-bonding to O(ATP), [N(Lys)-HL···O(ATP)]. Metastable structures with one hydrogen atom bonding with two heavy atoms (hydrogen acceptors) were also located by our dynamic simulations. This bonding mode can satisfy the hungering for hydrogen of the two heavy atoms simultaneously.

  5. Evidence for tertiary structural RNA-RNA interactions within the protein S4 binding site at the 5'-end of 16S ribosomal RNA of Escherichia coli.+.

    PubMed Central

    Ungewickell, E; Ehresmann, C; Stiegler, P; Garrett, R

    1975-01-01

    Evidence is presented for tertiary structural interaction(s) (interactions(s) between two regions of an RNA molecule that are widely separated in the RNA sequence) within the 5'-one third of the 16S ribosomal RNA of Escherichia coli that constitutes the binding site of protein S4. The two main interacting RNA regions were separated by about 120 nucleotides (sections Q to M) of the 16S RNA sequence. A second, smaller gap, of 13 nucleotides, occurred within section C". The two main interacting regions contain about 150 nucleotides (sections H" to Q) and 160 nucleotides (sections M to C"). They are folded back on one another and, especially in the presence of protein S4, are strongly protected against ribonuclease digestion. The intermediate region (sections Q to M), however, is relatively accessible to ribonucleases in the S4-RNP. By partial removal of subfragments from the RNA complex it was possible to localise the two main interacting sites within sections H" - H and sections I" - C". Three main criteria for the specificity of the RNA-RNA interactions were invoked and satisfied. The possibility of other tertiary structural RNA-RNA interactions occurring in other regions of the 16S RNA is discussed. Finally, all the structural information on the S4-RNP is summarised and a tentative model is proposed. Images PMID:1103089

  6. Effect of D23N mutation on the dimer conformation of amyloid β-proteins: ab initio molecular simulations in water.

    PubMed

    Okamoto, Akisumi; Yano, Atsushi; Nomura, Kazuya; Higai, Shin'ichi; Kurita, Noriyuki

    2014-05-01

    The molecular pathogenesis of Alzheimer's disease (AD) is deeply involved in aggregations of amyloid β-proteins (Aβ) in a diseased brain. The recent experimental studies indicated that the mutation of Asp23 by Asn (D23N) within the coding sequence of Aβ increases the risk for the pathogeny of cerebral amyloid angiopathy and early-onset familial ADs. Fibrils of the D23N mutated Aβs can form both parallel and antiparallel structures, and the parallel one is considered to be associated with the pathogeny. However, the structure and the aggregation mechanism of the mutated Aβ fibrils are not elucidated at atomic and electronic levels. We here investigated solvated structures of the two types of Aβ dimers, each of which is composed of the wild-type or the D23N mutated Aβ, using classical molecular mechanics and ab initio fragment molecular orbital (FMO) methods, in order to reveal the effect of the D23N mutation on the structure of Aβ dimer as well as the specific interactions between the Aβ monomers. The results elucidate that the effect of the D23N mutation is significant for the parallel structure of Aβ dimer and that the solvating water molecules around the Aβ dimer have significant contribution to the stability of Aβ dimer.

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

    PubMed

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

    2012-12-01

    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.

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

    PubMed Central

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

    2012-01-01

    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. PMID:23151633

  9. 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.

  10. 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.

  11. Exploring the potential of global protein-protein docking: an overview and critical assessment of current programs for automatic ab initio docking.

    PubMed

    Huang, Sheng-You

    2015-08-01

    Protein-protein docking is an important computational tool for studying protein-protein interactions. A variety of docking programs with different sampling algorithms and scoring functions as well as computational efficiencies have been subsequently developed over the last decades. Here, we have reviewed the trend and performance of current global docking programs through a comprehensive assessment of the 18 docking/scoring protocols of 14 global docking programs on the latest protein docking benchmark 4.0. The effects of docking algorithms, interaction types, and conformational changes on the docking performance were investigated and discussed. The findings are expected to provide a general guideline for the choice of an appropriate docking protocol and offer insights into the optimization and development of docking and scoring algorithms.

  12. eThread: A Highly Optimized Machine Learning-Based Approach to Meta-Threading and the Modeling of Protein Tertiary Structures

    PubMed Central

    Brylinski, Michal; Lingam, Daswanth

    2012-01-01

    Template-based modeling that employs various meta-threading techniques is currently the most accurate, and consequently the most commonly used, approach for protein structure prediction. Despite the evident progress in this field, accurate structure models cannot be constructed for a significant fraction of gene products, thus the development of new algorithms is required. Here, we describe the development, optimization and large-scale benchmarking of eThread, a highly accurate meta-threading procedure for the identification of structural templates and the construction of corresponding target-to-template alignments. eThread integrates ten state-of-the-art threading/fold recognition algorithms in a local environment and extensively uses various machine learning techniques to carry out fully automated template-based protein structure modeling. Tertiary structure prediction employs two protocols based on widely used modeling algorithms: Modeller and TASSER-Lite. As a part of eThread, we also developed eContact, which is a Bayesian classifier for the prediction of inter-residue contacts and eRank, which effectively ranks generated multiple protein models and provides reliable confidence estimates as structure quality assessment. Excluding closely related templates from the modeling process, eThread generates models, which are correct at the fold level, for >80% of the targets; 40–50% of the constructed models are of a very high quality, which would be considered accurate at the family level. Furthermore, in large-scale benchmarking, we compare the performance of eThread to several alternative methods commonly used in protein structure prediction. Finally, we estimate the upper bound for this type of approach and discuss the directions towards further improvements. PMID:23185577

  13. Semiautomatic sequence-specific assignment of proteins based on the tertiary structure--the program st2nmr.

    PubMed

    Pristovsek, Primoz; Rüterjans, Heinz; Jerala, Roman

    2002-02-01

    The sequence-specific assignment of resonances is still the most time-consuming procedure that is necessary as the first step in high-resolution NMR studies of proteins. In many cases a reliable three-dimensional (3D) structure of the protein is available, for example, from X-ray spectroscopy or homology modeling. Here we introduce the st2nmr program that uses the 3D structure and Nuclear Overhauser Effect spectroscopy (NOESY) peak list(s) to evaluate and optimize trial sequence-specific assignments of spin systems derived from correlation spectra to residues of the protein. A distance-dependent target function that scores trial assignments based on the presence of expected NOESY crosspeaks is optimized in a Monte Carlo fashion. The performance of the program st2nmr is tested on real NMR data of an alpha-helical (cytochrome c) and beta-sheet (lipocalin) protein using homology models and/or X-ray structures; it succeeded in completely reproducing the correct sequence-specific assignments in most cases using 2D and/or 15N/13C Nuclear Overhauser Effect (NOE) data. Additionally to amino acid residues the program can also handle ligands that are bound to the protein, such as heme, and can be used as a complementary tool to fully automated assignment procedures. PMID:11908496

  14. 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.

  15. Tertiary Interactions within the Ribosomal Exit Tunnel

    PubMed Central

    Kosolapov, Andrey; Deutsch, Carol

    2009-01-01

    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 β-hairpin as well as an α-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. PMID:19270700

  16. Ab initio molecular dynamics.

    PubMed

    Laasonen, Kari

    2013-01-01

    In this chapter, an introduction to ab initio molecular dynamics (AIMD) has been given. Many of the basic concepts, like the Hellman-Feynman forces, the difference between the Car-Parrinello molecular dynamics and AIMD, have been explained. Also a very versatile AIMD code, the CP2K, has been introduced. On the application, the emphasis was on the aqueous systems and chemical reactions. The biochemical applications have not been discussed in depth.

  17. 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

  18. 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

    Khoury, George A; Smadbeck, James; Tamamis, Phanourios; Vandris, Andrew C; Kieslich, Chris A; Floudas, Christodoulos A

    2014-12-19

    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.

  19. Tertiary Basins of Spain

    NASA Astrophysics Data System (ADS)

    Friend, Peter F.; Dabrio, Cristino J.

    1996-01-01

    During the Tertiary, Spain suffered compressional collision between France and Africa, and its Atlantic and Mediterranean coasts have been further modified by extensional rifting. Because it includes sectors of two separate foreland basins, and an intervening craton with basins that have been influenced by extensional and strikeSHslip deformation, Spain provides excellent material for the development and testing of theories on the study of sedimentary basin formation and filling. This book is one of the few studies available in English of the important Tertiary geology of Spain.

  20. Diversification of Tertiary Education.

    ERIC Educational Resources Information Center

    Crausaz, Roselyne

    A working party of representatives from the Federal Republic of Germany, France, Norway, Switzerland, and the United Kingdom, visited five capitals to hear accounts of noteworthy innovations or experiments at the tertiary (post secondary) level of education. Diversification as opposed to expansion is currently being tried in many countries because…

  1. 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…

  2. Visibility of natural tertiary rainbows.

    PubMed

    Lee, Raymond L; Laven, Philip

    2011-10-01

    Naturally occurring tertiary rainbows are extraordinarily rare and only a handful of reliable sightings and photographs have been published. Indeed, tertiaries are sometimes assumed to be inherently invisible because of sun glare and strong forward scattering by raindrops. To analyze the natural tertiary's visibility, we use Lorenz-Mie theory, the Debye series, and a modified geometrical optics model (including both interference and nonspherical drops) to calculate the tertiary's (1) chromaticity gamuts, (2) luminance contrasts, and (3) color contrasts as seen against dark cloud backgrounds. Results from each model show that natural tertiaries are just visible for some unusual combinations of lighting conditions and raindrop size distributions.

  3. Visibility of natural tertiary rainbows.

    PubMed

    Lee, Raymond L; Laven, Philip

    2011-10-01

    Naturally occurring tertiary rainbows are extraordinarily rare and only a handful of reliable sightings and photographs have been published. Indeed, tertiaries are sometimes assumed to be inherently invisible because of sun glare and strong forward scattering by raindrops. To analyze the natural tertiary's visibility, we use Lorenz-Mie theory, the Debye series, and a modified geometrical optics model (including both interference and nonspherical drops) to calculate the tertiary's (1) chromaticity gamuts, (2) luminance contrasts, and (3) color contrasts as seen against dark cloud backgrounds. Results from each model show that natural tertiaries are just visible for some unusual combinations of lighting conditions and raindrop size distributions. PMID:22016239

  4. Tertiary Element Interaction in HIV-1 TAR.

    PubMed

    Krawczyk, Konrad; Sim, Adelene Y L; Knapp, Bernhard; Deane, Charlotte M; Minary, Peter

    2016-09-26

    HIV-1 replication requires binding to occur between Trans-activation Response Element (TAR) RNA and the TAT protein. This TAR-TAT binding depends on the conformation of TAR, and therapeutic development has attempted to exploit this dynamic behavior. Here we simulate TAR dynamics in the context of mutations inhibiting TAR binding. We find that two tertiary elements, the apical loop and the bulge, can interact directly, and this interaction may be linked to the affinity of TAR for TAT. PMID:27500460

  5. 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.

  6. Towards AB Initio Calculation of the Circular Dichroism of Peptides

    NASA Astrophysics Data System (ADS)

    Molteni, E.; Onida, G.; Tiana, G.

    2012-08-01

    In this work we plan to use ab initio spectroscopy calculations to compute circular dichroism (CD) spectra of peptides. CD provides information on protein secondary structure content; peptides, instead, remain difficult to address, due to their tendency to adopt multiple conformations in equilibrium. Therefore peptides are an interesting test-case for ab initio calculation of CD spectra. As a first application, we focus on the (83-92) fragment of HIV-1 protease, which is known to be involved in the folding and dimerization of this protein. As a preliminary step, we performed classical molecular dynamics (MD) simulations, in order to obtain a set of representative conformers of the peptide. Then, on some of the obtained conformations, we calculated absorption spectra at the independent particle, RPA and TDLDA levels, showing the presence of charge transfer excitations, and their influence on spectral features.

  7. Inactivation, aggregation, secondary and tertiary structural changes of germin-like protein in Satsuma mandarine with high polyphenol oxidase activity induced by ultrasonic processing.

    PubMed

    Huang, Nana; Cheng, Xi; Hu, Wanfeng; Pan, Siyi

    2015-02-01

    The inhibition of Polyphenol oxidase (PPO) in plants has been widely researched for their important roles in browning reaction. A newly found germin-like protein (GLP) with high PPO activity in Satsuma mandarine was inactivated by low-frequency high-intensity ultrasonic (20 kHz) processing. The effects of ultrasound on PPO activity and structure of GLP were investigated using dynamic light scattering (DLS) analysis, transmission electron microscopy (TEM), circular dichroism (CD) spectral measurement and fluorescence spectral measurement. The lowest PPO activity achieved was 27.4% following ultrasonication for 30 min at 400 W. DLS analysis showed ultrasound caused both aggregation and dissociation of GLP particles. TEM images also demonstrated protein aggregation phenomena. CD spectra exhibited a certain number of loss in α-helix structure content. Fluorescence spectra showed remarkable increase in fluorescence intensity with tiny blue-shift following ultrasonication. In conclusion, ultrasound applied in this study induced structural changes of GLP and eventually inactivated PPO activity.

  8. Structural basis of light chain amyloidogenicity: comparison of the thermodynamic properties, fibrillogenic potential and tertiary structural features of four Vlambda6 proteins.

    PubMed

    Wall, Jonathan S; Gupta, Vibha; Wilkerson, Matthew; Schell, Maria; Loris, Remy; Adams, Paul; Solomon, Alan; Stevens, Fred; Dealwis, Chris

    2004-01-01

    Primary (AL) amyloidosis results from the pathologic deposition of monoclonal light chains as amyloid fibrils. Studies of recombinant-derived variable region (VL) fragments of these proteins have shown an inverse relationship between thermodynamic stability and fibrillogenic potential. Further, ionic interactions within the VL domain were predicted to influence the kinetics of light chain fibrillogenicity, as evidenced from our analyses of a relatively stable Vlambda6 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 Vlambda6 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 immunoglobulin light chains.

  9. 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

  10. Co-evolution of quaternary organization and novel RNA tertiary interactions revealed in the crystal structure of a bacterial protein-RNA toxin-antitoxin system.

    PubMed

    Rao, Feng; Short, Francesca L; Voss, Jarrod E; Blower, Tim R; Orme, Anastasia L; Whittaker, Tom E; Luisi, Ben F; Salmond, George P C

    2015-10-30

    Genes encoding toxin-antitoxin (TA) systems are near ubiquitous in bacterial genomes and they play key roles in important aspects of bacterial physiology, including genomic stability, formation of persister cells under antibiotic stress, and resistance to phage infection. The CptIN locus from Eubacterium rectale is a member of the recently-discovered Type III class of TA systems, defined by a protein toxin suppressed by direct interaction with a structured RNA antitoxin. Here, we present the crystal structure of the CptIN protein-RNA complex to 2.2 Å resolution. The structure reveals a new heterotetrameric quaternary organization for the Type III TA class, and the RNA antitoxin bears a novel structural feature of an extended A-twist motif within the pseudoknot fold. The retention of a conserved ribonuclease active site as well as traits normally associated with TA systems, such as plasmid maintenance, implicates a wider functional role for Type III TA systems. We present evidence for the co-variation of the Type III component pair, highlighting a distinctive evolutionary process in which an enzyme and its substrate co-evolve.

  11. 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.

  12. The role of C-reactive protein as a diagnostic predictor of sepsis in a multidisciplinary Intensive Care Unit of a tertiary care center in Nepal

    PubMed Central

    Pradhan, Saurabh; Ghimire, Ashish; Bhattarai, Balkrishna; Khanal, Bashudha; Pokharel, Krishna; Lamsal, Madhab; Koirala, Sidhhartha

    2016-01-01

    Aim: C-reactive protein (CRP) is a commonly used biomarker of sepsis, the leading cause of mortality in Intensive Care Units (ICUs). However, sufficient data are still lacking to strongly recommend it in clinical practice. The present study is aimed to find out its reliability in diagnosing sepsis. Materials and Methods: CRP was measured in ICU-admitted patients with systemic inflammatory response syndrome and compared using a cutoff of 50 mg/L with the gold standard for diagnosing sepsis, taken as isolation of organism from a suspected source of infection or the Centers for Disease Control criteria for clinical sepsis. Results: CRP had a sensitivity and specificity of 84.3% and 46.15%, respectively. Area under the receiver operating characteristics curve was calculated to be 0.683 (±0.153, P < 0.05). The cutoff value with the best diagnostic accuracy was found to be 61 mg/L. Conclusion: CRP is a sensitive marker of sepsis, but it is not specific. PMID:27555697

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

    PubMed

    Palopoli, Nicolas; Monzon, Alexander Miguel; 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

  14. 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

  15. 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.

  16. 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…

  17. An ab initio MO study of butalene

    NASA Astrophysics Data System (ADS)

    Ohta, Katsuhisa; Shima, Toru

    1994-01-01

    Butalene as a structural isomer of p-benzyne has been studied by using an ab initio GVB wavefunction. The geometry of butalene, which is shown to be almost rectangular, is first optimized as a local minimum on the energy surface at the ab initio level. However, the energy barrier of conversion to p-benzyne is as small as 1.6 kcal/mol, and experimental isolation of butalene is predicted to be difficult from a force-constant analysis.

  18. 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…

  19. A fragmentation and reassembly method for ab initio phasing.

    PubMed

    Shrestha, Rojan; Zhang, Kam Y J

    2015-02-01

    Ab initio phasing with de novo models has become a viable approach for structural solution from protein crystallographic diffraction data. This approach takes advantage of the known protein sequence information, predicts de novo models and uses them for structure determination by molecular replacement. However, even the current state-of-the-art de novo modelling method has a limit as to the accuracy of the model predicted, which is sometimes insufficient to be used as a template for successful molecular replacement. A fragment-assembly phasing method has been developed that starts from an ensemble of low-accuracy de novo models, disassembles them into fragments, places them independently in the crystallographic unit cell by molecular replacement and then reassembles them into a whole structure that can provide sufficient phase information to enable complete structure determination by automated model building. Tests on ten protein targets showed that the method could solve structures for eight of these targets, although the predicted de novo models cannot be used as templates for successful molecular replacement since the best model for each target is on average more than 4.0 Å away from the native structure. The method has extended the applicability of the ab initio phasing by de novo models approach. The method can be used to solve structures when the best de novo models are still of low accuracy. PMID:25664740

  20. 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)

  1. Parathyroid carcinoma in tertiary hyperparathyroidism.

    PubMed

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

    2016-10-01

    Parathyroid carcinoma is a rare disease of unknown etiology. This study presents a case of parathyroid carcinoma in a patient with tertiary hyperparathyroidism. Despite a successful kidney transplantation, the intact parathyroid hormone (iPTH) level of the patient was elevated consistently and could not be controlled by medical therapy. Due to the development of tertiary hyperparathyroidism with bone pain and osteoporosis, subtotal parathyroidectomy was performed 4 months after the kidney transplantation. Histological evaluation revealed that one of four parathyroid lesions was a parathyroid carcinoma, while the others were diffuse hyperplasia. Postoperative laboratory studies indicated a decreased level of iPTH. A positron emission tomography-computed tomography performed 6 months after the operation revealed no evidence of local recurrence or distant metastasis. PMID:27664600

  2. 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.

  3. 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. PMID:23106040

  4. Regulation and 3 dimensional culture of tertiary follicle growth

    PubMed Central

    2012-01-01

    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. PMID:23106040

  5. A Multi-Objective Approach for Protein Structure Prediction Based on an Energy Model and Backbone Angle Preferences.

    PubMed

    Tsay, Jyh-Jong; Su, Shih-Chieh; Yu, Chin-Sheng

    2015-07-03

    Protein structure prediction (PSP) is concerned with the prediction of protein tertiary structure from primary structure and is a challenging calculation problem. After decades of research effort, numerous solutions have been proposed for optimisation methods based on energy models. However, further investigation and improvement is still needed to increase the accuracy and similarity of structures. This study presents a novel backbone angle preference factor, which is one of the factors inducing protein folding. The proposed multiobjective optimisation approach simultaneously considers energy models and backbone angle preferences to solve the ab initio PSP. To prove the effectiveness of the multiobjective optimisation approach based on the energy models and backbone angle preferences, 75 amino acid sequences with lengths ranging from 22 to 88 amino acids were selected from the CB513 data set to be the benchmarks. The data sets were highly dissimilar, therefore indicating that they are meaningful. The experimental results showed that the root-mean-square deviation (RMSD) of the multiobjective optimization approach based on energy model and backbone angle preferences was superior to those of typical energy models, indicating that the proposed approach can facilitate the ab initio PSP.

  6. A Multi-Objective Approach for Protein Structure Prediction Based on an Energy Model and Backbone Angle Preferences

    PubMed Central

    Tsay, Jyh-Jong; Su, Shih-Chieh; Yu, Chin-Sheng

    2015-01-01

    Protein structure prediction (PSP) is concerned with the prediction of protein tertiary structure from primary structure and is a challenging calculation problem. After decades of research effort, numerous solutions have been proposed for optimisation methods based on energy models. However, further investigation and improvement is still needed to increase the accuracy and similarity of structures. This study presents a novel backbone angle preference factor, which is one of the factors inducing protein folding. The proposed multiobjective optimisation approach simultaneously considers energy models and backbone angle preferences to solve the ab initio PSP. To prove the effectiveness of the multiobjective optimisation approach based on the energy models and backbone angle preferences, 75 amino acid sequences with lengths ranging from 22 to 88 amino acids were selected from the CB513 data set to be the benchmarks. The data sets were highly dissimilar, therefore indicating that they are meaningful. The experimental results showed that the root-mean-square deviation (RMSD) of the multiobjective optimization approach based on energy model and backbone angle preferences was superior to those of typical energy models, indicating that the proposed approach can facilitate the ab initio PSP. PMID:26151847

  7. Tertiary hypothyroidism in a dog

    PubMed Central

    2007-01-01

    A nine-year-old male entire Labrador was diagnosed with pituitary dependent hyperadrenocorticism. Following seven months of successful mitotane therapy, the dog presented with marked weight gain, seborrhoea and alopecia. Routine clinicopathological analyses revealed marked hypercholesterolaemia. Serum total and free thyroxine (T4) concentrations were below their respective reference ranges. Serum thyroid stimulating hormone (cTSH) concentration was within reference range. TSH and thyrotropin releasing hormone (TRH) response tests revealed adequate stimulation of total T4 in both, and cTSH in the latter test. Magnetic resonance imaging revealed a mass arising from the pituitary fossa, with suprasellar extension. A diagnosis of tertiary hypothyroidism was made. Following four weeks of levothyroxine therapy, circulating cholesterol concentration had declined, weight loss had ensued and dermatological abnormalities had improved. Euthanasia was performed four months later due to the development of neurological signs. A highly infiltrative pituitary adenoma, with effacement of the overlying hypothalamus was identified on post mortem examination. Tertiary hypothyroidism has not been previously reported in dogs. PMID:21851691

  8. 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…

  9. Towards Tertiary Education. Staff and Staff Development.

    ERIC Educational Resources Information Center

    Ratcliffe, Joan

    This report is intended as a resource for all those interested in staff development, especially in the tertiary education context. It describes the staff development project in the first two years of a new tertiary college--Harlow Technical College in England. An introduction and a description of the context of the project begin the report.…

  10. Engaging Heterogeneity: Tertiary Literacy in New Times.

    ERIC Educational Resources Information Center

    Hirst, Elizabeth Wyshe

    The "massification" of higher education in Australia and the associated increasing student diversity have significant implications for tertiary education. In particular, students seem to be struggling with the demands of tertiary literacy with commentators claiming that literacy standards are in decline. The solution has been to provide study…

  11. 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

  12. Changing Tertiary Education in Modern European Society.

    ERIC Educational Resources Information Center

    Council for Cultural Cooperation, Strasbourg (France).

    Reports on recent developments and problems in the diversification of tertiary education in seven Western European countries are presented by members of the Working Party on the Diversification of Tertiary Education. Policy analysis and evaluation and recommendations for future policy are also provided. As a policy, diversification refers to the…

  13. Nodular tertiary syphilis in an immunocompetent patient.

    PubMed

    Bittencourt, Maraya de Jesus Semblano; Brito, Arival Cardoso de; 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

  14. 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,…

  15. Like-charge guanidinium pairing from molecular dynamics and ab initio calculations.

    PubMed

    Vazdar, Mario; Vymětal, Jiři; Heyda, Jan; Vondrášek, Jiři; Jungwirth, Pavel

    2011-10-20

    Pairing of guanidinium moieties in water is explored by molecular dynamics simulations of short arginine-rich peptides and ab initio calculations of a pair of guanidinium ions in water clusters of increasing size. Molecular dynamics simulations show that, in an aqueous environment, the diarginine guanidinium like-charged ion pairing is sterically hindered, whereas in the Arg-Ala-Arg tripeptide, this pairing is significant. This result is supported by the survey of protein structure databases, where it is found that stacked arginine pairs in dipeptide fragments exist solely as being imposed by the protein structure. In contrast, when two arginines are separated by a single amino acid, their guanidinium groups can freely approach each other and they frequently form stacked pairs. Molecular dynamics simulations results are also supported by ab initio calculations, which show stabilization of stacked guanidinium pairs in sufficiently large water clusters.

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

    PubMed

    Zheng, Fan; Zhang, Jian; Grigoryan, Gevorg

    2015-05-01

    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.

  17. 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.

  18. 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.

  19. 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

  20. The Cretaceous/Tertiary Extinction Controversy Reconsidered.

    ERIC Educational Resources Information Center

    McCartney, Kevin; Nienstedt, Jeffrey

    1986-01-01

    Reviews varying positions taken in the Cretaceous/Tertiary (K/Y) extinction controversy. Analyzes and contests the meteoritic impact theory known as the Alvarez Model. Presents an alternative working hypothesis explaining the K/T transition. (ML)

  1. Ab initio melting curve of osmium

    NASA Astrophysics Data System (ADS)

    Burakovsky, L.; Burakovsky, N.; Preston, D. L.

    2015-11-01

    The melting curve of osmium up to a pressure P of 500 GPa is obtained from an extensive suite of ab initio quantum molecular dynamics (QMD) simulations using the Z method. The ab initio P =0 melting point of Os is 3370 ±75 K; this range encompasses all of the available data in the literature and corroborates the conclusion of J. W. Arblaster [Platinum Metals Rev. 49, 166 (2005)], 10.1595/147106705X70264 that the melting temperature of pure Os is 3400 ±50 K and that the 3300 K typically quoted in the literature is the melting point of impure Os. The T =0 equation of state (EOS) of Os and the P dependence of the optimized c /a ratio for the hexagonal unit cell, both to pressures ˜900 GPa, are obtained in the ab initio approach as validation of its use. Although excellent agreement with the available experimental data (P ≲80 GPa) is found, it is the third-order Birch-Murnaghan EOS with B0'=5 rather than the more widely accepted B0'=4 that describes the QMD data to higher pressures, in agreement with the more recent experimental EOS by Godwal et al. The theoretical melting curve of Os obtained earlier by Joshi et al. is shown to be inconsistent with our QMD results, and the possible reason for this discrepancy is suggested. Regularities in the melting curves of Os and five other third-row transition metals (Ta, W, Re, Pt, Au) could be used to estimate the currently unknown melting curves of Hf and Ir.

  2. 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

  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. 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.

  5. Ab initio Study of HZnF

    NASA Astrophysics Data System (ADS)

    Hayashi, S.; Léonard, C.; Chambaud, G.

    2009-11-01

    On the basis of highly correlated ab initio calculations, an accurate determination of the electronic structure and of the rovibrational spectroscopy has been performed for the electronic ground state of the HZnF system. Using effective core pseudopotentials for the Zn and F atoms and associated aug-cc-pVQZ basis sets, we have calculated, at the multireference configuration interaction level including the Davidson correction, the three-dimensional potential energy surface of the X1Σ+ ground state. The rovibrational energy levels have been obtained variationally, and the results have been discussed and compared with existing experimental data on the ground state of the close system HZnCl, which exhibits a complicated vibration-rotation spectrum. Our analysis shows that the nature of the H-ZnF bond is quite similar to that of the H-ZnCl bond, according to their bond lengths, harmonic frequencies of the H-Zn stretching mode, and dissociation energies into H and ZnF/ZnCl. The ab initio study of the electronic ground and excited states of ZnH and ZnH+ are also presented using similar level of calculations. Characteristic constants are given for the first bounded electronic states correlating to the first two dissociation asymptotes of the neutral and ionic diatomics.

  6. 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.

  7. Ab initio non-relativistic spin dynamics

    NASA Astrophysics Data System (ADS)

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

    2014-12-01

    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 Li3 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. 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. PMID:27148634

  9. 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

  10. Formation of Tertiary Interactions during rRNA GTPase Center Folding.

    PubMed

    Rau, Michael J; Welty, Robb; Tom Stump, W; Hall, Kathleen B

    2015-08-28

    The 60-nt GTPase center (GAC) of 23S rRNA has a phylogenetically conserved secondary structure with two hairpin loops and a 3-way junction. It folds into an intricate tertiary structure upon addition of Mg(2+) ions, which is stabilized by the L11 protein in cocrystal structures. Here, we monitor the kinetics of its tertiary folding and Mg(2+)-dependent intermediate states by observing selected nucleobases that contribute specific interactions to the GAC tertiary structure in the cocrystals. The fluorescent nucleobase 2-aminopurine replaced three individual adenines, two of which make long-range stacking interactions and one that also forms hydrogen bonds. Each site reveals a unique response to Mg(2+) addition and temperature, reflecting its environmental change from secondary to tertiary structure. Stopped-flow fluorescence experiments revealed that kinetics of tertiary structure formation upon addition of MgCl2 are also site specific, with local conformational changes occurring from 5 ms to 4s and with global folding from 1 to 5s. Site-specific substitution with (15)N-nucleobases allowed observation of stable hydrogen bond formation by NMR experiments. Equilibrium titration experiments indicate that a stable folding intermediate is present at stoichiometric concentrations of Mg(2+) and suggest that there are two initial sites of Mg(2+) ion association. PMID:26210661

  11. Tertiary filtration in small wastewater treatment plants.

    PubMed

    Naddeo, V; Belgiorno, V

    2007-01-01

    Tertiary filtration can be proposed in small wastewater treatment plants with impact on protected water bodies. Rotating disk filters may be adopted, in respect to conventional sand filters, when low availability of space and low investment costs are the prevailing conditions. The overall objective of this research was to evaluate the filtration efficiency of rotating disk filters; to compare effectiveness with traditional sand filters; to analyse thoroughly the importance of particle size distribution in wastewater tertiary filtration. In the experimental activity, conventional wastewater quality parameters were investigated and particle size distribution (PSD) was characterized to discuss the filter effectiveness. The effect of design and operation parameters of tertiary filters were discussed related to particle removal curves derived from particles counts. Analysis of particle size distribution can be very useful to help comprehension of filtration processes, design of filtration treatments and to decide the best measures to improve filter performance.

  12. 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. PMID:27536341

  13. Ab initio quantum mechanical models of peptide helices and their vibrational spectra.

    PubMed

    Bour, Petr; Kubelka, Jan; Keiderling, Timothy A

    2002-10-01

    Structural parameters for standard peptide helices (alpha, 3(10), 3(1) left-handed) were fully ab initio optimized for Ac-(L-Ala)(9)-NHMe and for Ac-(L-Pro)(9)-NHMe (poly-L-proline-PLP I and PLP II-forms), in order to better understand the relative stability and minimum energy geometries of these conformers and the dependence of the ir absorption and vibrational CD (VCD) spectra on detailed variation in these conformations. Only the 3(10)-helical Ala-based conformation was stable in vacuum for this decaamide structure, but both Pro-based conformers minimized successfully. Inclusion of solvent effects, by use of the conductor-like screening solvent model (COSMO), enabled ab initio optimizations [at the DFT/B3LYP/SV(P) level] without any constraints for the alpha- and 3(10)-helical Ala-based peptides as well as the two Pro-based peptides. The geometries obtained compare well with peptide chain torsion angles and hydrogen-bond distances found for these secondary structure types in x-ray structures of peptides and proteins. For the simulation of VCD spectra, force field and intensity response tensors were obtained ab initio for the complete Ala-based peptides in vacuum, but constrained to the COSMO optimized torsional angles, due to limitations of the solvent model. Resultant spectral patterns reproduce well many aspects of the experimental spectra and capture the differences observed for these various helical types.

  14. 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.

  15. 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

  16. 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.

  17. 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.

  18. Discovering chemistry with an ab initio nanoreactor

    DOE PAGES

    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 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. 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.

  20. Ab initio derivation of model energy density functionals

    NASA Astrophysics Data System (ADS)

    Dobaczewski, Jacek

    2016-08-01

    I propose a simple and manageable method that allows for deriving coupling constants of model energy density functionals (EDFs) directly from ab initio calculations performed for finite fermion systems. A proof-of-principle application allows for linking properties of finite nuclei, determined by using the nuclear nonlocal Gogny functional, to the coupling constants of the quasilocal Skyrme functional. The method does not rely on properties of infinite fermion systems but on the ab initio calculations in finite systems. It also allows for quantifying merits of different model EDFs in describing the ab initio results.

  1. On the hierarchical parallelization of ab initio simulations

    NASA Astrophysics Data System (ADS)

    Ruiz-Barragan, Sergi; Ishimura, Kazuya; Shiga, Motoyuki

    2016-02-01

    A hierarchical parallelization has been implemented in a new unified code PIMD-SMASH for ab initio simulation where the replicas and the Born-Oppenheimer forces are parallelized. It is demonstrated that ab initio path integral molecular dynamics simulations can be carried out very efficiently for systems up to a few tens of water molecules. The code was then used to study a Diels-Alder reaction of cyclopentadiene and butenone by ab initio string method. A reduction in the reaction energy barrier is found in the presence of hydrogen-bonded water, in accordance with experiment.

  2. Ab initio alpha-alpha scattering.

    PubMed

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

    2015-12-01

    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

  3. Ab initio alpha-alpha scattering.

    PubMed

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

    2015-12-01

    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

  4. Molecular alterations of Ras-Raf-mitogen-activated protein kinase and phosphatidylinositol 3-kinase-Akt signaling pathways in colorectal cancers from a tertiary hospital at Kuala Lumpur, Malaysia.

    PubMed

    Yip, Wai Kien; Choo, Chee Wei; Leong, Vincent Ching-Shian; Leong, Pooi Pooi; Jabar, Mohd Faisal; Seow, Heng Fong

    2013-10-01

    Molecular alterations in KRAS, BRAF, PIK3CA, and PTEN have been implicated in designing targeted therapy for colorectal cancer (CRC). The present study aimed to determine the status of these molecular alterations in Malaysian CRCs as such data are not available in the literature. We investigated the mutations of KRAS, BRAF, and PTEN, the gene amplification of PIK3CA, and the protein expression of PTEN and phosphatidylinositol 3-kinase (PI3K) catalytic subunit (p110α) by direct DNA sequencing, quantitative real-time PCR, and immunohistochemistry, respectively, in 49 CRC samples. The frequency of KRAS (codons 12, 13, and 61), BRAF (V600E), and PTEN mutations, and PIK3CA amplification was 25.0% (11/44), 2.3% (1/43), 0.0% (0/43), and 76.7% (33/43), respectively. Immunohistochemical staining demonstrated loss of PTEN protein in 54.5% (24/44) of CRCs and no significant difference in PI3K p110α expression between CRCs and the adjacent normal colonic mucosa (p = 0.380). PIK3CA amplification was not associated with PI3K p110α expression level, but associated with male cases (100% of male cases vs 56% of female cases harbored amplified PIK3CA, p = 0.002). PI3K p110α expression was significantly higher (p = 0.041) in poorly/moderately differentiated carcinoma compared with well-differentiated carcinoma. KRAS mutation, PIK3CA amplification, PTEN loss, and PI3K p110α expression did not correlate with Akt phosphorylation or Ki-67 expression. KRAS mutation, PIK3CA amplification, and PTEN loss were not mutually exclusive. This is the first report on CRC in Malaysia showing comparable frequency of KRAS mutation and PTEN loss, lower BRAF mutation rate, higher PIK3CA amplification frequency, and rare PTEN mutation, as compared with published reports.

  5. 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)

  6. 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.

  7. Rural Professionals: A Tertiary Preparation Model.

    ERIC Educational Resources Information Center

    Krynowsky, Bernie

    An outline is proposed for a tertiary course in rural studies for professionals such as teachers, nurses, and social workers that would better prepare them for rural service. The course could be an elective in general studies or give credit toward professional certification. Key components for effective rural preparation of professionals should be…

  8. 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…

  9. 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…

  10. 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…

  11. 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…

  12. 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…

  13. Early Tertiary climates of the Arctic Ocean

    SciTech Connect

    Marincovich, L.; Zinsmeister, W.J.

    1985-01-01

    Knowledge of Early Tertiary high latitude marine faunas (north of 65 N) is extremely limited. What published data that are available were based on small collections obtained during the early part of the 20th century. Recent work along the western part of the Arctic Ocean has greatly increased the knowledge of the composition of these faunas and climatic conditions of the high northern latitudes during the Early Tertiary. Early Eocene shallow marine faunas from the Eureka Sound Formation, Ellesmere Island (79/sup 0/ 30'N), together with similar aged faunas from Ocean Point, Alaska (72/sup 0/N) and Spitsbergen trough, Svalbard, (78/sup 0/N) indicate that temperature conditions prevailed in the high Arctic during the early Tertiary. These high latitude temperate conditions are also supported by the presence of a diverse terrestrial mammalian faunas (currently known only from Ellesmere Island) and floras. Preliminary comparisons of these faunas from the Arctic ocean with the diverse subtropical faunas from West Greenland (70/sup 0/N) indicates the presence of a major faunal discontinuity existed in the high northern latitudes during the early Tertiary. The cause of this faunal discontinuity is uncertain. It may be due to the presence of a physical barrier between the Arctic Ocean and the North Atlantic or it may reflect cooler climatic conditions north of 70 N.

  14. The Cretaceous/Tertiary Extinction Controversy.

    ERIC Educational Resources Information Center

    McCartney, Kevin

    1984-01-01

    The cause of the Cretaceous/Tertiary extinction has become a major geologic controversy. Current evidence for the two opposing views is reviewed to provide an introduction to the controversy and to form the basis for a seminar of discussion topic. (Author/JN)

  15. Quarterly Technical Progress Report - West Hackberry Tertiary Project

    SciTech Connect

    Demetrios Yannimaras; Travis Gillham

    1998-07-14

    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.

  16. Quarterly Technical Progress Report - West Hackberry Tertiary Project

    SciTech Connect

    Bruce Cerveny; Tor Kragas; Travis Gillham

    1998-01-13

    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.

  17. 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.

  18. 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.

  19. 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…

  20. 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)

  1. Protein

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Proteins are the major structural and functional components of all cells in the body. They are macromolecules that comprise 1 or more chains of amino acids that vary in their sequence and length and are folded into specific 3-dimensional structures. The sizes and conformations of proteins, therefor...

  2. 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.

  3. 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)

  4. 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.

  5. 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.

  6. 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.

  7. 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.

  8. Ab initio two-component Ehrenfest dynamics

    NASA Astrophysics Data System (ADS)

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

    2015-09-01

    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 H2 and O2. 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.

  9. Ab Initio Studies of Calcium Carbonate Hydration.

    PubMed

    Lopez-Berganza, Josue A; Diao, Yijue; Pamidighantam, Sudhakar; Espinosa-Marzal, Rosa M

    2015-11-25

    Ab initio simulations of large hydrated calcium carbonate clusters are challenging due to the existence of multiple local energy minima. Extensive conformational searches around hydrated calcium carbonate clusters (CaCO3·nH2O for n = 1-18) were performed to find low-energy hydration structures using an efficient combination of Monte Carlo searches, density-functional tight binding (DFTB+) method, and density-functional theory (DFT) at the B3LYP level, or Møller-Plesset perturbation theory at the MP2 level. This multilevel optimization yields several low-energy structures for hydrated calcium carbonate. Structural and energetics analysis of the hydration of these clusters revealed a first hydration shell composed of 12 water molecules. Bond-length and charge densities were also determined for different cluster sizes. The solvation of calcium carbonate in bulk water was investigated by placing the explicitly solvated CaCO3·nH2O clusters in a polarizable continuum model (PCM). The findings of this study provide new insights into the energetics and structure of hydrated calcium carbonate and contribute to the understanding of mechanisms where calcium carbonate formation or dissolution is of relevance.

  10. Phonocatalysis. An ab initio simulation experiment

    NASA Astrophysics Data System (ADS)

    Kim, Kwangnam; Kaviany, Massoud

    2016-06-01

    Using simulations, we postulate and show that heterocatalysis on large-bandgap semiconductors can be controlled by substrate phonons, i.e., phonocatalysis. With ab initio calculations, including molecular dynamic simulations, the chemisorbed dissociation of XeF6 on h-BN surface leads to formation of XeF4 and two surface F/h-BN bonds. The reaction pathway and energies are evaluated, and the sorption and reaction emitted/absorbed phonons are identified through spectral analysis of the surface atomic motion. Due to large bandgap, the atomic vibration (phonon) energy transfer channels dominate and among them is the match between the F/h-BN covalent bond stretching and the optical phonons. We show that the chemisorbed dissociation (the pathway activation ascent) requires absorption of large-energy optical phonons. Then using progressively heavier isotopes of B and N atoms, we show that limiting these high-energy optical phonons inhibits the chemisorbed dissociation, i.e., controllable phonocatalysis.

  11. Proteins

    NASA Astrophysics Data System (ADS)

    Regnier, Fred E.; Gooding, Karen M.

    Because of the complexity of cellular material and body fluids, it is seldom possible to analyze a natural product directly. Qualitative and quantitative analyses must often be preceded by some purification step that separates the molecular species being examined from interfering materials. In the case of proteins, column liquid chromatography has been used extensively for these fractionations. With the advent of gel permeation, cation exchange, anion exchange, hydrophobic, and affinity chromatography, it became possible to resolve proteins through their fundamental properties of size, charge, hydrophobicity, and biological affinity. The chromatographic separations used in the early isolation and characterization of many proteins later became analytical tools in their routine analysis. Unfortunately, these inherently simple and versatile column chromatographic techniques introduced in the 50s and 60s have a severe limitation in routine analysis-separation time. It is common to encounter 1-24 h separation times with the classical gel-type supports.

  12. 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.

  13. 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

  14. Eclipsing Binaries with Possible Tertiary Components

    NASA Astrophysics Data System (ADS)

    Snyder, LeRoy F.

    2013-05-01

    Many eclipsing binary star systems (EBS) show long-term variations in their orbital periods which are evident in their O-C (observed minus calculated period) diagrams. This research carried out an analysis of 324 eclipsing binary systems taken from the systems analyzed in the Bob Nelson's O-C Files database. Of these 18 systems displayed evidence of periodic variations of the arrival times of the eclipses. These rates of period changes are sinusoidal variations. The sinusoidal character of these variations is suggestive of Keplerian motion caused by an orbiting companion. The reason for these changes is unknown, but mass loss, apsidal motion, magnetic activity and the presence of a third body have been proposed. This paper has assumed light time effect as the cause of the sinusoidal variations caused by the gravitational pull of a tertiary companion orbiting around the eclipsing binary systems. An observed minus calculated (O-C) diagram of the 324 systems was plotted using a quadratic ephemeris to determine if the system displayed a sinusoidal trend in theO-C residuals. After analysis of the 18 systems, seven systems, AW UMa, BB PEG, OO Aql, V508 Oph, VW Cep, WCrv and YY ERI met the benchmark of the criteria of a possible orbiting companion. The other 11 systems displayed a sinusoidal variation in the O-C residuals of the primary eclipses but these systems in the Bob Nelson's O-C Files did not contain times of minimum (Tmin) of the secondary eclipses and therefore not conclusive in determining the presents of the effects of a tertiary companion. An analysis of the residuals of the seven systems yields a light-time semi-amplitude, orbital period, eccentricity and mass of the tertiary companion as the amplitude of the variation is proportional to the mass, period and inclination of the 3rd orbiting body. Knowing the low mass of the tertiary body in the seven cases the possibility of five of these tertiary companions being brown dwarfs is discussed.

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

    PubMed

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

    2014-07-01

    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 alkaline earth dications with the carbonyl group remain difficult to assign and controversial to interpret. Herein, we directly compute the infrared (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. Because 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.

  19. Tertiary lymphoid organs in infection and autoimmunity.

    PubMed

    Neyt, Katrijn; Perros, Frédéric; GeurtsvanKessel, Corine H; Hammad, Hamida; Lambrecht, Bart N

    2012-06-01

    The lymph nodes (LNs) and spleen have an optimal structure that allows the interaction between T cells, B cells and antigen-presenting dendritic cells (DCs) on a matrix made up by stromal cells. Such a highly organized structure can also be formed in tertiary lymphoid organs (TLOs) at sites of infection or chronic immune stimulation. This review focuses on the molecular mechanisms of TLO formation and maintenance, the controversies surrounding the nature of the inducing events, and the functions of these structures in infection, transplantation and autoimmunity. PMID:22622061

  20. 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.

  1. 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.

  2. 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.

  3. The prediction of T- and B-combined epitope and tertiary structure of the Eg95 antigen of Echinococcus granulosus

    PubMed Central

    MA, XIUMIN; ZHOU, XIAOTAO; ZHU, YUEJIE; LI, YANHUA; WANG, HONGYING; MAMUTI, WULAMU; LI, YUJIAO; WEN, HAO; DING, JIANBING

    2013-01-01

    Echinococcosis, also known as hydatid disease, is a type of zoonotic parasitic disease caused by the Echinococcus larvae infection. The disease is severely harmful to both humans and animals. Research and development of an epitope vaccine is crucial. To determine the dominant epitopes of the Eg95 antigen, the tertiary structure and the T- and B-combined epitope of the Eg95 protein for Echinococcus granulosus were predicted and analyzed in the present study. The tertiary structure of the Eg95 protein was predicted using the 3DLigandsite server and RasMol software. The T- and B-combined epitope of the Eg95 antigen was analyzed using the DNAStar (V5.0), IEDB, SYFPEITHI and BIMAS. Tertiary structure prediction results showed that there were potential epitopes in Eg95 antigen. Bioinformatics analysis revealed the T- and B-combined epitopes of Eg95 antigen. Four and six T- and B-combined epitopes induced immune responses in humans and mice. Additionally, four T- and B-combined epitopes induced immune responses in both humans and mice. The tertiary structure and T- and B-combined epitopes of the Eg95 protein were also determined. The results obtained in the present study may be beneficial in the investigation of Eg95 antigenicity and the development of dominant epitope vaccines. PMID:24137242

  4. 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.

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

    PubMed Central

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

    2015-01-01

    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. PMID:25791957

  6. Ab Initio No-Core Shell Model

    SciTech Connect

    Barrett, B R; Navratil, P; Vary, J P

    2011-04-11

    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

  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. 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.

  9. An effective evolutionary algorithm for protein folding on 3D FCC HP model by lattice rotation and generalized move sets

    PubMed Central

    2013-01-01

    Background Proteins are essential biological molecules which play vital roles in nearly all biological processes. It is the tertiary structure of a protein that determines its functions. Therefore the prediction of a protein's tertiary structure based on its primary amino acid sequence has long been the most important and challenging subject in biochemistry, molecular biology and biophysics. In the past, the HP lattice model was one of the ab initio methods that many researchers used to forecast the protein structure. Although these kinds of simplified methods could not achieve high resolution, they provided a macrocosm-optimized protein structure. The model has been employed to investigate general principles of protein folding, and plays an important role in the prediction of protein structures. Methods In this paper, we present an improved evolutionary algorithm for the protein folding problem. We study the problem on the 3D FCC lattice HP model which has been widely used in previous research. Our focus is to develop evolutionary algorithms (EA) which are robust, easy to implement and can handle various energy functions. We propose to combine three different local search methods, including lattice rotation for crossover, K-site move for mutation, and generalized pull move; these form our key components to improve previous EA-based approaches. Results We have carried out experiments over several data sets which were used in previous research. The results of the experiments show that our approach is able to find optimal conformations which were not found by previous EA-based approaches. Conclusions We have investigated the geometric properties of the 3D FCC lattice and developed several local search techniques to improve traditional EA-based approaches to the protein folding problem. It is known that EA-based approaches are robust and can handle arbitrary energy functions. Our results further show that by extensive development of local searches, EA can also be very

  10. 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...

  11. 40 CFR 721.10669 - Tertiary amine alkyl ether (generic).

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... 40 Protection of Environment 32 2013-07-01 2013-07-01 false Tertiary amine alkyl ether (generic... Specific Chemical Substances § 721.10669 Tertiary amine alkyl ether (generic). (a) Chemical substance and... alkyl ether (PMN P-13-78) is subject to reporting under this section for the significant new...

  12. 40 CFR 721.10669 - Tertiary amine alkyl ether (generic).

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... 40 Protection of Environment 31 2014-07-01 2014-07-01 false Tertiary amine alkyl ether (generic... Specific Chemical Substances § 721.10669 Tertiary amine alkyl ether (generic). (a) Chemical substance and... alkyl ether (PMN P-13-78) is subject to reporting under this section for the significant new...

  13. 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…

  14. 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...

  15. 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...

  16. 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...

  17. 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.…

  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. 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...

  20. 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...

  1. 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...

  2. 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…

  3. 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.

  4. 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.

  5. Ab initio calculations in three-body cluster systems

    SciTech Connect

    Romero-Redondo, C.; Navratil, P.; Quaglioni, S.

    2013-06-10

    In this work we briefly outline the extension of the ab initio no-core shell model/Resonating group method (NCSM/RGM) to three-body cluster states. We present the results for {sup 6}He ground state within a {sup 4}He+n+n cluster basis under this approach.

  6. Ab Initio Modeling of the Herpesvirus VP26 Core Domain Assessed by CryoEM Density

    PubMed Central

    Baker, Matthew L; Jiang, Wen; Wedemeyer, William J; Rixon, Frazer J; Baker, David; Chiu, Wah

    2006-01-01

    Efforts in structural biology have targeted the systematic determination of all protein structures through experimental determination or modeling. In recent years, 3-D electron cryomicroscopy (cryoEM) has assumed an increasingly important role in determining the structures of these large macromolecular assemblies to intermediate resolutions (6–10 Å). While these structures provide a snapshot of the assembly and its components in well-defined functional states, the resolution limits the ability to build accurate structural models. In contrast, sequence-based modeling techniques are capable of producing relatively robust structural models for isolated proteins or domains. In this work, we developed and applied a hybrid modeling approach, utilizing cryoEM density and ab initio modeling to produce a structural model for the core domain of a herpesvirus structural protein, VP26. Specifically, this method, first tested on simulated data, utilizes the cryoEM density map as a geometrical constraint in identifying the most native-like models from a gallery of models generated by ab initio modeling. The resulting model for the core domain of VP26, based on the 8.5-Å resolution herpes simplex virus type 1 (HSV-1) capsid cryoEM structure and mutational data, exhibited a novel fold. Additionally, the core domain of VP26 appeared to have a complementary interface to the known upper-domain structure of VP5, its cognate binding partner. While this new model provides for a better understanding of the assembly and interactions of VP26 in HSV-1, the approach itself may have broader applications in modeling the components of large macromolecular assemblies. PMID:17069457

  7. 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

  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

    SciTech Connect

    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. Tertiary Lymphoid Organs in Cancer Tissues.

    PubMed

    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

  12. Neurosarcoidosis in a Tertiary Referral Center

    PubMed Central

    Leonhard, Sonja E.; Fritz, Daan; Eftimov, Filip; van der Kooi, Anneke J.; van de Beek, Diederik; Brouwer, Matthijs C.

    2016-01-01

    Abstract The aim of this study was to evaluate clinical characteristics, diagnostic strategy, and treatment in patients with neurosarcoidosis in a tertiary referral centre. In a cross-sectional study, we included all patients with neurosarcoidosis treated at our tertiary referral center between September 2014 and April 2015. We identified 52 patients, among them 1 patient was categorized as having definite neurosarcoidosis, 37 probable neurosarcoidosis, and 14 possible neurosarcoidosis. Neurologic symptoms were the first manifestation of sarcoidosis in 37 patients (71%). Chronic aseptic meningitis was the most common presentation (19/52 patients [37%]), followed by cranial neuropathy (16/52 patients [31%]). Serum angiotensin-converting enzyme and lysozyme levels were elevated in 18 of 41 (44%) and 12 of 26 cases (46%). Pulmonary or lymph node sarcoidosis was identified by chest X-ray in 21 of 39 cases (54%) and by computed tomography of the chest in 25 of 31 cases (81%); 18Fluorodeoxyglucose-Positron emission tomography showed signs of sarcoidosis in 15 of 19 cases (79%). Thirty-one of the 46 cases receiving treatment (67%) improved, 13 cases (28%) stabilized, and 2 cases (4%) deteriorated. First-line treatment with corticosteroids resulted in satisfactory reduction of symptoms in 21 of 43 patients (49%). Seventeen patients (33%) needed second-line cytostatic treatment, and 10 patients (19%) were treated with tumor necrosis factor-α inhibitors. The majority of patients with neurosarcoidosis present with chronic meningitis without a history of systemic sarcoidosis. The diagnosis can be difficult to make because of the poor sensitivity of most diagnostic tests. Half of patients had a satisfactory reduction of symptoms on first-line therapy. PMID:27057889

  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. Elucidation of the Covalent and Tertiary Structures of Biologically Active Ts3 Toxin.

    PubMed

    Dang, Bobo; Kubota, Tomoya; Mandal, Kalyaneswar; Correa, Ana M; Bezanilla, Francisco; Kent, Stephen B H

    2016-07-18

    Ts3 is an alpha scorpion toxin from the venom of the Brazilian scorpion Tityus serrulatus. Ts3 binds to the domain IV voltage sensor of voltage-gated sodium channels (Nav ) and slows down their fast inactivation. The covalent structure of the Ts3 toxin is uncertain, and the structure of the folded protein molecule is unknown. Herein, we report the total chemical synthesis of four candidate Ts3 toxin protein molecules and the results of structure-activity studies that enabled us to establish the covalent structure of biologically active Ts3 toxin. We also report the synthesis of the mirror image form of the Ts3 protein molecule, and the use of racemic protein crystallography to determine the folded (tertiary) structure of biologically active Ts3 toxin by X-ray diffraction. PMID:27244051

  15. Roles of long-range tertiary interactions in limiting dynamics of the Tetrahymena group I ribozyme.

    PubMed

    Shi, Xuesong; Bisaria, Namita; Benz-Moy, Tara L; Bonilla, Steve; Pavlichin, Dmitri S; Herschlag, Daniel

    2014-05-01

    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.

  16. 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

  17. 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.

  18. 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.

  19. Ab-initio calculations on melting of thorium

    NASA Astrophysics Data System (ADS)

    Mukherjee, D.; Sahoo, B. D.; Joshi, K. D.; Kaushik, T. C.; Gupta, Satish C.

    2016-05-01

    Ab-initio molecular dynamics study has been performed on face centered cubic structured thorium to determine its melting temperature at room pressure. The ion-electron interaction potential energy calculated as a function of temperature for three volumes (a0)3 and (1.02a0)3 and (1.04a0)3 increases gradually with temperature and undergoes a sharp jump at ~2200 K, ~2100 K and ~1800 K, respectively. Here, a0 = 5.043 Å is the equilibrium lattice parameter at 0 K obtained from ab-initio calculations. These jumps in interaction energy are treated as due to the onset of melting and corresponding temperatures as melting point. The melting point of 2100 K is close to the experimental value of 2023K. Further, the same has been verified by plotting the atomic arrangement evolved at various temperatures and corresponding pair correlation functions.

  20. Ab initio molecular dynamics: Concepts, recent developments, and future trends

    PubMed Central

    Iftimie, Radu; Minary, Peter; Tuckerman, Mark E.

    2005-01-01

    The methodology of ab initio molecular dynamics, wherein finite-temperature dynamical trajectories are generated by using forces computed “on the fly” from electronic structure calculations, has had a profound influence in modern theoretical research. Ab initio molecular dynamics allows chemical processes in condensed phases to be studied in an accurate and unbiased manner, leading to new paradigms in the elucidation of microscopic mechanisms, rationalization of experimental data, and testable predictions of new phenomena. The purpose of this work is to give a brief introduction to the technique and to review several important recent developments in the field. Several illustrative examples showing the power of the technique have been chosen. Perspectives on future directions in the field also will be given. PMID:15870204

  1. Ab Initio Electronic Relaxation Times and Transport in Noble Metals

    NASA Astrophysics Data System (ADS)

    Mustafa, Jamal I.; Bernardi, Marco; Neaton, Jeffrey B.; Louie, Steven G.

    Relaxation times employed to study electron transport in metals are typically assumed to be constants and obtained empirically using the Drude model. Here, we employ ab initio calculations to compute the electron-phonon relaxation times of Cu, Ag, and Au, and find that they vary significantly on the Fermi surface, spanning ~15 -45 fs. We compute room temperature resistivities in excellent agreement with experiment by combining GW bandstructures, Wannier-interpolated band velocities, and ab initio relaxation times. Our calculations are compared to other approximations used for the relaxation times. Additionally, an importance sampling scheme is introduced to speed up the convergence of resistivity and transport calculations by sampling directly points on the Fermi surface. This work was supported by NSF Grant No. DMR15-1508412 and U.S. DOE under Contract No. DE-AC02-05CH11231. Computational resources have been provided by DOE at LBNL's NERSC facility.

  2. 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.

  3. 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.

  4. 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.

  5. Minor Structural Change to Tertiary Sulfonamide RORc Ligands Led to Opposite Mechanisms of Action

    PubMed Central

    2014-01-01

    A minor structural change to tertiary sulfonamide RORc ligands led to distinct mechanisms of action. Co-crystal structures of two compounds revealed mechanistically consistent protein conformational changes. Optimized phenylsulfonamides were identified as RORc agonists while benzylsulfonamides exhibited potent inverse agonist activity. Compounds behaving as agonists in our biochemical assay also gave rise to an increased production of IL-17 in human PBMCs whereas inverse agonists led to significant suppression of IL-17 under the same assay conditions. The most potent inverse agonist compound showed >180-fold selectivity over the ROR isoforms as well as all other nuclear receptors that were profiled. PMID:25815138

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

    NASA Astrophysics Data System (ADS)

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

    2014-08-01

    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.

  7. 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.

  8. Acceleration of the Convergence in ab initio Atomic Relaxations

    NASA Astrophysics Data System (ADS)

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

    2006-03-01

    Atomic relaxations is often required to accurately describe the properties of nanosystems. In ab initio calculations, a common practice is to use a standard search algorithm, such as BFGS (Broyden-Fletcher-Goldfarb-Shanno) or CG (conjugate gradient) method, which starts the atomic relaxations without any knowledge of the Hessian matrix of the system. For example, the initial Hessian in BFGS method is often set to identity, and there is no preconditioning to CG method. One way to accelerate the convergence of the atomic relaxations is to estimate an approximate Hessian matrix of the system and then use it as the initial Hessian in BFGS method or a preconditioner in CG method. Previous attempts to obtain the approximated Hessian were focused on the use of classical force field models which rely on the existence of good parameters. Here, we present an alternative method to estimate the Hessian matrix of a nanosystem. First, we decompose the system into motifs which consist of a few atoms, then calculate the Hessian matrix elements on different motif types from ab initio calculations for small prototype systems. Then we generate the Hessian Matrix of the whole system by putting together these motif Hessians. We have applied our motif-based Hessian matrix in ab initio atomic relaxations in several bulk (with/without impurity) and quantum dot systems, and have found a speed up factor of 2 to 4 depending on the system size.

  9. 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.

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

    PubMed

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

    2016-09-14

    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 (12)CH4 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. PMID:27634258

  11. 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.

  12. 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).

  13. Ab initio calculations of reactions with light nuclei

    NASA Astrophysics Data System (ADS)

    Quaglioni, Sofia; Hupin, Guillaume; Calci, Angelo; Navrátil, Petr; Roth, Robert

    2016-03-01

    An ab initio (i.e., from first principles) theoretical framework capable of providing a unified description of the structure and low-energy reaction properties of light nuclei is desirable to further our understanding of the fundamental interactions among nucleons, and provide accurate predictions of crucial reaction rates for nuclear astrophysics, fusion-energy research, and other applications. In this contribution we review ab initio calculations for nucleon and deuterium scattering on light nuclei starting from chiral two- and three-body Hamiltonians, obtained within the framework of the ab initio no-core shell model with continuum. This is a unified approach to nuclear bound and scattering states, in which square-integrable energy eigenstates of the A-nucleon system are coupled to (A-a)+a target-plus-projectile wave functions in the spirit of the resonating group method to obtain an efficient description of the many-body nuclear dynamics both at short and medium distances and at long ranges.

  14. 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.

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

    PubMed

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

    2016-09-14

    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 (12)CH4 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 multiple cloning algorithm for quantum nonadiabatic molecular dynamics.

    PubMed

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

    2014-08-01

    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. PMID:25106573

  17. 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...

  18. 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.

  19. Tertiary Aquifer Modeling Within the Mississippi Embayment

    NASA Astrophysics Data System (ADS)

    Csontos, R.; Waldron, B.; Anderson, J.

    2008-12-01

    The geologic and hydrogeologic characterization of the aquifers and their recharge area within the Central United States in west Tennessee, northern Mississippi and eastern Arkansas are poorly understood. Previous investigations have utilized overly generalized outcrop boundaries of the primary Tertiary aquifers based on sparse well log information and stream down-cutting to show formation location. Acquisition of data in the form of deep oil and gas wells along with shallow lignite borehole data from the North American Coal Company is enabling us to improve upon these prior formational boundaries and recharge area delineations. Additionally, utilization of those geophysical logs with numerous well log curves is allowing us to characterize each geologic unit as to the sand/clay composition, porosity, and depiction of facies changes within a three- dimensional context. This is made possible through the utilization of the oil industry standard mapping package, Petrel®. We use a combination of methods to illustrate the presence of clay bodies within the primary drinking water aquifer, historically modeled solely as a sand unit. Identification of these clay bodies will impact ground-water flow patterns and assist water utilities in reducing contamination threats. We will illustrate aquifer thickness variability owning to faulting and paleo-erosion that again may impact ground-water pathways.

  20. 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.

  1. 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…

  2. Pd/C-Catalyzed Aminocarbonylation of Aryl Iodides via Oxidative C-N Bond Activation of Tertiary Amines to Tertiary Amides.

    PubMed

    Mane, Rajendra S; Bhanage, Bhalchandra M

    2016-02-01

    This work reports oxidative N-dealkylation/carbonylation of tertiary amines to tertiary amides by using molecular oxygen as a sole oxidant using a Pd/C catalyst. This protocol is free from ligands, additives, bases, and cocatalysts. Different tertiary amines as well as aryl iodides have been examined for this transformation, providing desired products in good to excellent yield. PMID:26756705

  3. 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.

  4. Polymeric nitrogen in a graphene matrix: An ab initio study

    NASA Astrophysics Data System (ADS)

    Timoshevskii, V.; Ji, Wei; Abou-Rachid, Hakima; Lussier, Louis-Simon; Guo, H.

    2009-09-01

    A hybrid material where polymeric nitrogen chains are sandwiched between graphene sheets in the form of a three-dimensional crystal, is predicted by means of ab initio simulations. It is demonstrated that chainlike polymeric nitrogen phase becomes stable at ambient pressure when intercalated in a multilayer graphene matrix. The physical origin of this stabilization is identified by studying the electronic properties of the system. This approach of stabilizing polymeric nitrogen by means of external three-dimensional matrix constitutes a path toward synthesizing different types of nitrogen-based high-energy materials.

  5. 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.

  6. 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.

  7. 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.

  8. 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.

  9. Exploring Transition Metal Catalyzed Reactions via AB Initio Reaction Pathways

    NASA Astrophysics Data System (ADS)

    Hratchian, Hrant P.

    2011-06-01

    The study and prediction of chemical reactivity is one of the most influential contributions of quantum chemistry. A central concept in the theoretical treatment of chemical reactions is the reaction pathway, which can be quite difficult to integrate accurately and efficiently. This talk will outline our developments in the integration of these pathways on ab initio potential energy surfaces. We will also describe results from recent studies on the kinetics of transition metal catalyzed reactions, including the importance of vibrational coupling to the reaction coordinate and the role of this coupling in catalytic rate enhancement.

  10. Ab-initio study of napthelene based conducting polymer

    SciTech Connect

    Ruhela, Ankur; Kanchan, Reena; Srivastava, Anurag; Sinha, O. P.

    2014-04-24

    In this paper, we have identified structural and electronic properties of conducting polymers by using DFT based ATK-VNL ab-initio tool. Naphthalene derivative structures were stabilized by varying the bond length between two atoms of the molecule C-N and C-C. We have also studied the molecular energy spectrum of naphthalene derivatives and found the HOMOLUMO for the same. A comparison of structural and electronic properties of naphthalene derivatives by attaching the functional group of amine, have been performed and found that they show good semi conducting properties.

  11. Ab Initio Computation of the Energies of Circular Quantum Dots

    SciTech Connect

    Lohne, M. Pedersen; Hagen, Gaute; Hjorth-Jensen, M.; Kvaal, S.; Pederiva, F.

    2011-01-01

    We perform coupled-cluster and diffusion Monte Carlo calculations of the energies of circular quantum dots up to 20 electrons. The coupled-cluster calculations include triples corrections and a renormalized Coulomb interaction defined for a given number of low-lying oscillator shells. Using such a renormalized Coulomb interaction brings the coupled-cluster calculations with triples correlations in excellent agreement with the diffusion Monte Carlo calculations. This opens up perspectives for doing ab initio calculations for much larger systems of electrons.

  12. 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.

  13. 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.

  14. 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.

  15. Emulsifying and interfacial properties of vicilins: role of conformational flexibility at quaternary and/or tertiary levels.

    PubMed

    Liang, Han-Ni; Tang, Chuan-He

    2013-11-20

    Although the functionality of plant proteins (and soy proteins in particular) has been widely investigated in the last decades, the importance of conformational characteristics to their functionalities is still far away from being understood. The aim of the present work was to unravel the role of conformational flexibility at the quaternary and/or tertiary levels in the emulsifying and interfacial properties of phaseolin, an ideal vicilin (or 7S globulin) from red kidney bean. The conformational flexibility at quaternary and tertiary levels of phaseolin was modulated by urea with increasing concentrations from 0 to 8 M, as characterized by using dynamic light scattering (DLS), intrinsic fluorescence and derivative UV spectroscopy, and differential scanning calorimetry (DSC). The emulsifying and interfacial properties, including emulsifying ability, flocculated state of oil droplets (in fresh emulsions), emulsion stability against creaming, and adsorption dynamics at the oil-water interface, were characterized at a specific protein concentration of 0.5% (w/v). The results indicated that increasing the urea concentration resulted in a progressive dissociation of trimeric phaseolin molecules into monomeric subunits, and even a structural unfolding of dissociated subunits; the urea-induced conformational changes at quaternary and/or tertiary levels were reversible, and the molecules at high urea concentrations shared similar structural features to the "molten globule state". On the other hand, increasing the urea concentration progressively improved the emulsifying ability of the protein, and flocculated extent of oil droplets in the fresh emulsions, but led to a progressive decrease in interfacial protein concentration. The improvement of the emulsifying ability was not related to diffusion (during initial adsorption) and penetration at the interface, but highly dependent on ease of structural rearrangement of the adsorbed proteins. These observations clearly

  16. Aspergillus surveillance project at a large tertiary-care hospital.

    PubMed

    Curtis, L; Cali, S; Conroy, L; Baker, K; Ou, C-H; Hershow, R; Norlock-Cruz, F; Scheff, P

    2005-03-01

    A one-year surveillance project was conducted at a large tertiary hospital, which had extensive indoor renovation and extensive demolition/building at several nearby sites. This study collected viable fungi samples in the hospital every six days and analysed 74 duct dust samples for Aspergillus fumigatus mycelial asp f1 protein. Mean total fungi were 257.8 cfu/m3 outdoors, 53.2 cfu/m3 in all indoor samples and 83.5 cfu/m3 in the bone marrow transplant patient rooms. Mean total aspergillus was 6.8 cfu/m3 outdoors, 12.1 cfu/m3 in all indoor samples and 7.3 cfu/m3 in the bone marrow transplant patient rooms. The five most prevalent Aspergillus species collected inside the hospital (mean cfu/m3) were Aspergillus niger 7.57 cfu/m3, Aspergillus candidus 1.72 cfu/m3, Aspergillus flavus 0.97 cfu/m3, A. fumigatus 0.88 cfu/m3 and Aspergillus glaucus 0.45 cfu/m3. In rooms undergoing duct cleaning, mean A. fumigatus concentrations were 11.0 cfu/m3. Forty-eight of 74 (65%) duct dust samples had measurable levels of asp f1 protein, with a mean level of 0.41 ppm and maximum level of 1.94 ppm. Three major incidents involved increased hospital aspergillus concentrations. A. niger levels reached 680 cfu/m3 in an organ transplant room after a water leak from a ceiling pipe. Total aspergillus concentrations rose to 77 cfu/m3 in a bone marrow transplant patient room after improper sealing and water infiltration of the unit's dedicated high-efficiency particulate air filter system. Total aspergillus levels of 160 cfu/m3 were recorded in a renovation area during wood cutting. The higher concentrations of aspergillus seen inside the hospital compared with outdoors and the various moisture/HEPA filter/renovation incidents suggest that numerous small to moderate sources of aspergillus exist in the hospital. PMID:15694975

  17. Summation of Parquet diagrams as an ab initio method in nuclear structure calculations

    SciTech Connect

    Bergli, Elise; Hjorth-Jensen, Morten

    2011-05-15

    Research Highlights: > We present a Green's function based approach for doing ab initio nuclear structure calculations. > In particular the sum the subset of so-called Parquet diagrams. > Applying the theory to a simple but realistic model, results in good agreement with other ab initio methods. > This opens up for ab initio calculations for medium-heavy nuclei. - Abstract: In this work we discuss the summation of the Parquet class of diagrams within Green's function theory as a possible framework for ab initio nuclear structure calculations. The theory is presented and some numerical details are discussed, in particular the approximations employed. We apply the Parquet method to a simple model, and compare our results with those from an exact solution. The main conclusion is that even at the level of approximation presented here, the results shows good agreement with other comparable ab initio approaches.

  18. 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.

  19. 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.

  20. Tertiary paleomagnetism of the North Cascade Range, Washington

    NASA Astrophysics Data System (ADS)

    Beck, Myrl E., Jr.; Burmester, R. F.; Schoonover, Ruth

    1982-05-01

    We have obtained paleomagnetic data for the southern tip of the middle Tertiary Chilliwack Composite Batholith, located on the Canada-United States border about 125 km E of Vancouver, B.C. Thirty-four separately oriented samples were collected along a road traverse 1.5 km long located along State Highway 22, about 20 km NE of Marblemount, Washington. The mean direction after magnetic cleaning is: D, 182.8° I, -65.0° α95, 1.5°. This corresponds to a paleomagnetic pole at 87.5°N, 267.5°E, close to other poles for Tertiary plutons from the North Cascades and only slightly displaced from Tertiary reference poles from the craton. We conclude that the North Cascades block has not been rotated or suffered major internal disruption since perhaps late Eocene time, in marked contrast to all the terranes that surround it.

  1. 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.

  2. 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

  3. Finite Elements in Ab Initio Electronic-Structure Calulations

    NASA Astrophysics Data System (ADS)

    Pask, J. E.; Sterne, P. A.

    Over the course of the past two decades, the density functional theory (DFT) (see e.g., [1]) of Hohenberg, Kohn, and Sham has proven to be an accurate and reliable basis for the understanding and prediction of a wide range of materials properties from first principles (ab initio), with no experimental input or empirical parameters. However, the solution of the Kohn-Sham equations of DFT is a formidable task and this has limited the range of physical systems which can be investigated by such rigorous, quantum mechanical means. In order to extend the interpretive and predictive power of such quantum mechanical theories further into the domain of "real materials", involving nonstoichiometric deviations, defects, grain boundaries, surfaces, interfaces, and the like; robust and efficient methods for the solution of the associated quantum mechanical equations are critical. The finite-element (FE) method (see e.g., [2]) is a general method for the solution of partial differential and integral equations which has found wide application in diverse fields ranging from particle physics to civil engineering. Here, we discuss its application to large-scale ab initio electronic-structure calculations.

  4. 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.

  5. 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.

  6. Unified ab initio approaches to nuclear structure and reactions

    NASA Astrophysics Data System (ADS)

    Navrátil, Petr; Quaglioni, Sofia; Hupin, Guillaume; Romero-Redondo, Carolina; Calci, Angelo

    2016-05-01

    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 7Be {({{p}},γ )}8{{B}} radiative capture. Finally, we highlight our efforts to describe transfer reactions including the 3H{({{d}},{{n}})}4He fusion.

  7. 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.

  8. Entropy of Liquid Water from Ab Initio Molecular Dynamics

    NASA Astrophysics Data System (ADS)

    Spanu, Leonardo; Zhang, Cui; Galli, Giulia

    2012-02-01

    The debate on the structural properties of water has been mostly based on the calculation of pair correlation functions. However, the simulation of thermodynamic and spectroscopic quantities may be of great relevance for the characterization of liquid water properties. We have computed the entropy of liquid water using a two-phase thermodynamic model and trajectories generated by ab initio molecular dynamics simulations [1]. In an attempt to better understand the performance of several density functionals in simulating liquid water, we have performed ab initio molecular dynamics using semilocal, hybrid [2] and van der Waals density functionals [3]. We show that in all cases, at the experimental equilibrium density and at temperatures in the vicinity of 300 K, the computed entropies are underestimated, with respect to experiment, and the liquid exhibits a degree of tetrahedral order higher than in experiments. We also discuss computational strategies to simulate spectroscopic properties of water, including infrared and Raman spectra.[4pt] [1] C.Zhang, L.Spanu and G.Galli, J.Phys.Chem. B 2011 (in press)[0pt] [2] C.Zhang, D.Donadio, F.Gygi and G.Galli, J. Chem. Theory Comput. 7, 1443 (2011)[0pt] [3] C.Zhang, J.Wu, G.Galli and F.Gygi, J. Chem. Theory Comput. 7, 3061 (2011)

  9. 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.

  10. 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

  11. 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.

  12. Late Tertiary paleogeographic and tectonic evolution of the Mediterranean area

    SciTech Connect

    Arnott, R.J.; Haan, E.A.

    1988-08-01

    The present geography of the Mediterranean Sea is the result of late Tertiary tectonic processes and hardly reflects its Mesozoic and early Tertiary evolution. This paper outlines a plate tectonics model for the Mediterranean area from the Oligocene to the Pliocene. Seismic and well data have been integrated into the regional structural framework to produce a set of paleogeographic maps, which includes the Oligocene, early and middle Miocene, late Miocene, and Pliocene. These maps highlight the changes in sedimentation patterns in response to the tectonic development of the Mediterranean area. Special attention will be given to the Messinian desiccation event.

  13. Tertiary foraminiferal rock samples from the western Solomon Sea

    NASA Astrophysics Data System (ADS)

    Haig, David W.

    1986-12-01

    Rock fragments dredged from four R/VNatsushima stations contain Tertiary foraminifera. The oldest sample is an upper bathyal biomicrite of Early Eocene age (52 to 53.5 Ma) from the the Trobriand Platform. Upper Oligocene-Lower Miocene neritic limestones were located off the Trobriand Platform and on the inner wall of the New Britain Trench. Miocene bathyal sediments come from the Trobriand Platform; similar Pliocene rocks were recovered here as well as from the inner wall of the New Britain Trench and the central part of the Solomon Sea Basin. No reworked pre-Tertiary foraminifera are present in any sample.

  14. 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.

  15. Resistance of spiders to Cretaceous-Tertiary extinction events.

    PubMed

    Penney, David; Wheater, C Philip; Selden, Paul A

    2003-11-01

    Throughout Earth history a small number of global catastrophic events leading to biotic crises have caused mass extinctions. Here, using a technique that combines taxonomic and numerical data, we consider the effects of the Cenomanian-Turonian and Cretaceous-Tertiary mass extinctions on the terrestrial spider fauna in the light of new fossil data. We provide the first evidence that spiders suffered no decline at the family level during these mass extinction events. On the contrary, we show that they increased in relative numbers through the Cretaceous and beyond the Cretaceous-Tertiary extinction event. PMID:14686534

  16. Transmembrane beta-barrel protein structure prediction

    NASA Astrophysics Data System (ADS)

    Randall, Arlo; Baldi, Pierre

    Transmembrane β-barrel (TMB) proteins are embedded in the outer membranes of mitochondria, Gram-negative bacteria, and chloroplasts. These proteins perform critical functions, including active ion-transport and passive nutrient intake. Therefore, there is a need for accurate prediction of secondary and tertiary structures of TMB proteins. A variety of methods have been developed for predicting the secondary structure and these predictions are very useful for constructing a coarse topology of TMB structure; however, they do not provide enough information to construct a low-resolution tertiary structure for a TMB protein. In addition, while the overall structural architecture is well conserved among TMB proteins, the amino acid sequences are highly divergent. Thus, traditional homology modeling methods cannot be applied to many putative TMB proteins. Here, we describe the TMBpro: a pipeline of methods for predicting TMB secondary structure, β-residue contacts, and finally tertiary structure. The tertiary prediction method relies on the specific construction rules that TMB proteins adhere to and on the predicted β-residue contacts to dramatically reduce the search space for the model building procedure.

  17. Protein Residue Contacts and Prediction Methods

    PubMed Central

    Adhikari, Badri

    2016-01-01

    In the field of computational structural proteomics, contact predictions have shown new prospects of solving the longstanding problem of ab initio protein structure prediction. In the last few years, application of deep learning algorithms and availability of large protein sequence databases, combined with improvement in methods that derive contacts from multiple sequence alignments, have shown a huge increase in the precision of contact prediction. In addition, these predicted contacts have also been used to build three-dimensional models from scratch. In this chapter, we briefly discuss many elements of protein residue–residue contacts and the methods available for prediction, focusing on a state-of-the-art contact prediction tool, DNcon. Illustrating with a case study, we describe how DNcon can be used to make ab initio contact predictions for a given protein sequence and discuss how the predicted contacts may be analyzed and evaluated. PMID:27115648

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

    PubMed

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

    2016-07-01

    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

  19. 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

  20. Global Trends in Tertiary Education Quality Assurance: Implications for the Anglophone Caribbean.

    ERIC Educational Resources Information Center

    Roberts, Vivienne

    2001-01-01

    Review of literature on trends in quality-assurance systems for tertiary education throughout the world followed by a discussion of the implications of these trends for tertiary education in the Caribbean. (Contains 26 references.) (PKP)

  1. 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.

  2. 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)…

  3. Teaching the Attributes of Venture Teamwork in Tertiary Entrepreneurship Programmes

    ERIC Educational Resources Information Center

    Kotey, Bernice

    2007-01-01

    Purpose: The paper seeks to demonstrate the characteristics of group work that are required to teach the attributes of real world venture teamwork in tertiary entrepreneurship programmes. Design/methodology/approach: One-tailed Spearman correlation analysis is used to assess the associations between students' grades in four group assessment tasks…

  4. Autonomous Language Learning: Hong Kong Tertiary Students' Attitudes and Behaviors.

    ERIC Educational Resources Information Center

    Chan, Victoria; Spratt, Mary; Humphreys, Gillian

    2002-01-01

    Studied students' views of their responsibilities and decision-making abilities in learning English, motivation, and learning activities of 508 tertiary students learning English at Hong Kong Polytechnic University, Hong Kong. Presents the student profile generated from the study and discusses the pedagogical implications. (SLD)

  5. 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)

  6. 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…

  7. Constructing Knowledge Societies: New Challenges for Tertiary Education.

    ERIC Educational Resources Information Center

    Salmi, Jamil

    2003-01-01

    The principal set of challenges facing tertiary education today is that set which links it to the construction of knowledge societies. Governments, the private sector, and the World Bank have specific tasks to perform in meeting these challenges. Countries--depending upon whether or not they are transition economies, low-income countries, or small…

  8. Endosymbiotic gene transfer in tertiary plastid-containing dinoflagellates.

    PubMed

    Burki, Fabien; Imanian, Behzad; Hehenberger, Elisabeth; Hirakawa, Yoshihisa; Maruyama, Shinichiro; Keeling, Patrick J

    2014-02-01

    Plastid establishment involves the transfer of endosymbiotic genes to the host nucleus, a process known as endosymbiotic gene transfer (EGT). Large amounts of EGT have been shown in several photosynthetic lineages but also in present-day plastid-lacking organisms, supporting the notion that endosymbiotic genes leave a substantial genetic footprint in the host nucleus. Yet the extent of this genetic relocation remains debated, largely because the long period that has passed since most plastids originated has erased many of the clues to how this process unfolded. Among the dinoflagellates, however, the ancestral peridinin-containing plastid has been replaced by tertiary plastids on several more recent occasions, giving us a less ancient window to examine plastid origins. In this study, we evaluated the endosymbiotic contribution to the host genome in two dinoflagellate lineages with tertiary plastids. We generated the first nuclear transcriptome data sets for the "dinotoms," which harbor diatom-derived plastids, and analyzed these data in combination with the available transcriptomes for kareniaceans, which harbor haptophyte-derived plastids. We found low level of detectable EGT in both dinoflagellate lineages, with only 9 genes and 90 genes of possible tertiary endosymbiotic origin in dinotoms and kareniaceans, respectively, suggesting that tertiary endosymbioses did not heavily impact the host dinoflagellate genomes.

  9. 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…

  10. Competition and Reform of the New Zealand Tertiary Education Sector

    ERIC Educational Resources Information Center

    Abbott, Malcolm

    2006-01-01

    The purpose of this paper is to use an historical approach to examine the changing nature, size and diversification of education and training in New Zealand. In particular, attention will be concentrated on the impact of the introduction of competition into the New Zealand tertiary education industry since 1989. It will examine the relationship…

  11. Appropriate Selection Procedures for a Multicultural Tertiary Institution.

    ERIC Educational Resources Information Center

    Malan, D. Johann

    1994-01-01

    If entrance to tertiary education in South Africa is restricted to successful school final-examination scores, blacks may be underrepresented for many years. Difficulties in ridding South African education of racism and alternative strategies for conditional enrollment in higher education are discussed. (SLD)

  12. Predictors of Attrition and Achievement in a Tertiary Bridging Program

    ERIC Educational Resources Information Center

    Whannell, Robert

    2013-01-01

    This study examines the attrition and achievement of a sample of 295 students in an on-campus tertiary bridging program at a regional university. A logistic regression analysis using enrolment status, age and the number of absences from scheduled classes at week three of the semester as predictor variables correctly predicted 92.8 percent of…

  13. Initial Educational Experiences of Tertiary Students. LSAY Briefing Number 14

    ERIC Educational Resources Information Center

    Hillman, Kylie

    2008-01-01

    This "Briefing" presents information about the initial tertiary education experiences, such as satisfaction with aspects of student life and changes to initial enrolments, of two groups of young people, based on two recent Longitudinal Surveys of Australian Youth (LSAY) research reports. One study focused on the first year experiences of a group…

  14. 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…

  15. Annual Technical Progress Report - West Hackberry Tertiary Project

    SciTech Connect

    Allen Fornea; Bruce Cerveny; Travis H. Gillham

    1997-09-30

    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. Air injection on the west flank 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 downstructure well.

  16. 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…

  17. 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…

  18. 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…

  19. English Textbooks in Parallel-Language Tertiary Education

    ERIC Educational Resources Information Center

    Pecorari, Diane; Shaw, Philip; Malmstrom, Hans; Irvine, Aileen

    2011-01-01

    Tertiary education in many countries is increasingly bilingual, with English used in parallel with the national language, particularly as a reading language. This article describes the results of a survey of student attitudes toward, and reading practices regarding, English language textbooks. Over 1,000 students at three Swedish universities…

  20. Reform and Development of Tertiary Education in Europe. Recommendations.

    ERIC Educational Resources Information Center

    de Moor, R. A.; Vedel, Doyer Georges

    Tertiary education policies in seven Western European and seven Southern European countries are evaluated in two reports. In the first report by R. A. de Moor, attention is focused on France, the Federal Republic of Germany, the Netherlands, Norway, Sweden, Switzerland, and the United Kingdom. The evaluation and policy recommendations for the…

  1. Primary, secondary, and tertiary effects of phototherapy: a review

    NASA Astrophysics Data System (ADS)

    Dyson, Mary

    2006-02-01

    The classification of the cellular effects of phototherapy into primary, secondary and tertiary types is an aid to understanding variation in the predictability of the events that follow its application. Primary effects are generally restricted to the absorption of photons by cytochromes and catalytic interactions with these and other intracellular molecules. If suprathreshold, they stimulate cell activity, initiating secondary anabolic effects in those cells affected by the photons. These events can also be initiated by nonphotonic stimuli. Some of the secondary effects, such as growth factor secretion, can produce effects in cells that did not absorb photons. It is proposed that this group of effects be classified as tertiary. Primary effects are strongly predictable, secondary effects less so, being dependent on cell sensitivity, while tertiary effects are the least predictable, being affected by variation in both the internal and external environment and by intercellular interactions. The investigation of primary and secondary effects of phototherapy can be used to determine which irradiation parameters are ineffective in vitro and therefore cannot be effective in vivo. Since tertiary effects predominate in vivo only clinical testing can demonstrate which parameters are most likely to be effective, and with what level of predictability. It is essential that all relevant exposure conditions be recorded and disseminated if experimental work is to be of clinical value. It is also essential that all relevant information about the target of phototherapy, be it molecule, organelle, cell, healthy volunteer or patient, be recorded and disseminated.

  2. 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…

  3. 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,…

  4. 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…

  5. A Comparison of Career Success between Graduates of Vocational and Academic Tertiary Education

    ERIC Educational Resources Information Center

    Backes-Gellner, Uschi; Geel, Regula

    2014-01-01

    This paper analyses whether tertiary education of different types, i.e., academic or vocational tertiary education, leads to more or less favorable labor market outcomes. We study the problem for Switzerland, where more than two thirds of the workforce gain vocational secondary degrees and a substantial number go on to a vocational tertiary degree…

  6. 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…

  7. 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)

  8. 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)…

  9. 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...

  10. 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...

  11. 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...

  12. 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...

  13. 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...

  14. 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…

  15. 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].

  16. 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.

  17. Quasi-Ab initio molecular dynamic study of Fe melting

    PubMed

    Belonoshko; Ahuja; Johansson

    2000-04-17

    We have investigated the melting of hcp Fe at high pressure by employing molecular dynamics simulations in conjunction with the full potential linear muffin tin orbital method. Apart from being of fundamental value, the melting of iron at high pressure is also important for our understanding of the Earth. The subject of iron melting at high pressures is controversial. The experimental data for the iron melting temperature can be separated into two regions, "low" and "high." Here we present an ab initio simulated iron melting curve which is in agreement with the low temperatures at lower pressures, but is in excellent agreement with the high-mostly shockwave-temperatures at high pressures. A comparison with available data lends support to the presented iron melting curve.

  18. Effective pair potentials using an ab initio variational approach

    NASA Astrophysics Data System (ADS)

    Faussurier, Gérald; Blancard, Christophe; Silvestrelli, Pier Luigi

    2010-01-01

    We used a variational approach adapted to a quantum molecular-dynamics code to determine the best reference potential for warm dense aluminum. This ab initio variational approach was based on the Gibbs-Bogolyubov inequality. We used many-body reference systems interacting through inverse-power-law potentials, among which the Coulomb potential was a particular case defining the classical one-component plasma model. By comparisons with full quantum molecular-dynamics simulations, we found that the Coulomb potential was not always the best reference potential. We calculated the self-diffusion coefficient and the shear viscosity and discussed the results obtained using the Chisolm-Wallace relation in the warm dense matter regime.

  19. Ab initio calculation of the shock Hugoniot of bulk silicon

    NASA Astrophysics Data System (ADS)

    Strickson, Oliver; Artacho, Emilio

    2016-03-01

    We describe how ab initio molecular dynamics can be used to determine the Hugoniot locus (states accessible by a shock wave) for materials with a number of stable phases, and with an approximate treatment of plasticity and yield, without having to simulate these phenomena directly. We consider the case of bulk silicon, with forces from density-functional theory, up to 70 GPa. The fact that shock waves can split into multiple waves due to phase transitions or yielding is taken into account here by specifying the strength of any preceding waves explicitly based on their yield strain. Points corresponding to uniaxial elastic compression along three crystal axes and a number of postshock phases are given, including a plastically yielded state, approximated by an isotropic stress configuration following an elastic wave of predetermined strength. The results compare well to existing experimental data for shocked silicon.

  20. Ab Initio Calculations of Excited Carrier Dynamics in Gallium Nitride

    NASA Astrophysics Data System (ADS)

    Jhalani, Vatsal; Bernardi, Marco

    Bulk wurtzite GaN is the primary material for blue light-emission technology. The radiative processes in GaN are regulated by the dynamics of excited (or so-called ``hot'') carriers, through microscopic processes not yet completely understood. We present ab initio calculations of electron-phonon (e-ph) scattering rates for hot carriers in GaN. Our work combines density functional theory to compute the electronic states, and density functional perturbation theory to obtain the phonon dispersions and e-ph coupling matrix elements. These quantities are interpolated on fine Brillouin zone grids with maximally localized Wannier functions, to converge the e-ph scattering rates within 5 eV of the band edges. We resolve the contribution of the different phonon modes to the total scattering rate, and study the impact on the relaxation times of the long-range Fröhlich interaction due to the longitudinal-optical phonon modes.

  1. 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.

  2. Ab initio study of guanine damage by hydroxyl radical.

    PubMed

    Chaban, Galina M; Wang, Dunyou; Huo, Winifred M

    2015-01-15

    Multiconfigurational ab initio methods are used in this study to examine two initial reactions that take place during the OH radical attack of the DNA base guanine: a ring opening reaction and a hydrogen transfer reaction. The same reactions are also studied in the presence of a single water molecule. The ring opening reaction has a moderate barrier height of ∼20-25 kcal/mol that is relatively insensitive to the presence of water. The barrier of the H-transfer reaction, on the other hand, is lowered from ∼50 to ∼22 kcal/mol when one water molecule is added, thus becoming comparable to the barrier height of the ring opening reaction. PMID:25517252

  3. 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.

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

    PubMed

    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.

  5. Ab initio study of palladium and silicon carbide

    SciTech Connect

    Schuck, Paul C; Stoller, Roger E; Shrader, David

    2011-01-01

    Ab initio methods have been used to investigate the properties of Pd as impurity in bulk SiC at five charge states within the framework of density functional theory using the local density spin approximation. Pd interstitials and substitutionals have similar energy to their intrinsic counterparts. In addition, Pd substitutes for a vacancy, di-vacancy, and tri-vacancy with similar energies. Pd will also diffuse through SiC via an interstitial mechanism employing the tetrahedral sites and Pd can substitute for Si and C at positive charge states. Removing electrons (p-type doping) from SiC lowers the formation and migration energies of Pd defects in SiC for most configurations.

  6. 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.

  7. Ab initio and RRKM calculations of o-benzyne pyrolysis

    NASA Astrophysics Data System (ADS)

    Deng, Wei-Qiao; Han, Ke-Li; Zhan, Ji-Ping; He, Guo-Zhong

    1998-05-01

    Recently, a new mechanism has been provided in the phenyl pyrolysis, that is, the phenyl dissociation favours the benzyne channel by losing an H atom [H. Wang, M. Frenklach, J. Phys. Chem., 98 (1994) 11465]. In this Letter, the dissociation of o-benzyne has been investigated by means of ab initio theory. The geometries and structures of o-benzyne with its pyrolysis products C 4H 2, C 2H 2 and also the transition state were optimized at the UHF/6-31G* level. The single point energies were refined by B3LYP/6-31G* calculations. The unimolecular rate constants for o-benzyne pyrolysis in different pressures were calculated by the Rice-Ramsperger-Kassel-Marcus (RRKM) method.

  8. 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. PMID:27015491

  9. 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. PMID:25687650

  10. Reactive Monte Carlo sampling with an ab initio potential

    NASA Astrophysics Data System (ADS)

    Leiding, Jeff; Coe, Joshua D.

    2016-05-01

    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 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). We find that there are regions of state space for which RxMC sampling is much more efficient than AIMD due to the "rare-event" character of chemical reactions.

  11. Ab initio X-Ray Absorption Fine Structure Cumulants

    NASA Astrophysics Data System (ADS)

    Vila, F.; Rehr, J. J.; Rossner, H. H.; Krappe, H. J.

    2006-03-01

    Theoretical calculations of vibrational effects in x-ray absorption spectra typically employ semi-phenomenological models, e.g. empirical force constants or correlated Debye or Einstein models. Instead we introduce an efficient and generally applicable ab initio approach based on electronic structure calculations of the dynamical matrix together with the Lanczos recursion algorithm [1] and relations between the cumulants. The approach yields 1) the thermal expansion coefficients (first cumulant of the vibrational distribution function); 2) correlated Debye-Waller factors (second cumulants) and 3) anharmonic contributions (third cumulants). Results are presented for crystalline (Cu, Au, Ge, GaAs) and molecular (GeCl4, C6H6) systems. Our results for the Debye-Waller factors agree well with experiment. [1]H.J. Krappe and H.H. Rossner, Phys. Rev. B70, 104102 (2004).

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

    PubMed

    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.

  13. 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

  14. Ab Initio Force Fields for Imidazolium-Based Ionic Liquids.

    PubMed

    McDaniel, Jesse G; Choi, Eunsong; Son, Chang Yun; Schmidt, J R; Yethiraj, Arun

    2016-07-21

    We develop ab initio force fields for alkylimidazolium-based ionic liquids (ILs) that predict the density, heats of vaporization, diffusion, and conductivity that are in semiquantitative agreement with experimental data. These predictions are useful in light of the scarcity of and sometimes inconsistency in experimental heats of vaporization and diffusion coefficients. We illuminate physical trends in the liquid cohesive energy with cation chain length and anion. These trends are different than those based on the experimental heats of vaporization. Molecular dynamics prediction of the room temperature dynamics of such ILs is more difficult than is generally realized in the literature due to large statistical uncertainties and sensitivity to subtle force field details. We believe that our developed force fields will be useful for correctly determining the physics responsible for the structure/property relationships in neat ILs.

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

    PubMed

    Olsson, P; Vidal, J; Lincot, D

    2011-10-12

    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 ZnTe(2) 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.

  16. 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.

  17. 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.

  18. 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.

  19. Isofulminic acid, HONC: Ab initio theory and microwave spectroscopy.

    PubMed

    Mladenović, Mirjana; Lewerenz, Marius; McCarthy, Michael C; Thaddeus, Patrick

    2009-11-01

    Isofulminic acid, HONC, the most energetic stable isomer of isocyanic acid HNCO, higher in energy by 84 kcal/mol, has been detected spectroscopically by rotational spectroscopy supported by coupled cluster electronic structure calculations. The fundamental rotational transitions of the normal, carbon-13, oxygen-18, and deuterium isotopic species have been detected in the centimeter band in a molecular beam by Fourier transform microwave spectroscopy, and rotational constants and nitrogen and deuterium quadrupole coupling constants have been derived. The measured constants agree well with those predicted by ab initio calculations. A number of other electronic and spectroscopic parameters of isofulminic acid, including the dipole moment, vibrational frequencies, infrared intensities, and centrifugal distortion constants have been calculated at a high level of theory. Isofulminic acid is a good candidate for astronomical detection with radio telescopes because it is highly polar and its more stable isomers (HNCO, HOCN, and HCNO) have all been identified in space. PMID:19895013

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

    PubMed Central

    Wu, Henry; Mayeshiba, Tam; Morgan, Dane

    2016-01-01

    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. PMID:27434308

  1. Vibrational and ab initio molecular dynamics studies of bradykinin

    NASA Astrophysics Data System (ADS)

    Święch, Dominika; Kubisiak, Piotr; Andrzejak, Marcin; Borowski, Piotr; Proniewicz, Edyta

    2016-07-01

    In this study, the comprehensive theoretical and experimental investigations of Raman (RS) and infrared absorption (IR) spectra of bradykinin (BK) are presented. The ab initio Born-Oppenheimer molecular dynamics (BOMD) calculations, in the presence of water molecules that form the first coordination sphere, were used for conformational analysis of the BK structure. Based on the Density Functional Theory (DFT) calculations at the B3LYP/6-311G(d) level the vibrational spectra were interpreted. The calculated frequencies were scaled by means of the effective scaling frequency factor (ESFF) method. The theoretical data, which confirm the compact structure of BK in the presence of the water molecules revealed the remarkable effect of the intermolecular hydrogen bonding on the BK structural properties.

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

    NASA Astrophysics Data System (ADS)

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

    2015-01-01

    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.

  3. 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.

  4. 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.

  5. RNA chaperone StpA loosens interactions of the tertiary structure in the td group I intron in vivo

    PubMed Central

    Waldsich, Christina; Grossberger, Rupert; Schroeder, Renée

    2002-01-01

    Efficient splicing of the td group I intron in vivo is dependent on the ribosome. In the absence of translation, the pre-mRNA is trapped in nonnative-splicing-incompetent conformations. Alternatively, folding of the pre-mRNA can be promoted by the RNA chaperone StpA or by the group I intron-specific splicing factor Cyt-18. To understand the mechanism of action of RNA chaperones, we probed the impact of StpA on the structure of the td intron in vivo. Our data suggest that StpA loosens tertiary interactions. The most prominent structural change was the opening of the base triples, which are involved in the correct orientation of the two major intron core domains. In line with the destabilizing activity of StpA, splicing of mutant introns with a reduced structural stability is sensitive to StpA. In contrast, Cyt-18 strengthens tertiary contacts, thereby rescuing splicing of structurally compromised td mutants in vivo. Our data provide direct evidence for protein-induced conformational changes within catalytic RNA in vivo. Whereas StpA resolves tertiary contacts enabling the RNA to refold, Cyt-18 contributes to the overall compactness of the td intron in vivo. PMID:12208852

  6. 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

  7. Ab-Initio Based Computation of Rate Constants for Spin Forbidden Metalloprotein-Substrate Reactions

    NASA Astrophysics Data System (ADS)

    Ozkanlar, Abdullah; Rodriguez, Jorge H.

    2007-03-01

    Some chemical and biochemical reactions are non-adiabatic processes whereby the total spin angular momentum, before and after the reaction, is not conserved. These are named spin- forbidden reactions. The application of ab-initio methods, such as spin density functional theory (SDFT), to the prediction of rate constants is a challenging task of fundamental and practical importance. We apply non-adiabatic transition state theory (NA-TST) in conjuntion with SDFT to predict the rate constant of the spin- forbidden recombination of carbon monoxide with iron tetracarbonyl. To model the surface hopping probability between singlet and triplet states, the Landau-Zener formalism is used. The lowest energy point for singlet-triplet crossing, known as minimum energy crossing point (MECP), was located and used to compute, in a semi-quantum approach, reaction rate constants at 300 K. The predicted rates are in very good agreement with experiment. In addition, we present results for the spin- forbidden ligand binding reactions of iron-containing heme proteins such as myoglobin.

  8. Ab initio structure determination from prion nanocrystals at atomic resolution by MicroED

    PubMed Central

    Sawaya, Michael R.; Rodriguez, Jose; Cascio, Duilio; Collazo, Michael J.; Shi, Dan; Reyes, Francis E.; Gonen, Tamir; Eisenberg, David S.

    2016-01-01

    Electrons, because of their strong interaction with matter, produce high-resolution diffraction patterns from tiny 3D crystals only a few hundred nanometers thick in a frozen-hydrated state. This discovery offers the prospect of facile structure determination of complex biological macromolecules, which cannot be coaxed to form crystals large enough for conventional crystallography or cannot easily be produced in sufficient quantities. Two potential obstacles stand in the way. The first is a phenomenon known as dynamical scattering, in which multiple scattering events scramble the recorded electron diffraction intensities so that they are no longer informative of the crystallized molecule. The second obstacle is the lack of a proven means of de novo phase determination, as is required if the molecule crystallized is insufficiently similar to one that has been previously determined. We show with four structures of the amyloid core of the Sup35 prion protein that, if the diffraction resolution is high enough, sufficiently accurate phases can be obtained by direct methods with the cryo-EM method microelectron diffraction (MicroED), just as in X-ray diffraction. The success of these four experiments dispels the concern that dynamical scattering is an obstacle to ab initio phasing by MicroED and suggests that structures of novel macromolecules can also be determined by direct methods. PMID:27647903

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

    PubMed

    Tu, Liwei; Khanna, Pooja; Deutsch, Carol

    2014-01-01

    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.

  10. Transmembrane Segments Form Tertiary Hairpins in the Folding Vestibule of the Ribosome.

    PubMed Central

    Tu, LiWei; Khanna, Pooja; Deutsch, Carol

    2013-01-01

    Folding of membrane proteins begins in the ribosome as the peptide is elongated. During this process, the nascent peptide navigates along 100 Å 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. PMID:24055377

  11. 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.

  12. Influence of Cononsolvency on the Aggregation of Tertiary Butyl Alcohol in Methanol-Water Mixtures.

    PubMed

    Mochizuki, Kenji; Pattenaude, Shannon R; Ben-Amotz, Dor

    2016-07-27

    The term cononsolvency has been used to describe a situation in which a polymer is less soluble (and so is more likely to collapse and aggregate) in a mixture of two cosolvents than it is in either one of the pure solvents. Thus, cononsolvency is closely related to the suppression of protein denaturation by stabilizing osmolytes. Here, we show that cononsolvency behavior can also influence the aggregation of tertiary butyl alcohol in mixtures of water and methanol, as demonstrated using both Raman multivariate curve resolution spectroscopy and molecular dynamics simulations. Our results imply that cononsolvency results from the cosolvent-mediated enhancement of the attractive (solvophobic) mean force between nonpolar groups, driven by preferential solvation of the aggregates, in keeping with Wyman-Tanford theory. PMID:27363494

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

    PubMed

    Tu, Liwei; Khanna, Pooja; Deutsch, Carol

    2014-01-01

    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. PMID:24055377

  14. Tertiary paleomagnetism of regions around the South China Sea

    NASA Astrophysics Data System (ADS)

    Fuller, M.; Haston, R.; Lin, Jin-Lu; Richter, B.; Schmidtke, E.; Almasco, J.

    Paleomagnetic data from the Philippine Sea Plate (PSP) reveal a history of plate-wide clockwise (CW) rotation and northerly translation since the late Eocene about a nearby pole to the east. The motion has generated left lateral oblique convergence between the Philippine Sea Plate and S.E. Asia. Paleomagnetic data from Luzon in the northern Philippines show early Miocene CCW rotation followed by late Miocene CW rotation. In contrast, the Southern and Central Philippines display early Miocene CW rotation and unrotated late Miocene directions. These results define two different paleomagnetic domains with distinct post early Miocene histories. Pre-Miocene CCW rotation is suggested by data from Zambales, the Visayas and the Celebes Sea. In Borneo, a history of Tertiary CCW rotation has been found in Sarawak, and Sabah. Conflicting results have been reported from Kalimantan, some show no rotation with respect to Eurasia, while others give CCW rotations. In the Malaysian peninsula, the Segamat basalts and Kuantan dykes, of probable late Cretaceous early Tertiary age show CCW rotations similar to those seen in Sarawak. To the north peninsular Thailand, CW rotations have been found in two Miocene non-marine basins. Late Tertiary basalts from Northern and Central Thailand yield similar CW rotations while coeval flows on the Khorat plateau in Eastern Thailand are unrotated. The tectonic implications of the results remain problematical. In particular, the relative importance of true plate rotations and localized rotation of upper crustal blocks in distributed shear zones is unclear. The substantial region of CCW rotation in Borneo, the Celebes Sea and the Philippines is consistent with the broad features of the Holloway model, although the timing of the rotations precludes simple coherent rotation. The model must also be modified to include the effect of the left lateral oblique convergence between the PSP and Eurasia. The CW rotations seen in peninsular Thailand and Malaysia

  15. 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.

  16. Stable conformation of full-length amyloid-β (1-42) monomer in water: Replica exchange molecular dynamics and ab initio molecular orbital simulations

    NASA Astrophysics Data System (ADS)

    Okamoto, Akisumi; Yano, Atsushi; Nomura, Kazuya; Higai, Shin'ichi; Kurita, Noriyuki

    2013-07-01

    Aggregation of amyloid β-proteins (Aβ) plays a key role in the mechanism of molecular pathogenesis of Alzheimer’s disease (AD). It is known that full-length Aβ(1-42) is more prone to aggregation than Aβ(1-40). We here search stable conformations of solvated Aβ(1-42) monomer by replica exchange molecular dynamics simulations based on classical force fields, and the most stable conformation is determined from the total energies evaluated by the ab initio fragment molecular orbital (FMO) calculations. In addition, based on the FMO results, the amino acid residues of Aβ(1-42) contributing to the stabilization of the monomer are highlighted.

  17. Ab-initio modeling of an anion C- 60 pseudopotential for fullerene-based compounds

    NASA Astrophysics Data System (ADS)

    Vrubel, Ivan I.; Polozkov, Roman G.; Ivanov, Vadim K.

    2016-08-01

    An anion C- 60 pseudopotential is determined from an ab-initio-based approach. First, ab-initio calculations are performed to calculate the electronic charge density and the total electrostatic potential. Second, the effective dependence of the pseudopotential on the radial degree of freedom is extracted from the angular average of the total electrostatic potential. Finally, the resulting effective pseudopotential is fitted to a simple analytical form which can be applied in further dynamical simulations of fullerene-based compounds.

  18. 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

  19. Contributions of a hydrogen bond/salt bridge network to the stability of secondary and tertiary structure in lambda repressor.

    PubMed Central

    Marqusee, S.; Sauer, R. T.

    1994-01-01

    In the N-terminal domain of lambda repressor, the Asp 14 side chain forms an intrahelical, hydrogen bond/salt bridge with the Arg 17 side chain and a tertiary hydrogen bond with the Ser 77 side chain. By measuring the stabilities to urea denaturation of the wild-type N-terminal domain and variants containing single, double, and triple alanine substitutions at positions 14, 17, and 77, the side-chain interaction energies, the coupling energy between interactions, and the intrinsic effects of each wild-type side chain on protein stability have been estimated. These studies indicate that the Asp 14-Arg 17 and Asp 14-Ser 77 interactions are stabilizing by roughly 0.8 and 1.5 kcal/mol, respectively, but that Asp 14, by itself, is destabilizing by roughly 0.9 kcal/mol. We also show that a peptide model of alpha-helix 1, which contains Asp 14 and Arg 17, forms a reasonably stable, monomeric helix in solution and responds to alanine mutations at positions 14 and 17 in the fashion expected from the intact protein studies. These studies suggest that it is possible to view the stability effects of mutations in intact proteins in a hierarchical fashion, with the stability of units of secondary structure being distinguishable from the stability of tertiary structure. PMID:7756981

  20. 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.

  1. 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

  2. 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.

  3. TMT tertiary mirror axis calibration with laser tracker

    NASA Astrophysics Data System (ADS)

    An, Qi-chang; Zhang, Jing-xu; Yang, Fei; Sun, Jing-wei

    2015-03-01

    To calibrate the tracing performance of the thirty meter telescope (TMT) tertiary mirror, for the special requirement of the TMT, the laser tracker is used to verify the motion. Firstly, the deviation is divided into two parts, namely, the repeatable error and the unrepeatable part. Then, based on the laser tracker, the mearturement and evalutation methods of the rigid body motion for the mirror are established, and the Monte Carol method is used to determine the accuracy of the mothod. Lastly, the mothod is applied to the turn table of a classical telescope and the residual error is about 4 arc second. The work of this paper will guide the next desgin and construction work of the thirty meter telescope tertiary mirror.

  4. Extraterrestrial cause for the Cretaceous-Tertiary extinction

    NASA Technical Reports Server (NTRS)

    Alvarez, L. W.; Alvarez, W.; Asaro, F.; Michel, H. V.

    1980-01-01

    Direct physical evidence is presented for an unusual event at exactly the time of extinctions in the planktonic realm. Deep-sea limestones exposed in Italy, Denmark, and New Zealand indicate 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 that this iridium is of extraterrestrial origin, but did not come from a nearby supernova. A hypothesis is set forth which accounts for the extinctions and the iridium observations. One prediction of this hypothesis is verified, that 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 chemically similar Cretaceous and Tertiary limestones.

  5. 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. PMID:26708122

  6. 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.

  7. Major wildfires at the Cretaceous-Tertiary boundary

    NASA Astrophysics Data System (ADS)

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

    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.

  8. 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.

  9. 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

  10. 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

  11. Operator evolution for ab initio theory of light nuclei

    NASA Astrophysics Data System (ADS)

    Schuster, Micah; Quaglioni, Sofia; Johnson, Calvin; Jurgenson, Eric; Navrátil, Petr

    2014-09-01

    The past two decades have seen a revolution in ab initio calculations of nuclear properties. One key element has been the development of a rigorous effective interaction theory, applying unitary transformations to soften the nuclear Hamiltonian and hence accelerate the convergence as a function of the model space size. For consistency, however, one ought to apply the same transformation to other operators when calculating transitions and mean values from the eigenstates of the renormalized Hamiltonian. Working in a translationally invariant harmonic oscillator basis for the two- and three-nucleon systems, we evolve the Hamiltonian, square radius, and total dipole strength operators by the similarity renormalization group (SRG). The inclusion of up to three-body matrix elements in the 4He nucleus all but completely restores the invariance of the expectation values under the transformation. We also consider a Gaussian operator with adjustable range; short ranges have the largest absolute renormalization when including two- and three-body induced terms, while at long ranges the induced three-body contribution takes on increased relative importance. The past two decades have seen a revolution in ab initio calculations of nuclear properties. One key element has been the development of a rigorous effective interaction theory, applying unitary transformations to soften the nuclear Hamiltonian and hence accelerate the convergence as a function of the model space size. For consistency, however, one ought to apply the same transformation to other operators when calculating transitions and mean values from the eigenstates of the renormalized Hamiltonian. Working in a translationally invariant harmonic oscillator basis for the two- and three-nucleon systems, we evolve the Hamiltonian, square radius, and total dipole strength operators by the similarity renormalization group (SRG). The inclusion of up to three-body matrix elements in the 4He nucleus all but completely restores

  12. Towards an ab initio description of correlated materials

    NASA Astrophysics Data System (ADS)

    Yee, Chuck-Hou

    Strongly-correlated materials are a rich playground for physical phenomena, exhibiting complex phase diagrams with many competing orders. Ab initio insights into materials combined with physical ideas provide the ability to identify the organizing principles driving the correlated electronic behavior and pursue first-principles design of new compounds. Realistic modeling of correlated materials is an active area of research, especially with the recent merger of density functional theory (DFT) with dynamical mean-field theory (DMFT). This thesis is structured in two parts. The first describes the methods and algorithmic developments which drive advances in DFT+DMFT. In Ch. 2 and 3, we provide an overview of the two foundational theories, DMFT and DFT. In the second half of Ch. 3, we describe some of the principles guiding the combination of the two theories to form DFT+DMFT. In Ch. 4, we describe the algorithm lying at the heart of modern DFT+DMFT implementations, the hybridization expansion formulation of continuous-time quantum monte carlo (CTQMC) for the general Anderson impurity problem, as well as a fast rejection algorithm for speeding-up the local trace evaluation. The final chapter in the methods section describes an algorithm for direct sampling of the partition function, and thus the free energy and entropy, of simple Anderson impurity models within CTQMC. The second part of the thesis is a collection of applications of our ab initio approach to key correlated materials. We first apply our method to plutonium binary alloys (Ch. 6), which when supplemented with slave-boson mean-field theory, allows us to understand the observed photoemission spectra. Ch. 7 describes the computation of spectra and optical conductivity for rare-earth nickelates grown as epitaxial thin films. In the final two chapters, we turn our attention to the high-temperature superconductors. In the first, we show that the charge-transfer energy is a key chemical variable which controls

  13. 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.

  14. 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.

  15. Latitudinal gradients in tertiary molluscan faunas of the Pacific coast

    USGS Publications Warehouse

    Addicott, W.O.

    1970-01-01

    Tertiary molluscan faunas of the middle latitudes of the marginal eastern North Pacific are characterized by warm-water taxa whose descendants now live in more southerly latitudes. A series of profiles in which cumulative percentages of warm-water faunal elements are plotted against latitude show progressive northward decreases in the percentage of these elements in the faunas of Pacific coast Tertiary stages. Systematic changes in the relative position of these latitudinal gradients during the Middle and Late Tertiary are related to climatic change in the Pacific Basin. Widespread tropical marine climate in the middle latitudes of the eastern North Pacific during the Eocene is indicated by widespread faunal units characterized by high levels of taxonomic diversity. Succeeding Early Oligocene faunas are less diverse, suggesting cooler climatic conditions. Unusually low representations of warm-water genera characterize the molluscan faunas of the Acila shumardi Zone in central California (latitude 34??-37??N). The anomalously cool-water aspect of these faunas may record the occurrence of upwelling along a bold linear segment of the Pacific coast. During the Late Oligocene or the Early Miocene, they are replaced by faunas of unusually warm-water aspect resulting in positive anomalies in Miocene latitudinal faunal gradients in central California. The Miocene anomalies seem to result from the development of an irregular Neogene coastline with extensive, newly established shallow-water embayments. ?? 1970.

  16. Oil potential of Tertiary sediments in northern Nevada

    SciTech Connect

    Duey, H.; Osborne, S.

    1987-08-01

    Expansion of the earth's crust in the Basin and Range in the Tertiary resulted in the formation of structural and stratigraphic basins between mountain ranges. From the surrounding mountains, these basins have accumulated sediments in which herbaceous and lacustrine sediments were deposited, along with a great volume of clastic material. Much of this material was buried rapidly enough to preserve it for generation of liquid and gaseous hydrocarbons. The presence of documented hydrocarbons from Tertiary source rocks in Nevada, and recent drilling through those rocks indicate a large potential for commercial production from the structurally young basins in the Basin and Range. Oil shows from Tertiary sediments indicate the areal extent of the potential. Shows are present from the Carson Sink and Black Rock Desert in northwest Nevada to Toano draw in northeast Nevada, with oil production from Currant, Eagle Springs, and Trap Springs fields in central Nevada. Lopatin calculations indicate that oil generation may be attained from Miocene source rocks as shallow as 7000 ft. The presence of source rocks and the proper geothermal gradient are critical in petroleum exploration in the Basin and Range of Nevada.

  17. Oil potential of Tertiary sediments in northern Nevada

    SciTech Connect

    Duey, H.D.; Osborne, S.

    1988-03-01

    Expansion of the earth's crust in the Basin and Range provide during the Tertiary resulted in the formation of structural and stratigraphic basins between mountain ranges. From the surrounding mountains, these basins have accumulated sediments in which herbaceous and lacustrine sediments were deposited, along with a great volume of clastic material. Much of this material was buried rapidly enough to preserve it for generation of liquid and gaseous hydrocarbons. The presence of documented hydrocarbons from Tertiary source rocks in Nevada and recent drilling through those rocks indicate a large potential for commercial production from the structurally young basins in the Basin and Range province. Oil shows from Tertiary sediments indicate the areal extent of the potential basins. Shows are present from the Carson Sink and Black Rock Desert in northwest Nevada to Toano Draw in northeast Nevada, with oil production from currant, Eagle Springs, and Trap Springs fields in central Nevada. Lopatin calculations indicate that oil generation may be attained in Miocene source rocks as shallow as 7000 ft.

  18. 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. PMID:26301853

  19. 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...

  20. In vitro effects of recombinant Otoconin 90 upon calcite crystal growth. Significance of tertiary structure

    PubMed Central

    Lu, Wenfu; Zhou, Dan; Freeman, John J.; Thalmann, Isolde; Ornitz, David M.; Thalmann, Ruediger

    2010-01-01

    Otoconia are biomineral particles of microscopic size essential for perception of gravity and maintenance of balance. Millions of older Americans are affected in their mobility, quality of life and in their health by progressive demineralization of otoconia. Currently, no effective means to prevent or counteract this process are available. Because of prohibitive anatomical and biological constraints, otoconial research is lagging far behind other systems such as bone and teeth. We have overcome these obstacles by generating otoconial matrix proteins by recombinant techniques. In the present study, we evaluated the effects of recombinant Otoconin 90 (OC90), the principal soluble matrix protein upon calcite crystal growth patterns in vitro. Our findings highlight multiple effects, including facilitation of nucleation, and inhibition of crystal growth in a concentration-dependent manner. Moreover, OC90 induces morphologic changes characteristic of native otoconia. OC90 is considerably less acidic than the prototypical invertebrate CaCO3 –associated protein, but is nevertheless an effective modulator of calcite crystal growth. Based on homology modeling of the sPLA2-like domains of OC90, we propose that the lower density of acidic residues of the primary sequence is compensated by formation of major anionic surface clusters upon folding into tertiary conformation. PMID:20595020

  1. 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.

  2. Ab initio calculations of As-vacancy interactions in silicon

    SciTech Connect

    Xie, J.; Chen, S.P.

    1999-04-01

    Atomistic simulation of a vacancy-assisted dopant diffusion in silicon needs details of the dopant-vacancy interaction, i.e., the potential as a functional of dopant-vacancy separations. In this paper, the authors present a detailed study on the energetics of As-vacancy reaction in silicon and the lattice distortions surrounding the As-vacancy defect by using an ab initio plane wave pseudopotential method and the density functional theory (DFT). A potential-energy diagram as a function of As-vacancy separation is provided, which can be used in the atomistic diffusion simulations. The authors also calculate the binding energy and the formation energy of different complexes such as AsV, As{sub 2}V and AsV{sub 2} (V represents vacancy). They find that the stable configuration of As{sub 2}V is As-V-As, while the stable configuration of AsV{sub 2} is As-V-V. The nature of the binding between As and vacancy is explained from the lattice distortions and the change of chemical bond configuration introduced by the As-vacancy complex.

  3. 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.

  4. 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. PMID:27357850

  5. Ab initio simulations of MgO under extreme conditions

    NASA Astrophysics Data System (ADS)

    Cebulla, Daniel; Redmer, Ronald

    2014-04-01

    We determined the phase diagram of magnesium oxide with finite-temperature density functional theory molecular dynamics simulations up to temperatures and pressures as relevant for the deep interior of super-Earths and in rocky cores of giant planets such as Jupiter. The equation of state data, the Hugoniot, and a ramp compression curve are computed and compared to earlier results from diamond anvil cell and (decaying) shock wave experiments. In addition, the dynamical electrical conductivity and the reflectivity along the experimental Hugoniot curve are calculated in order to characterize electronic structure changes under compression. The structural properties of MgO are identified using pair correlation functions and self-diffusion coefficients. The solid-solid coexistence line is calculated by comparing the free enthalpies of the B1 and the B2 phase. The free energy of the solid phases is determined via thermodynamic relations using the ab initio simulation results and phonon calculations in the harmonic approximation. Our results indicate that the solid B2 phase of MgO does not occur in the interior of the Earth but may play an important role in super-Earths and in rocky planetary cores.

  6. 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

  7. 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.

  8. Engineering Room-temperature Superconductors Via ab-initio Calculations

    NASA Astrophysics Data System (ADS)

    Gulian, Mamikon; Melkonyan, Gurgen; Gulian, Armen

    The BCS, or bosonic model of superconductivity, as Little and Ginzburg have first argued, can bring in superconductivity at room temperatures in the case of high-enough frequency of bosonic mode. It was further elucidated by Kirzhnitset al., that the condition for existence of high-temperature superconductivity is closely related to negative values of the real part of the dielectric function at finite values of the reciprocal lattice vectors. In view of these findings, the task is to calculate the dielectric function for real materials. Then the poles of this function will indicate the existence of bosonic excitations which can serve as a "glue" for Cooper pairing, and if the frequency is high enough, and the dielectric matrix is simultaneously negative, this material is a good candidate for very high-Tc superconductivity. Thus, our approach is to elaborate a methodology of ab-initio calculation of the dielectric function of various materials, and then point out appropriate candidates. We used the powerful codes (TDDF with the DP package in conjunction with ABINIT) for computing dielectric responses at finite values of the wave vectors in the reciprocal lattice space. Though our report is concerned with the particular problem of superconductivity, the application range of the data processing methodology is much wider. The ability to compute the dielectric function of existing and still non-existing (though being predicted!) materials will have many more repercussions not only in fundamental sciences but also in technology and industry.

  9. 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.

  10. Local Environment Distribution in Ab Initio Liquid Water

    NASA Astrophysics Data System (ADS)

    Santra, Biswajit; Distasio, Robert A., Jr.; Car, Roberto

    2013-03-01

    We have analyzed the distribution of local environments in liquid water at ambient conditions and its inherent potential energy surface (IPES) based on state-of-the-art ab initio molecular dynamics simulations performed on 128 molecules implementing hybrid PBE0 exchange [PRB 79, 085102 (2009)] and van der Waals (vdW) interactions [PRL 102, 073005 (2009)]. The local environments of molecules are characterized in terms of the local structure index (LSI) [JCP 104, 7671 (1996)] which is able to distinguish high- and low-density molecular environments. In agreement with simulations based on model potentials, we find that the distribution of LSI is unimodal at ambient conditions and bimodal in the IPES, consistent with the existence of polymorphism in amorphous phases of water. At ambient conditions spatial LSI fluctuations extend up to ~7 Å and their dynamical correlation decays on a time scale of ~3 ps, as found for density fluctuations in a recent study [PRL 106, 037801 (2011)]. DOE: DE-SC0008626, DOE: DE-SC0005180, NSF: CHE-0956500

  11. FTIR, Raman spectra and ab initio calculations of 2-mercaptobenzothiazole.

    PubMed

    Rai, Amareshwar K; Singh, Rachana; Singh, K N; Singh, V B

    2006-02-01

    FTIR and Raman spectra of a rubber vulcanization accelerator, 2-mercaptobenzothiazole (MBT), were recorded in the solid phase. The harmonic vibrational wavenumbers, for both the toutomeric forms of MBT, as well as for its dimeric complex, have been calculated, using ab initio RHF and density functional B3LYP methods invoking different basis sets upto RHF/6-31G** and B3LYP/6-31G** and the results were compared with the experimental values. Conformational studies have been also carried out regarding its toutomeric monomer forms and its dimer form. With all the basis sets the thione form of MBT (II) is predicted to be more stable than thiol form (I) and dimeric conformation (III) is predicted to be more stable with monomeric conformations (I) and (II). Vibrational assignments have been made, and it has been found that the calculated normal mode frequencies of dimeric conformation (III) are required for the analysis of IR and Raman bands of the MBT. The predicted shift in NH- stretching vibration towards the lower wave number side with the B3LYP/6-31G** calculations for the most stable dimer form (III), is in better agreement with experimental results. The intermolecular sulfur-nitrogen distance in N-H...S hydrogen bond was found to be 3.35 angstroms from these calculations, is also in agreement to the experimental value. PMID:16098806

  12. 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.

  13. 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.

  14. Microsolvation of methyl hydrogen peroxide: Ab initio quantum chemical approach

    NASA Astrophysics Data System (ADS)

    Kulkarni, Anant D.; Rai, Dhurba; Bartolotti, Libero J.; Pathak, Rajeev K.

    2009-08-01

    Methyl hydrogen peroxide (MHP), one of the simplest organic hydroperoxides, is a strong oxidant, with enhanced activity in aqueous ambience. The present study investigates, at the molecular level, the role of hydrogen bonding that is conducive to cluster formation of MHP with water molecules from its peroxide end, with the methyl group remaining hydrophobic for up to five water molecules. Ab initio quantum chemical computations on MHP⋯(H2O)n, [n =1-5] are performed at second order Møller-Plesset (MP2) perturbation theory employing the basis sets 6-31G(d,p) and 6-311++G(2d,2p) to study the cluster formation of MHP with water molecules from its peroxide end and hydrophobic hydration due to the methyl group. Successive addition of water molecules alters the hydrogen bonding pattern, which leads to changes in overall cluster geometry and in turn to IR vibrational frequency shifts. Molecular co-operativity in these clusters is gauged directly through a detailed many-body interaction energy analysis. Molecular electrostatic potential maps are shown to have a bearing on predicting further growth of these clusters, which is duly corroborated through sample calculations for MHP⋯(H2O)8. Further, a continuum solvation model calculation for energetically stable clusters suggests that this study should serve as a precursor for pathways to aqueous solvation of MHP.

  15. Ab initio modelling of methane hydrate thermophysical properties.

    PubMed

    Jendi, Z M; Servio, P; Rey, A D

    2016-04-21

    The key thermophysical properties of methane hydrate were determined using ab initio modelling. Using density functional theory, the second-order elastic constants, heat capacity, compressibility, and thermal expansion coefficient were calculated. A wide and relevant range of pressure-temperature conditions were considered, and the structures were assessed for stability using the mean square displacement and radial distribution functions. Methane hydrate was found to be elastically isotropic with a linear dependence of the bulk modulus on pressure. Equally significant, multi-body interactions were found to be important in hydrates, and water-water interactions appear to strongly influence compressibility like in ice Ih. While the heat capacity of hydrate was found to be higher than that of ice, the thermal expansion coefficient was significantly lower, most likely due to the lower rigidity of hydrates. The mean square displacement gave important insight into stability, heat capacity, and elastic moduli, and the radial distribution functions further confirmed stability. The presented results provide a much needed atomistic thermoelastic characterization of methane hydrates and are essential input for the large-scale applications of hydrate detection and production. PMID:27019976

  16. 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.

  17. An efficient approach to ab initio Monte Carlo simulation

    SciTech Connect

    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{sup 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.

  18. Ab initio description of p-shell hypernuclei.

    PubMed

    Wirth, Roland; Gazda, Daniel; Navrátil, Petr; Calci, Angelo; Langhammer, Joachim; Roth, Robert

    2014-11-01

    We present the first ab initio calculations for p-shell single-Λ hypernuclei. For the solution of the many-baryon problem, we develop two variants of the no-core shell model with explicit Λ and Σ(+),Σ(0),Σ(-) hyperons including Λ-Σ conversion, optionally supplemented by a similarity renormalization group transformation to accelerate model-space convergence. In addition to state-of-the-art chiral two- and three-nucleon interactions, we use leading-order chiral hyperon-nucleon interactions and a recent meson-exchange hyperon-nucleon interaction. We validate the approach for s-shell hypernuclei and apply it to p-shell hypernuclei, in particular to (Λ)(7)Li, (Λ)(9)Be, and (Λ)(13)C. We show that the chiral hyperon-nucleon interactions provide ground-state and excitation energies that generally agree with experiment within the cutoff dependence. At the same time we demonstrate that hypernuclear spectroscopy provides tight constraints on the hyperon-nucleon interactions. PMID:25415901

  19. Ab initio calculations of free-energy reaction barriers.

    PubMed

    Bucko, T

    2008-02-13

    The theoretical description of chemical reactions was until recently limited to a 'static' approach in which important parameters such as the rate constant are deduced from the local topology of the potential energy surface close to minima and saddle points. Such an approach has, however, serious limitations. The growing computational power allows us now to use advanced simulation techniques to determine entropic effects accurately for medium-sized systems at ab initio level. Recently, we have implemented free-energy simulation techniques based on molecular dynamics, in particular on the blue-moon ensemble technique and on metadynamics, in the popular DFT code VASP. In the thermodynamic integration (blue-moon ensemble) technique, the free-energy profile is calculated as the path integral over the restoring forces along a parametrized reaction coordinate. In metadynamics, an image of the free-energy surface is constructed on the fly during the simulation by adding small repulsive Gaussian-shaped hills to the Lagrangian driving the dynamics. The two methods are tested on a simple chemical reaction-the nucleophilic substitution of methyl chloride by a chlorine anion.

  20. Ab initio calculations of free-energy reaction barriers

    NASA Astrophysics Data System (ADS)

    Bucko, T.

    2008-02-01

    The theoretical description of chemical reactions was until recently limited to a 'static' approach in which important parameters such as the rate constant are deduced from the local topology of the potential energy surface close to minima and saddle points. Such an approach has, however, serious limitations. The growing computational power allows us now to use advanced simulation techniques to determine entropic effects accurately for medium-sized systems at ab initio level. Recently, we have implemented free-energy simulation techniques based on molecular dynamics, in particular on the blue-moon ensemble technique and on metadynamics, in the popular DFT code VASP. In the thermodynamic integration (blue-moon ensemble) technique, the free-energy profile is calculated as the path integral over the restoring forces along a parametrized reaction coordinate. In metadynamics, an image of the free-energy surface is constructed on the fly during the simulation by adding small repulsive Gaussian-shaped hills to the Lagrangian driving the dynamics. The two methods are tested on a simple chemical reaction—the nucleophilic substitution of methyl chloride by a chlorine anion.

  1. 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.

  2. 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.

  3. Exploring the free energy surface using ab initio molecular dynamics.

    PubMed

    Samanta, Amit; Morales, Miguel A; Schwegler, Eric

    2016-04-28

    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. PMID:27131525

  4. 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.

  5. Rational design of electrolyte components by ab initio calculations

    NASA Astrophysics Data System (ADS)

    Johansson, Patrik; Jacobsson, Per

    This paper is a small review of the use of computer simulations and especially the use of standard quantum-mechanical ab initio electronic structure calculations to rationally design and investigate different choices of chemicals/systems for lithium battery electrolytes. Covered systems and strategies to enhance the performance of electrolytes will range from assisting the interpretation of vibrational spectroscopy experiments over development of potentials for molecular dynamics simulations, to the design of new lithium salts and the lithium ion coordination in liquid, polymer, and gel polymer electrolytes. Examples of studied properties include the vibrational spectra of anions and ion pairs to characterize the nature and extent of the interactions present, the lithium ion affinities of anions, important for the salt solvation and the ability to provide a high concentration of charge carriers, the HOMO energies of the anions to estimate the stability versus oxidation, the anion volumes that correlate to the anion mobility, the lithium ion coordination and dynamics to reveal the limiting steps of lithium ion transport, etc.

  6. Ab initio molecular dynamics calculations of ion hydration free energies

    SciTech Connect

    Leung, Kevin; Rempe, Susan B.; Lilienfeld, O. Anatole von

    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{sup +}, Cl{sup -}, and Ag{sup +} 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 ({Delta}G{sub 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{sup +}/Cl{sup -} and Ag{sup +}/Cl{sup -} AIMD {Delta}G{sub 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{sup +}+Ni{sup +}{yields}Ag+Ni{sup 2+} in water. The predictions for this reaction suggest that existing estimates of {Delta}G{sub hyd} for unstable radiolysis intermediates such as Ni{sup +} may need to be extensively revised.

  7. 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.

  8. The AB Initio Mia Method: Theoretical Development and Practical Applications

    NASA Astrophysics Data System (ADS)

    Peeters, Anik

    The bottleneck in conventional ab initio Hartree -Fock calculations is the storage of the electron repulsion integrals because their number increases with the fourth power of the number of basis functions. This problem can be solved by a combination of the multiplicative integral approximation (MIA) and the direct SCF method. The MIA approach was successfully applied in the geometry optimisation of some biologically interesting compounds like the neurolepticum Haloperidol and two TIBO derivatives, inactivators of HIV1. In this thesis the potency of the MIA-method is shown by the application of this method in the calculation of the forces on the nuclei. In addition, the MIA method enabled the development of a new model for performing crystal field studies: the supermolecule model. The results for this model are in better agreement with experimental data than the results for the point charge model. This is illustrated by the study of some small molecules in the solid state: 2,3-diketopiperazine, formamide oxime and two polymorphic forms of glycine, alpha-glycine and beta-glycine.

  9. Topological constraints are major determinants of tRNA tertiary structure and dynamics and provide basis for tertiary folding cooperativity.

    PubMed

    Mustoe, Anthony M; Brooks, Charles L; Al-Hashimi, Hashim M

    2014-10-01

    Recent studies have shown that basic steric and connectivity constraints encoded at the secondary structure level are key determinants of 3D structure and dynamics in simple two-way RNA junctions. However, the role of these topological constraints in higher order RNA junctions remains poorly understood. Here, we use a specialized coarse-grained molecular dynamics model to directly probe the thermodynamic contributions of topological constraints in defining the 3D architecture and dynamics of transfer RNA (tRNA). Topological constraints alone restrict tRNA's allowed conformational space by over an order of magnitude and strongly discriminate against formation of non-native tertiary contacts, providing a sequence independent source of folding specificity. Topological constraints also give rise to long-range correlations between the relative orientation of tRNA's helices, which in turn provides a mechanism for encoding thermodynamic cooperativity between distinct tertiary interactions. These aspects of topological constraints make it such that only several tertiary interactions are needed to confine tRNA to its native global structure and specify functionally important 3D dynamics. We further show that topological constraints are conserved across tRNA's different naturally occurring secondary structures. Taken together, our results emphasize the central role of secondary-structure-encoded topological constraints in defining RNA 3D structure, dynamics and folding.

  10. Protein Repeats from First Principles.

    PubMed

    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

  11. 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.

  12. 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

  13. 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.

  14. In solution cation-induced secondary and tertiary structure alterations of human calprotectin.

    PubMed

    Imani, Mehdi; Bahrami, Yaser; Jaliani, Hossein Zarei; Ardestani, Sussan Kaboudanian

    2014-10-01

    Calprotectin (CP) is widely considered to have diverse roles including growth inhibitory and apoptosis induction in a number of tumor cell lines and antimicrobial activities. As CP has been proposed to bind metal ions with high affinity, we have studied its functional and primarily its structural behavior upon Zn(2+) and Mn(2+) chelation solely and along with Ca(2+). We employed fluorescence spectroscopy and circular dichroism to determine the resulting modifications. Based upon our findings it is clear that treating CP with ions effectively weakened its natural growth inhibitory activity. Moreover, structural analysis of Zn(2+) and Mn(2+)-treated CPs indicated remarkable alterations in the regular secondary structures in favor of irregular structures while Zn(2+) and Mn(2+) treatment of CP after incubation with Ca(2+) displayed no remarkable shifts. Tertiary structure investigation using fluorescence spectroscopy showed that CP undergoes conformational changes upon Zn(2+) and Mn(2+) treatment whereby Trp residues of protein is slightly exposed to the hydrophilic environment, compactness of CP is compromised, whereas in Ca(2+)-treated CP, the tertiary structure integrity is intact upon Zn(2+) and Mn(2+) chelation. Interestingly, CP structural modifications upon Zn(2+) and Mn(2+) treatment was significantly comparable, probably due to similar radii and charges of ions. Taken all together, we have concluded that CP maintains its normal nature in Ca(2+)-loaded state when treated with Zn(2+) and Mn(2+) ions. It can be suggested that Ca(2+) not only stabilize CP structure but also helps CP to keep its structure upon metal ions chelation which is involved in host organism defense system.

  15. Secondary and tertiary structure of the A-state of cytochrome c from resonance Raman spectroscopy.

    PubMed Central

    Jordan, T.; Eads, J. C.; Spiro, T. G.

    1995-01-01

    Ferricytochrome c can be converted to the partially folded A-state at pH 2.2 in the presence of 1.5 M NaCl. The structure of the A-state has been studied in comparison with the native and unfolded states, using resonance Raman spectroscopy with visible and ultraviolet excitation wavelengths. Spectra obtained with 200 nm excitation show a decrease in amide II intensity consistent with loss of structure for the 50s and 70s helices. The 230-nm spectra contain information on vibrational modes of the single Trp 59 side chain and the four tyrosine side chains (Tyr 48, 67, 74, and 97). The Trp 59 modes indicate that the side chain remains in a hydrophobic environment but loses its tertiary hydrogen bond and is rotationally disordered. The tyrosine modes Y8b and Y9a show disruption of tertiary hydrogen bonding for the Tyr 48, 67, and 74 side chains. The high-wavenumber region of the 406.7-nm resonance Raman spectrum reveals a mixed spin heme iron atom, which arises from axial coordination to His 18 and a water molecule. The low-frequency spectral region reports on heme distortions and indicates a reduced degree of interaction between the heme and the polypeptide chain. A structural model for the A-state is proposed in which a folded protein subdomain, consisting of the heme and the N-terminal, C-terminal, and 60s helices, is stabilized through nonbonding interactions between helices and with the heme. PMID:7613469

  16. Secondary and tertiary structure of the A-state of cytochrome c from resonance Raman spectroscopy.

    PubMed

    Jordan, T; Eads, J C; Spiro, T G

    1995-04-01

    Ferricytochrome c can be converted to the partially folded A-state at pH 2.2 in the presence of 1.5 M NaCl. The structure of the A-state has been studied in comparison with the native and unfolded states, using resonance Raman spectroscopy with visible and ultraviolet excitation wavelengths. Spectra obtained with 200 nm excitation show a decrease in amide II intensity consistent with loss of structure for the 50s and 70s helices. The 230-nm spectra contain information on vibrational modes of the single Trp 59 side chain and the four tyrosine side chains (Tyr 48, 67, 74, and 97). The Trp 59 modes indicate that the side chain remains in a hydrophobic environment but loses its tertiary hydrogen bond and is rotationally disordered. The tyrosine modes Y8b and Y9a show disruption of tertiary hydrogen bonding for the Tyr 48, 67, and 74 side chains. The high-wavenumber region of the 406.7-nm resonance Raman spectrum reveals a mixed spin heme iron atom, which arises from axial coordination to His 18 and a water molecule. The low-frequency spectral region reports on heme distortions and indicates a reduced degree of interaction between the heme and the polypeptide chain. A structural model for the A-state is proposed in which a folded protein subdomain, consisting of the heme and the N-terminal, C-terminal, and 60s helices, is stabilized through nonbonding interactions between helices and with the heme.

  17. Kinetic and thermodynamic framework for P4-P6 RNA reveals tertiary motif modularity and modulation of the folding preferred pathway.

    PubMed

    Bisaria, Namita; Greenfeld, Max; Limouse, Charles; Pavlichin, Dmitri S; Mabuchi, Hideo; Herschlag, Daniel

    2016-08-23

    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

  18. 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

  19. Nonadiabatic ab initio dynamics of a model protonated Schiff base of 9-cis retinal.

    PubMed

    Chung, Wilfredo Credo; Nanbu, Shinkoh; Ishida, Toshimasa

    2010-08-19

    The dynamics of the photoisomerization of a model protonated Schiff base of 9-cis retinal in isorhodopsin is investigated using nonadiabatic molecular dynamics simulation combined with ab initio quantum chemical calculations on-the-fly. The quantum chemical part is treated at the complete-active space self-consistent field level for six electrons in six active pi orbitals with the 6-31G basis set (CASSCF(6,6)/6-31G). The probabilities of nonadiabatic transitions between the S(1) ((1)pipi*) and S(0) states are estimated in light of the Zhu-Nakamura theory. The photoinduced cis-trans isomerization of 9-cis retinal proceeds slower than that of its 11-cis analogue and at a lower quantum yield, confirming experimental observations. An energetic barrier in the excited state impedes the elongation and twist of the C(9)=C(10) stretch and torsion coordinates, respectively, resulting in the trapping of trajectories before transition. Consequently, the isomerization takes longer time and the transition more often occurs at smaller twist angle of =C(8)-C(9)=C(10)-C(11)=, which leads to regeneration of the 9-cis reactant. Thus, neither the smaller twist observed in the X-ray crystal nor the slower movement of nuclei in the transition region would be the main reason for the longer reaction time and lower yield. A well-known space-saving asynchronous bicycle pedal or crankshaft photoisomerization mechanism is found to be operational in 9-cis retinal. The simulation in vacuo suggests that the excited-state barrier and the photoisomerization itself are intrinsic properties of the visual chromophore and not triggered mainly by the protein environment that surrounds the chromophore. PMID:20666503

  20. Limitations of Ab Initio Predictions of Peptide Binding to MHC Class II Molecules

    PubMed Central

    Xu, Ying; Sette, Alessandro; Bourne, Philip E.; Lund, Ole; Ponomarenko, Julia; Nielsen, Morten; Peters, Bjoern

    2010-01-01

    Successful predictions of peptide MHC binding typically require a large set of binding data for the specific MHC molecule that is examined. Structure based prediction methods promise to circumvent this requirement by evaluating the physical contacts a peptide can make with an MHC molecule based on the highly conserved 3D structure of peptide:MHC complexes. While several such methods have been described before, most are not publicly available and have not been independently tested for their performance. We here implemented and evaluated three prediction methods for MHC class II molecules: statistical potentials derived from the analysis of known protein structures; energetic evaluation of different peptide snapshots in a molecular dynamics simulation; and direct analysis of contacts made in known 3D structures of peptide:MHC complexes. These methods are ab initio in that they require structural data of the MHC molecule examined, but no specific peptide:MHC binding data. Moreover, these methods retain the ability to make predictions in a sufficiently short time scale to be useful in a real world application, such as screening a whole proteome for candidate binding peptides. A rigorous evaluation of each methods prediction performance showed that these are significantly better than random, but still substantially lower than the best performing sequence based class II prediction methods available. While the approaches presented here were developed independently, we have chosen to present our results together in order to support the notion that generating structure based predictions of peptide:MHC binding without using binding data is unlikely to give satisfactory results. PMID:20174654

  1. A Initio Studies of Polarisabilities of Ions in Crystals.

    NASA Astrophysics Data System (ADS)

    Tole, Philip

    Available from UMI in association with The British Library. This thesis is concerned with the ab initio calculation of polarisabilities of ions in crystals. For a binary salt the Clausius-Mossotti equation relates the refractive index to the in-crystal polarisability of the ion-pair. However, there is no experimental means of separating the sum into anion and cation components. Theoretical models which use isolated ion polarisabilities to do this are physically unrealistic and have met with little success. A much better model has been developed using ab initio all-electron CHF calculations. The in-crystal environment is represented by a 'molecular' cluster embedded in a point-charge lattice. The physical features important to the success of the model are the nearest-neighbour overlap compression and the isotropic part of the electrostatic potential arising from the point -charge lattice. Calculations on simple first row alkali halides show the cation to be independent of these forces whereas the anion becomes, smaller, more bound and less polarisable in the crystal. When corrections for correlation are added the agreement with Clausius-Mossotti polarisabilities is at the 5% level or better. This implies a reduction in polarisability by factors of up to 2 with respect to the free ion. The polarisabilities for the anions in LiF, NaF, KF, LiCl, NaCl, KCl, LiBr, NaBr, KBr, CaF _2, BeO, MgO, CaO, Li_2O, Na_2O, K_2O, BeS, CaS, Li_2S, Na_2 S and K_2S were calculated. Anion polarisability is found to vary with lattice parameter but hardly at all with coordination number. Calculations on Be_2C show that in-crystal compression is sufficient to stabilise even C^{4 -}, which has a polarisability of over 20 au. Anions at the surface of LiF and MgO were also modelled. Because anisotropic overlap and electrostatic factors tend to cancel, the ion in 5-, 4- and 3-coordinate surface sites has a polarisability only a few per cent greater than in the bulk solid. Implications for

  2. Chiroptical properties of unsubstituted carbohydrates: Ab initio and semiempirical studies

    NASA Astrophysics Data System (ADS)

    Parra C., Alejandro

    Ab initio calculations support assignment of the vacuum ultraviolet circular dichroism (CD) of simple saccharides to 11A 1 --> 21B1 and 11A 1 --> 11A2 transitions centered on the oxygen atoms of the acetal group treated as two weakly coupled ether chromophores. The calculations are consistent with assignments previously made on the basis of a deconvolution of CD spectra. Estimates of the oxygen centered contributions to magnetic transition dipole moments were made. Semiempirical calculations were performed to model the NaD molar optical rotation of 1,6- and 3,6- anhydrosugars. For 1,6-anhydrosugars, current parameters produce reasonable agreement with experimental values. For 3,6-anhydrosugars, modifications to the ether parameters had to be introduced. The most relevant included a reorientation of the bond-centered s-->s* transition dipole charges in the ether chromophore to a C2v orientation, and a shift from prolate polarizability ellipsoids to general ellipsoids. These changes result in good agreement with experimental Na D molar rotations for 3,6-anhydrosugars. A low energy CD band arises in 3,6- and 1,6-anhydrosugars when agreement with the experimental NaD molar rotations is achieved. It is proposed that this band is a real feature in the spectrum. The origin of the band is primarily the interaction between b1 symmetry- oriented transition dipoles in the COC groups with other transition dipoles in the molecule. Comparison with experimental spectra leads to an assignment of this band to 11A1 --> 21B1 transitions centered on the COC groups.

  3. Ab initio molecular dynamics study of ferroelectric phase transitions

    NASA Astrophysics Data System (ADS)

    Srinivasan, Varadharajan

    We have undertaken the first ever fully first-principles simulations of ferroelectric crystals at finite temperature with an aim to understand the nature of their phase transitions. In particular, we have studied the different aspects of phase transitions in two protypical ferroelectrics - PbTiO3 and KH2PO4. In PbTiO3, we have successfully reproduced the temperature-driven transition from a tetragonal to a cubic phase by using constant-pressure Car-Parrinello molecular dynamics. By defining suitable order parameters in terms of atomic displacements, we are able to monitor the approach of the cubic phase. Using a quasi-harmonic analysis, with the inclusion of a temperature dependent volume and the average thermal atomic displacements as the most basic effects of anharmonicity, we are also able to recover the softening of ferroelectric modes as well as other features seen in experiments. These observations confirm the predominantly displacive nature of the transition, while our simulations also indicate a possible build-up of disorder near the transition temperature. We have also studied the isotope effects in the ferroelectric transition in KH2PO4 by quantifying the temperature and mass dependence of the extent of delocalization of the hydrogens. Using a recently developed ab initio Open Path-integral Molecular Dynamics scheme we have calculated both the real and momentum-space distribution of the hydrogens in both protonated and deuterated KDP above and below their respective transition temperatures. We find that the two crystals not only involve different transition mechanisms but also the fluctuations above the transition temperature are of a qualitatively different nature.

  4. 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.

  5. Ab initio cluster study of crystalline NaF

    SciTech Connect

    Temple, D.K.

    1992-01-01

    A highly-accurate ab initio cluster model of crystalline NaF has been constructed to explore the limits of cluster methods in the treatment of ionic solids. The focus of this model was the characterization of the lattice environment and its influence on the easily-polarizable fluorine anion. The model consisted of a central all-electron fluorine anion coordinated by pseudopotentials, to represent the nearest-neighbor sodium cations, and a finite array of point charges chosen to generate the correct crystal field from the surrounding infinite ionic lattice. The wavefunction and properties of the anion were calculated using the restricted Hartree-Fock and configuration interaction techniques from quantum chemistry. An extensive analysis of basis set incompleteness errors in the anion wavefunction was performed. Important features were identified in the embedded anion, such as its distortion under the influence of the lattice compressions, its stabilization from the Madelung potential, and its changes in size due to electron correlations. Bulk properties of the rocksalt-structure (B1) NaF crystal were derived from the total mode energies, calculated as a function of the crystal volume. The properties included the zero-pressure lattice constant, cohesive energy, and bulk modulus, and the pressure-volume equation-of-state. A series of test calculations explored the relationships, and their underlying physical mechanisms, between the features of the embedded anion and the bulk properties of the crystal. These features often produced opposing changes in the properties, demonstrating the importance of a thorough and systematic treatment of the embedded anion. The most thorough test calculation gave bulk properties that were within 1% of experiment. Using an embedded anion model for the high-pressure cesium-chloride (B2) phase of NaF, the B1-to-B2 structural transition was correctly predicted at 25 GPa, in excellent agreement with the experimental values of 23 to 27 GPa.

  6. Lithium insertion in silicon nanowires: an ab initio study.

    PubMed

    Zhang, Qianfan; Zhang, Wenxing; Wan, Wenhui; Cui, Yi; Wang, Enge

    2010-09-01

    The ultrahigh specific lithium ion storage capacity of Si nanowires (SiNWs) has been demonstrated recently and has opened up exciting opportunities for energy storage. However, a systematic theoretical study on lithium insertion in SiNWs remains a challenge, and as a result, understanding of the fundamental interaction and microscopic dynamics during lithium insertion is still lacking. This paper focuses on the study of single Li atom insertion into SiNWs with different sizes and axis orientations by using full ab initio calculations. We show that the binding energy of interstitial Li increases as the SiNW diameter grows. The binding energies at different insertion sites, which can be classified as surface, intermediate, and core sites, are quite different. We find that surface sites are energetically the most favorable insertion positions and that intermediate sites are the most unfavorable insertion positions. Compared with the other growth directions, the [110] SiNWs with different diameters always present the highest binding energies on various insertion locations, which indicates that [110] SiNWs are more favorable by Li doping. Furthermore, we study Li diffusion inside SiNWs. The results show that the Li surface diffusion has a much higher chance to occur than the surface to core diffusion, which is consistent with the experimental observation that the Li insertion in SiNWs is layer by layer from surface to inner region. After overcoming a large barrier crossing surface-to-intermediate region, the diffusion toward center has a higher possibility to occur than the inverse process.

  7. 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.

  8. Ab initio kinetics of gas phase decomposition reactions.

    PubMed

    Sharia, Onise; Kuklja, Maija M

    2010-12-01

    The thermal and kinetic aspects of gas phase decomposition reactions can be extremely complex due to a large number of parameters, a variety of possible intermediates, and an overlap in thermal decomposition traces. The experimental determination of the activation energies is particularly difficult when several possible reaction pathways coexist in the thermal decomposition. Ab initio calculations intended to provide an interpretation of the experiment are often of little help if they produce only the activation barriers and ignore the kinetics of the decomposition process. To overcome this ambiguity, a theoretical study of a complete picture of gas phase thermo-decomposition, including reaction energies, activation barriers, and reaction rates, is illustrated with the example of the β-octahydro-1,3,5,7-tetranitro-1,3,5,7-tetrazocine (HMX) molecule by means of quantum-chemical calculations. We study three types of major decomposition reactions characteristic of nitramines: the HONO elimination, the NONO rearrangement, and the N-NO(2) homolysis. The reaction rates were determined using the conventional transition state theory for the HONO and NONO decompositions and the variational transition state theory for the N-NO(2) homolysis. Our calculations show that the HMX decomposition process is more complex than it was previously believed to be and is defined by a combination of reactions at any given temperature. At all temperatures, the direct N-NO(2) homolysis prevails with the activation barrier at 38.1 kcal/mol. The nitro-nitrite isomerization and the HONO elimination, with the activation barriers at 46.3 and 39.4 kcal/mol, respectively, are slow reactions at all temperatures. The obtained conclusions provide a consistent interpretation for the reported experimental data. PMID:21077597

  9. Tertiary siRNAs mediate paramutation in C. elegans.

    PubMed

    Sapetschnig, Alexandra; Sarkies, Peter; Lehrbach, Nicolas J; Miska, Eric A

    2015-03-01

    In the nematode Caenorhabditis elegans, different small RNA-dependent gene silencing mechanisms act in the germline to initiate transgenerational gene silencing. Piwi-interacting RNAs (piRNAs) can initiate transposon and gene silencing by acting upstream of endogenous short interfering RNAs (siRNAs), which engage a nuclear RNA interference (RNAi) pathway to trigger transcriptional gene silencing. Once gene silencing has been established, it can be stably maintained over multiple generations without the requirement of the initial trigger and is also referred to as RNAe or paramutation. This heritable silencing depends on the integrity of the nuclear RNAi pathway. However, the exact mechanism by which silencing is maintained across generations is not understood. Here we demonstrate that silencing of piRNA targets involves the production of two distinct classes of small RNAs with different genetic requirements. The first class, secondary siRNAs, are localized close to the direct target site for piRNAs. Nuclear import of the secondary siRNAs by the Argonaute HRDE-1 leads to the production of a distinct class of small RNAs that map throughout the transcript, which we term tertiary siRNAs. Both classes of small RNAs are necessary for full repression of the target gene and can be maintained independently of the initial piRNA trigger. Consistently, we observed a form of paramutation associated with tertiary siRNAs. Once paramutated, a tertiary siRNA generating allele confers dominant silencing in the progeny regardless of its own transmission, suggesting germline-transmitted siRNAs are sufficient for multigenerational silencing. This work uncovers a multi-step siRNA amplification pathway that promotes germline integrity via epigenetic silencing of endogenous and invading genetic elements. In addition, the same pathway can be engaged in environmentally induced heritable gene silencing and could therefore promote the inheritance of acquired traits. PMID:25811365

  10. 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.

  11. Mesozoic and early Tertiary rift tectonics in East Africa

    NASA Astrophysics Data System (ADS)

    Bosworth, William

    1992-08-01

    A complex history of crustal extension occurred in east and central Africa during the Mesozoic and early Tertiary. Beginning in the Late Jurassic, this resulted in a large system of rifts, the Central African rift system, that spanned from central Sudan to southern Kenya. Late Jurassic rifting is best documented in the White and Blue Nile rifts of the Sudan, and records east-west extension in half-graben that were connected by large-scale shear zones and pull-apart basins. Early Cretaceous rifting re-activated Jurassic basins and spread to the large South Sudan rifts and Anza rift in Kenya. By the Late Cretaceous, the extension direction shifted to the NE-SW, and the presently observed large-scale rift geometry was established. In the early Tertiary, some Mesozoic basins were again reactivated, while other regions underwent wrench faulting and basin inversion. The large number of basins preserved in the Central African rift system can be used to construct an evolutionary model of continental rift tectonics. Early phases of extension at low strains produced alternating half-graben/accommodation zone geometries similar to those observed in most young and active continental rifts. At higher strains, some border faults were abandoned so that through-going, simpler active fault systems could evolve. This is interpreted as representing a switch from complex, oppositely dipping detachment structures, with strike dimensions of 50-150 km, to regional detachment structures that continue for hundreds of kilometers parallel to the rift. This change in the type of detachment was accompanied by a shift in the position of the subsidence away from the breakaway to a position focused further within the regional upper plate. Non-rotational, high angle, normal faulting dominates in the development of these late basin geometries. Deciphering similar rift basin histories from passive continental margins may, in many cases, exceed the limits of available reflection seismic data. East

  12. 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.

  13. The rotational spectrum of tertiary-butyl alcohol

    NASA Astrophysics Data System (ADS)

    Cohen, E. A.; Drouin, B. J.; Valenzuela, E. A.; Woods, R. C.; Caminati, W.; Maris, A.; Melandri, S.

    2010-03-01

    The rotational spectrum of tertiary-butyl alcohol has been recorded in selected regions between 8 and 500 GHz. Early data from the University of Wisconsin in the 8-40 GHz region have been combined with recent measurements from the University of Bologna and the Jet Propulsion Laboratory in the millimeter and submillimeter wavelength regions. The spectrum was fit over a wide range of J's and K's using a common set of parameters for both the A and E states. This paper describes the initial assignment at Wisconsin and the final procedure used to assign and fit the higher rotational states. The resulting molecular constants and their interpretation are discussed.

  14. Integral Membrane Proteins and Bilayer Proteomics

    PubMed Central

    Whitelegge, Julian P.

    2013-01-01

    Integral membrane proteins reside within the bilayer membranes that surround cells and organelles, playing critical roles in movement of molecules across them and the transduction of energy and signals. While their extreme amphipathicity presents technical challenges, biological mass spectrometry has been applied to all aspects of membrane protein chemistry and biology, including analysis of primary, secondary, tertiary and quaternary structure, as well as the dynamics that accompany functional cycles and catalysis. PMID:23301778

  15. Role of the tertiary structure in the diphenol oxidase activity of Octopus vulgaris hemocyanin.

    PubMed

    Campello, S; Beltramini, M; Giordano, G; Di Muro, P; Marino, S M; Bubacco, L

    2008-03-15

    The functional differences between the oxygen transport protein Hemocyanin and the enzymes Tyrosinase and Catechol oxidase are believed to be governed, at least in part, by the tertiary structure, which differs in these molecules and controls the accessibility of their copper containing active site for substrate(s). Accordingly, Octopus vulgaris Hemocyanin catalyses the o-diphenol oxidation to o-quinone at a very low rate. The crystallographic structure of one of the functional units (called Odg) of O. dofleini Hemocyanin shows two domains, a mainly alpha-helical domain that directly binds the copper ions of the reaction center and a beta-strand domain that precludes access to the active site to ligands bigger than molecular oxygen. In this work, we have first cleaved the whole protein and then purified different oxygen binding functional units from O. vulgaris Hemocyanin. These functional units were used in activity assays with l-DOPA, the paradigmatic substrate for Catechol oxidase. All functional units show a negligible enzymatic activity. The procedure to generate the functional units induces in only one of them a proteolytic cleavage. Amino terminal sequencing and mass spectroscopy of the fragments allow to place the cleavage site between the alpha and beta domains of the functional unit homologous to Odd, in the O. dofleini sequence. An increase, up to three orders of magnitude, of Tyrosinase-like activity was observed when the cleaved Odd-like was incubated with the substrate in the presence of trifluoroethanol or hexafluoroisopropanol. PMID:18237542

  16. 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.

  17. Tertiary lymphoid organ development coincides with determinant spreading of the myelin-specific T cell response.

    PubMed

    Kuerten, Stefanie; Schickel, Achim; Kerkloh, Christian; Recks, Mascha S; Addicks, Klaus; Ruddle, Nancy H; Lehmann, Paul V

    2012-12-01

    While the role of T cells has been studied extensively in multiple sclerosis (MS), the pathogenic contribution of B cells has only recently attracted major attention, when it was shown that B cell aggregates can develop in the meninges of a subset of MS patients and were suggested to be correlates of late-stage and more aggressive disease in this patient population. However, whether these aggregates actually exist has subsequently been questioned and their functional significance has remained unclear. Here, we studied myelin basic protein (MBP)-proteolipid protein (PLP)-induced experimental autoimmune encephalomyelitis (EAE), which is one of the few animal models for MS that is dependent on B cells. We provide evidence that B cell aggregation is reflective of lymphoid neogenesis in the central nervous system (CNS) in MBP-PLP-elicited EAE. B cell aggregation was present already few days after disease onset. With disease progression CNS B cell aggregates increasingly displayed the phenotype of tertiary lymphoid organs (TLOs). Our results further imply that these TLOs were not merely epiphenomena of the disease, but functionally active, supporting intrathecal determinant spreading of the myelin-specific T cell response. Our data suggest that the CNS is not a passive "immune-privileged" target organ, but rather a compartment, in which highly active immune responses can perpetuate and amplify the autoimmune pathology and thereby autonomously contribute to disease progression.

  18. An Efficient Time-Stepping Scheme for Ab Initio Molecular Dynamics Simulations

    NASA Astrophysics Data System (ADS)

    Tsuchida, Eiji

    2016-08-01

    In ab initio molecular dynamics simulations of real-world problems, the simple Verlet method is still widely used for integrating the equations of motion, while more efficient algorithms are routinely used in classical molecular dynamics. We show that if the Verlet method is used in conjunction with pre- and postprocessing, the accuracy of the time integration is significantly improved with only a small computational overhead. We also propose several extensions of the algorithm required for use in ab initio molecular dynamics. The validity of the processed Verlet method is demonstrated in several examples including ab initio molecular dynamics simulations of liquid water. The structural properties obtained from the processed Verlet method are found to be sufficiently accurate even for large time steps close to the stability limit. This approach results in a 2× performance gain over the standard Verlet method for a given accuracy. We also show how to generate a canonical ensemble within this approach.

  19. 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.

  20. Ab initio calculations of free energy barriers for chemical reactions in solution: proton transfer in [FHF]-.

    PubMed

    Muller, R P; Warshel, A

    1996-01-01

    This paper describes a hybrid ab initio quantum mechanical/molecular mechanics (QM/MM) method for calculating activation free energies of chemical reactions in solution, using molecular mechanics force fields for the solvent and an ab initio technique that incorporates the potential from the solvent in its Hamiltonian for the solute. The empirical valence bond (EVB) method is used as a reference potential for the ab initio free energy calculation, and drives the reaction along the proper coordinate, thus overcoming problems encountered by direct attempts to use molecular orbital methods in calculations of activation free energies. The utility of our method is illustrated by calculating the activation free energy for proton transfer between fluoride ions in the [FHF]-system, in both polar and nonpolar solution.

  1. 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.

  2. LSST primary, secondary, and tertiary mirror support systems

    NASA Astrophysics Data System (ADS)

    Cuerden, Brian; Sebag, Jacques; Mathews, Scott; Cho, Myung; Lee, Joon; West, Steven

    2004-09-01

    The current LSST Baseline Configuration has a field of view of 3.5 degrees and an optical etendue of 302 meters square degrees square. The etendue calculation includes the effect of gradual vignetting by the camera as the field angle increases. A current optical point design includes an 8.4 m spun cast light-weighted borosilicate primary mirror, a 3.2 m secondary mirror and a 5.0 m tertiary mirror. The goal of this study is to determine if these mirrors can be actively supported and retain figure control over elevation angles without closed-loop control based on wave-front measurement. Support systems for the tertiary and primary mirrors are adapted from proven systems utilized on 6.5 and 8.4 m class primaries developed by the University of Arizona"s Mirror Laboratory. The number and locations of axial and lateral supports is determined for each mirror and the gravitational and support induced surface distortions are calculated and are shown to be within budgeted limits. The support components and their performance are described and it is demonstrated that predicted mirror distortion attributable to the support system is consistent with the known performance of the support components.

  3. Mortality in newborns referred to tertiary hospital: An introspection

    PubMed Central

    Aggarwal, Kailash Chandra; Gupta, Ratan; Sharma, Shobha; Sehgal, Rachna; Roy, Manas Pratim

    2015-01-01

    Background: India is one of the largest contributors in the pool of neonatal death in the world. However, there are inadequate data on newborns referred to tertiary care centers. The present study aimed to find out predictors of mortality among newborns delivered elsewhere and admitted in a tertiary hospital in New Delhi between February and September 2014. Materials and Methods: Hospital data for were retrieved and analyzed for determining predictors for mortality of the newborns. Time of admission, referral and presenting clinical features were considered. Results: Out of 1496 newborns included in the study, there were 300 deaths. About 43% deaths took place in first 24 hours of life. Asphyxia and low birth weight were the main causes of death in early neonatal period, whereas sepsis had maximum contribution in deaths during late neonatal period. Severe hypothermia, severe respiratory distress, admission within first 24 hours of life, absence of health personnel during transport and referral from any hospital had significant correlation with mortality. Conclusions: There is need for ensure thermoregulation, respiratory sufficiency and presence of health personnel during transport. PMID:26288788

  4. Prevalence of Keratoconus Among a Palestinian Tertiary Student Population

    PubMed Central

    Shehadeh, Mohammad M.; Diakonis, Vasilios F.; Jalil, Sara A.; Younis, Rania; Qadoumi, Jamal; Al-Labadi, Liana

    2015-01-01

    Purpose: To screen for keratoconus and potential associated risk factors in a tertiary student population sample. Population and Methods: This cross sectional study included 1234 students attending An-Najah National University (Nablus, West Bank, Palestine), that were randomly selected from a total of 20,000 university students. 634 (51.3%) student participants responded by completing a self-administered questionnaire and were assessed by means of corneal topography. Following initial evaluation, participants were referred for Pentacam evaluation if they demonstrated either a mean keratometry of more than 45 diopters, corneal astigmatism of more than 2 diopters and/or if asymmetric topographic patterns were present. Pentacam images were analyzed by an experienced ophthalmologist based on a number of indices and the participants were classified as normal, keratoconus suspects, and keratoconus patients. Results: A total of 620 participants (mean age, 20.1±1.6 years) were included in this study, 379 (61.1%) were females and 241 (38.9%) were males. Nine subjects were diagnosed with keratoconus, demonstrating a prevalence of 1.5%. 52 (8.4%) participants showed at least one abnormal pentacam index, and were considered as KC suspects. Conclusion: Keratoconus is a prevalent disease among the tertiary Palestinian student population. This may be related to a combination of genetic and environmental factors. The results of this study signal the need for public health outreach and intervention for keratoconus. PMID:26962381

  5. 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.

  6. 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.

  7. 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.

  8. 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.

  9. Knowledge of HIV and AIDS among tertiary students in Bangladesh.

    PubMed

    Hossain, Mohammad Bellal; Kabir, Alamgir; Ferdous, Hasina

    To examine the levels and predictors of knowledge on HIV and AIDS, a survey was conducted among 392 tertiary level students in the University of Dhaka, Bangladesh. Students demonstrated a high knowledge of transmission and prevention of HIV and AIDS yet with considerable misconception. All students said that unprotected sex with an HIV-positive man or woman can transmit the HIV virus to a negative man or woman but at the same time 43.6% of students believed that there is a preventive vaccine for HIV and 39.8% understood that HIV can be cured if it is diagnosed early. Multivariate regression analysis indicated that the students who had more knowledge on HIV and AIDS were: older boys, fathers having more income, business or service as father's occupation, having more mass media exposure, being senior students, living in a university dormitory, and being students of faculty of arts, social sciences, and science. The findings of this study suggest that a special course on health education, including risk perceptions of HIV and AIDS and issues related to sexual and other high risk behavior, should be included in the course curricula irrespective of disciplines at tertiary levels.

  10. Ab initio centroid molecular dynamics: a fully quantum method for condensed-phase dynamics simulations

    NASA Astrophysics Data System (ADS)

    Pavese, Marc; Berard, Daniel R.; Voth, Gregory A.

    1999-01-01

    A fully quantum molecular dynamics method is presented which combines ab initio Car-Parrinello molecular dynamics with centroid molecular dynamics. The first technique allows the forces on the atoms to be obtained from ab initio electronic structure. The second technique, given the forces on the atoms, allows one to calculate an approximate quantum time evolution for the nuclei. The combination of the two, therefore, represents the first feasible approach to simulating the fully quantum dynamics of a many-body system. An application to excess proton translocation along a model water wire will be presented.

  11. Exploring the ab initio/classical free energy perturbation method: The hydration free energy of water

    NASA Astrophysics Data System (ADS)

    Sakane, Shinichi; Yezdimer, Eric M.; Liu, Wenbin; Barriocanal, Jose A.; Doren, Douglas J.; Wood, Robert H.

    2000-08-01

    The ab initio/classical free energy perturbation (ABC-FEP) method proposed previously by Wood et al. [J. Chem. Phys. 110, 1329 (1999)] uses classical simulations to calculate solvation free energies within an empirical potential model, then applies free energy perturbation theory to determine the effect of changing the empirical solute-solvent interactions to corresponding interactions calculated from ab initio methods. This approach allows accurate calculation of solvation free energies using an atomistic description of the solvent and solute, with interactions calculated from first principles. Results can be obtained at a feasible computational cost without making use of approximations such as a continuum solvent or an empirical cavity formation energy. As such, the method can be used far from ambient conditions, where the empirical parameters needed for approximate theories of solvation may not be available. The sources of error in the ABC-FEP method are the approximations in the ab initio method, the finite sample of configurations, and the classical solvent model. This article explores the accuracy of various approximations used in the ABC-FEP method by comparing to the experimentally well-known free energy of hydration of water at two state points (ambient conditions, and 973.15 K and 600 kg/m3). The TIP4P-FQ model [J. Chem. Phys. 101, 6141 (1994)] is found to be a reliable solvent model for use with this method, even at supercritical conditions. Results depend strongly on the ab initio method used: a gradient-corrected density functional theory is not adequate, but a localized MP2 method yields excellent agreement with experiment. Computational costs are reduced by using a cluster approximation, in which ab initio pair interaction energies are calculated between the solute and up to 60 solvent molecules, while multi-body interactions are calculated with only a small cluster (5 to 12 solvent molecules). Sampling errors for the ab initio contribution to

  12. 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.

  13. Accurate ab initio quartic force fields for borane and BeH2

    NASA Technical Reports Server (NTRS)

    Martin, J. M. L.; Lee, Timothy J.

    1992-01-01

    The quartic force fields of BH3 and BeH2 have been computed ab initio using an augmented coupled cluster (CCSD(T)) method and basis sets of spdf and spdfg quality. For BH3, the computed spectroscopic constants are in very good agreement with recent experimental data, and definitively confirm misassignments in some older work, in agreement with recent ab initio studies. Using the computed spectroscopic constants, the rovibrational partition function for both molecules has been constructed using a modified direct numerical summation algorithm, and JANAF-style thermochemical tables are presented.

  14. 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.

  15. Semiempirical prediction of protein folds

    NASA Astrophysics Data System (ADS)

    Fernández, Ariel; Colubri, Andrés; Appignanesi, Gustavo

    2001-08-01

    We introduce a semiempirical approach to predict ab initio expeditious pathways and native backbone geometries of proteins that fold under in vitro renaturation conditions. The algorithm is engineered to incorporate a discrete codification of local steric hindrances that constrain the movements of the peptide backbone throughout the folding process. Thus, the torsional state of the chain is assumed to be conditioned by the fact that hopping from one basin of attraction to another in the Ramachandran map (local potential energy surface) of each residue is energetically more costly than the search for a specific (Φ, Ψ) torsional state within a single basin. A combinatorial procedure is introduced to evaluate coarsely defined torsional states of the chain defined ``modulo basins'' and translate them into meaningful patterns of long range interactions. Thus, an algorithm for structure prediction is designed based on the fact that local contributions to the potential energy may be subsumed into time-evolving conformational constraints defining sets of restricted backbone geometries whereupon the patterns of nonbonded interactions are constructed. The predictive power of the algorithm is assessed by (a) computing ab initio folding pathways for mammalian ubiquitin that ultimately yield a stable structural pattern reproducing all of its native features, (b) determining the nucleating event that triggers the hydrophobic collapse of the chain, and (c) comparing coarse predictions of the stable folds of moderately large proteins (N~100) with structural information extracted from the protein data bank.

  16. Ab Initio Treatment of Lower Mantle Mineral Solvi.

    NASA Astrophysics Data System (ADS)

    Jung, D. Y.; Oganov, A. R.; Schmidt, M. W.

    2006-12-01

    The lower mantle of the Earth extends from about 670 to 2980 km depth and consists mainly of MgSiO3- perovskite (~ 70 vol%), (Mg,Fe)O magnesiowüstite (~ 20 vol%) and CaSiO3-perovskite (~ 10 vol%). To obtain a realistic picture of the lower mantle, it is necessary to consider the perovskite minerals as coexisting solid solutions with a large miscibility gap, as this is the case in nature. In this work we investigate the solvi of the three binaries in the Ca-perovskite - Mg-perovskite - corundum ternary, i.e. the solid solutions relevant for the Earth's lower mantle minerals in a simplified CMAS system. It is possible to calculate thermodynamic properties, structures and energetics of the individual minerals at extreme conditions of the mantle using ab initio methods, such as the density functional theory (DFT). We use the DFT together with the generalized gradient approximation (GGA) and the projector augmented wave (PAW) method, as implemented in the VASP code. The binary solvi are modelled through a subregular solid solution model together with point defect calculations at different pressures in the lower mantle regime. Point defects in the (Ca,Mg)-perovskite system are simple substitutions, but in MgSiO3-Al2O3 there is a coupled charge substitution of 2Al3+ with Mg2+Si^{4+}. Additionally, different symmetries of the perovskite (and akimotoite/ilmenite for MgSiO3) structures have been taken into account, thus allowing for phase transitions in solid solutions. At pressures and temperatures of the lower mantle, the solvus in the (Ca,Mg)SiO3 system remains wide open and solubilities of Ca in Mg-perovskite and Mg in Ca-perovskite decrease with pressure (at constant temperature and along any adiabatic geotherm). Calculations on the MgSiO3-Al2O3 (akimotoite-corundum) solvus show higher solubilities. Still, we find it unlikely that Ca-perovskite would disappear (i.e. fully dissolve in Mg-perovskite) at conditions of the lower mantle, at last not in the simplified CMAS

  17. Ab initio Calculations of Solvation Processes in Volcanic Gases

    NASA Astrophysics Data System (ADS)

    Lemke, K.; Seward, T.

    2006-12-01

    The structures and thermochemical properties of hydrated ions and neutral molecules play an important role in our understanding of solvent clustering and hydrogen bonding in the gas phase. Considerable effort therefore has been devoted to both the experimental and theoretical determination of stepwise hydration energies of geochemically important ions and neutral molecules with solvents, for instance H2O or H2S, over a broad range of temperatures typical of those encountered in volcanic gases. Because volcanic gases contain mutiple solute and solvent components which are subject to proton transfer, competive solvation and solvent switching, characterizing individual clusters has been a fundamental challenge to a molecular-level understanding of high temperature gas-phase solvation. However, recent advances in computational chemistry methods, especially Pople´s Gaussian (G-n) and complete basis set limit (CBS-x) model chemistries, now allow characterization of the dominant cluster structures and thermochemical properties of solute-solvent and solvent-solvent interactions in high temperature volcanic gases. Building on reported measurements of volcanic gases at Vesuvio, Italy, and Showa-Shinzan, Japan, as well as our recent investigations of ion-hydration we have re-examined the high temperature clustering equilibria of the small hydronium (H3O+) and ammonium (NH4+) ions as well as neutral ammonia and sulphur species with H2O and/or H2S using ab initio quantum chemical methods. From our study, we find that most of the gas phase ions tend to associate with a small number of H2O and H2S molecules to yield a hydrated ion cluster even at low humidities. Furthermore, inspection of van´t Hoff data demonstrate that (1) hydration energies of ions are shifted to less exergonic values as the solvent shell grows and the composition shifts from water-rich to hydrogen sulphide rich, (2) ion-cluster size increases with decreasing temperature at constant humidity, (3) attachment

  18. An efficient generation of a functionalized tertiary-alkyl radical for copper-catalyzed tertiary-alkylative Mizoroki-Heck type reaction.

    PubMed

    Nishikata, Takashi; Noda, Yushi; Fujimoto, Ryo; Sakashita, Tomomi

    2013-11-01

    α-Halocarbonyl compounds undergo β-hydrogen elimination to give conjugated olefins in the presence of a transition-metal catalyst. However, a copper/triamine catalyst system can induce the alkylative Mizoroki–Heck reaction of styrenes with tertiary-alkyl halides possessing a withdrawing group under very mild conditions. This reaction provides an efficient synthetic methodology for tertiary-alkylated styrenes. PMID:24143934

  19. 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…

  20. Cost-Sharing Reform of Tertiary Education in China and Its Equity Impact

    ERIC Educational Resources Information Center

    Wang, Catherine Yan

    2013-01-01

    China has made huge strides in expanding access to higher education since the 1980s. The main approach to achieve mass higher education was cost-sharing reforms of tertiary education. This article examines the policy reforms that affected tuition, fees and subsidies for tertiary students since the end of the 1980s and looks at the effects in terms…

  1. An Investigation of Tertiary-Level Learning in Some Practical Physics Courses

    ERIC Educational Resources Information Center

    Wang, Weili; Coll, Richard K.

    2005-01-01

    Experimental physics is seen as an essential part of tertiary physics education. Students are supposed to develop practical skills and advance from closed "cookbook" experiments to open experiment and design experiment procedures independently. As a consequence tertiary practical physics courses increase in the level of challenge throughout an…

  2. 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…

  3. Challenges Faced by Key Stakeholders Using Educational Online Technologies in Blended Tertiary Environments

    ERIC Educational Resources Information Center

    Tuapawa, Kimberley

    2016-01-01

    Traditional learning spaces have evolved into dynamic blended tertiary environments (BTEs), providing a modern means through which tertiary education institutes (TEIs) can augment delivery to meet stakeholder needs. Despite the significant demand for web-enabled learning, there are obstacles concerning the use of EOTs, which challenge the…

  4. Collaboration/Competition Crossroads: National/Supranational Tertiary Education Policies on a Collision Course

    ERIC Educational Resources Information Center

    Patterson, Glenys

    2005-01-01

    In the context of tertiary education, the paper explores the nature of the General Agreement on Trade in Services (GATS) negotiation process and obligation framework, with examples, considers whether GATS is needed to support a country's "export education" and what a country could do to protect its tertiary education system from the impact of a…

  5. 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…

  6. 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…

  7. 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…

  8. 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…

  9. Information Literacy: The Link between Secondary and Tertiary Education Project and Its Wider Implications

    ERIC Educational Resources Information Center

    Crawford, John; Irving, Christine

    2007-01-01

    The study reviews a research project which, inter alia, is constructing an information literacy framework linking secondary and tertiary education and arises out of research conducted in both the secondary and tertiary sectors. The Project is firmly situated in a Scottish context but draws on UK and indeed worldwide experience. It began in October…

  10. Students' Conceptions of the Particulate Nature of Matter at Secondary and Tertiary Level

    ERIC Educational Resources Information Center

    Ayas, Alipasa; Ozmen, Haluk; Calik, Muammer

    2010-01-01

    The aim of the present study is to elicit students' understanding of the particulate nature of matter via a cross-age study ranging from secondary to tertiary educational levels. A questionnaire with five-item open-ended questions was administered to 166 students from the secondary to tertiary levels of education. In light of the findings, it can…

  11. Transition and Tertiary Education: A Case Study of Mzuzu University, Malawi

    ERIC Educational Resources Information Center

    Zozie, Paxton Andrew; Kayira, Peter Benwell

    2012-01-01

    This article reviews the role of guidance and counselling in Malawi in reducing dropout and easing the transition of students to tertiary education, as well as in helping them during their time in tertiary education. It begins by identifying key success factors in guidance and counselling services for learners in both developed and developing…

  12. 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…

  13. The Impact of HECS Debt on Australian Students' Tertiary Academic Performance

    ERIC Educational Resources Information Center

    Birch, Elisa R.; Miller, Paul W.

    2006-01-01

    The Australian literature suggests that students' academic success in tertiary education is principally influenced by their university entrance score. Personal, secondary school and university characteristics have more minor impacts on tertiary outcomes. Little research has been undertaken into the relationship between students' marks and the…

  14. Benzoyl peroxide (BPO)-promoted oxidative trifluoromethylation of tertiary amines with trimethyl(trifluoromethyl)silane.

    PubMed

    Chu, Lingling; Qing, Feng-Ling

    2010-09-14

    The benzoyl peroxide (BPO)-promoted oxidative functionalization of tertiary amines under transition-metal-free reaction conditions was developed. Various 1-trifluoromethylated tetrahydroisoquinoline derivatives were prepared by employing this method. It constitutes the first example of direct trifluoromethylation of tertiary amines.

  15. 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…

  16. Widening Access to Tertiary Education for Women in Ghana through Distance Education

    ERIC Educational Resources Information Center

    Kwapong, Olivia Adwoa Tiwaah Frimpong

    2007-01-01

    Distance education (DE) is seen as a tool for widening access to education at all levels. It is an educational tool that breaks most of the divides in education--age, gender, race, income, space, time etc. For the past decades, irrespective of the extensive expansion of tertiary institutions in the country, provision of tertiary education in Ghana…

  17. 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…

  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. 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,…

  20. The School-Tertiary Interface in Mathematics: Teaching Style and Assessment Practice

    ERIC Educational Resources Information Center

    Thomas, Michael O. J.; Klymchuk, Sergiy

    2012-01-01

    Issues arising in the transition from secondary school to tertiary mathematics study are increasingly coming under scrutiny. In this paper, we analyse two practical aspects of the school-tertiary interface: teaching style; and assessment. We present some of the findings arising from a 2-year national project in New Zealand titled "Analysing the…

  1. 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…

  2. 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…

  3. 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…

  4. 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…

  5. A General Method for Insertion of Functional Proteins within Proteins via Combinatorial Selection of Permissive Junctions.

    PubMed

    Peng, Yingjie; Zeng, Wenwen; Ye, Hui; Han, Kyung Ho; Dharmarajan, Venkatasubramanian; Novick, Scott; Wilson, Ian A; Griffin, Patrick R; Friedman, Jeffrey M; Lerner, Richard A

    2015-08-20

    A major goal of modern protein chemistry is to create new proteins with different functions. One approach is to amalgamate secondary and tertiary structures from different proteins. This is difficult for several reasons, not the least of which is the fact that the junctions between secondary and tertiary structures are not degenerate and usually affect the function and folding of the entire complex. Here, we offer a solution to this problem by coupling a large combinatorial library of about 10(7) different N- and C-terminal junctions to a powerful system that selects for function. Using this approach, the entire Leptin and follicle-stimulating hormone (FSH) were inserted into an antibody. Complexes with full retention of function in vivo and in vitro, although rare, were found easily by using an autocrine selection system to search for hormonal activity. Such large diversity systems, when coupled to robust selection systems, should enable construction of novel therapeutic proteins.

  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. Ab initio charge-carrier mobility model for amorphous molecular semiconductors

    NASA Astrophysics Data System (ADS)

    Massé, Andrea; Friederich, Pascal; Symalla, Franz; Liu, Feilong; Nitsche, Robert; Coehoorn, Reinder; Wenzel, Wolfgang; Bobbert, Peter A.

    2016-05-01

    Accurate charge-carrier mobility models of amorphous organic molecular semiconductors are essential to describe the electrical properties of devices based on these materials. The disordered nature of these semiconductors leads to percolative charge transport with a large characteristic length scale, posing a challenge to the development of such models from ab initio simulations. Here, we develop an ab initio mobility model using a four-step procedure. First, the amorphous morphology together with its energy disorder and intermolecular charge-transfer integrals are obtained from ab initio simulations in a small box. Next, the ab initio information is used to set up a stochastic model for the morphology and transfer integrals. This stochastic model is then employed to generate a large simulation box with modeled morphology and transfer integrals, which can fully capture the percolative charge transport. Finally, the charge-carrier mobility in this simulation box is calculated by solving a master equation, yielding a mobility function depending on temperature, carrier concentration, and electric field. We demonstrate the procedure for hole transport in two important molecular semiconductors, α -NPD and TCTA. In contrast to a previous study, we conclude that spatial correlations in the energy disorder are unimportant for α -NPD. We apply our mobility model to two types of hole-only α -NPD devices and find that the experimental temperature-dependent current density-voltage characteristics of all devices can be well described by only slightly decreasing the simulated energy disorder strength.

  8. 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.

  9. 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.

  10. 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

    2016-07-01

    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.

  11. 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.

  12. New approaches for molecular conformer force field analysis in combination with ab initio results

    NASA Astrophysics Data System (ADS)

    Kuramshina, G. M.; Pentin, Yu. A.; Yagola, A. G.

    1999-10-01

    Ab initio and DFT results on harmonic force constants for trans- and gauche-conformers of CH 3CH 2CH 2Cl, CF 3CH 2CH 2Cl and CCl 3CH 2CH 2Cl are used for formulating constraints in molecular force field models described compounds with hindered internal rotation around the C-C bond.

  13. 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

    2016-07-01

    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. PMID:27394094

  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. The Use of Ab Initio Wavefunctions in Line-Shape Calculations for Water Vapor

    NASA Astrophysics Data System (ADS)

    Gamache, Robert R.; Lamouroux, Julien; Schwenke, David W.

    2014-06-01

    In semi-classical line-shape calculations, the internal motions of the colliding pair are treated via quantum mechanics and the collision trajectory is determined by classical dynamics. The quantum mechanical component, i.e. the determination of reduced matrix elements (RME) for the colliding pair, requires the wavefunctions of the radiating and the perturbing molecules be known. Here the reduced matrix elements for collisions in the ground vibrational state of water vapor are calculated by two methods and compared. First, wavefunctions determined by diagonalizing an effective (Watson) Hamiltonian are used to calculate the RMEs and, second, the ab initio wavefunctions of Partridge and Schwenke are used. While the ground vibrational state will yield the best approximation of the wavefunctions from the effective Hamiltonian approach, this study clearly identifies problems for states not included in the fit of the Hamiltonian and for extrapolated states. RMEs determined using ab initio wavefunctions use ˜100000 times more computational time; however, all ro-vibrational interactions are included. Hence, the ab initio approach will yield better RMEs as the number of vibrational quanta exchanged in the optical transition increases, resulting in improvements in calculated half-widths and line shifts. It is important to note that even for pure rotational transitions the use of ab initio wavefunctions will yield improved results.

  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. Raman and infrared spectra of minerals from ab initio molecular dynamics simulations: The spodumene crystal

    NASA Astrophysics Data System (ADS)

    Pagliai, Marco; Muniz-Miranda, Maurizio; Cardini, Gianni; Schettino, Vincenzo

    2011-05-01

    Ab initio molecular dynamics simulations with the Car-Parrinello method have been performed on the spodumene crystal at standard conditions and high pressure. Starting from the computed trajectories, accurate Raman and infrared spectra have been obtained and compared with available experimental measurements in the low and high pressure phases. The structural and spectroscopic changes due to the pressure effects are discussed.

  18. Clinical pharmacy service practice in a Chinese tertiary hospital.

    PubMed

    Chen, Bing; Huang, Jing-Jing; Chen, He-feng; Xu, Bei-ming

    2015-12-01

    Clinical pharmacy service is focused on the rationality and safety of medication therapy. Clinical pharmacists play an important role in designing therapeutic regimen, preventing medication errors, reducing the incidence of adverse drug reaction, and saving medical costs. Although clinical pharmacy service in China is in its early stage, its development is rapid. In this manuscript, the working model of clinical pharmacists in a Chinese tertiary hospital is introduced, including ward rounds, consultation, stewardship of antimicrobial therapy, drug adverse reaction monitoring, therapeutic drug monitoring, clinical pharmacokinetics and pharmacogenetics, and training system. With the efforts of clinical pharmacists, there will be a significant increase in the optimization of medication therapy and a notable reduction in preventable adverse drug events as well as health-care cost in China. PMID:26457791

  19. Volume XIII: The tertiary insects of North America

    USGS Publications Warehouse

    Scudder, Samuel H.

    1890-01-01

    Another point to which attention may be drawn is the very considerable number and quite extraordinary proportion of species which so far are represented by a single specimen. Leaving out of consideration certain marvelously prevalent forms in the beds of Florissant, such as certain Formicidae, Alydina, etc., one working these beds, from which many thousands of insects have already been taken, may confidently expect that every third or fourth specimen will prove something new. A quite similar statement can be made of all, or all but one, of the other localities where insects have been found in our Tertiary deposits: it surely indicates that with all the rich results of the explorations so far undertaken we are only upon the threshold of our possible kno

  20. An asterid flower from neotropical mid-Tertiary amber.

    PubMed

    Poinar, George O; Struwe, Lena

    2016-01-01

    Fossils preserved in amber may provide significant palaeoevolutionary and biogeographical data regarding the evolution of life on Earth(1). Although amber is particularly noted for its detailed preservation of arthropods, the same degree of preservation can be found for vascular plant remains(2). Mid-Tertiary Dominican amber is a rich source for such fossils, and representatives of several angiosperm families have been described. However, no fossilized examples of the large asterid plant clade have yet been reported. Here we describe the first fossil neotropical flowers found in amber from a representative of the asterids. The asterids are one of the largest lineages of flowering plants, containing groups such as the sunflower, potato, coffee and mint families, totalling over 80,000 species(3). The new fossils are only known as flowers, more precisely corollas with stamens and styles. We here describe them as a new species, Strychnos electri sp. nov, in the plant family Loganiaceae (Gentianales). PMID:27249345