Evaluating a new test of whole English collocations

DEFF Research Database (Denmark)

Revier, Robert Lee

2009-01-01

in their own right and, as such, feature formal, semantic, and usage properties similar to those borne by single words. Third, the semantic properties of the constituent words that combine to form collocations are likely to play a role in EFL learners' ability to 'produce' English collocations. Forth, testing...... of L2 collocation knowledge needs to focus on the recognition and production of whole collocations. It is this set of assumptions that the new collocation test presented in this chapter is desined to probe. More specifically, the test is designed to assess L2 learners' productive knowledge of whole...

The Presentation and Treatment of Collocations as Secondary ...

African Journals Online (AJOL)

Although the discussion primarily focuses on printed dictionaries proposals are also made for the presentation of collocations in online dictionaries. Keywords: Article structure, collocation, complex collocation, cotext, example sentences, integrated microstructure, non-grouped ordering, search zone, semi-integrated ...

Testing controlled productive knowledge of adverb-verb collocations ...

African Journals Online (AJOL)

A controlled productive test of adverb-verb collocations ..... The third approach to studying collocations, corpus analysis, ..... The collocation web model is thought to match Nation's (2001) psychological .... Theory, analysis, and applications. .... Canadian Modern ... Focus on vocabulary: Mastering the Academic Word List.

Productive knowledge of collocations may predict academic literacy

Directory of Open Access Journals (Sweden)

Van Dyk, Tobie

2016-12-01

Full Text Available The present study examines the relationship between productive knowledge of collocations and academic literacy among first year students at North-West University. Participants were administered a collocation test, the items of which were selected from Nation’s (2006 word frequency bands, i.e. the 2000-word, 3000-word, 5000-word bands; and the Academic Word List (Coxhead, 2000. The scores from the collocation test were compared to those from the Test of Academic Literacy Levels (version administered in 2012. The results of this study indicate that, overall, knowledge of collocations is significantly correlated with academic literacy, which is also observed at each of the frequency bands from which the items were selected. These results support Nizonkiza’s (2014 findings that a significant correlation between mastery of collocations of words from the Academic Word List and academic literacy exists; which is extended here to words from other frequency bands. They also confirm previous findings that productive knowledge of collocations increases alongside overall proficiency (cf. Gitsaki, 1999; Bonk, 2001; Eyckmans et al., 2004; Boers et al., 2006; Nizonkiza, 2011; among others. This study therefore concludes that growth in productive knowledge of collocations may entail growth in academic literacy; suggesting that productive use of collocations is linked to academic literacy to a considerable extent. In light of these findings, teaching strategies aimed to assist first year students meet academic demands posed by higher education and avenues to explore for further research are discussed. Especially, we suggest adopting a productive oriented approach to teaching collocations, which we believe may prove useful.

Testing controlled productive knowledge of adverb-verb collocations ...

African Journals Online (AJOL)

The study also reveals that controlled productive knowledge of adverbverb collocations is less problematic. Based on these results, teaching strategies aimed at improving the use of adverb-verb collocations among EFL users are proposed. Keywords: academic writing, adverb-verb collocations, productive knowledge of ...

Pseudospectral collocation methods for fourth order differential equations

Science.gov (United States)

Malek, Alaeddin; Phillips, Timothy N.

1994-01-01

Collocation schemes are presented for solving linear fourth order differential equations in one and two dimensions. The variational formulation of the model fourth order problem is discretized by approximating the integrals by a Gaussian quadrature rule generalized to include the values of the derivative of the integrand at the boundary points. Collocation schemes are derived which are equivalent to this discrete variational problem. An efficient preconditioner based on a low-order finite difference approximation to the same differential operator is presented. The corresponding multidomain problem is also considered and interface conditions are derived. Pseudospectral approximations which are C1 continuous at the interfaces are used in each subdomain to approximate the solution. The approximations are also shown to be C3 continuous at the interfaces asymptotically. A complete analysis of the collocation scheme for the multidomain problem is provided. The extension of the method to the biharmonic equation in two dimensions is discussed and results are presented for a problem defined in a nonrectangular domain.

The relationship between productive knowledge of collocations and ...

African Journals Online (AJOL)

This research explores tertiary level L2 students' mastery of the collocations pertaining to the Academic Word List (AWL) and the extent to which their knowledge of collocations grows alongside their academic literacy. A collocation test modelled on Laufer and Nation (1999), with target words selected from Coxhead's (2000) ...

Measuring receptive collocational competence across proficiency ...

African Journals Online (AJOL)

The present study investigates (i) English as Foreign Language (EFL) learners' receptive collocational knowledge growth in relation to their linguistic proficiency level; (ii) how much receptive collocational knowledge is acquired as linguistic proficiency develops; and (iii) the extent to which receptive knowledge of ...

Teaching collocations

DEFF Research Database (Denmark)

Revier, Robert Lee; Henriksen, Birgit

2006-01-01

Very little pedadagoy has been made available to teachers interested in teaching collocations in foreign and/or second language classroom. This paper aims to contribute to and promote efforts in developing L2-based pedagogy for the teaching of phraseology. To this end, it presents pedagogical...

On Collocations and Their Interaction with Parsing and Translation

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Violeta Seretan

2013-10-01

Full Text Available We address the problem of automatically processing collocations—a subclass of multi-word expressions characterized by a high degree of morphosyntactic flexibility—in the context of two major applications, namely, syntactic parsing and machine translation. We show that parsing and collocation identification are processes that are interrelated and that benefit from each other, inasmuch as syntactic information is crucial for acquiring collocations from corpora and, vice versa, collocational information can be used to improve parsing performance. Similarly, we focus on the interrelation between collocations and machine translation, highlighting the use of translation information for multilingual collocation identification, as well as the use of collocational knowledge for improving translation. We give a panorama of the existing relevant work, and we parallel the literature surveys with our own experiments involving a symbolic parser and a rule-based translation system. The results show a significant improvement over approaches in which the corresponding tasks are decoupled.

A Study on the Phenomenon of Collocations: Methodology of Teaching English and German Collocations to Russian Students

Science.gov (United States)

Varlamova, Elena V.; Naciscione, Anita; Tulusina, Elena A.

2016-01-01

Relevance of the issue stated in the article is determined by the fact that there is a lack of research devoted to the methods of teaching English and German collocations. The aim of our work is to determine methods of teaching English and German collocations to Russian university students studying foreign languages through experimental testing.…

Verb-Noun Collocations in Written Discourse of Iranian EFL Learners

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Fatemeh Ebrahimi-Bazzaz

2015-07-01

Full Text Available When native speakers of English write, they employ both grammatical rules and collocations. Collocations are words that are present in the memory of native speakers as ready-made prefabricated chunks. Non-native speakers who wish to acquire native-like fluency should give appropriate attention to collocations in writing in order not to produce sentences that native speakers may consider odd. The present study tries to explore the use of verb-noun collocations in written discourse of English as foreign language (EFL among Iranian EFL learners from one academic year to the next in Iran. To measure the use of verb-noun collocations in written discourse, there was a 60-minute task of writing story  based on a series of six pictures whereby for each picture, three verb-noun collocations were measured, and nouns were provided to limit the choice of collocations. The results of the statistical analysis of ANOVA for the research question indicated that there was a significant difference in the use of lexical verb-noun collocations in written discourse both between and within the four academic years. The results of a post hoc multiple comparison tests confirmed that the means are significantly different between the first year and the third and fourth years, between the second and the fourth, and between the third and the fourth academic year which indicate substantial development in verb-noun collocation proficiency.  The vital implication is that the learners could use verb-noun collocations in productive skill of writing.

Meshfree Local Radial Basis Function Collocation Method with Image Nodes

Energy Technology Data Exchange (ETDEWEB)

Baek, Seung Ki; Kim, Minjae [Pukyong National University, Busan (Korea, Republic of)

2017-07-15

We numerically solve two-dimensional heat diffusion problems by using a simple variant of the meshfree local radial-basis function (RBF) collocation method. The main idea is to include an additional set of sample nodes outside the problem domain, similarly to the method of images in electrostatics, to perform collocation on the domain boundaries. We can thereby take into account the temperature profile as well as its gradients specified by boundary conditions at the same time, which holds true even for a node where two or more boundaries meet with different boundary conditions. We argue that the image method is computationally efficient when combined with the local RBF collocation method, whereas the addition of image nodes becomes very costly in case of the global collocation. We apply our modified method to a benchmark test of a boundary value problem, and find that this simple modification reduces the maximum error from the analytic solution significantly. The reduction is small for an initial value problem with simpler boundary conditions. We observe increased numerical instability, which has to be compensated for by a sufficient number of sample nodes and/or more careful parameter choices for time integration.

Rectangular spectral collocation

KAUST Repository

Driscoll, Tobin A.; Hale, Nicholas

2015-01-01

Boundary conditions in spectral collocation methods are typically imposed by removing some rows of the discretized differential operator and replacing them with others that enforce the required conditions at the boundary. A new approach based upon

Improving academic literacy by teaching collocations | Nizonkiza ...

African Journals Online (AJOL)

Stellenbosch Papers in Linguistics ... Abstract. This study explores the effect of teaching collocations on building academic vocabulary and hence improving academic writing abilities. ... They were presented with a completion task and an essay-writing task before and after being exposed to a collocation-based syllabus.

Testing knowledge of whole English collocations available for use in written production

DEFF Research Database (Denmark)

Revier, Robert Lee

2014-01-01

Testing knowledge of whole English collocations available for use in written production: Developing tests for use with intermediate and advanced Danish learners (dansk resume nedenfor) The present foreign language acquisition research derives its impetus from four assumptions regarding knowledge...... of English collocations. These are: (a) collocation knowledge can be conceptualized as an independent knowledge construct, (b) collocations are lexical items in their own right, (c) testing of collocation knowledge should also target knowledge of whole collocations, and (d) the learning burden of a whole...... the development of Danish EFL learners’ productive knowledge of whole English collocations. Five empirical studies were designed to generate information that would shed light on the reliability and validity of the CONTRIX as a measure of collocation knowledge available for use in written production. Study 1...

Extending Binary Collocations: (Lexicographical Implications of Going beyond the Prototypical a – b

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Dušan Gabrovšek

2014-05-01

Full Text Available The paper focuses primarily on the Sinclairian concept of extended units of meaning in general and on extended collocations in particular, investigating their nature and types. Such extended units are extremely varied and diverse; they are regarded as instances of the functioning of the coselection principle. Some extended forms are used far more commonly that the corresponding prototypical (binary sequences. The final section delves into the ABCs of extended collocations in the context of lexicography, suggesting that dictionaries should make an effort to include a selection of such strings, especially for encoding tasks that are to be shown as examples of use. Most dictionaries incorporate very few such “loose” units, probably because of a powerful tradition to include as examples of use chiefly binary collocations and full sentences.

Modified Chebyshev Collocation Method for Solving Differential Equations

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M Ziaul Arif

2015-05-01

Full Text Available This paper presents derivation of alternative numerical scheme for solving differential equations, which is modified Chebyshev (Vieta-Lucas Polynomial collocation differentiation matrices. The Scheme of modified Chebyshev (Vieta-Lucas Polynomial collocation method is applied to both Ordinary Differential Equations (ODEs and Partial Differential Equations (PDEs cases. Finally, the performance of the proposed method is compared with finite difference method and the exact solution of the example. It is shown that modified Chebyshev collocation method more effective and accurate than FDM for some example given.

Supporting Collocation Learning with a Digital Library

Science.gov (United States)

Wu, Shaoqun; Franken, Margaret; Witten, Ian H.

2010-01-01

Extensive knowledge of collocations is a key factor that distinguishes learners from fluent native speakers. Such knowledge is difficult to acquire simply because there is so much of it. This paper describes a system that exploits the facilities offered by digital libraries to provide a rich collocation-learning environment. The design is based on…

"Minimum input, maximum output, indeed!" Teaching Collocations ...

African Journals Online (AJOL)

Fifty-nine EFL college students participated in the study, and they received two 75-minute instructions between pre- and post-tests: one on the definition of colloca-tion and its importance, and the other on the skill of looking up collocational information in the Naver Dictionary — an English–Korean online dictionary. During ...

The structure of an Afrikaans collocation and phrase dictionary | Otto ...

African Journals Online (AJOL)

As one of the target groups is unsophisticated learners with a limited grammatical background, the ideal would be to enter lexical collocations both at their bases and at the collocators. To save space however, more information such as examples could then be provided at the bases only. Grammatical collocations should be ...

Recent advances in radial basis function collocation methods

CERN Document Server

Chen, Wen; Chen, C S

2014-01-01

This book surveys the latest advances in radial basis function (RBF) meshless collocation methods which emphasis on recent novel kernel RBFs and new numerical schemes for solving partial differential equations. The RBF collocation methods are inherently free of integration and mesh, and avoid tedious mesh generation involved in standard finite element and boundary element methods. This book focuses primarily on the numerical algorithms, engineering applications, and highlights a large class of novel boundary-type RBF meshless collocation methods. These methods have shown a clear edge over the traditional numerical techniques especially for problems involving infinite domain, moving boundary, thin-walled structures, and inverse problems. Due to the rapid development in RBF meshless collocation methods, there is a need to summarize all these new materials so that they are available to scientists, engineers, and graduate students who are interest to apply these newly developed methods for solving real world’s ...

47 CFR 51.323 - Standards for physical collocation and virtual collocation.

Science.gov (United States)

2010-10-01

... standards or any other performance standards. An incumbent LEC that denies collocation of a competitor's equipment, citing safety standards, must provide to the competitive LEC within five business days of the... incumbent LEC contends the competitor's equipment fails to meet. This affidavit must set forth in detail...

An empirical understanding of triple collocation evaluation measure

Science.gov (United States)

Scipal, Klaus; Doubkova, Marcela; Hegyova, Alena; Dorigo, Wouter; Wagner, Wolfgang

2013-04-01

Triple collocation method is an advanced evaluation method that has been used in the soil moisture field for only about half a decade. The method requires three datasets with an independent error structure that represent an identical phenomenon. The main advantages of the method are that it a) doesn't require a reference dataset that has to be considered to represent the truth, b) limits the effect of random and systematic errors of other two datasets, and c) simultaneously assesses the error of three datasets. The objective of this presentation is to assess the triple collocation error (Tc) of the ASAR Global Mode Surface Soil Moisture (GM SSM 1) km dataset and highlight problems of the method related to its ability to cancel the effect of error of ancillary datasets. In particular, the goal is to a) investigate trends in Tc related to the change in spatial resolution from 5 to 25 km, b) to investigate trends in Tc related to the choice of a hydrological model, and c) to study the relationship between Tc and other absolute evaluation methods (namely RMSE and Error Propagation EP). The triple collocation method is implemented using ASAR GM, AMSR-E, and a model (either AWRA-L, GLDAS-NOAH, or ERA-Interim). First, the significance of the relationship between the three soil moisture datasets was tested that is a prerequisite for the triple collocation method. Second, the trends in Tc related to the choice of the third reference dataset and scale were assessed. For this purpose the triple collocation is repeated replacing AWRA-L with two different globally available model reanalysis dataset operating at different spatial resolution (ERA-Interim and GLDAS-NOAH). Finally, the retrieved results were compared to the results of the RMSE and EP evaluation measures. Our results demonstrate that the Tc method does not eliminate the random and time-variant systematic errors of the second and the third dataset used in the Tc. The possible reasons include the fact a) that the TC

First-year University Students' Productive Knowledge of Collocations ...

African Journals Online (AJOL)

The present study examines productive knowledge of collocations of tertiary-level second language (L2) learners of English in an attempt to make estimates of the size of their knowledge. Participants involved first-year students at North-West University who sat a collocation test modelled on that developed by Laufer and ...

Corpus-Aided Business English Collocation Pedagogy: An Empirical Study in Chinese EFL Learners

Science.gov (United States)

Chen, Lidan

2017-01-01

This study reports an empirical study of an explicit instruction of corpus-aided Business English collocations and verifies its effectiveness in improving learners' collocation awareness and learner autonomy, as a result of which is significant improvement of learners' collocation competence. An eight-week instruction in keywords' collocations,…

Teachability of collocations: The role of word frequency counts ...

African Journals Online (AJOL)

... beginner/low-intermediate students and only exceed the 2 000-word band from the upper-intermediate learning stage onwards, a suggestion in line with Nation's (2006) discussion on how to teach vocabulary. Keywords: collocation size, controlled productive knowledge, teachability of collocations, word frequency counts, ...

Developing and Evaluating a Web-Based Collocation Retrieval Tool for EFL Students and Teachers

Science.gov (United States)

Chen, Hao-Jan Howard

2011-01-01

The development of adequate collocational knowledge is important for foreign language learners; nonetheless, learners often have difficulties in producing proper collocations in the target language. Among the various ways of learning collocations, the DDL (data-driven learning) approach encourages independent learning of collocations and allows…

A Stochastic Collocation Method for Elliptic Partial Differential Equations with Random Input Data

KAUST Repository

Babuška, Ivo; Nobile, Fabio; Tempone, Raul

2010-01-01

This work proposes and analyzes a stochastic collocation method for solving elliptic partial differential equations with random coefficients and forcing terms. These input data are assumed to depend on a finite number of random variables. The method consists of a Galerkin approximation in space and a collocation in the zeros of suitable tensor product orthogonal polynomials (Gauss points) in the probability space, and naturally leads to the solution of uncoupled deterministic problems as in the Monte Carlo approach. It treats easily a wide range of situations, such as input data that depend nonlinearly on the random variables, diffusivity coefficients with unbounded second moments, and random variables that are correlated or even unbounded. We provide a rigorous convergence analysis and demonstrate exponential convergence of the “probability error” with respect to the number of Gauss points in each direction of the probability space, under some regularity assumptions on the random input data. Numerical examples show the effectiveness of the method. Finally, we include a section with developments posterior to the original publication of this work. There we review sparse grid stochastic collocation methods, which are effective collocation strategies for problems that depend on a moderately large number of random variables.

Examining Second Language Receptive Knowledge of Collocation and Factors That Affect Learning

Science.gov (United States)

Nguyen, Thi My Hang; Webb, Stuart

2017-01-01

This study investigated Vietnamese EFL learners' knowledge of verb-noun and adjective-noun collocations at the first three 1,000 word frequency levels, and the extent to which five factors (node word frequency, collocation frequency, mutual information score, congruency, and part of speech) predicted receptive knowledge of collocation. Knowledge…

Translating English Idioms and Collocations

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Rochayah Machali

2004-01-01

Full Text Available Learners of English should be made aware of the nature, types, and use of English idioms. This paper disensses the nature of idioms and collocations and translation issues related to them

Learning and Teaching L2 Collocations: Insights from Research

Science.gov (United States)

Szudarski, Pawel

2017-01-01

The aim of this article is to present and summarize the main research findings in the area of learning and teaching second language (L2) collocations. Being a large part of naturally occurring language, collocations and other types of multiword units (e.g., idioms, phrasal verbs, lexical bundles) have been identified as important aspects of L2…

English collocations: A novel approach to teaching the language's last bastion

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Rafe S. Zaabalawi

2017-01-01

Full Text Available Collocations are a class of idiomatic expressions comprised of a sequence of words which, for mostly arbitrary reasons, occur together in a prescribed order. Collocations are not necessarily grammatical and/or cannot be generated through knowledge of rules or formulae. Therefore, they are often not easily mastered by EFL learners and typically only dealt with during the latter phase of second language apprenticeship. Literature has mostly examined the phenomenon of collocations from one of two perspectives. First, there are studies focusing on error analysis and contingent pedagogical advice. Second, there is research concerned with theory development; a genre associated with a specific methodological limitations. This study reports on data pertaining to a novel approach to learning collocations; one based on a learner's incidental discovery of such structures in written texts. Our research question is: will students who have been introduced to and practiced specific collocations in reading texts be inclined to naturally use such exemplars appropriately in novel/unfamiliar subsequent contexts? Findings have implications for EFL teachers and those concerned with curriculum development.

Analysis of an upstream weighted collocation approximation to the transport equation

International Nuclear Information System (INIS)

Shapiro, A.; Pinder, G.F.

1981-01-01

The numerical behavior of a modified orthogonal collocation method, as applied to the transport equations, can be examined through the use of a Fourier series analysis. The necessity of such a study becomes apparent in the analysis of several techniques which emulate classical upstream weighting schemes. These techniques are employed in orthogonal collocation and other numerical methods as a means of handling parabolic partial differential equations with significant first-order terms. Divergent behavior can be shown to exist in one upstream weighting method applied to orthogonal collocation

Corpora and Collocations in Chinese-English Dictionaries for Chinese Users

Science.gov (United States)

Xia, Lixin

2015-01-01

The paper identifies the major problems of the Chinese-English dictionary in representing collocational information after an extensive survey of nine dictionaries popular among Chinese users. It is found that the Chinese-English dictionary only provides the collocation types of "v+n" and "v+n," but completely ignores those of…

Collocational Relations in Japanese Language Textbooks and Computer-Assisted Language Learning Resources

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Irena SRDANOVIĆ

2011-05-01

Full Text Available In this paper, we explore presence of collocational relations in the computer-assisted language learning systems and other language resources for the Japanese language, on one side, and, in the Japanese language learning textbooks and wordlists, on the other side. After introducing how important it is to learn collocational relations in a foreign language, we examine their coverage in the various learners’ resources for the Japanese language. We particularly concentrate on a few collocations at the beginner’s level, where we demonstrate their treatment across various resources. A special attention is paid to what is referred to as unpredictable collocations, which have a bigger foreign language learning-burden than the predictable ones.

Crosstalk statistics via collocation method

NARCIS (Netherlands)

Diouf, F.; Canavero, Flavio

2009-01-01

A probabilistic model for the evaluation of transmission lines crosstalk is proposed. The geometrical parameters are assumed to be unknown and the exact solution is decomposed into two functions, one depending solely on the random parameters and the other on the frequency. The stochastic collocation

Collocations of High Frequency Noun Keywords in Prescribed Science Textbooks

Science.gov (United States)

Menon, Sujatha; Mukundan, Jayakaran

2012-01-01

This paper analyses the discourse of science through the study of collocational patterns of high frequency noun keywords in science textbooks used by upper secondary students in Malaysia. Research has shown that one of the areas of difficulty in science discourse concerns lexis, especially that of collocations. This paper describes a corpus-based…

B-spline Collocation with Domain Decomposition Method

International Nuclear Information System (INIS)

Hidayat, M I P; Parman, S; Ariwahjoedi, B

2013-01-01

A global B-spline collocation method has been previously developed and successfully implemented by the present authors for solving elliptic partial differential equations in arbitrary complex domains. However, the global B-spline approximation, which is simply reduced to Bezier approximation of any degree p with C 0 continuity, has led to the use of B-spline basis of high order in order to achieve high accuracy. The need for B-spline bases of high order in the global method would be more prominent in domains of large dimension. For the increased collocation points, it may also lead to the ill-conditioning problem. In this study, overlapping domain decomposition of multiplicative Schwarz algorithm is combined with the global method. Our objective is two-fold that improving the accuracy with the combination technique, and also investigating influence of the combination technique to the employed B-spline basis orders with respect to the obtained accuracy. It was shown that the combination method produced higher accuracy with the B-spline basis of much lower order than that needed in implementation of the initial method. Hence, the approximation stability of the B-spline collocation method was also increased.

Bessel collocation approach for approximate solutions of Hantavirus infection model

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Suayip Yuzbasi

2017-11-01

Full Text Available In this study, a collocation method is introduced to find the approximate solutions of Hantavirus infection model which is a system of nonlinear ordinary differential equations. The method is based on the Bessel functions of the first kind, matrix operations and collocation points. This method converts Hantavirus infection model into a matrix equation in terms of the Bessel functions of first kind, matrix operations and collocation points. The matrix equation corresponds to a system of nonlinear equations with the unknown Bessel coefficients. The reliability and efficiency of the suggested scheme are demonstrated by numerical applications and all numerical calculations have been done by using a program written in Maple.

GUESSING VERB-ADVERB COLLOCATIONS: ARAB EFL ...

African Journals Online (AJOL)

user

In the sections to follow, the concept and meaning of collocation is defined ... expressions (Alexander 1984); formulaic language or speech (Weinert 1995); multi- ... Two further studies reported Arab EFL learners' overall ignorance of col-.

Translating Legal Collocations in Contract Agreements by Iraqi EFL Students-Translators

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Muntaha A. Abdulwahid

2017-01-01

Full Text Available Legal translation of contract agreements is a challenge to translators as it involves combining the literary translation with the technical terminological precision. In translating legal contract agreements, a legal translator must utilize the lexical or syntactic precision and, more importantly, the pragmatic awareness of the context. This will guarantee an overall communicative process and avoid inconsistency in legal translation. However, the inability of the translator to meet these two functions in translating the contract item not only affects the contractors’ comprehension of the contract item but also affects the parties’ contractual obligations. In light of this, the purpose of this study was to find out how legal collocations used in contract agreements are translated from Arabic into English by student-translators in terms of (1 purely technical, (2 semi-technical, and (3 everyday vocabulary collocations. For the data collection, a multiple-choice collocation test was used to be answered by 35 EFL Iraqi undergraduate translator-students to decide on the aspects of weaknesses and strengths of their translation, thus decide on the aspects of correction. The findings showed that these students had serious problems in translating legal collocations as they lack the linguistic knowledge and pragmatic awareness needed to achieve the legal meaning and effect. They were also unable to make a difference among the three categories of legal collocations, purely technical, semi-technical, and everyday vocabulary collocations. These students should be exposed to more legal translation practices to obtain the required experience needed for their future career.

Presenting collocates in a dictionary of computing and the Internet according to user needs

DEFF Research Database (Denmark)

Leroyer, Patrick; L'Homme, Marie-Claude; Jousse, Anne-Laure

2011-01-01

This paper presents a novel method for organizing and presenting collocations in a specialized dictionary of computing and the Internet. This work is undertaken in order to meet a specific user need, i.e. that of searching for a collocate (or a short list of collocates) that expresses a specific...

High-frequency collocations of nouns in research articles across eight disciplines

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Matthew Peacock

2012-04-01

Full Text Available This paper describes a corpus-based analysis of the distribution of the high-frequency collocates of abstract nouns in 320 research articles across eight disciplines: Chemistry, Computer Science, Materials Science, Neuroscience, Economics, Language and Linguistics, Management, and Psychology. Disciplinary variation was also examined – very little previous research seems to have investigated this. The corpus was analysed using WordSmith Tools. The 16 highest-frequency nouns across all eight disciplines were identified, followed by the highest-frequency collocates for each noun. Five disciplines showed over 50% variance from the overall results. Conclusions are that the differing patterns revealed are disciplinary norms and represent standard terminology within the disciplines arising from the topics discussed, research methods, and content of discussions. It is also concluded that the collocations are an important part of the meanings and functions of the nouns, and that this evidence of sharp discipline differences underlines the importance of discipline-specific collocation research.

COLLOCATION PHRASES IN RELATION TO OTHER LEXICAL PHRASES IN CROATIAN

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Goranka Blagus Bartolec

2012-01-01

Full Text Available The paper analyzes the semantic and lexicological aspects of collocation phrases in Croatian with tendency to separate them from other lexical phrases in Croatian (terms, idioms, names. The collocation phrase is defined as a special lexical phrase on a syntagmatic level, based on the semantic correlation of the two individual lexical components in which their meanings are specified.

Relation work in collocated and distributed collaboration

DEFF Research Database (Denmark)

Christensen, Lars Rune; Jensen, Rasmus Eskild; Bjørn, Pernille

2014-01-01

Creating social ties are important for collaborative work; however, in geographically distributed organizations e.g. global software development, making social ties requires extra work: Relation work. We find that characteristics of relation work as based upon shared history and experiences......, emergent in personal and often humorous situations. Relation work is intertwined with other activities such as articulation work and it is rhythmic by following the work patterns of the participants. By comparing how relation work is conducted in collocated and geographically distributed settings we...... in this paper identify basic differences in relation work. Whereas collocated relation work is spontaneous, place-centric, and yet mobile, relation work in a distributed setting is semi-spontaneous, technology-mediated, and requires extra efforts....

Age of Acquisition Effects in Chinese EFL learners’ Delexicalized Verb and Collocation Acquisition

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Miao Haiyan

2015-05-01

Full Text Available This paper investigates age of acquisition (AoA effects and the acquisition of delexicalized verbs and collocations in Chinese EFL learners, and explores the underlying reasons from the connectionist model for these learners’ acquisition characteristics. The data were collected through a translation test consisted of delexialized verb information section and English-Chinese and Chinese-English collocation parts, aiming to focus on Chinese EFL learners’ receptive and productive abilities respectively. As Chinese EFL is a nationally classroom-based practice beginning from early primary school, the pedagogical value and different phases of acquisition are thus taken into consideration in designing the translation test. Research results show that the effects of AoA are significant not only in the learners’ acquisition of individual delexicalized verbs but also in delexicalized collocations. Although learners have long begun to learn delexicalized verbs, their production indicates that early learning does not guarantee total acquisition, because their grasp of delexicalized verbs still stay at the senior middle school level. AoA effects significantly affect the recognition but not the production of collocations. Furthermore, a plateau effect occurs in learners’ acquisition of college-level delexicalized collocations, as their recognition and production have no processing advantages over earlier learned collocations.

Not Just "Small Potatoes": Knowledge of the Idiomatic Meanings of Collocations

Science.gov (United States)

Macis, Marijana; Schmitt, Norbert

2017-01-01

This study investigated learner knowledge of the figurative meanings of 30 collocations that can be both literal and figurative. One hundred and seven Chilean Spanish-speaking university students of English were asked to complete a meaning-recall collocation test in which the target items were embedded in non-defining sentences. Results showed…

The multi-element probabilistic collocation method (ME-PCM): Error analysis and applications

International Nuclear Information System (INIS)

Foo, Jasmine; Wan Xiaoliang; Karniadakis, George Em

2008-01-01

Stochastic spectral methods are numerical techniques for approximating solutions to partial differential equations with random parameters. In this work, we present and examine the multi-element probabilistic collocation method (ME-PCM), which is a generalized form of the probabilistic collocation method. In the ME-PCM, the parametric space is discretized and a collocation/cubature grid is prescribed on each element. Both full and sparse tensor product grids based on Gauss and Clenshaw-Curtis quadrature rules are considered. We prove analytically and observe in numerical tests that as the parameter space mesh is refined, the convergence rate of the solution depends on the quadrature rule of each element only through its degree of exactness. In addition, the L 2 error of the tensor product interpolant is examined and an adaptivity algorithm is provided. Numerical examples demonstrating adaptive ME-PCM are shown, including low-regularity problems and long-time integration. We test the ME-PCM on two-dimensional Navier-Stokes examples and a stochastic diffusion problem with various random input distributions and up to 50 dimensions. While the convergence rate of ME-PCM deteriorates in 50 dimensions, the error in the mean and variance is two orders of magnitude lower than the error obtained with the Monte Carlo method using only a small number of samples (e.g., 100). The computational cost of ME-PCM is found to be favorable when compared to the cost of other methods including stochastic Galerkin, Monte Carlo and quasi-random sequence methods

Vocabulary and Receptive Knowledge of English Collocations among Swedish Upper Secondary School Students

OpenAIRE

Bergström, Kerstin

2008-01-01

The aim of this study is to examine the vocabulary and receptive collocation knowledge in English among Swedish upper secondary school students. The primary material consists of two vocabulary tests, one collocation test, and a background questionnaire. The first research question concerns whether the students who receive a major part of their education in English have a higher level of vocabulary and receptive collocation knowledge in English than those who are taught primarily in Swedish. T...

Measuring receptive collocational competence across proficiency ...

African Journals Online (AJOL)

Kate H

frequency bands. A proficiency measure and a collocation test were administered to English ... battery may negatively impact the test-takers' performance. ..... examples. The major finding is that raising learners' awareness constitutes the best way forward ..... Amsterdam: John Benjamins Publishing Company. Green, R.

Least-squares collocation meshless approach for radiative heat transfer in absorbing and scattering media

Science.gov (United States)

Liu, L. H.; Tan, J. Y.

2007-02-01

A least-squares collocation meshless method is employed for solving the radiative heat transfer in absorbing, emitting and scattering media. The least-squares collocation meshless method for radiative transfer is based on the discrete ordinates equation. A moving least-squares approximation is applied to construct the trial functions. Except for the collocation points which are used to construct the trial functions, a number of auxiliary points are also adopted to form the total residuals of the problem. The least-squares technique is used to obtain the solution of the problem by minimizing the summation of residuals of all collocation and auxiliary points. Three numerical examples are studied to illustrate the performance of this new solution method. The numerical results are compared with the other benchmark approximate solutions. By comparison, the results show that the least-squares collocation meshless method is efficient, accurate and stable, and can be used for solving the radiative heat transfer in absorbing, emitting and scattering media.

Least-squares collocation meshless approach for radiative heat transfer in absorbing and scattering media

International Nuclear Information System (INIS)

Liu, L.H.; Tan, J.Y.

2007-01-01

A least-squares collocation meshless method is employed for solving the radiative heat transfer in absorbing, emitting and scattering media. The least-squares collocation meshless method for radiative transfer is based on the discrete ordinates equation. A moving least-squares approximation is applied to construct the trial functions. Except for the collocation points which are used to construct the trial functions, a number of auxiliary points are also adopted to form the total residuals of the problem. The least-squares technique is used to obtain the solution of the problem by minimizing the summation of residuals of all collocation and auxiliary points. Three numerical examples are studied to illustrate the performance of this new solution method. The numerical results are compared with the other benchmark approximate solutions. By comparison, the results show that the least-squares collocation meshless method is efficient, accurate and stable, and can be used for solving the radiative heat transfer in absorbing, emitting and scattering media

The treatment of lexical collocations in EFL coursebooks in the Estonian secondary school context

Directory of Open Access Journals (Sweden)

Liina Vassiljev

2015-04-01

Full Text Available The article investigates lexical collocations encountered in English as a Foreign Language (EFL instruction in Estonian upper secondary schools. This is achieved through a statistical analysis of collocations featuring in three coursebooks where the collocations found are analysed in terms of their type, frequency and usefulness index by studying them through an online language corpus (Collins Wordbanks Online. The coursebooks are systematically compared and contrasted relying upon the data gathered. The results of the study reveal that the frequency and range of lexical collocations in a language corpus have not been regarded as an essential criterion for their selection and practice by any of the coursebook authors under discussion.

English Collocation Learning through Corpus Data: On-Line Concordance and Statistical Information

Science.gov (United States)

Ohtake, Hiroshi; Fujita, Nobuyuki; Kawamoto, Takeshi; Morren, Brian; Ugawa, Yoshihiro; Kaneko, Shuji

2012-01-01

We developed an English Collocations On Demand system offering on-line corpus and concordance information to help Japanese researchers acquire a better command of English collocation patterns. The Life Science Dictionary Corpus consists of approximately 90,000,000 words collected from life science related research papers published in academic…

THE INVESTIGATION OF PRODUCTIVE AND RECEPTIVE COMPETENCE IN V+N AND ADJ+N COLLOCATIONS AMONG INDONESIAN EFL LEARNERS

Directory of Open Access Journals (Sweden)

Saudin Saudin

2017-05-01

Full Text Available The important role of collocation in learners’ language proficiency has been acknowledged widely. In Systemic Functional Linguistics (SFL, collocation is known as one prominent member of the super-ordinate lexical cohesion, which contributes significantly to the textual coherence, together with grammatical cohesion and structural cohesion (Halliday & Hasan, 1985. Collocation is also viewed as the hallmark of truly advanced English learners since the higher the learners’ proficiency is, the more they tend to use collocation (Bazzaz & Samad, 2011; Hsu, 2007; Zhang, 1993. Further, knowledge of collocation is regarded as part of the native speakers’ communicative competence (Bazzaz & Samad, 2011; and lack of the knowledge is the most important sign of foreignness among foreign language learners (McArthur, 1992; McCarthy, 1990. Taking the importance of collocation into account, this study is aimed to shed light on Indonesian EFL learners’ levels of collocational competence. In the study, the collocational competence is restricted to v+n and adj+n of collocation but broken down into productive and receptive competence, about which little work has been done (Henriksen, 2013. For this purpose, 49 second-year students of an English department in a state polytechnic were chosen as the subjects. Two sets of tests (filling in the blanks and multiple-choice were administered to obtain the data of the subjects’ levels of productive and receptive competence and to gain information of which type was more problematic for the learners. The test instruments were designed by referring to Brashi’s (2006 test model, and Koya’s (2003. In the analysis of the data, interpretive-qualitative method was used primarily to obtain broad explanatory information. The data analysis showed that the scores of productive competence were lower than those of receptive competence in both v+n and adj+n collocation. The analysis also revealed that the scores of productive

The Effects of Input Flood and Consciousness-Raising Approach on Collocation Knowledge Development of Language Learners

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Elaheh Hamed Mahvelati

2012-11-01

Full Text Available Many researchers stress the importance of lexical coherence and emphasize the need for teaching collocations at all levels of language proficiency. Thus, this study was conducted to measure the relative effectiveness of explicit (consciousness-raising approach versus implicit (input flood collocation instruction with regard to learners’ knowledge of both lexical and grammatical collocations. Ninety-five upper-intermediate learners, who were randomly assigned to the control and experimental groups, served as the participants of this study. While one of the experimental groups was provided with input flood treatment, the other group received explicit collocation instruction. In contrast, the participants in the control group did not receive any instruction on learning collocations. The results of the study, which were collected through pre-test, immediate post-test and delayed post-test, revealed that although both methods of teaching collocations proved effective, the explicit method of consciousness-raising approach was significantly superior to the implicit method of input flood treatment.

Teaching vocabulary using collocations versus using definitions in EFL classes

OpenAIRE

Altınok, Şerife İper

2000-01-01

Ankara : Institute of Economics and Social Sciences of Bilkent Univ., 2000. Thesis (Master's) -- Bilkent University, 2000. Includes bibliographical references leaves 40-43 Teaching words in collocations is a comparatively new technique and it is accepted as an effective one in vocabulary teaching. The purpose of this study was to find out whether teaching vocabulary would result in better learning and remembering vocabulary items. This study investigated the differences betw...

A collocation--Galerkin finite element model of cardiac action potential propagation.

Science.gov (United States)

Rogers, J M; McCulloch, A D

1994-08-01

A new computational method was developed for modeling the effects of the geometric complexity, nonuniform muscle fiber orientation, and material inhomogeneity of the ventricular wall on cardiac impulse propagation. The method was used to solve a modification to the FitzHugh-Nagumo system of equations. The geometry, local muscle fiber orientation, and material parameters of the domain were defined using linear Lagrange or cubic Hermite finite element interpolation. Spatial variations of time-dependent excitation and recovery variables were approximated using cubic Hermite finite element interpolation, and the governing finite element equations were assembled using the collocation method. To overcome the deficiencies of conventional collocation methods on irregular domains, Galerkin equations for the no-flux boundary conditions were used instead of collocation equations for the boundary degrees-of-freedom. The resulting system was evolved using an adaptive Runge-Kutta method. Converged two-dimensional simulations of normal propagation showed that this method requires less CPU time than a traditional finite difference discretization. The model also reproduced several other physiologic phenomena known to be important in arrhythmogenesis including: Wenckebach periodicity, slowed propagation and unidirectional block due to wavefront curvature, reentry around a fixed obstacle, and spiral wave reentry. In a new result, we observed wavespeed variations and block due to nonuniform muscle fiber orientation. The findings suggest that the finite element method is suitable for studying normal and pathological cardiac activation and has significant advantages over existing techniques.

Improving academic literacy by teaching collocations

African Journals Online (AJOL)

Kate H

version of McCarthy and O'Dell's (2005) collocation web model were the techniques adopted ... both cued recall and essay writing, supporting earlier findings (cf. ..... from a 'holistic' representation of formulaic sequences in memory” (Boers et al. ... their study indicate that non-native speakers also retain words as they appear ...

Numerical simulation of GEW equation using RBF collocation method

Directory of Open Access Journals (Sweden)

Hamid Panahipour

2012-08-01

Full Text Available The generalized equal width (GEW equation is solved numerically by a meshless method based on a global collocation with standard types of radial basis functions (RBFs. Test problems including propagation of single solitons, interaction of two and three solitons, development of the Maxwellian initial condition pulses, wave undulation and wave generation are used to indicate the efficiency and accuracy of the method. Comparisons are made between the results of the proposed method and some other published numerical methods.

Impact of WhatsApp on Learning and Retention of Collocation Knowledge among Iranian EFL Learners

Directory of Open Access Journals (Sweden)

Zahra Ashiyan

2016-10-01

Full Text Available During the recent technological years, language learning has been attempted to transform its path from the conventional methods to instrumental applications. Mobile phone provides people to reach and exchange information through chats (WhatsApp. It is a tool or mode that means the facilities are used for main purposes. The unique features of the application are its compatibility to exchange information, enhance communication and relationship. A mobile phone provides to download, upload and store learning materials and information files. The purpose of the current study was to investigate the use and effect of mobile applications such as WhatsApp on school work and out of school work. In this way, Oxford Placement Test (OPT was conducted among 80 learners in order to select intermediate EFL learners.  In total, 60 participants whose scores were 70 or higher were elected as the intermediate level and were divided into experimental and control groups. In order to control the reliability of the collocation pretest, the test was pilot studied on 15 learners. Then, the pretest was conducted to measure the learner’s collocation knowledge in both of the groups. The experimental group frequently installed WhatsApp application in order to learning and practicing new collocations in order to learning and practicing new collocations, while the control group did not use any tool for learning them. An immediate posttest after the treatment was administered. The results in each group were statistically evaluated and the findings manifested that the experimental group who used WhatsApp application in learning collocation significantly outperformed the control group in posttest. Thus usage of WhatsApp application to acquire collocations can reinforce and enhance the process of collocations acquisition and it can guarantee retention of collocations. This study also prepares pedagogical implications for utilizing mobile application as an influential instrument

Communication Collocations of the Lexeme Geld in General and Business German

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Mirna Hocenski-Dreiseidl

2010-07-01

Full Text Available The authors aim to analyse and compare the lexeme Geld and its collocations on the grammatical and semantic levels in general and in business German. A special emphasis will be put on the importance of the communicative function that this lexeme and its collocations have in the language of banking. The paper also has a practical purpose. Its applicability in teaching is envisaged to improve the communicative competence of students of economics.

A moving boundary problem and orthogonal collocation in solving a dynamic liquid surfactant membrane model including osmosis and breakage

Directory of Open Access Journals (Sweden)

E.C. Biscaia Junior

2001-06-01

Full Text Available A dynamic kinetic-diffusive model for the extraction of metallic ions from aqueous liquors using liquid surfactant membranes is proposed. The model incorporates undesirable intrinsic phenomena such as swelling and breakage of the emulsion globules that have to be controlled during process operation. These phenomena change the spatial location of the chemical reaction during the course of extraction, resulting in a transient moving boundary problem. The orthogonal collocation method was used to transform the partial differential equations into an ordinary differential equation set that was solved by an implicit numerical routine. The model was found to be numerically stable and reliable in predicting the behaviour of zinc extraction with acidic extractant for long residence times.

Block Hybrid Collocation Method with Application to Fourth Order Differential Equations

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Lee Ken Yap

2015-01-01

Full Text Available The block hybrid collocation method with three off-step points is proposed for the direct solution of fourth order ordinary differential equations. The interpolation and collocation techniques are applied on basic polynomial to generate the main and additional methods. These methods are implemented in block form to obtain the approximation at seven points simultaneously. Numerical experiments are conducted to illustrate the efficiency of the method. The method is also applied to solve the fourth order problem from ship dynamics.

Language Proficiency, Collocational Knowledge and the Role of L1 Transfer: A Correlational Study of Iranian EFL Learners

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Mustapha Hajebi

2017-12-01

Full Text Available The present study investigates the correlation between language proficiency, collocations and the role of L1 transfer with collocations. This is a quantitative research. The research places more emphases on collecting data in the form of numbers. It is also experimental research in the sense that it tests participants to measure their variables. The participants of the study were 57 Persian B.A students, both male and female from Islamic Azad University of Bandar Abbas, Iran. The results showed that there is a significant relationship between Iranian subjects’ language proficiency, as measured by the Michigan proficiency test and their knowledge of collocations, as measured by their performance on a collocation test designed for the current study. The results obtained from the research indicate that Iranian EFL learners are more likely to use the right collocation in cases of L1 transfer. This suggests that positive transfer plays a major role when it comes to EFL learners’ ability to produce the right collocations in their L2. The findings of this study have some implications for language teaching. Teachers can put emphasis on the inclusion of selected grammatical and lexical collocations in reading comprehension passages.

Rectangular spectral collocation

KAUST Repository

Driscoll, Tobin A.

2015-02-06

Boundary conditions in spectral collocation methods are typically imposed by removing some rows of the discretized differential operator and replacing them with others that enforce the required conditions at the boundary. A new approach based upon resampling differentiated polynomials into a lower-degree subspace makes differentiation matrices, and operators built from them, rectangular without any row deletions. Then, boundary and interface conditions can be adjoined to yield a square system. The resulting method is both flexible and robust, and avoids ambiguities that arise when applying the classical row deletion method outside of two-point scalar boundary-value problems. The new method is the basis for ordinary differential equation solutions in Chebfun software, and is demonstrated for a variety of boundary-value, eigenvalue and time-dependent problems.

THE CASE FOR VERB-ADJECTIVE COLLOCATIONS: CORPUS-BASED ANALYSIS AND LEXICOGRAPHICAL TREATMENT

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Moisés Almela

2011-10-01

Full Text Available This article explores a type of co-occurrence pattern which cannot be adequately described by existing models of collocation, and for which combinatory dictionaries have yet failed to provide sufficient information. The phenomenon of “oblique inter-collocation”, as I propose to call it, is characterised by a concatenation of syntagmatic preferences which partially contravenes the habitual grammatical order of semantic selection. In particular, I will examine some of the effects which the verb cause exerts on the distribution of attributive adjectives in the context of specific noun classes. The procedure for detecting and describing patterns of oblique inter-collocation is illustrated by means of SketchEngine corpus query tools. Based on the data extracted from a large-scale corpus, this paper carries out a critical analysis of the micro-structure in Oxford Collocations Dictionary.

A collocation finite element method with prior matrix condensation

International Nuclear Information System (INIS)

Sutcliffe, W.J.

1977-01-01

For thin shells with general loading, sixteen degrees of freedom have been used for a previous finite element solution procedure using a Collocation method instead of the usual variational based procedures. Although the number of elements required was relatively small, nevertheless the final matrix for the simultaneous solution of all unknowns could become large for a complex compound structure. The purpose of the present paper is to demonstrate a method of reducing the final matrix size, so allowing solution for large structures with comparatively small computer storage requirements while retaining the accuracy given by high order displacement functions. Collocation points, a number are equilibrium conditions which must be satisfied independently of the overall compatibility of forces and deflections for a complete structure. (Auth.)

Entropy Stable Spectral Collocation Schemes for the Navier-Stokes Equations: Discontinuous Interfaces

Science.gov (United States)

Carpenter, Mark H.; Fisher, Travis C.; Nielsen, Eric J.; Frankel, Steven H.

2013-01-01

Nonlinear entropy stability and a summation-by-parts framework are used to derive provably stable, polynomial-based spectral collocation methods of arbitrary order. The new methods are closely related to discontinuous Galerkin spectral collocation methods commonly known as DGFEM, but exhibit a more general entropy stability property. Although the new schemes are applicable to a broad class of linear and nonlinear conservation laws, emphasis herein is placed on the entropy stability of the compressible Navier-Stokes equations.

Multimodal interaction design in collocated mobile phone use

NARCIS (Netherlands)

El-Ali, A.; Lucero, A.; Aaltonen, V.

2011-01-01

In the context of the Social and Spatial Interactions (SSI) platform, we explore how multimodal interaction design (input and output) can augment and improve the experience of collocated, collaborative activities using mobile phones. Based largely on our prototype evaluations, we reflect on and

RBF Multiscale Collocation for Second Order Elliptic Boundary Value Problems

KAUST Repository

Farrell, Patricio

2013-01-01

In this paper, we discuss multiscale radial basis function collocation methods for solving elliptic partial differential equations on bounded domains. The approximate solution is constructed in a multilevel fashion, each level using compactly supported radial basis functions of smaller scale on an increasingly fine mesh. On each level, standard symmetric collocation is employed. A convergence theory is given, which builds on recent theoretical advances for multiscale approximation using compactly supported radial basis functions. We are able to show that the convergence is linear in the number of levels. We also discuss the condition numbers of the arising systems and the effect of simple, diagonal preconditioners, now proving rigorously previous numerical observations. © 2013 Society for Industrial and Applied Mathematics.

Collocations and grammatical patterns in a Multilingual Online Term ...

African Journals Online (AJOL)

user

equivalents for key concepts in the African languages, but also additional con- ... for, inter alia, computational identification and extraction of collocations exist; .... sult' is to be followed by a prepositional phrase in which the preposition is.

Responding to Research Challenges Related to Studying L2 Collocational Use in Professional Academic Discourse

DEFF Research Database (Denmark)

Henriksen, Birgit; Westbrook, Pete

2017-01-01

and classifying collocations used by L2 speakers in advanced, domain-specific oral academic discourse. The main findings seem to suggest that to map an informant’s complete collocational use and to get an understanding of disciplinary differences, we need to not only take account of general, academic and domain...

Preconditioning cubic spline collocation method by FEM and FDM for elliptic equations

Energy Technology Data Exchange (ETDEWEB)

Kim, Sang Dong [KyungPook National Univ., Taegu (Korea, Republic of)

1996-12-31

In this talk we discuss the finite element and finite difference technique for the cubic spline collocation method. For this purpose, we consider the uniformly elliptic operator A defined by Au := -{Delta}u + a{sub 1}u{sub x} + a{sub 2}u{sub y} + a{sub 0}u in {Omega} (the unit square) with Dirichlet or Neumann boundary conditions and its discretization based on Hermite cubic spline spaces and collocation at the Gauss points. Using an interpolatory basis with support on the Gauss points one obtains the matrix A{sub N} (h = 1/N).

RBF Multiscale Collocation for Second Order Elliptic Boundary Value Problems

KAUST Repository

Farrell, Patricio; Wendland, Holger

2013-01-01

In this paper, we discuss multiscale radial basis function collocation methods for solving elliptic partial differential equations on bounded domains. The approximate solution is constructed in a multilevel fashion, each level using compactly

Solutions of First-Order Volterra Type Linear Integrodifferential Equations by Collocation Method

Directory of Open Access Journals (Sweden)

Olumuyiwa A. Agbolade

2017-01-01

Full Text Available The numerical solutions of linear integrodifferential equations of Volterra type have been considered. Power series is used as the basis polynomial to approximate the solution of the problem. Furthermore, standard and Chebyshev-Gauss-Lobatto collocation points were, respectively, chosen to collocate the approximate solution. Numerical experiments are performed on some sample problems already solved by homotopy analysis method and finite difference methods. Comparison of the absolute error is obtained from the present method and those from aforementioned methods. It is also observed that the absolute errors obtained are very low establishing convergence and computational efficiency.

Adaptive wavelet collocation methods for initial value boundary problems of nonlinear PDE's

Science.gov (United States)

Cai, Wei; Wang, Jian-Zhong

1993-01-01

We have designed a cubic spline wavelet decomposition for the Sobolev space H(sup 2)(sub 0)(I) where I is a bounded interval. Based on a special 'point-wise orthogonality' of the wavelet basis functions, a fast Discrete Wavelet Transform (DWT) is constructed. This DWT transform will map discrete samples of a function to its wavelet expansion coefficients in O(N log N) operations. Using this transform, we propose a collocation method for the initial value boundary problem of nonlinear PDE's. Then, we test the efficiency of the DWT transform and apply the collocation method to solve linear and nonlinear PDE's.

Runge-Kutta and Hermite Collocation for a biological invasion problem modeled by a generalized Fisher equation

International Nuclear Information System (INIS)

Athanasakis, I E; Papadopoulou, E P; Saridakis, Y G

2014-01-01

Fisher's equation has been widely used to model the biological invasion of single-species communities in homogeneous one dimensional habitats. In this study we develop high order numerical methods to accurately capture the spatiotemporal dynamics of the generalized Fisher equation, a nonlinear reaction-diffusion equation characterized by density dependent non-linear diffusion. Working towards this direction we consider strong stability preserving Runge-Kutta (RK) temporal discretization schemes coupled with the Hermite cubic Collocation (HC) spatial discretization method. We investigate their convergence and stability properties to reveal efficient HC-RK pairs for the numerical treatment of the generalized Fisher equation. The Hadamard product is used to characterize the collocation discretized non linear equation terms as a first step for the treatment of generalized systems of relevant equations. Numerical experimentation is included to demonstrate the performance of the methods

Collocation methods for the solution of eigenvalue problems for singular ordinary differential equations

Directory of Open Access Journals (Sweden)

Winfried Auzinger

2006-01-01

Full Text Available We demonstrate that eigenvalue problems for ordinary differential equations can be recast in a formulation suitable for the solution by polynomial collocation. It is shown that the well-posedness of the two formulations is equivalent in the regular as well as in the singular case. Thus, a collocation code equipped with asymptotically correct error estimation and adaptive mesh selection can be successfully applied to compute the eigenvalues and eigenfunctions efficiently and with reliable control of the accuracy. Numerical examples illustrate this claim.

The Challenge of English Language Collocation Learning in an ES/FL Environment: PRC Students in Singapore

Science.gov (United States)

Ying, Yang

2015-01-01

This study aimed to seek an in-depth understanding about English collocation learning and the development of learner autonomy through investigating a group of English as a Second Language (ESL) learners' perspectives and practices in their learning of English collocations using an AWARE approach. A group of 20 PRC students learning English in…

Improvement of neutron kinetics module in TRAC-BF1code: one-dimensional nodal collocation method

Energy Technology Data Exchange (ETDEWEB)

Jambrina, Ana; Barrachina, Teresa; Miro, Rafael; Verdu, Gumersindo, E-mail: ajambrina@iqn.upv.es, E-mail: tbarrachina@iqn.upv.es, E-mail: rmiro@iqn.upv.es, E-mail: gverdu@iqn.upv.es [Universidade Politecnica de Valencia (UPV), Valencia (Spain); Soler, Amparo, E-mail: asoler@iberdrola.es [SEA Propulsion S.L., Madrid (Spain); Concejal, Alberto, E-mail: acbe@iberdrola.es [Iberdrola Ingenieria y Construcion S.A.U., Madrid (Spain)

2013-07-01

The TRAC-BF1 one-dimensional kinetic model is a formulation of the neutron diffusion equation in the two energy groups' approximation, based on the analytical nodal method (ANM). The advantage compared with a zero-dimensional kinetic model is that the axial power profile may vary with time due to thermal-hydraulic parameter changes and/or actions of the control systems but at has the disadvantages that in unusual situations it fails to converge. The nodal collocation method developed for the neutron diffusion equation and applied to the kinetics resolution of TRAC-BF1 thermal-hydraulics, is an adaptation of the traditional collocation methods for the discretization of partial differential equations, based on the development of the solution as a linear combination of analytical functions. It has chosen to use a nodal collocation method based on a development of Legendre polynomials of neutron fluxes in each cell. The qualification is carried out by the analysis of the turbine trip transient from the NEA benchmark in Peach Bottom NPP using both the original 1D kinetics implemented in TRAC-BF1 and the 1D nodal collocation method. (author)

Non-standard finite difference and Chebyshev collocation methods for solving fractional diffusion equation

Science.gov (United States)

Agarwal, P.; El-Sayed, A. A.

2018-06-01

In this paper, a new numerical technique for solving the fractional order diffusion equation is introduced. This technique basically depends on the Non-Standard finite difference method (NSFD) and Chebyshev collocation method, where the fractional derivatives are described in terms of the Caputo sense. The Chebyshev collocation method with the (NSFD) method is used to convert the problem into a system of algebraic equations. These equations solved numerically using Newton's iteration method. The applicability, reliability, and efficiency of the presented technique are demonstrated through some given numerical examples.

A Comparative Study of the Use of Collocation in Iranian High School Textbooks and American English File Books

Directory of Open Access Journals (Sweden)

Mohsen Shahrokhi

2014-05-01

Full Text Available The present study investigates the extent to which lexical and grammatical collocations are used in Iranian high school English textbooks, compared with the American English File books. To achieve the purposes of this study, this study had to be carried out in two phases. In the first phase, the content of the instructional textbooks, that is, American English File book series, Book 2 and Iranian high school English Book 3, were analyzed to find the frequencies and proportions of the collocations used in the textbooks. Since the instructional textbooks used in the two teaching environments (i.e., Iranian high schools and language institutes were not equal with regard to the density of texts, from each textbook just the first 6000 words, content words as well as function words, were considered. Then, the frequencies of the collocations among the first 6000 words in high school English Book 3 and American English File Book 2 were determined.The results of the statistical analyses revealed that the two text book series differ marginally in terms of frequency and type of collocations. Major difference existed between them when it came to lexical collocations in American English File book 2.

Lexical richness and collocational competence in second-language writing

NARCIS (Netherlands)

Vedder, I.; Benigno, V.

2016-01-01

In this article we report on an experiment set up to investigate lexical richness and collocational competence in the written production of 39 low-intermediate and intermediate learners of Italian L2. Lexical richness was assessed by means of a lexical profiling method inspired by Laufer and Nation

Sinc-collocation method for solving the Blasius equation

International Nuclear Information System (INIS)

Parand, K.; Dehghan, Mehdi; Pirkhedri, A.

2009-01-01

Sinc-collocation method is applied for solving Blasius equation which comes from boundary layer equations. It is well known that sinc procedure converges to the solution at an exponential rate. Comparison with Howarth and Asaithambi's numerical solutions reveals that the proposed method is of high accuracy and reduces the solution of Blasius' equation to the solution of a system of algebraic equations.

Using Small Parallel Corpora to Develop Collocation-Centred Activities in Specialized Translation Classes

Directory of Open Access Journals (Sweden)

Postolea Sorina

2016-12-01

Full Text Available The research devoted to special languages as well as the activities carried out in specialized translation classes tend to focus primarily on one-word or multi-word terminological units. However, a very important part in the making of specialist registers and texts is played by specialised collocations, i.e. relatively stable word combinations that do not designate concepts but are nevertheless of frequent use in a given field of activity. This is why helping students acquire competences relative to the identification and processing of collocations should become an important objective in specialised translation classes. An easily accessible and dependable resource that may be successfully used to this purpose is represented by corpora and corpus analysis tools, whose usefulness in translator training has been highlighted by numerous studies. This article proposes a series of practical, task-based activities-developed with the help of a small-size parallel corpus of specialised texts-that aim to raise the translation trainees′ awareness of the collocations present in specialised texts and to provide suggestions about their processing in translation.

Numerical simulation for fractional order stationary neutron transport equation using Haar wavelet collocation method

Energy Technology Data Exchange (ETDEWEB)

Saha Ray, S., E-mail: santanusaharay@yahoo.com; Patra, A.

2014-10-15

Highlights: • A stationary transport equation has been solved using the technique of Haar wavelet collocation method. • This paper intends to provide the great utility of Haar wavelets to nuclear science problem. • In the present paper, two-dimensional Haar wavelets are applied. • The proposed method is mathematically very simple, easy and fast. - Abstract: In this paper the numerical solution for the fractional order stationary neutron transport equation is presented using Haar wavelet Collocation Method (HWCM). Haar wavelet collocation method is efficient and powerful in solving wide class of linear and nonlinear differential equations. This paper intends to provide an application of Haar wavelets to nuclear science problems. This paper describes the application of Haar wavelets for the numerical solution of fractional order stationary neutron transport equation in homogeneous medium with isotropic scattering. The proposed method is mathematically very simple, easy and fast. To demonstrate about the efficiency and applicability of the method, two test problems are discussed.

A Line-Tau Collocation Method for Partial Differential Equations ...

African Journals Online (AJOL)

This paper deals with the numerical solution of second order linear partial differential equations with the use of the method of lines coupled with the tau collocation method. The method of lines is used to convert the partial differential equation (PDE) to a sequence of ordinary differential equations (ODEs) which is then ...

Corpus-Based Websites to Promote Learner Autonomy in Correcting Writing Collocation Errors

Directory of Open Access Journals (Sweden)

Pham Thuy Dung

2016-12-01

Full Text Available The recent yet powerful emergence of E-learning and using online resources in learning EFL (English as a Foreign Language has helped promote learner autonomy in language acquisition including self-correcting their mistakes. This pilot study despite conducted on a modest sample of 25 second year students majoring in Business English at Hanoi Foreign Trade University is an initial attempt to investigate the feasibility of using corpus-based websites to promote learner autonomy in correcting collocation errors in EFL writing. The data is collected using a pre-questionnaire and a post-interview aiming to find out the participants’ change in belief and attitude toward learner autonomy in collocation errors in writing, the extent of their success in using the corpus-based websites to self-correct the errors and the change in their confidence in self-correcting the errors using the websites. The findings show that a significant majority of students have shifted their belief and attitude toward a more autonomous mode of learning, enjoyed a fair success of using the websites to self-correct the errors and become more confident. The study also yields an implication that a face-to-face training of how to use these online tools is vital to the later confidence and success of the learners

Metaphors in terminological collocations in English language and their equivalents in Serbian

Directory of Open Access Journals (Sweden)

Orčić Lidija S.

2017-01-01

Full Text Available The framework of this paper is the theory of conceptual metaphor where metaphor is the transfer of a more concrete source domain into a more abstract target domain. Metaphor is a fundamental human ability to speak about abstract concepts using specific terms where the meaning of a term is transferred to another, thus achieving semantic extensions. Although it was thought that in terminology polysemantic expressions are not desirable, in recent decades this traditional view has been abandoned. Metaphor is used not only as a linguistic decoration in language, but as a means of argumentation. It may be noted that the metaphor, as a universal phenomenon, is also common in business English discourse. The subject of our interest is to investigate collocations made up of those nouns and adjectives, which, according to the Oxford Business English Dictionary for Learners of English, are most frequently used in this field. The main objective of this work is to identify and analyze the source and target domains in metaphors in English collocations that contain these nouns and adjectives, and detect mechanisms applied in translating into Serbian. We categorised metaphors in collocations into four groups. The first group consists of metaphors in which the source domain is expressed with the living beings: inanimate entities are described as if they were alive. In these examples, the personification is used to explain abstract concepts, forces and processes in order to present them in a more understandable way. The second group consists of metaphors in which animals are the source domain and their behavior and characteristics serve as a starting point. In business discourse people and institutions are described with such metaphors. In the third group we included the metaphors based on objects that users are familiar with in everyday life. The fourth group consists of metaphors in which the source domain are natural phenomena. When translating a metaphor we

Application of collocation meshless method to eigenvalue problem

International Nuclear Information System (INIS)

Saitoh, Ayumu; Matsui, Nobuyuki; Itoh, Taku; Kamitani, Atsushi; Nakamura, Hiroaki

2012-01-01

The numerical method for solving the nonlinear eigenvalue problem has been developed by using the collocation Element-Free Galerkin Method (EFGM) and its performance has been numerically investigated. The results of computations show that the approximate solution of the nonlinear eigenvalue problem can be obtained stably by using the developed method. Therefore, it can be concluded that the developed method is useful for solving the nonlinear eigenvalue problem. (author)

Robust Topology Optimization Based on Stochastic Collocation Methods under Loading Uncertainties

Directory of Open Access Journals (Sweden)

Qinghai Zhao

2015-01-01

Full Text Available A robust topology optimization (RTO approach with consideration of loading uncertainties is developed in this paper. The stochastic collocation method combined with full tensor product grid and Smolyak sparse grid transforms the robust formulation into a weighted multiple loading deterministic problem at the collocation points. The proposed approach is amenable to implementation in existing commercial topology optimization software package and thus feasible to practical engineering problems. Numerical examples of two- and three-dimensional topology optimization problems are provided to demonstrate the proposed RTO approach and its applications. The optimal topologies obtained from deterministic and robust topology optimization designs under tensor product grid and sparse grid with different levels are compared with one another to investigate the pros and cons of optimization algorithm on final topologies, and an extensive Monte Carlo simulation is also performed to verify the proposed approach.

An adaptive multi-element probabilistic collocation method for statistical EMC/EMI characterization

KAUST Repository

Yücel, Abdulkadir C.

2013-12-01

An adaptive multi-element probabilistic collocation (ME-PC) method for quantifying uncertainties in electromagnetic compatibility and interference phenomena involving electrically large, multi-scale, and complex platforms is presented. The method permits the efficient and accurate statistical characterization of observables (i.e., quantities of interest such as coupled voltages) that potentially vary rapidly and/or are discontinuous in the random variables (i.e., parameters that characterize uncertainty in a system\\'s geometry, configuration, or excitation). The method achieves its efficiency and accuracy by recursively and adaptively dividing the domain of the random variables into subdomains using as a guide the decay rate of relative error in a polynomial chaos expansion of the observables. While constructing local polynomial expansions on each subdomain, a fast integral-equation-based deterministic field-cable-circuit simulator is used to compute the observable values at the collocation/integration points determined by the adaptive ME-PC scheme. The adaptive ME-PC scheme requires far fewer (computationally costly) deterministic simulations than traditional polynomial chaos collocation and Monte Carlo methods for computing averages, standard deviations, and probability density functions of rapidly varying observables. The efficiency and accuracy of the method are demonstrated via its applications to the statistical characterization of voltages in shielded/unshielded microwave amplifiers and magnetic fields induced on car tire pressure sensors. © 2013 IEEE.

A stochastic collocation method for the second order wave equation with a discontinuous random speed

KAUST Repository

Motamed, Mohammad

2012-08-31

In this paper we propose and analyze a stochastic collocation method for solving the second order wave equation with a random wave speed and subjected to deterministic boundary and initial conditions. The speed is piecewise smooth in the physical space and depends on a finite number of random variables. The numerical scheme consists of a finite difference or finite element method in the physical space and a collocation in the zeros of suitable tensor product orthogonal polynomials (Gauss points) in the probability space. This approach leads to the solution of uncoupled deterministic problems as in the Monte Carlo method. We consider both full and sparse tensor product spaces of orthogonal polynomials. We provide a rigorous convergence analysis and demonstrate different types of convergence of the probability error with respect to the number of collocation points for full and sparse tensor product spaces and under some regularity assumptions on the data. In particular, we show that, unlike in elliptic and parabolic problems, the solution to hyperbolic problems is not in general analytic with respect to the random variables. Therefore, the rate of convergence may only be algebraic. An exponential/fast rate of convergence is still possible for some quantities of interest and for the wave solution with particular types of data. We present numerical examples, which confirm the analysis and show that the collocation method is a valid alternative to the more traditional Monte Carlo method for this class of problems. © 2012 Springer-Verlag.

An adaptive multi-element probabilistic collocation method for statistical EMC/EMI characterization

KAUST Repository

Yü cel, Abdulkadir C.; Bagci, Hakan; Michielssen, Eric

2013-01-01

polynomial chaos expansion of the observables. While constructing local polynomial expansions on each subdomain, a fast integral-equation-based deterministic field-cable-circuit simulator is used to compute the observable values at the collocation

A Sparse Stochastic Collocation Technique for High-Frequency Wave Propagation with Uncertainty

KAUST Repository

Malenova, G.

2016-09-08

We consider the wave equation with highly oscillatory initial data, where there is uncertainty in the wave speed, initial phase, and/or initial amplitude. To estimate quantities of interest related to the solution and their statistics, we combine a high-frequency method based on Gaussian beams with sparse stochastic collocation. Although the wave solution, uϵ, is highly oscillatory in both physical and stochastic spaces, we provide theoretical arguments for simplified problems and numerical evidence that quantities of interest based on local averages of |uϵ|2 are smooth, with derivatives in the stochastic space uniformly bounded in ϵ, where ϵ denotes the short wavelength. This observable related regularity makes the sparse stochastic collocation approach more efficient than Monte Carlo methods. We present numerical tests that demonstrate this advantage.

A Sparse Stochastic Collocation Technique for High-Frequency Wave Propagation with Uncertainty

KAUST Repository

Malenova, G.; Motamed, M.; Runborg, O.; Tempone, Raul

2016-01-01

We consider the wave equation with highly oscillatory initial data, where there is uncertainty in the wave speed, initial phase, and/or initial amplitude. To estimate quantities of interest related to the solution and their statistics, we combine a high-frequency method based on Gaussian beams with sparse stochastic collocation. Although the wave solution, uϵ, is highly oscillatory in both physical and stochastic spaces, we provide theoretical arguments for simplified problems and numerical evidence that quantities of interest based on local averages of |uϵ|2 are smooth, with derivatives in the stochastic space uniformly bounded in ϵ, where ϵ denotes the short wavelength. This observable related regularity makes the sparse stochastic collocation approach more efficient than Monte Carlo methods. We present numerical tests that demonstrate this advantage.

Collocation mismatch uncertainties in satellite aerosol retrieval validation

Science.gov (United States)

Virtanen, Timo H.; Kolmonen, Pekka; Sogacheva, Larisa; Rodríguez, Edith; Saponaro, Giulia; de Leeuw, Gerrit

2018-02-01

Satellite-based aerosol products are routinely validated against ground-based reference data, usually obtained from sun photometer networks such as AERONET (AEROsol RObotic NETwork). In a typical validation exercise a spatial sample of the instantaneous satellite data is compared against a temporal sample of the point-like ground-based data. The observations do not correspond to exactly the same column of the atmosphere at the same time, and the representativeness of the reference data depends on the spatiotemporal variability of the aerosol properties in the samples. The associated uncertainty is known as the collocation mismatch uncertainty (CMU). The validation results depend on the sampling parameters. While small samples involve less variability, they are more sensitive to the inevitable noise in the measurement data. In this paper we study systematically the effect of the sampling parameters in the validation of AATSR (Advanced Along-Track Scanning Radiometer) aerosol optical depth (AOD) product against AERONET data and the associated collocation mismatch uncertainty. To this end, we study the spatial AOD variability in the satellite data, compare it against the corresponding values obtained from densely located AERONET sites, and assess the possible reasons for observed differences. We find that the spatial AOD variability in the satellite data is approximately 2 times larger than in the ground-based data, and the spatial variability correlates only weakly with that of AERONET for short distances. We interpreted that only half of the variability in the satellite data is due to the natural variability in the AOD, and the rest is noise due to retrieval errors. However, for larger distances (˜ 0.5°) the correlation is improved as the noise is averaged out, and the day-to-day changes in regional AOD variability are well captured. Furthermore, we assess the usefulness of the spatial variability of the satellite AOD data as an estimate of CMU by comparing the

Fibonacci collocation method with a residual error Function to solve linear Volterra integro differential equations

Directory of Open Access Journals (Sweden)

Salih Yalcinbas

2016-01-01

Full Text Available In this paper, a new collocation method based on the Fibonacci polynomials is introduced to solve the high-order linear Volterra integro-differential equations under the conditions. Numerical examples are included to demonstrate the applicability and validity of the proposed method and comparisons are made with the existing results. In addition, an error estimation based on the residual functions is presented for this method. The approximate solutions are improved by using this error estimation.

Metagenome Analysis of Protein Domain Collocation within Cellulase Genes of Goat Rumen Microbes

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SooYeon Lim

2013-08-01

Full Text Available In this study, protein domains with cellulase activity in goat rumen microbes were investigated using metagenomic and bioinformatic analyses. After the complete genome of goat rumen microbes was obtained using a shotgun sequencing method, 217,892,109 pair reads were filtered, including only those with 70% identity, 100-bp matches, and thresholds below E−10 using METAIDBA. These filtered contigs were assembled and annotated using blastN against the NCBI nucleotide database. As a result, a microbial community structure with 1431 species was analyzed, among which Prevotella ruminicola 23 bacteria and Butyrivibrio proteoclasticus B316 were the dominant groups. In parallel, 201 sequences related with cellulase activities (EC.3.2.1.4 were obtained through blast searches using the enzyme.dat file provided by the NCBI database. After translating the nucleotide sequence into a protein sequence using Interproscan, 28 protein domains with cellulase activity were identified using the HMMER package with threshold E values below 10−5. Cellulase activity protein domain profiling showed that the major protein domains such as lipase GDSL, cellulase, and Glyco hydro 10 were present in bacterial species with strong cellulase activities. Furthermore, correlation plots clearly displayed the strong positive correlation between some protein domain groups, which was indicative of microbial adaption in the goat rumen based on feeding habits. This is the first metagenomic analysis of cellulase activity protein domains using bioinformatics from the goat rumen.

A multi-dimensional Smolyak collocation method in curvilinear coordinates for computing vibrational spectra

International Nuclear Information System (INIS)

Avila, Gustavo; Carrington, Tucker

2015-01-01

In this paper, we improve the collocation method for computing vibrational spectra that was presented in Avila and Carrington, Jr. [J. Chem. Phys. 139, 134114 (2013)]. Using an iterative eigensolver, energy levels and wavefunctions are determined from values of the potential on a Smolyak grid. The kinetic energy matrix-vector product is evaluated by transforming a vector labelled with (nondirect product) grid indices to a vector labelled by (nondirect product) basis indices. Both the transformation and application of the kinetic energy operator (KEO) scale favorably. Collocation facilitates dealing with complicated KEOs because it obviates the need to calculate integrals of coordinate dependent coefficients of differential operators. The ideas are tested by computing energy levels of HONO using a KEO in bond coordinates

Let's collocate: student generated worksheets as a motivational tool

OpenAIRE

Simpson, Adam John

2006-01-01

This article discusses the process of producing collocation worksheets and the values of these worksheets as a motivational tool within a tertiary level preparatory English program. Firstly, the method by which these worksheets were produced is described, followed by an analysis of their effectiveness as a resource in terms of student motivation, personalisation, involvement in the development of the curriculum and in raising awareness of corpus linguistics and its applications.

A Highly Accurate Regular Domain Collocation Method for Solving Potential Problems in the Irregular Doubly Connected Domains

Directory of Open Access Journals (Sweden)

Zhao-Qing Wang

2014-01-01

Full Text Available Embedding the irregular doubly connected domain into an annular regular region, the unknown functions can be approximated by the barycentric Lagrange interpolation in the regular region. A highly accurate regular domain collocation method is proposed for solving potential problems on the irregular doubly connected domain in polar coordinate system. The formulations of regular domain collocation method are constructed by using barycentric Lagrange interpolation collocation method on the regular domain in polar coordinate system. The boundary conditions are discretized by barycentric Lagrange interpolation within the regular domain. An additional method is used to impose the boundary conditions. The least square method can be used to solve the overconstrained equations. The function values of points in the irregular doubly connected domain can be calculated by barycentric Lagrange interpolation within the regular domain. Some numerical examples demonstrate the effectiveness and accuracy of the presented method.

Gimme Context – towards New Domain-Specific Collocational Dictionaries

Directory of Open Access Journals (Sweden)

Sylvana Krausse

2011-04-01

Full Text Available The days of traditional drudgery-filled lexicography are long gone. Fortunately today, computers help in the enormous task of storing and analysing language in order to condense and store the found information in the form of dictionaries. In this paper, the way from a corpus to a small domain-specific collocational dictionary will be described and thus exemplified based on the example of the domain-specific language of mining reclamation, which can be duplicated for other specific languages too. So far, domain-specific dictionaries are mostly rare as their creation is very labour- and thus cost-effective and all too often they are just a collection of terms plus translation without any information on how to use them in speech. Particular small domains which do not involve a lot of users have been disregarded by lexicographers as there is also always the question of how well it sells afterwards. Following this, I will describe the creation of a small collocational dictionary on mining reclamation language which is based on the consequent use of corpus information. It is relatively quick to realize in the design phase and is thought to provide the sort of linguistic information engineering experts need when they communicate in English or read specialist texts in the specific domain.

Strategies in Translating Collocations in Religious Texts from Arabic into English

Science.gov (United States)

Dweik, Bader S.; Shakra, Mariam M. Abu

2010-01-01

The present study investigated the strategies adopted by students in translating specific lexical and semantic collocations in three religious texts namely, the Holy Quran, the Hadith and the Bible. For this purpose, the researchers selected a purposive sample of 35 MA translation students enrolled in three different public and private Jordanian…

Adaptive probabilistic collocation based Kalman filter for unsaturated flow problem

Science.gov (United States)

Man, J.; Li, W.; Zeng, L.; Wu, L.

2015-12-01

The ensemble Kalman filter (EnKF) has gained popularity in hydrological data assimilation problems. As a Monte Carlo based method, a relatively large ensemble size is usually required to guarantee the accuracy. As an alternative approach, the probabilistic collocation based Kalman filter (PCKF) employs the Polynomial Chaos to approximate the original system. In this way, the sampling error can be reduced. However, PCKF suffers from the so called "cure of dimensionality". When the system nonlinearity is strong and number of parameters is large, PCKF is even more computationally expensive than EnKF. Motivated by recent developments in uncertainty quantification, we propose a restart adaptive probabilistic collocation based Kalman filter (RAPCKF) for data assimilation in unsaturated flow problem. During the implementation of RAPCKF, the important parameters are identified and active PCE basis functions are adaptively selected. The "restart" technology is used to alleviate the inconsistency between model parameters and states. The performance of RAPCKF is tested by unsaturated flow numerical cases. It is shown that RAPCKF is more efficient than EnKF with the same computational cost. Compared with the traditional PCKF, the RAPCKF is more applicable in strongly nonlinear and high dimensional problems.

Fourier analysis of finite element preconditioned collocation schemes

Science.gov (United States)

Deville, Michel O.; Mund, Ernest H.

1990-01-01

The spectrum of the iteration operator of some finite element preconditioned Fourier collocation schemes is investigated. The first part of the paper analyses one-dimensional elliptic and hyperbolic model problems and the advection-diffusion equation. Analytical expressions of the eigenvalues are obtained with use of symbolic computation. The second part of the paper considers the set of one-dimensional differential equations resulting from Fourier analysis (in the tranverse direction) of the 2-D Stokes problem. All results agree with previous conclusions on the numerical efficiency of finite element preconditioning schemes.

Spline Collocation Method for Nonlinear Multi-Term Fractional Differential Equation

OpenAIRE

Choe, Hui-Chol; Kang, Yong-Suk

2013-01-01

We study an approximation method to solve nonlinear multi-term fractional differential equations with initial conditions or boundary conditions. First, we transform the nonlinear multi-term fractional differential equations with initial conditions and boundary conditions to nonlinear fractional integral equations and consider the relations between them. We present a Spline Collocation Method and prove the existence, uniqueness and convergence of approximate solution as well as error estimatio...

Parallel algorithm of trigonometric collocation method in nonlinear dynamics of rotors

Czech Academy of Sciences Publication Activity Database

Musil, Tomáš; Jakl, Ondřej

2007-01-01

Roč. 1, č. 2 (2007), s. 555-564 ISSN 1802-680X. [Výpočtová mechanika 2007. Hrad Nečtiny, 05.11.2007-07.11.2007] Institutional research plan: CEZ:AV0Z20760514; CEZ:AV0Z30860518 Keywords : rotor system * trigonometric collocation * parallel computation Subject RIV: JR - Other Machinery

Simulation of electrically driven jet using Chebyshev collocation method

Institute of Scientific and Technical Information of China (English)

无

2011-01-01

The model of electrically driven jet is governed by a series of quasi 1D dimensionless partial differential equations(PDEs).Following the method of lines,the Chebyshev collocation method is employed to discretize the PDEs and obtain a system of differential-algebraic equations(DAEs).By differentiating constrains in DAEs twice,the system is transformed into a set of ordinary differential equations(ODEs) with invariants.Then the implicit differential equations solver "ddaskr" is used to solve the ODEs and ...

Approximate solutions of the hyperchaotic Rössler system by using the Bessel collocation scheme

Directory of Open Access Journals (Sweden)

Şuayip Yüzbaşı

2015-02-01

Full Text Available The purpose of this study is to give a Bessel polynomial approximation for the solutions of the hyperchaotic Rössler system. For this purpose, the Bessel collocation method applied to different problems is developed for the mentioned system. This method is based on taking the truncated Bessel expansions of the functions in the hyperchaotic Rössler systems. The suggested secheme converts the problem into a system of nonlinear algebraic equations by means of the matrix operations and collocation points, The accuracy and efficiency of the proposed approach are demonstrated by numerical applications and performed with the help of a computer code written in Maple. Also, comparison between our method and the differential transformation method is made with the accuracy of solutions.

Implementation of optimal Galerkin and Collocation approximations of PDEs with Random Coefficients

KAUST Repository

Beck, Joakim; Nobile, F.; Tamellini, L.; Tempone, Raul

2011-01-01

We consider then the Stochastic Collocation method, and use the previous estimates to introduce a new effective class of Sparse Grids, based on the idea of selecting a priori the most profitable hierarchical surpluses, that, again, features better convergence properties compared to standard Smolyak or tensor product grids.

FTA Corpus: a parallel corpus of English and Spanish Free Trade Agreements for the study of specialized collocations

Directory of Open Access Journals (Sweden)

Pedro Patiño García

2013-04-01

Full Text Available This paper describes the Corpus of Free Trade Agreements (henceforth FTA, a specialized parallel corpus in English and Spanish from Europe and America and a smaller subcorpus in English-Norwegian and Spanish-Norwegian that was prepared and then aligned with Translation Corpus Aligner 2 (Hofland & Johansson, 1998. The data was taken from Free Trade Agreements. These agreements are specialized texts officially signed and ratified by several countries and blocks of countries in the last twenty years. Thus, FTAs are a rich repository for terminology and phraseology that is used in different fields of business activity throughout the world. The corpus contains around 1.37 million words in the English section and 1.48 million words in its Spanish counterpart, plus 60,000 words each in the Spanish-Norwegian and English-Norwegian subcorpus. The corpus is being used primarily to study the terms and specialized collocations that include these terms in this kind of specialized texts.Keywords: specialized collocation, specialized parallel corpus, corpus linguistics, Free Trade Agreement

Application of adaptive hierarchical sparse grid collocation to the uncertainty quantification of nuclear reactor simulators

Energy Technology Data Exchange (ETDEWEB)

Yankov, A.; Downar, T. [University of Michigan, 2355 Bonisteel Blvd, Ann Arbor, MI 48109 (United States)

2013-07-01

Recent efforts in the application of uncertainty quantification to nuclear systems have utilized methods based on generalized perturbation theory and stochastic sampling. While these methods have proven to be effective they both have major drawbacks that may impede further progress. A relatively new approach based on spectral elements for uncertainty quantification is applied in this paper to several problems in reactor simulation. Spectral methods based on collocation attempt to couple the approximation free nature of stochastic sampling methods with the determinism of generalized perturbation theory. The specific spectral method used in this paper employs both the Smolyak algorithm and adaptivity by using Newton-Cotes collocation points along with linear hat basis functions. Using this approach, a surrogate model for the outputs of a computer code is constructed hierarchically by adaptively refining the collocation grid until the interpolant is converged to a user-defined threshold. The method inherently fits into the framework of parallel computing and allows for the extraction of meaningful statistics and data that are not within reach of stochastic sampling and generalized perturbation theory. This paper aims to demonstrate the advantages of spectral methods-especially when compared to current methods used in reactor physics for uncertainty quantification-and to illustrate their full potential. (authors)

Stochastic spectral Galerkin and collocation methods for PDEs with random coefficients: A numerical comparison

KAUST Repository

Bä ck, Joakim; Nobile, Fabio; Tamellini, Lorenzo; Tempone, Raul

2010-01-01

Much attention has recently been devoted to the development of Stochastic Galerkin (SG) and Stochastic Collocation (SC) methods for uncertainty quantification. An open and relevant research topic is the comparison of these two methods

The Application of the Probabilistic Collocation Method to a Transonic Axial Flow Compressor

NARCIS (Netherlands)

Loeven, G.J.A.; Bijl, H.

2010-01-01

In this paper the Probabilistic Collocation method is used for uncertainty quantification of operational uncertainties in a transonic axial flow compressor (i.e. NASA Rotor 37). Compressor rotors are components of a gas turbine that are highly sensitive to operational and geometrical uncertainties.

A Modified Generalized Laguerre-Gauss Collocation Method for Fractional Neutral Functional-Differential Equations on the Half-Line

Directory of Open Access Journals (Sweden)

Ali H. Bhrawy

2014-01-01

Full Text Available The modified generalized Laguerre-Gauss collocation (MGLC method is applied to obtain an approximate solution of fractional neutral functional-differential equations with proportional delays on the half-line. The proposed technique is based on modified generalized Laguerre polynomials and Gauss quadrature integration of such polynomials. The main advantage of the present method is to reduce the solution of fractional neutral functional-differential equations into a system of algebraic equations. Reasonable numerical results are achieved by choosing few modified generalized Laguerre-Gauss collocation points. Numerical results demonstrate the accuracy, efficiency, and versatility of the proposed method on the half-line.

An h-adaptive stochastic collocation method for stochastic EMC/EMI analysis

KAUST Repository

Yücel, Abdulkadir C.

2010-07-01

The analysis of electromagnetic compatibility and interference (EMC/EMI) phenomena is often fraught by randomness in a system\\'s excitation (e.g., the amplitude, phase, and location of internal noise sources) or configuration (e.g., the routing of cables, the placement of electronic systems, component specifications, etc.). To bound the probability of system malfunction, fast and accurate techniques to quantify the uncertainty in system observables (e.g., voltages across mission-critical circuit elements) are called for. Recently proposed stochastic frameworks [1-2] combine deterministic electromagnetic (EM) simulators with stochastic collocation (SC) methods that approximate system observables using generalized polynomial chaos expansion (gPC) [3] (viz. orthogonal polynomials spanning the entire random domain) to estimate their statistical moments and probability density functions (pdfs). When constructing gPC expansions, the EM simulator is used solely to evaluate system observables at collocation points prescribed by the SC-gPC scheme. The frameworks in [1-2] therefore are non-intrusive and straightforward to implement. That said, they become inefficient and inaccurate for system observables that vary rapidly or are discontinuous in the random variables (as their representations may require very high-order polynomials). © 2010 IEEE.

Application of a nodal collocation approximation for the multidimensional PL equations to the 3D Takeda benchmark problems

International Nuclear Information System (INIS)

Capilla, M.; Talavera, C.F.; Ginestar, D.; Verdú, G.

2012-01-01

Highlights: ► The multidimensional P L approximation to the nuclear transport equation is reviewed. ► A nodal collocation method is developed for the spatial discretization of P L equations. ► Advantages of the method are lower dimension and good characterists of the associated algebraic eigenvalue problem. ► The P L nodal collocation method is implemented into the computer code SHNC. ► The SHNC code is verified with 2D and 3D benchmark eigenvalue problems from Takeda and Ikeda, giving satisfactory results. - Abstract: P L equations are classical approximations to the neutron transport equations, which are obtained expanding the angular neutron flux in terms of spherical harmonics. These approximations are useful to study the behavior of reactor cores with complex fuel assemblies, for the homogenization of nuclear cross-sections, etc., and most of these applications are in three-dimensional (3D) geometries. In this work, we review the multi-dimensional P L equations and describe a nodal collocation method for the spatial discretization of these equations for arbitrary odd order L, which is based on the expansion of the spatial dependence of the fields in terms of orthonormal Legendre polynomials. The performance of the nodal collocation method is studied by means of obtaining the k eff and the stationary power distribution of several 3D benchmark problems. The solutions are obtained are compared with a finite element method and a Monte Carlo method.

Part 6. Internationalization and collocation of FBR fuel cycle facilities

International Nuclear Information System (INIS)

Stevenson, M.G.; Abramson, P.B.; LeSage, L.G.

1980-01-01

This report examines some of the non-proliferation, technical, and institutional aspects of internationalization and/or collocation of major facilities of the Fast Breeder Reactor (FBR) fuel cycle. The national incentives and disincentives for establishment of FBR Fuel Cycle Centers are enumerated. The technical, legal, and administrative considerations in determining the feasibility of FBR Fuel Cycle Centers are addressed by making comparisons with Light Water Reactor (LWR) centers which have been studied in detail by the IAEA and UNSRC

Stochastic Collocation Applications in Computational Electromagnetics

Directory of Open Access Journals (Sweden)

Dragan Poljak

2018-01-01

Full Text Available The paper reviews the application of deterministic-stochastic models in some areas of computational electromagnetics. Namely, in certain problems there is an uncertainty in the input data set as some properties of a system are partly or entirely unknown. Thus, a simple stochastic collocation (SC method is used to determine relevant statistics about given responses. The SC approach also provides the assessment of related confidence intervals in the set of calculated numerical results. The expansion of statistical output in terms of mean and variance over a polynomial basis, via SC method, is shown to be robust and efficient approach providing a satisfactory convergence rate. This review paper provides certain computational examples from the previous work by the authors illustrating successful application of SC technique in the areas of ground penetrating radar (GPR, human exposure to electromagnetic fields, and buried lines and grounding systems.

Application of Legendre spectral-collocation method to delay differential and stochastic delay differential equation

Science.gov (United States)

Khan, Sami Ullah; Ali, Ishtiaq

2018-03-01

Explicit solutions to delay differential equation (DDE) and stochastic delay differential equation (SDDE) can rarely be obtained, therefore numerical methods are adopted to solve these DDE and SDDE. While on the other hand due to unstable nature of both DDE and SDDE numerical solutions are also not straight forward and required more attention. In this study, we derive an efficient numerical scheme for DDE and SDDE based on Legendre spectral-collocation method, which proved to be numerical methods that can significantly speed up the computation. The method transforms the given differential equation into a matrix equation by means of Legendre collocation points which correspond to a system of algebraic equations with unknown Legendre coefficients. The efficiency of the proposed method is confirmed by some numerical examples. We found that our numerical technique has a very good agreement with other methods with less computational effort.

On the hybrid stability of the collocated virtual holonomic constraints basedwalking design

Czech Academy of Sciences Publication Activity Database

Anderle, Milan; Čelikovský, Sergej

2017-01-01

Roč. 6, č. 2 (2017), s. 47-56 ISSN 2223-7038 R&D Projects: GA ČR(CZ) GA17-04682S Institutional support: RVO:67985556 Keywords : Underactuated walking * Virtual holonomic constraints * Poincaré section method * collocated constraints Subject RIV: BC - Control Systems Theory OBOR OECD: Automation and control systems http://lib.physcon.ru/doc?id=60655c1961ed

Benchmarking the Collocation Stand-Alone Library and Toolkit (CSALT)

Science.gov (United States)

Hughes, Steven; Knittel, Jeremy; Shoan, Wendy; Kim, Youngkwang; Conway, Claire; Conway, Darrel J.

2017-01-01

This paper describes the processes and results of Verification and Validation (VV) efforts for the Collocation Stand Alone Library and Toolkit (CSALT). We describe the test program and environments, the tools used for independent test data, and comparison results. The VV effort employs classical problems with known analytic solutions, solutions from other available software tools, and comparisons to benchmarking data available in the public literature. Presenting all test results are beyond the scope of a single paper. Here we present high-level test results for a broad range of problems, and detailed comparisons for selected problems.

Comparing multiple model-derived aerosol optical properties to spatially collocated ground-based and satellite measurements

Science.gov (United States)

Ocko, Ilissa B.; Ginoux, Paul A.

2017-04-01

Anthropogenic aerosols are a key factor governing Earth's climate and play a central role in human-caused climate change. However, because of aerosols' complex physical, optical, and dynamical properties, aerosols are one of the most uncertain aspects of climate modeling. Fortunately, aerosol measurement networks over the past few decades have led to the establishment of long-term observations for numerous locations worldwide. Further, the availability of datasets from several different measurement techniques (such as ground-based and satellite instruments) can help scientists increasingly improve modeling efforts. This study explores the value of evaluating several model-simulated aerosol properties with data from spatially collocated instruments. We compare aerosol optical depth (AOD; total, scattering, and absorption), single-scattering albedo (SSA), Ångström exponent (α), and extinction vertical profiles in two prominent global climate models (Geophysical Fluid Dynamics Laboratory, GFDL, CM2.1 and CM3) to seasonal observations from collocated instruments (AErosol RObotic NETwork, AERONET, and Cloud-Aerosol Lidar with Orthogonal Polarization, CALIOP) at seven polluted and biomass burning regions worldwide. We find that a multi-parameter evaluation provides key insights on model biases, data from collocated instruments can reveal underlying aerosol-governing physics, column properties wash out important vertical distinctions, and improved models does not mean all aspects are improved. We conclude that it is important to make use of all available data (parameters and instruments) when evaluating aerosol properties derived by models.

Full-Wave Analysis of the Shielding Effectiveness of Thin Graphene Sheets with the 3D Unidirectionally Collocated HIE-FDTD Method

Directory of Open Access Journals (Sweden)

Arne Van Londersele

2017-01-01

Full Text Available Graphene-based electrical components are inherently multiscale, which poses a real challenge for finite-difference time-domain (FDTD solvers due to the stringent time step upper bound. Here, a unidirectionally collocated hybrid implicit-explicit (UCHIE FDTD method is put forward that exploits the planar structure of graphene to increase the time step by implicitizing the critical dimension. The method replaces the traditional Yee discretization by a partially collocated scheme that allows a more accurate numerical description of the material boundaries. Moreover, the UCHIE-FDTD method preserves second-order accuracy even for nonuniform discretization in the direction of collocation. The auxiliary differential equation (ADE approach is used to implement the graphene sheet as a dispersive Drude medium. The finite grid is terminated by a uniaxial perfectly matched layer (UPML to permit open-space simulations. Special care is taken to elaborate on the efficient implementation of the implicit update equations. The UCHIE-FDTD method is validated by computing the shielding effectiveness of a typical graphene sheet.

An improved triple collocation algorithm for decomposing autocorrelated and white soil moisture retrieval errors

Science.gov (United States)

If not properly account for, auto-correlated errors in observations can lead to inaccurate results in soil moisture data analysis and reanalysis. Here, we propose a more generalized form of the triple collocation algorithm (GTC) capable of decomposing the total error variance of remotely-sensed surf...

A stochastic collocation method for the second order wave equation with a discontinuous random speed

KAUST Repository

Motamed, Mohammad; Nobile, Fabio; Tempone, Raul

2012-01-01

In this paper we propose and analyze a stochastic collocation method for solving the second order wave equation with a random wave speed and subjected to deterministic boundary and initial conditions. The speed is piecewise smooth in the physical

Application of a modified collocation method to the one dimensional, one group neutron transport equation

International Nuclear Information System (INIS)

Maschek, W.

1976-07-01

A modified collocation method is used for solving the one group criticality problem for a uniform multiplying slab. The critical parameters and the angular fluxes for a number of slabs are displayed and compared with previously published values. (orig.) [de

Acoustic scattering by multiple elliptical cylinders using collocation multipole method

International Nuclear Information System (INIS)

Lee, Wei-Ming

2012-01-01

This paper presents the collocation multipole method for the acoustic scattering induced by multiple elliptical cylinders subjected to an incident plane sound wave. To satisfy the Helmholtz equation in the elliptical coordinate system, the scattered acoustic field is formulated in terms of angular and radial Mathieu functions which also satisfy the radiation condition at infinity. The sound-soft or sound-hard boundary condition is satisfied by uniformly collocating points on the boundaries. For the sound-hard or Neumann conditions, the normal derivative of the acoustic pressure is determined by using the appropriate directional derivative without requiring the addition theorem of Mathieu functions. By truncating the multipole expansion, a finite linear algebraic system is derived and the scattered field can then be determined according to the given incident acoustic wave. Once the total field is calculated as the sum of the incident field and the scattered field, the near field acoustic pressure along the scatterers and the far field scattering pattern can be determined. For the acoustic scattering of one elliptical cylinder, the proposed results match well with the analytical solutions. The proposed scattered fields induced by two and three elliptical–cylindrical scatterers are critically compared with those provided by the boundary element method to validate the present method. Finally, the effects of the convexity of an elliptical scatterer, the separation between scatterers and the incident wave number and angle on the acoustic scattering are investigated.

A fourth order spline collocation approach for a business cycle model

Science.gov (United States)

Sayfy, A.; Khoury, S.; Ibdah, H.

2013-10-01

A collocation approach, based on a fourth order cubic B-splines is presented for the numerical solution of a Kaleckian business cycle model formulated by a nonlinear delay differential equation. The equation is approximated and the nonlinearity is handled by employing an iterative scheme arising from Newton's method. It is shown that the model exhibits a conditionally dynamical stable cycle. The fourth-order rate of convergence of the scheme is verified numerically for different special cases.

The current strain distribution in the North China Basin of eastern China by least-squares collocation

Science.gov (United States)

Wu, J. C.; Tang, H. W.; Chen, Y. Q.; Li, Y. X.

2006-07-01

In this paper, the velocities of 154 stations obtained in 2001 and 2003 GPS survey campaigns are applied to formulate a continuous velocity field by the least-squares collocation method. The strain rate field obtained by the least-squares collocation method shows more clear deformation patterns than that of the conventional discrete triangle method. The significant deformation zones obtained are mainly located in three places, to the north of Tangshan, between Tianjing and Shijiazhuang, and to the north of Datong, which agree with the places of the Holocene active deformation zones obtained by geological investigations. The maximum shear strain rate is located at latitude 38.6°N and longitude 116.8°E, with a magnitude of 0.13 ppm/a. The strain rate field obtained can be used for earthquake prediction research in the North China Basin.

Two-dimensional Haar wavelet Collocation Method for the solution of Stationary Neutron Transport Equation in a homogeneous isotropic medium

International Nuclear Information System (INIS)

Patra, A.; Saha Ray, S.

2014-01-01

Highlights: • A stationary transport equation has been solved using the technique of Haar wavelet Collocation Method. • This paper intends to provide the great utility of Haar wavelets to nuclear science problem. • In the present paper, two-dimensional Haar wavelets are applied. • The proposed method is mathematically very simple, easy and fast. - Abstract: This paper emphasizes on finding the solution for a stationary transport equation using the technique of Haar wavelet Collocation Method (HWCM). Haar wavelet Collocation Method is efficient and powerful in solving wide class of linear and nonlinear differential equations. Recently Haar wavelet transform has gained the reputation of being a very effective tool for many practical applications. This paper intends to provide the great utility of Haar wavelets to nuclear science problem. In the present paper, two-dimensional Haar wavelets are applied for solution of the stationary Neutron Transport Equation in homogeneous isotropic medium. The proposed method is mathematically very simple, easy and fast. To demonstrate about the efficiency of the method, one test problem is discussed. It can be observed from the computational simulation that the numerical approximate solution is much closer to the exact solution

ANALYSIS OF SPECIALISED COLLOCATIONS IN THE AREA OF REMOTE SENSING IN THE PERSPECTIVE OF PHRASEOLOGY

Directory of Open Access Journals (Sweden)

Diva Cardoso de CAMARGO

2013-12-01

Full Text Available The aim of this research is to build and analyze a parallel corpus in the field of remote sensing in order to identify, according to its frequency, specialized collocations in English and then search for their equivalents in Portuguese. The research is based on the interdisciplinary approach of Corpus-Based Translation Studies (BAKER, 1995; CAMARGO, 2007, Corpus Linguistics (BERBER SARDINHA, 2004; TOGNINI-BONELLI, 2001, Phraseology (ORENHA-OTTAIANO, 2009; PAVEL, 1993, and some principles of Terminology (BARROS, 2004. For manipulating the corpora, the program WordSmith Tools (SCOTT, 2012 version 6.0 is used. To support this study, two comparable corpora in English and Portuguese were also built from articles published in both national and international journals in remote sensing. The results show that the collocations in Portuguese seem to be still in the process of conventionalization, as the translators made use of greater variation in their translational options, which can be a way to make the text clearer for the reader.

Comparison of multiphase mixing simulations performed on a staggered and a collocated grid

International Nuclear Information System (INIS)

Leskovar, M.

2000-01-01

During a severe reactor accident following core meltdown when the molten fuel comes into contact with the coolant water a steam explosion may occur. The premixing phase of a steam explosion covers the interaction of the melt jet or droplets with the water prior to any steam explosion occurrence. To get a better insight of the hydrodynamic processes during the premixing phase beside hot premixing experiments, where the water evaporation is significant, also cold isothermal premixing experiments are performed. To analyze the cold premixing experiments the computer code ESE has been developed. The specialty of ESE is that it uses a combined single-multiphase flow model. Because of problems with the convergence of the momentum equation written in conservative form on a staggered grid, the development of a collocated grid version of ESE was planed. But since we obtained the commercial code CFX-4.3, which uses a collocated variable arrangement, we decided first to test the capabilities of CFX-4.3. With ESE and CFX-4.3 the cold premixing experiment Q08 has been simulated. In the paper the simulation results performed with both codes are presented and commented in comparison to experimental data. (author)

Entropy Stable Staggered Grid Spectral Collocation for the Burgers' and Compressible Navier-Stokes Equations

Science.gov (United States)

Carpenter, Mark H.; Parsani, Matteo; Fisher, Travis C.; Nielsen, Eric J.

2015-01-01

Staggered grid, entropy stable discontinuous spectral collocation operators of any order are developed for Burgers' and the compressible Navier-Stokes equations on unstructured hexahedral elements. This generalization of previous entropy stable spectral collocation work [1, 2], extends the applicable set of points from tensor product, Legendre-Gauss-Lobatto (LGL) to a combination of tensor product Legendre-Gauss (LG) and LGL points. The new semi-discrete operators discretely conserve mass, momentum, energy and satisfy a mathematical entropy inequality for both Burgers' and the compressible Navier-Stokes equations in three spatial dimensions. They are valid for smooth as well as discontinuous flows. The staggered LG and conventional LGL point formulations are compared on several challenging test problems. The staggered LG operators are significantly more accurate, although more costly to implement. The LG and LGL operators exhibit similar robustness, as is demonstrated using test problems known to be problematic for operators that lack a nonlinearly stability proof for the compressible Navier-Stokes equations (e.g., discontinuous Galerkin, spectral difference, or flux reconstruction operators).

Classical solutions of two dimensional Stokes problems on non smooth domains. 2: Collocation method for the Radon equation

International Nuclear Information System (INIS)

Lubuma, M.S.

1991-05-01

The non uniquely solvable Radon boundary integral equation for the two-dimensional Stokes-Dirichlet problem on a non smooth domain is transformed into a well posed one by a suitable compact perturbation of the velocity double layer potential operator. The solution to the modified equation is decomposed into a regular part and a finite linear combination of intrinsic singular functions whose coefficients are computed from explicit formulae. Using these formulae, the classical collocation method, defined by continuous piecewise linear vector-valued basis functions, which converges slowly because of the lack of regularity of the solution, is improved into a collocation dual singular function method with optimal rates of convergence for the solution and for the coefficients of singularities. (author). 34 refs

Transport survey calculations using the spectral collocation method

International Nuclear Information System (INIS)

Painter, S.L.; Lyon, J.F.

1989-01-01

A novel transport survey code has been developed and is being used to study the sensitivity of stellarator reactor performance to various transport assumptions. Instead of following one of the usual approaches, the steady-state transport equation are solved in integral form using the spectral collocation method. This approach effectively combine the computational efficiency of global models with the general nature of 1-D solutions. A compact torsatron reactor test case was used to study the convergence properties and flexibility of the new method. The heat transport model combined Shaing's model for ripple-induced neoclassical transport, the Chang-Hinton model for axisymmetric neoclassical transport, and neoalcator scaling for anomalous electron heat flux. Alpha particle heating, radiation losses, classical electron-ion heat flow, and external heating were included. For the test problem, the method exhibited some remarkable convergence properties. As the number of basis functions was increased, the maximum, pointwise error in the integrated power balance decayed exponentially until the numerical noise level as reached. Better than 10% accuracy in the globally-averaged quantities was achieved with only 5 basis functions; better than 1% accuracy was achieved with 10 basis functions. The numerical method was also found to be very general. Extreme temperature gradients at the plasma edge which sometimes arise from the neoclassical models and are difficult to resolve with finite-difference methods were easily resolved. 8 refs., 6 figs

A Legendre Wavelet Spectral Collocation Method for Solving Oscillatory Initial Value Problems

Directory of Open Access Journals (Sweden)

A. Karimi Dizicheh

2013-01-01

wavelet suitable for large intervals, and then the Legendre-Guass collocation points of the Legendre wavelet are derived. Using this strategy, the iterative spectral method converts the differential equation to a set of algebraic equations. Solving these algebraic equations yields an approximate solution for the differential equation. The proposed method is illustrated by some numerical examples, and the result is compared with the exponentially fitted Runge-Kutta method. Our proposed method is simple and highly accurate.

A Comparison of the Performance Improvement by Collocated and Noncollocated Active Damping in Motion Systems

NARCIS (Netherlands)

Babakhani, B.; de Vries, Theodorus J.A.; van Amerongen, J.

2012-01-01

In this paper, both collocated and noncollocated active vibration control (AVC) of a the vibrations in a motion system are considered. Pole-zero plots of both the AVC loop and the motion-control (MC) loop are used to analyze the effect of the applied active damping on the system dynamics. Using

A Survey of Symplectic and Collocation Integration Methods for Orbit Propagation

Science.gov (United States)

Jones, Brandon A.; Anderson, Rodney L.

2012-01-01

Demands on numerical integration algorithms for astrodynamics applications continue to increase. Common methods, like explicit Runge-Kutta, meet the orbit propagation needs of most scenarios, but more specialized scenarios require new techniques to meet both computational efficiency and accuracy needs. This paper provides an extensive survey on the application of symplectic and collocation methods to astrodynamics. Both of these methods benefit from relatively recent theoretical developments, which improve their applicability to artificial satellite orbit propagation. This paper also details their implementation, with several tests demonstrating their advantages and disadvantages.

Composite multi-modal vibration control for a stiffened plate using non-collocated acceleration sensor and piezoelectric actuator

International Nuclear Information System (INIS)

Li, Shengquan; Li, Juan; Mo, Yueping; Zhao, Rong

2014-01-01

A novel active method for multi-mode vibration control of an all-clamped stiffened plate (ACSP) is proposed in this paper, using the extended-state-observer (ESO) approach based on non-collocated acceleration sensors and piezoelectric actuators. Considering the estimated capacity of ESO for system state variables, output superposition and control coupling of other modes, external excitation, and model uncertainties simultaneously, a composite control method, i.e., the ESO based vibration control scheme, is employed to ensure the lumped disturbances and uncertainty rejection of the closed-loop system. The phenomenon of phase hysteresis and time delay, caused by non-collocated sensor/actuator pairs, degrades the performance of the control system, even inducing instability. To solve this problem, a simple proportional differential (PD) controller and acceleration feed-forward with an output predictor design produce the control law for each vibration mode. The modal frequencies, phase hysteresis loops and phase lag values due to non-collocated placement of the acceleration sensor and piezoelectric patch actuator are experimentally obtained, and the phase lag is compensated by using the Smith Predictor technology. In order to improve the vibration control performance, the chaos optimization method based on logistic mapping is employed to auto-tune the parameters of the feedback channel. The experimental control system for the ACSP is tested using the dSPACE real-time simulation platform. Experimental results demonstrate that the proposed composite active control algorithm is an effective approach for suppressing multi-modal vibrations. (paper)

A nonclassical Radau collocation method for solving the Lane-Emden equations of the polytropic index 4.75 ≤ α < 5

Science.gov (United States)

Tirani, M. D.; Maleki, M.; Kajani, M. T.

2014-11-01

A numerical method for solving the Lane-Emden equations of the polytropic index α when 4.75 ≤ α ≤ 5 is introduced. The method is based upon nonclassical Gauss-Radau collocation points and Freud type weights. Nonclassical orthogonal polynomials, nonclassical Radau points and weighted interpolation are introduced and are utilized in the interval [0,1]. A smooth, strictly monotonic transformation is used to map the infinite domain x ∈ [0,∞) onto a half-open interval t ∈ [0,1). The resulting problem on the finite interval is then transcribed to a system of nonlinear algebraic equations using collocation. The method is easy to implement and yields very accurate results.

Trajectory Planning of Satellite Formation Flying using Nonlinear Programming and Collocation

Directory of Open Access Journals (Sweden)

Hyung-Chu Lim

2008-12-01

Full Text Available Recently, satellite formation flying has been a topic of significant research interest in aerospace society because it provides potential benefits compared to a large spacecraft. Some techniques have been proposed to design optimal formation trajectories minimizing fuel consumption in the process of formation configuration or reconfiguration. In this study, a method is introduced to build fuel-optimal trajectories minimizing a cost function that combines the total fuel consumption of all satellites and assignment of fuel consumption rate for each satellite. This approach is based on collocation and nonlinear programming to solve constraints for collision avoidance and the final configuration. New constraints of nonlinear equality or inequality are derived for final configuration, and nonlinear inequality constraints are established for collision avoidance. The final configuration constraints are that three or more satellites should form a projected circular orbit and make an equilateral polygon in the horizontal plane. Example scenarios, including these constraints and the cost function, are simulated by the method to generate optimal trajectories for the formation configuration and reconfiguration of multiple satellites.

Big Data and HPC collocation: Using HPC idle resources for Big Data Analytics

OpenAIRE

MERCIER , Michael; Glesser , David; Georgiou , Yiannis; Richard , Olivier

2017-01-01

International audience; Executing Big Data workloads upon High Performance Computing (HPC) infrastractures has become an attractive way to improve their performances. However, the collocation of HPC and Big Data workloads is not an easy task, mainly because of their core concepts' differences. This paper focuses on the challenges related to the scheduling of both Big Data and HPC workloads on the same computing platform. In classic HPC workloads, the rigidity of jobs tends to create holes in ...

A fractional spline collocation-Galerkin method for the time-fractional diffusion equation

Directory of Open Access Journals (Sweden)

Pezza L.

2018-03-01

Full Text Available The aim of this paper is to numerically solve a diffusion differential problem having time derivative of fractional order. To this end we propose a collocation-Galerkin method that uses the fractional splines as approximating functions. The main advantage is in that the derivatives of integer and fractional order of the fractional splines can be expressed in a closed form that involves just the generalized finite difference operator. This allows us to construct an accurate and efficient numerical method. Several numerical tests showing the effectiveness of the proposed method are presented.

Generalized Lagrangian Jacobi Gauss collocation method for solving unsteady isothermal gas through a micro-nano porous medium

Science.gov (United States)

Parand, Kourosh; Latifi, Sobhan; Delkhosh, Mehdi; Moayeri, Mohammad M.

2018-01-01

In the present paper, a new method based on the Generalized Lagrangian Jacobi Gauss (GLJG) collocation method is proposed. The nonlinear Kidder equation, which explains unsteady isothermal gas through a micro-nano porous medium, is a second-order two-point boundary value ordinary differential equation on the unbounded interval [0, ∞). Firstly, using the quasilinearization method, the equation is converted to a sequence of linear ordinary differential equations. Then, by using the GLJG collocation method, the problem is reduced to solving a system of algebraic equations. It must be mentioned that this equation is solved without domain truncation and variable changing. A comparison with some numerical solutions made and the obtained results indicate that the presented solution is highly accurate. The important value of the initial slope, y'(0), is obtained as -1.191790649719421734122828603800159364 for η = 0.5. Comparing to the best result obtained so far, it is accurate up to 36 decimal places.

Synergistic multi-sensor and multi-frequency retrieval of cloud ice water path constrained by CloudSat collocations

International Nuclear Information System (INIS)

Islam, Tanvir; Srivastava, Prashant K.

2015-01-01

The cloud ice water path (IWP) is one of the major parameters that have a strong influence on earth's radiation budget. Onboard satellite sensors are recognized as valuable tools to measure the IWP in a global scale. Albeit, active sensors such as the Cloud Profiling Radar (CPR) onboard the CloudSat satellite has better capability to measure the ice water content profile, thus, its vertical integral, IWP, than any passive microwave (MW) or infrared (IR) sensors. In this study, we investigate the retrieval of IWP from MW and IR sensors, including AMSU-A, MHS, and HIRS instruments on-board the N19 satellite, such that the retrieval is consistent with the CloudSat IWP estimates. This is achieved through the collocations between the passive satellite measurements and CloudSat scenes. Potential benefit of synergistic multi-sensor multi-frequency retrieval is investigated. Two modeling approaches are explored for the IWP retrieval – generalized linear model (GLM) and neural network (NN). The investigation has been carried out over both ocean and land surface types. The MW/IR synergy is found to be retrieved more accurate IWP than the individual AMSU-A, MHS, or HIRS measurements. Both GLM and NN approaches have been able to exploit the synergistic retrievals. - Highlights: • MW/IR synergy is investigated for IWP retrieval. • The IWP retrieval is modeled using CloudSat collocations. • Two modeling approaches are explored – GLM and ANN. • MW/IR synergy performs better than the MW or IR only retrieval

Spectral collocation for multiparameter eigenvalue problems arising from separable boundary value problems

Science.gov (United States)

Plestenjak, Bor; Gheorghiu, Călin I.; Hochstenbach, Michiel E.

2015-10-01

In numerous science and engineering applications a partial differential equation has to be solved on some fairly regular domain that allows the use of the method of separation of variables. In several orthogonal coordinate systems separation of variables applied to the Helmholtz, Laplace, or Schrödinger equation leads to a multiparameter eigenvalue problem (MEP); important cases include Mathieu's system, Lamé's system, and a system of spheroidal wave functions. Although multiparameter approaches are exploited occasionally to solve such equations numerically, MEPs remain less well known, and the variety of available numerical methods is not wide. The classical approach of discretizing the equations using standard finite differences leads to algebraic MEPs with large matrices, which are difficult to solve efficiently. The aim of this paper is to change this perspective. We show that by combining spectral collocation methods and new efficient numerical methods for algebraic MEPs it is possible to solve such problems both very efficiently and accurately. We improve on several previous results available in the literature, and also present a MATLAB toolbox for solving a wide range of problems.

Nodal collocation approximation for the multidimensional PL equations applied to transport source problems

Energy Technology Data Exchange (ETDEWEB)

Verdu, G. [Departamento de Ingenieria Quimica Y Nuclear, Universitat Politecnica de Valencia, Cami de Vera, 14, 46022. Valencia (Spain); Capilla, M.; Talavera, C. F.; Ginestar, D. [Dept. of Nuclear Engineering, Departamento de Matematica Aplicada, Universitat Politecnica de Valencia, Cami de Vera, 14, 46022. Valencia (Spain)

2012-07-01

PL equations are classical high order approximations to the transport equations which are based on the expansion of the angular dependence of the angular neutron flux and the nuclear cross sections in terms of spherical harmonics. A nodal collocation method is used to discretize the PL equations associated with a neutron source transport problem. The performance of the method is tested solving two 1D problems with analytical solution for the transport equation and a classical 2D problem. (authors)

Nodal collocation approximation for the multidimensional PL equations applied to transport source problems

International Nuclear Information System (INIS)

Verdu, G.; Capilla, M.; Talavera, C. F.; Ginestar, D.

2012-01-01

PL equations are classical high order approximations to the transport equations which are based on the expansion of the angular dependence of the angular neutron flux and the nuclear cross sections in terms of spherical harmonics. A nodal collocation method is used to discretize the PL equations associated with a neutron source transport problem. The performance of the method is tested solving two 1D problems with analytical solution for the transport equation and a classical 2D problem. (authors)

Optimization of Low-Thrust Spiral Trajectories by Collocation

Science.gov (United States)

Falck, Robert D.; Dankanich, John W.

2012-01-01

As NASA examines potential missions in the post space shuttle era, there has been a renewed interest in low-thrust electric propulsion for both crewed and uncrewed missions. While much progress has been made in the field of software for the optimization of low-thrust trajectories, many of the tools utilize higher-fidelity methods which, while excellent, result in extremely high run-times and poor convergence when dealing with planetocentric spiraling trajectories deep within a gravity well. Conversely, faster tools like SEPSPOT provide a reasonable solution but typically fail to account for other forces such as third-body gravitation, aerodynamic drag, solar radiation pressure. SEPSPOT is further constrained by its solution method, which may require a very good guess to yield a converged optimal solution. Here the authors have developed an approach using collocation intended to provide solution times comparable to those given by SEPSPOT while allowing for greater robustness and extensible force models.

Stochastic spectral Galerkin and collocation methods for PDEs with random coefficients: A numerical comparison

KAUST Repository

Bäck, Joakim

2010-09-17

Much attention has recently been devoted to the development of Stochastic Galerkin (SG) and Stochastic Collocation (SC) methods for uncertainty quantification. An open and relevant research topic is the comparison of these two methods. By introducing a suitable generalization of the classical sparse grid SC method, we are able to compare SG and SC on the same underlying multivariate polynomial space in terms of accuracy vs. computational work. The approximation spaces considered here include isotropic and anisotropic versions of Tensor Product (TP), Total Degree (TD), Hyperbolic Cross (HC) and Smolyak (SM) polynomials. Numerical results for linear elliptic SPDEs indicate a slight computational work advantage of isotropic SC over SG, with SC-SM and SG-TD being the best choices of approximation spaces for each method. Finally, numerical results corroborate the optimality of the theoretical estimate of anisotropy ratios introduced by the authors in a previous work for the construction of anisotropic approximation spaces. © 2011 Springer.

Investigating electro-mechanical signals from collocated piezoelectric wafers for the reference-free damage diagnosis of a plate

International Nuclear Information System (INIS)

Kim, Eun Jin; Park, Hyun Woo; Kim, Min Koo; Sohn, Hoon

2011-01-01

The electro-mechanical (EM) signals from piezoelectric (PZT) wafers are investigated for reference-free damage diagnosis so that a notch in a plate can be detected without requiring direct comparison with a baseline EM signal. Two identical PZT wafers collocated on both surfaces of a plate are utilized for extracting the mode-converted Lamb wave signals created by a notch. As harmonic input voltage signals are exerted on the collocated PZT wafers, the corresponding mode-converted Lamb wave signals become steady-state in the presence of damage. Applying fast Fourier transform to these mode-converted Lamb wave signals followed by a proper normalization, the EM signals associated with the mode conversion can be obtained. The theoretical finding of this paper is validated through spectral element simulations of a cantilever beam with a notch. The effects of the size and the location of the notch on the mode-converted EM signals are investigated as well. Finally, the applicability of the decomposed EM signals to reference-free damage diagnosis is discussed

Numerical solution of sixth-order boundary-value problems using Legendre wavelet collocation method

Science.gov (United States)

Sohaib, Muhammad; Haq, Sirajul; Mukhtar, Safyan; Khan, Imad

2018-03-01

An efficient method is proposed to approximate sixth order boundary value problems. The proposed method is based on Legendre wavelet in which Legendre polynomial is used. The mechanism of the method is to use collocation points that converts the differential equation into a system of algebraic equations. For validation two test problems are discussed. The results obtained from proposed method are quite accurate, also close to exact solution, and other different methods. The proposed method is computationally more effective and leads to more accurate results as compared to other methods from literature.

A Numerical Method for Lane-Emden Equations Using Hybrid Functions and the Collocation Method

Directory of Open Access Journals (Sweden)

Changqing Yang

2012-01-01

Full Text Available A numerical method to solve Lane-Emden equations as singular initial value problems is presented in this work. This method is based on the replacement of unknown functions through a truncated series of hybrid of block-pulse functions and Chebyshev polynomials. The collocation method transforms the differential equation into a system of algebraic equations. It also has application in a wide area of differential equations. Corresponding numerical examples are presented to demonstrate the accuracy of the proposed method.

Multi-element probabilistic collocation method in high dimensions

International Nuclear Information System (INIS)

Foo, Jasmine; Karniadakis, George Em

2010-01-01

We combine multi-element polynomial chaos with analysis of variance (ANOVA) functional decomposition to enhance the convergence rate of polynomial chaos in high dimensions and in problems with low stochastic regularity. Specifically, we employ the multi-element probabilistic collocation method MEPCM and so we refer to the new method as MEPCM-A. We investigate the dependence of the convergence of MEPCM-A on two decomposition parameters, the polynomial order μ and the effective dimension ν, with ν<< N, and N the nominal dimension. Numerical tests for multi-dimensional integration and for stochastic elliptic problems suggest that ν≥μ for monotonic convergence of the method. We also employ MEPCM-A to obtain error bars for the piezometric head at the Hanford nuclear waste site under stochastic hydraulic conductivity conditions. Finally, we compare the cost of MEPCM-A against Monte Carlo in several hundred dimensions, and we find MEPCM-A to be more efficient for up to 600 dimensions for a specific multi-dimensional integration problem involving a discontinuous function.

Fermat collocation method for the solutions of nonlinear system of second order boundary value problems

Directory of Open Access Journals (Sweden)

Salih Yalcinbas

2016-01-01

Full Text Available In this study, a numerical approach is proposed to obtain approximate solutions of nonlinear system of second order boundary value problem. This technique is essentially based on the truncated Fermat series and its matrix representations with collocation points. Using the matrix method, we reduce the problem system of nonlinear algebraic equations. Numerical examples are also given to demonstrate the validity and applicability of the presented technique. The method is easy to implement and produces accurate results.

A fast collocation method for a variable-coefficient nonlocal diffusion model

Science.gov (United States)

Wang, Che; Wang, Hong

2017-02-01

We develop a fast collocation scheme for a variable-coefficient nonlocal diffusion model, for which a numerical discretization would yield a dense stiffness matrix. The development of the fast method is achieved by carefully handling the variable coefficients appearing inside the singular integral operator and exploiting the structure of the dense stiffness matrix. The resulting fast method reduces the computational work from O (N3) required by a commonly used direct solver to O (Nlog ⁡ N) per iteration and the memory requirement from O (N2) to O (N). Furthermore, the fast method reduces the computational work of assembling the stiffness matrix from O (N2) to O (N). Numerical results are presented to show the utility of the fast method.

On multilevel RBF collocation to solve nonlinear PDEs arising from endogenous stochastic volatility models

Science.gov (United States)

Bastani, Ali Foroush; Dastgerdi, Maryam Vahid; Mighani, Abolfazl

2018-06-01

The main aim of this paper is the analytical and numerical study of a time-dependent second-order nonlinear partial differential equation (PDE) arising from the endogenous stochastic volatility model, introduced in [Bensoussan, A., Crouhy, M. and Galai, D., Stochastic equity volatility related to the leverage effect (I): equity volatility behavior. Applied Mathematical Finance, 1, 63-85, 1994]. As the first step, we derive a consistent set of initial and boundary conditions to complement the PDE, when the firm is financed by equity and debt. In the sequel, we propose a Newton-based iteration scheme for nonlinear parabolic PDEs which is an extension of a method for solving elliptic partial differential equations introduced in [Fasshauer, G. E., Newton iteration with multiquadrics for the solution of nonlinear PDEs. Computers and Mathematics with Applications, 43, 423-438, 2002]. The scheme is based on multilevel collocation using radial basis functions (RBFs) to solve the resulting locally linearized elliptic PDEs obtained at each level of the Newton iteration. We show the effectiveness of the resulting framework by solving a prototypical example from the field and compare the results with those obtained from three different techniques: (1) a finite difference discretization; (2) a naive RBF collocation and (3) a benchmark approximation, introduced for the first time in this paper. The numerical results confirm the robustness, higher convergence rate and good stability properties of the proposed scheme compared to other alternatives. We also comment on some possible research directions in this field.

A consistent method for finite volume discretization of body forces on collocated grids applied to flow through an actuator disk

DEFF Research Database (Denmark)

Troldborg, Niels; Sørensen, Niels N.; Réthoré, Pierre-Elouan

2015-01-01

This paper describes a consistent algorithm for eliminating the numerical wiggles appearing when solving the finite volume discretized Navier-Stokes equations with discrete body forces in a collocated grid arrangement. The proposed method is a modification of the Rhie-Chow algorithm where the for...

Improved statistical models for limited datasets in uncertainty quantification using stochastic collocation

Energy Technology Data Exchange (ETDEWEB)

Alwan, Aravind; Aluru, N.R.

2013-12-15

This paper presents a data-driven framework for performing uncertainty quantification (UQ) by choosing a stochastic model that accurately describes the sources of uncertainty in a system. This model is propagated through an appropriate response surface function that approximates the behavior of this system using stochastic collocation. Given a sample of data describing the uncertainty in the inputs, our goal is to estimate a probability density function (PDF) using the kernel moment matching (KMM) method so that this PDF can be used to accurately reproduce statistics like mean and variance of the response surface function. Instead of constraining the PDF to be optimal for a particular response function, we show that we can use the properties of stochastic collocation to make the estimated PDF optimal for a wide variety of response functions. We contrast this method with other traditional procedures that rely on the Maximum Likelihood approach, like kernel density estimation (KDE) and its adaptive modification (AKDE). We argue that this modified KMM method tries to preserve what is known from the given data and is the better approach when the available data is limited in quantity. We test the performance of these methods for both univariate and multivariate density estimation by sampling random datasets from known PDFs and then measuring the accuracy of the estimated PDFs, using the known PDF as a reference. Comparing the output mean and variance estimated with the empirical moments using the raw data sample as well as the actual moments using the known PDF, we show that the KMM method performs better than KDE and AKDE in predicting these moments with greater accuracy. This improvement in accuracy is also demonstrated for the case of UQ in electrostatic and electrothermomechanical microactuators. We show how our framework results in the accurate computation of statistics in micromechanical systems.

Improved statistical models for limited datasets in uncertainty quantification using stochastic collocation

International Nuclear Information System (INIS)

Alwan, Aravind; Aluru, N.R.

2013-01-01

This paper presents a data-driven framework for performing uncertainty quantification (UQ) by choosing a stochastic model that accurately describes the sources of uncertainty in a system. This model is propagated through an appropriate response surface function that approximates the behavior of this system using stochastic collocation. Given a sample of data describing the uncertainty in the inputs, our goal is to estimate a probability density function (PDF) using the kernel moment matching (KMM) method so that this PDF can be used to accurately reproduce statistics like mean and variance of the response surface function. Instead of constraining the PDF to be optimal for a particular response function, we show that we can use the properties of stochastic collocation to make the estimated PDF optimal for a wide variety of response functions. We contrast this method with other traditional procedures that rely on the Maximum Likelihood approach, like kernel density estimation (KDE) and its adaptive modification (AKDE). We argue that this modified KMM method tries to preserve what is known from the given data and is the better approach when the available data is limited in quantity. We test the performance of these methods for both univariate and multivariate density estimation by sampling random datasets from known PDFs and then measuring the accuracy of the estimated PDFs, using the known PDF as a reference. Comparing the output mean and variance estimated with the empirical moments using the raw data sample as well as the actual moments using the known PDF, we show that the KMM method performs better than KDE and AKDE in predicting these moments with greater accuracy. This improvement in accuracy is also demonstrated for the case of UQ in electrostatic and electrothermomechanical microactuators. We show how our framework results in the accurate computation of statistics in micromechanical systems

Analytic regularity and collocation approximation for elliptic PDEs with random domain deformations

KAUST Repository

Castrillon, Julio

2016-03-02

In this work we consider the problem of approximating the statistics of a given Quantity of Interest (QoI) that depends on the solution of a linear elliptic PDE defined over a random domain parameterized by N random variables. The elliptic problem is remapped onto a corresponding PDE with a fixed deterministic domain. We show that the solution can be analytically extended to a well defined region in CN with respect to the random variables. A sparse grid stochastic collocation method is then used to compute the mean and variance of the QoI. Finally, convergence rates for the mean and variance of the QoI are derived and compared to those obtained in numerical experiments.

Implementation of optimal Galerkin and Collocation approximations of PDEs with Random Coefficients

KAUST Repository

Beck, Joakim

2011-12-22

In this work we first focus on the Stochastic Galerkin approximation of the solution u of an elliptic stochastic PDE. We rely on sharp estimates for the decay of the coefficients of the spectral expansion of u on orthogonal polynomials to build a sequence of polynomial subspaces that features better convergence properties compared to standard polynomial subspaces such as Total Degree or Tensor Product. We consider then the Stochastic Collocation method, and use the previous estimates to introduce a new effective class of Sparse Grids, based on the idea of selecting a priori the most profitable hierarchical surpluses, that, again, features better convergence properties compared to standard Smolyak or tensor product grids.

An estimation of the height system bias parameter N (0) using least squares collocation from observed gravity and GPS-levelling data

DEFF Research Database (Denmark)

Sadiq, Muhammad; Tscherning, Carl C.; Ahmad, Zulfiqar

2009-01-01

This paper deals with the analysis of gravity anomaly and precise levelling in conjunction with GPS-Levelling data for the computation of a gravimetric geoid and an estimate of the height system bias parameter N-o for the vertical datum in Pakistan by means of least squares collocation technique...... covariance parameters has facilitated to achieve gravimetric height anomalies in a global geocentric datum. Residual terrain modeling (RTM) technique has been used in combination with the EGM96 for the reduction and smoothing of the gravity data. A value for the bias parameter N-o has been estimated...... with reference to the local GPS-Levelling datum that appears to be 0.705 m with 0.07 m mean square error. The gravimetric height anomalies were compared with height anomalies obtained from GPS-Levelling stations using least square collocation with and without bias adjustment. The bias adjustment minimizes...

Non-collocated fuzzy logic and input shaping control strategy for elastic joint manipulator: vibration suppression and time response analysis

Energy Technology Data Exchange (ETDEWEB)

Rashidifar, Mohammed Amin [Faculty of Mechanical Engineering, Islamic Azad University, SHADEGAN (Iran, Islamic Republic of); Rashidifar, Ali Amin, E-mail: rashidifar_58@yahoo.com [Computer Science, Islamic Azad University, SHADEGAN (Iran, Islamic Republic of)

2014-07-01

Conventional model-based control strategies are very complex and difficult to synthesize due to high complexity of the dynamics of robots manipulator considering joint elasticity. This paper presents investigations into the development of hybrid control schemes for trajectory tracking and vibration control of a flexible joint manipulator. To study the effectiveness of the controllers, initially a collocated proportional-derivative (P D)-type Fuzzy Logic Controller (FLC) is developed for tip angular position control of a flexible joint manipulator. This is then extended to incorporate a non-collocated Fuzzy Logic Controller and input shaping scheme for vibration reduction of the flexible joint system. The positive zero-vibration-derivative-derivative (ZVDD) shaper is designed based on the properties of the system. Simulation results of the response of the flexible joint manipulator with the controllers are presented in time and frequency domains. The performances of the hybrid control schemes are examined in terms of input tracking capability, level of vibration reduction and time response specifications. Finally, a comparative assessment of the control techniques is presented and discussed. (Author)

Entropy Stable Staggered Grid Discontinuous Spectral Collocation Methods of any Order for the Compressible Navier--Stokes Equations

KAUST Repository

Parsani, Matteo

2016-10-04

Staggered grid, entropy stable discontinuous spectral collocation operators of any order are developed for the compressible Euler and Navier--Stokes equations on unstructured hexahedral elements. This generalization of previous entropy stable spectral collocation work [M. H. Carpenter, T. C. Fisher, E. J. Nielsen, and S. H. Frankel, SIAM J. Sci. Comput., 36 (2014), pp. B835--B867, M. Parsani, M. H. Carpenter, and E. J. Nielsen, J. Comput. Phys., 292 (2015), pp. 88--113], extends the applicable set of points from tensor product, Legendre--Gauss--Lobatto (LGL), to a combination of tensor product Legendre--Gauss (LG) and LGL points. The new semidiscrete operators discretely conserve mass, momentum, energy, and satisfy a mathematical entropy inequality for the compressible Navier--Stokes equations in three spatial dimensions. They are valid for smooth as well as discontinuous flows. The staggered LG and conventional LGL point formulations are compared on several challenging test problems. The staggered LG operators are significantly more accurate, although more costly from a theoretical point of view. The LG and LGL operators exhibit similar robustness, as is demonstrated using test problems known to be problematic for operators that lack a nonlinear stability proof for the compressible Navier--Stokes equations (e.g., discontinuous Galerkin, spectral difference, or flux reconstruction operators).

Coefficient of restitution in fractional viscoelastic compliant impacts using fractional Chebyshev collocation

Science.gov (United States)

Dabiri, Arman; Butcher, Eric A.; Nazari, Morad

2017-02-01

Compliant impacts can be modeled using linear viscoelastic constitutive models. While such impact models for realistic viscoelastic materials using integer order derivatives of force and displacement usually require a large number of parameters, compliant impact models obtained using fractional calculus, however, can be advantageous since such models use fewer parameters and successfully capture the hereditary property. In this paper, we introduce the fractional Chebyshev collocation (FCC) method as an approximation tool for numerical simulation of several linear fractional viscoelastic compliant impact models in which the overall coefficient of restitution for the impact is studied as a function of the fractional model parameters for the first time. Other relevant impact characteristics such as hysteresis curves, impact force gradient, penetration and separation depths are also studied.

Collocational Networks Supporting Strategic Planning of Brand Communication: Analysis of Quarterly Reports of Telecommunication Companies

Directory of Open Access Journals (Sweden)

Pentti Järvi

2004-10-01

Full Text Available This study addresses analysing quarterly reports from a brandtheoretical viewpoint. The study addresses the issue through a method which introduces both a quantitative tool based on linguistic theory and qualitative decisions of the researchers. The research objects of this study are two quarterly reports each of three telecommunications companies: Ericsson, Motorola and Nokia. The method used is a collocational network. The analyses show that there are differences in communication and message strategies among investigated companies and also changes during a quite short period in each company

An embedded formula of the Chebyshev collocation method for stiff problems

Science.gov (United States)

Piao, Xiangfan; Bu, Sunyoung; Kim, Dojin; Kim, Philsu

2017-12-01

In this study, we have developed an embedded formula of the Chebyshev collocation method for stiff problems, based on the zeros of the generalized Chebyshev polynomials. A new strategy for the embedded formula, using a pair of methods to estimate the local truncation error, as performed in traditional embedded Runge-Kutta schemes, is proposed. The method is performed in such a way that not only the stability region of the embedded formula can be widened, but by allowing the usage of larger time step sizes, the total computational costs can also be reduced. In terms of concrete convergence and stability analysis, the constructed algorithm turns out to have an 8th order convergence and it exhibits A-stability. Through several numerical experimental results, we have demonstrated that the proposed method is numerically more efficient, compared to several existing implicit methods.

Collocation lists as instruments for metaphor detection in corpora Listas de colocações como instrumentos para detecção de metáforas em corpora

Directory of Open Access Journals (Sweden)

Tony Berber Sardinha

2006-01-01

Full Text Available This paper reports a study on the use of collocation lists as instruments for detecting metaphors in corpora. A collocation list contains the collocations for selected words in corpora together with concordances for those words. As corpora become more available to metaphor researchers, there is a growing need for developing ways to gain access to as much data as the corpus can offer. The research described here has hopefully come some way toward meeting the challenges of developing tools for metaphor corpus research. Results suggest that the collocation lists seem to be a good pre-processing instrument for corpus research of metaphor, despite accuracy problems.Este trabalho apresenta uma pesquisa sobre o uso de listas de colocações como instrumentos para detecção de metáforas em corpora. Uma lista de colocação contém as colocações de palavras selecionadas de corpora juntamente com as concordâncias dessas palavras. Na medida que os corpora se tornam mais acessíveis aos pesquisadores de metáfora, começa a surgir uma necessidade de desenvolver maneiras de acessar a maior quantidade possível de dados que um corpus oferece. A pesquisa descrita aqui tentou enfrentar esse desafio, criando e testando ferramentas para pesquisa de metáfora baseada em corpus. Os resultados sugerem que as listas de colocações podem ser um instrumento eficaz de pré-processamento de corpus com vistas à análise humana de metáforas, a despeito de alguns problemas de precisão.

Multi-Index Monte Carlo and stochastic collocation methods for random PDEs

KAUST Repository

Nobile, Fabio; Haji Ali, Abdul Lateef; Tamellini, Lorenzo; Tempone, Raul

2016-01-01

In this talk we consider the problem of computing statistics of the solution of a partial differential equation with random data, where the random coefficient is parametrized by means of a finite or countable sequence of terms in a suitable expansion. We describe and analyze a Multi-Index Monte Carlo (MIMC) and a Multi-Index Stochastic Collocation method (MISC). the former is both a stochastic version of the combination technique introduced by Zenger, Griebel and collaborators and an extension of the Multilevel Monte Carlo (MLMC) method first described by Heinrich and Giles. Instead of using firstorder differences as in MLMC, MIMC uses mixed differences to reduce the variance of the hierarchical differences dramatically. This in turn yields new and improved complexity results, which are natural generalizations of Giles s MLMC analysis, and which increase the domain of problem parameters for which we achieve the optimal convergence, O(TOL-2). On the same vein, MISC is a deterministic combination technique based on mixed differences of spatial approximations and quadratures over the space of random data. Provided enough mixed regularity, MISC can achieve better complexity than MIMC. Moreover, we show that in the optimal case the convergence rate of MISC is only dictated by the convergence of the deterministic solver applied to a one-dimensional spatial problem. We propose optimization procedures to select the most effective mixed differences to include in MIMC and MISC. Such optimization is a crucial step that allows us to make MIMC and MISC computationally effective. We finally show the effectiveness of MIMC and MISC with some computational tests, including tests with a infinite countable number of random parameters.

Multi-Index Monte Carlo and stochastic collocation methods for random PDEs

KAUST Repository

Nobile, Fabio

2016-01-09

In this talk we consider the problem of computing statistics of the solution of a partial differential equation with random data, where the random coefficient is parametrized by means of a finite or countable sequence of terms in a suitable expansion. We describe and analyze a Multi-Index Monte Carlo (MIMC) and a Multi-Index Stochastic Collocation method (MISC). the former is both a stochastic version of the combination technique introduced by Zenger, Griebel and collaborators and an extension of the Multilevel Monte Carlo (MLMC) method first described by Heinrich and Giles. Instead of using firstorder differences as in MLMC, MIMC uses mixed differences to reduce the variance of the hierarchical differences dramatically. This in turn yields new and improved complexity results, which are natural generalizations of Giles s MLMC analysis, and which increase the domain of problem parameters for which we achieve the optimal convergence, O(TOL-2). On the same vein, MISC is a deterministic combination technique based on mixed differences of spatial approximations and quadratures over the space of random data. Provided enough mixed regularity, MISC can achieve better complexity than MIMC. Moreover, we show that in the optimal case the convergence rate of MISC is only dictated by the convergence of the deterministic solver applied to a one-dimensional spatial problem. We propose optimization procedures to select the most effective mixed differences to include in MIMC and MISC. Such optimization is a crucial step that allows us to make MIMC and MISC computationally effective. We finally show the effectiveness of MIMC and MISC with some computational tests, including tests with a infinite countable number of random parameters.

ENGLISH COLLOCATIONS OF THE VERBS “TO BE”, “TO HAVE” AND “TO TAKE” AND THEIR EQUIVALENTS IN GERMAN, FRENCH AND ITALIAN LANGUAGES: LINGUISTIC–CULTURAL ASPECT

Directory of Open Access Journals (Sweden)

Anna Nikolaevna Panamaryova

2013-10-01

Full Text Available The aim of this research is to find out conceptual characteristics of English, German, French, Italian languages world image. The subject of this paper is English collocations with the verbs “to be”, “to have” and “to take” and their equivalents in German, French and Italian languages. The task of this paper is to compare English collocations of the verbs “to be”, “to have” and “to take” and their equivalents in German, French and Italian languages in linguistic–cultural aspect. In Russian language studies such word groups are called “synlexis”. This term was coined by G. I. Klimovskaya, the professor ofTomskStateUniversity. The main method of the research is a comparative study of linguistic units. The conclusions made in the research are essential in the further study of European linguistic world image and can be used in textbooks on Cultural Linguistics.The practical result of the research can be a cross-cultural collocation dictionary of some languages. Such a dictionary is important for linguists, translators and people studying foreign languages.DOI: http://dx.doi.org/10.12731/2218-7405-2013-8-32

Nested sparse grid collocation method with delay and transformation for subsurface flow and transport problems

Science.gov (United States)

Liao, Qinzhuo; Zhang, Dongxiao; Tchelepi, Hamdi

2017-06-01

In numerical modeling of subsurface flow and transport problems, formation properties may not be deterministically characterized, which leads to uncertainty in simulation results. In this study, we propose a sparse grid collocation method, which adopts nested quadrature rules with delay and transformation to quantify the uncertainty of model solutions. We show that the nested Kronrod-Patterson-Hermite quadrature is more efficient than the unnested Gauss-Hermite quadrature. We compare the convergence rates of various quadrature rules including the domain truncation and domain mapping approaches. To further improve accuracy and efficiency, we present a delayed process in selecting quadrature nodes and a transformed process for approximating unsmooth or discontinuous solutions. The proposed method is tested by an analytical function and in one-dimensional single-phase and two-phase flow problems with different spatial variances and correlation lengths. An additional example is given to demonstrate its applicability to three-dimensional black-oil models. It is found from these examples that the proposed method provides a promising approach for obtaining satisfactory estimation of the solution statistics and is much more efficient than the Monte-Carlo simulations.

A nodal collocation approximation for the multi-dimensional PL equations - 2D applications

International Nuclear Information System (INIS)

Capilla, M.; Talavera, C.F.; Ginestar, D.; Verdu, G.

2008-01-01

A classical approach to solve the neutron transport equation is to apply the spherical harmonics method obtaining a finite approximation known as the P L equations. In this work, the derivation of the P L equations for multi-dimensional geometries is reviewed and a nodal collocation method is developed to discretize these equations on a rectangular mesh based on the expansion of the neutronic fluxes in terms of orthogonal Legendre polynomials. The performance of the method and the dominant transport Lambda Modes are obtained for a homogeneous 2D problem, a heterogeneous 2D anisotropic scattering problem, a heterogeneous 2D problem and a benchmark problem corresponding to a MOX fuel reactor core

An adaptive wavelet stochastic collocation method for irregular solutions of stochastic partial differential equations

Energy Technology Data Exchange (ETDEWEB)

Webster, Clayton G [ORNL; Zhang, Guannan [ORNL; Gunzburger, Max D [ORNL

2012-10-01

Accurate predictive simulations of complex real world applications require numerical approximations to first, oppose the curse of dimensionality and second, converge quickly in the presence of steep gradients, sharp transitions, bifurcations or finite discontinuities in high-dimensional parameter spaces. In this paper we present a novel multi-dimensional multi-resolution adaptive (MdMrA) sparse grid stochastic collocation method, that utilizes hierarchical multiscale piecewise Riesz basis functions constructed from interpolating wavelets. The basis for our non-intrusive method forms a stable multiscale splitting and thus, optimal adaptation is achieved. Error estimates and numerical examples will used to compare the efficiency of the method with several other techniques.

Modelling and Simulation of a Packed Bed of Pulp Fibers Using Mixed Collocation Method

Directory of Open Access Journals (Sweden)

Ishfaq Ahmad Ganaie

2013-01-01

Full Text Available A convenient computational approach for solving mathematical model related to diffusion dispersion during flow through packed bed is presented. The algorithm is based on the mixed collocation method. The method is particularly useful for solving stiff system arising in chemical and process engineering. The convergence of the method is found to be of order 2 using the roots of shifted Chebyshev polynomial. Model is verified using the literature data. This method has provided a convenient check on the accuracy of the results for wide range of parameters, namely, Peclet numbers. Breakthrough curves are plotted to check the effect of Peclet number on average and exit solute concentrations.

Collocated electrodynamic FDTD schemes using overlapping Yee grids and higher-order Hodge duals

Science.gov (United States)

Deimert, C.; Potter, M. E.; Okoniewski, M.

2016-12-01

The collocated Lebedev grid has previously been proposed as an alternative to the Yee grid for electromagnetic finite-difference time-domain (FDTD) simulations. While it performs better in anisotropic media, it performs poorly in isotropic media because it is equivalent to four overlapping, uncoupled Yee grids. We propose to couple the four Yee grids and fix the Lebedev method using discrete exterior calculus (DEC) with higher-order Hodge duals. We find that higher-order Hodge duals do improve the performance of the Lebedev grid, but they also improve the Yee grid by a similar amount. The effectiveness of coupling overlapping Yee grids with a higher-order Hodge dual is thus questionable. However, the theoretical foundations developed to derive these methods may be of interest in other problems.

Collocated Dataglyphs for large-message storage and retrieval

Science.gov (United States)

Motwani, Rakhi C.; Breidenbach, Jeff A.; Black, John R.

2004-06-01

In contrast to the security and integrity of electronic files, printed documents are vulnerable to damage and forgery due to their physical nature. Researchers at Palo Alto Research Center utilize DataGlyph technology to render digital characteristics to printed documents, which provides them with the facility of tamper-proof authentication and damage resistance. This DataGlyph document is known as GlyphSeal. Limited DataGlyph carrying capacity per printed page restricted the application of this technology to a domain of graphically simple and small-sized single-paged documents. In this paper the authors design a protocol motivated by techniques from the networking domain and back-up strategies, which extends the GlyphSeal technology to larger-sized, graphically complex, multi-page documents. This protocol provides fragmentation, sequencing and data loss recovery. The Collocated DataGlyph Protocol renders large glyph messages onto multiple printed pages and recovers the glyph data from rescanned versions of the multi-page documents, even when pages are missing, reordered or damaged. The novelty of this protocol is the application of ideas from RAID to the domain of DataGlyphs. The current revision of this protocol is capable of generating at most 255 pages, if page recovery is desired and does not provide enough data density to store highly detailed images in a reasonable amount of page space.

Application of the orthogonal collocation method to determination of temperature distribution in cylindrical conductors

International Nuclear Information System (INIS)

Fortini, Maria A.; Stamoulis, Michel N.; Ferreira, Angela F.M.; Pereira, Claubia; Costa, Antonella L.; Silva, Clarysson A.M.

2008-01-01

In this work, an analytical model for the determination of the temperature distribution in cylindrical heater components with characteristics of nuclear fuel rods, is presented. The heat conductor is characterized by an arbitrary number of solid walls and different types of materials, whose thermal properties are taken as function of temperature. The heat conduction fundamental equation is solved numerically with the method of weighted residuals (MWR) using a technique of orthogonal collocation. The results obtained with the proposed method are compared with the experimental data from tests performed in the TRIGA IPR-R1 research reactor localized at the CDTN/CNEN (Centro de Desenvolvimento da Tecnologia Nuclear/Comissao Nacional de Energia Nuclear) at Belo Horizonte in Brazil

Demonstration of non-collocated vibration control of a flexible manipulator using electrical dynamic absorbers

International Nuclear Information System (INIS)

Kim, Sang-Myeong; Kim, Heungseob; Boo, Kwangsuck; Brennan, Michael J

2013-01-01

This paper describes an experimental study into the vibration control of a servo system comprising a servo motor and a flexible manipulator. Two modes of the system are controlled by using the servo motor and an accelerometer attached to the tip of the flexible manipulator. The control system is thus non-collocated. It consists of two electrical dynamic absorbers, each of which consists of a modal filter and, in case of an out-of-phase mode, a phase inverter. The experimental results show that each absorber acts as a mechanical dynamic vibration absorber attached to each mode and significantly reduces the settling time for the system response to a step input. (technical note)

The collocated station Košetice - Kešín u Pacova, Czech Republic: an important research infrastructure in central Europe

Science.gov (United States)

Dvorska, Alice; Milan, Váňa; Vlastimil, Hanuš; Marian, Pavelka

2013-04-01

The collocated station Košetice - Křešín u Pacova, central Czech Republic, is a major research and monitoring infrastructure in the Czech Republic and central Europe. It consists of two basic components: the observatory Košetice run since 1988 by the Czech Hydrometeorological Institute and the atmospheric station (AS) Křešín u Pacova starting operation in 2013. The AS is built and run by CzechGlobe - Global Change Research Centre, Academy of Sciences of the Czech Republic and is situated 100 m far from the observatory. There are three research and monitoring activities at the collocated station providing data necessary for the research on climate and related changes. The AS Křešín u Pacova consists of a 250 m tall tower serving for ground-based and vertical gradient measurements of (i) concentrations of CO2, CO, CH4, total gaseous mercury and tropospheric ozone (continuously), (ii) elemental and organic carbon (semicontinuously), (iii) carbon and oxygen isotopes, radon, N2O, SF6 and other species (episodically), (iv) optical properties of atmospheric aerosols and (v) meteorological parameters and the boundary layer height. Further, eddy covariance measurements in the nearby agroecosystem provide data on CO2 and H2O fluxes between the atmosphere and the ecosystem. Finally, monitoring activities at the nearby small hydrological catchment Anenské povodí run under the GEOMON network enables studying local hydrological and biogeochemical cycles. These measurements are supported by the long-term monitoring of meteorological and air quality parameters at the observatory Košetice, that are representative for the central European background. The collocated station provides a big research opportunity and challenge due to (i) a broad spectra of monitored chemical species, meteorological, hydrological and other parameters, (ii) measurements in various environmental compartments and especially the atmosphere, (iii) provision of data suitable for conducting

Hybrid B-Spline Collocation Method for Solving the Generalized Burgers-Fisher and Burgers-Huxley Equations

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Imtiaz Wasim

2018-01-01

Full Text Available In this study, we introduce a new numerical technique for solving nonlinear generalized Burgers-Fisher and Burgers-Huxley equations using hybrid B-spline collocation method. This technique is based on usual finite difference scheme and Crank-Nicolson method which are used to discretize the time derivative and spatial derivatives, respectively. Furthermore, hybrid B-spline function is utilized as interpolating functions in spatial dimension. The scheme is verified unconditionally stable using the Von Neumann (Fourier method. Several test problems are considered to check the accuracy of the proposed scheme. The numerical results are in good agreement with known exact solutions and the existing schemes in literature.

Block preconditioners for linear systems arising from multiscale collocation with compactly supported RBFs

KAUST Repository

Farrell, Patricio

2015-04-30

© 2015John Wiley & Sons, Ltd. Symmetric collocation methods with RBFs allow approximation of the solution of a partial differential equation, even if the right-hand side is only known at scattered data points, without needing to generate a grid. However, the benefit of a guaranteed symmetric positive definite block system comes at a high computational cost. This cost can be alleviated somewhat by considering compactly supported RBFs and a multiscale technique. But the condition number and sparsity will still deteriorate with the number of data points. Therefore, we study certain block diagonal and triangular preconditioners. We investigate ideal preconditioners and determine the spectra of the preconditioned matrices before proposing more practical preconditioners based on a restricted additive Schwarz method with coarse grid correction. Numerical results verify the effectiveness of the preconditioners.

A nodal collocation method for the calculation of the lambda modes of the P L equations

International Nuclear Information System (INIS)

Capilla, M.; Talavera, C.F.; Ginestar, D.; Verdu, G.

2005-01-01

P L equations are classical approximations to the neutron transport equation admitting a diffusive form. Using this property, a nodal collocation method is developed for the P L approximations, which is based on the expansion of the flux in terms of orthonormal Legendre polynomials. This method approximates the differential lambda modes problem by an algebraic eigenvalue problem from which the fundamental and the subcritical modes of the system can be calculated. To test the performance of this method, two problems have been considered, a homogeneous slab, which admits an analytical solution, and a seven-region slab corresponding to a more realistic problem

A bivariate Chebyshev spectral collocation quasilinearization method for nonlinear evolution parabolic equations.

Science.gov (United States)

Motsa, S S; Magagula, V M; Sibanda, P

2014-01-01

This paper presents a new method for solving higher order nonlinear evolution partial differential equations (NPDEs). The method combines quasilinearisation, the Chebyshev spectral collocation method, and bivariate Lagrange interpolation. In this paper, we use the method to solve several nonlinear evolution equations, such as the modified KdV-Burgers equation, highly nonlinear modified KdV equation, Fisher's equation, Burgers-Fisher equation, Burgers-Huxley equation, and the Fitzhugh-Nagumo equation. The results are compared with known exact analytical solutions from literature to confirm accuracy, convergence, and effectiveness of the method. There is congruence between the numerical results and the exact solutions to a high order of accuracy. Tables were generated to present the order of accuracy of the method; convergence graphs to verify convergence of the method and error graphs are presented to show the excellent agreement between the results from this study and the known results from literature.

A Bivariate Chebyshev Spectral Collocation Quasilinearization Method for Nonlinear Evolution Parabolic Equations

Directory of Open Access Journals (Sweden)

S. S. Motsa

2014-01-01

Full Text Available This paper presents a new method for solving higher order nonlinear evolution partial differential equations (NPDEs. The method combines quasilinearisation, the Chebyshev spectral collocation method, and bivariate Lagrange interpolation. In this paper, we use the method to solve several nonlinear evolution equations, such as the modified KdV-Burgers equation, highly nonlinear modified KdV equation, Fisher's equation, Burgers-Fisher equation, Burgers-Huxley equation, and the Fitzhugh-Nagumo equation. The results are compared with known exact analytical solutions from literature to confirm accuracy, convergence, and effectiveness of the method. There is congruence between the numerical results and the exact solutions to a high order of accuracy. Tables were generated to present the order of accuracy of the method; convergence graphs to verify convergence of the method and error graphs are presented to show the excellent agreement between the results from this study and the known results from literature.

Adaptive collocation method for simultaneous heat and mass diffusion with phase change

International Nuclear Information System (INIS)

Chawla, T.C.; Leaf, G.; Minkowycz, W.J.; Pedersen, D.R.; Shouman, A.R.

1983-01-01

The present study is carried out to determine melting rates of a lead slab of various thicknesses by contact with sodium coolant and to evaluate the extent of penetration and the mixing rates of molten lead into liquid sodium by molecular diffusion alone. The study shows that these two calculations cannot be performed simultaneously without the use of adaptive coordinates which cause considerable stretching of the physical coordinates for mass diffusion. Because of the large difference in densities of these two liquid metals, the traditional constant density approximation for the calculation of mass diffusion cannot be used for studying their interdiffusion. The use of orthogonal collocation method along with adaptive coordinates produces extremely accurate results which are ascertained by comparing with the existing analytical solutions for concentration distribution for the case of constant density approximation and for melting rates for the case of infinite lead slab

Evaluating the performance of collocated optical disdrometers: LPM and PARSIVEL

Science.gov (United States)

Angulo-Martinez, Marta; Begueria, Santiago; Latorre, Borja

2017-04-01

Optical disdrometers are present weather sensors with the ability of providing integrate information of precipitation like intensity and reflectivity together with discrete information of drop sizes and velocities distribution (DSVD) of the hydrometeors crossing the laser beam sampling area. These sensors constitute a step forward in comparison with pluviometers towards a more complete characterisation of precipitation. Their use is spreading in many research fields for several applications. Understanding the differences from one another helps in the election of the sensor and point out limitations to be fixed in future versions. Four collocated optical disdrometers, two Laser Precipitation Monitors (LPM-Thies Clima) and two PARSIVEL, 1-minute measurements of 800 natural rainfall events were compared. Results showed a general agreement in integrated variables, like intensity or liquid water content. Nevertheless, comparing raw data, as the number of particles and DSVD, great differences were found. LPM generally measures more and smaller drops than PARSIVEL and this difference increases with rainfall intensity. These results may affect especially the reflectivity value every disdrometer provide. A complete description of the measurements obtained, quantifiying the differences is provided, indicating their possible sources.

Between initial familiarity and future use – a case of Collocated Collaborative Writing

DEFF Research Database (Denmark)

Bødker, Susanne; Polli, Anna Maria

2014-01-01

these with the three above forms of practice. The initial familiarity leads to two different early practices that get in the way of each other, and the collaborative writing idea. They point instead towards a discursive sharing of individual feelings, a different kind of past experiences than anticipated in design.......This paper reports on a design experiment in an art gallery, where we explored visitor practices of commenting on art, and how they were shaped in interaction with a newly designed collocated, collaborative writing technology. In particular we investigate what potentials previous practices carry...... with them that may affect early use and further development of use. We base our analyses on interviews in the art gallery and on socio-cultural theories of artefactmediated learning and collaboration. The analyses help identify three forms of collaborative writing, which are placed in the space between...

Non-stationary covariance function modelling in 2D least-squares collocation

Science.gov (United States)

Darbeheshti, N.; Featherstone, W. E.

2009-06-01

Standard least-squares collocation (LSC) assumes 2D stationarity and 3D isotropy, and relies on a covariance function to account for spatial dependence in the observed data. However, the assumption that the spatial dependence is constant throughout the region of interest may sometimes be violated. Assuming a stationary covariance structure can result in over-smoothing of, e.g., the gravity field in mountains and under-smoothing in great plains. We introduce the kernel convolution method from spatial statistics for non-stationary covariance structures, and demonstrate its advantage for dealing with non-stationarity in geodetic data. We then compared stationary and non- stationary covariance functions in 2D LSC to the empirical example of gravity anomaly interpolation near the Darling Fault, Western Australia, where the field is anisotropic and non-stationary. The results with non-stationary covariance functions are better than standard LSC in terms of formal errors and cross-validation against data not used in the interpolation, demonstrating that the use of non-stationary covariance functions can improve upon standard (stationary) LSC.

Parallel iterative solution of the Hermite Collocation equations on GPUs II

International Nuclear Information System (INIS)

Vilanakis, N; Mathioudakis, E

2014-01-01

Hermite Collocation is a high order finite element method for Boundary Value Problems modelling applications in several fields of science and engineering. Application of this integration free numerical solver for the solution of linear BVPs results in a large and sparse general system of algebraic equations, suggesting the usage of an efficient iterative solver especially for realistic simulations. In part I of this work an efficient parallel algorithm of the Schur complement method coupled with Bi-Conjugate Gradient Stabilized (BiCGSTAB) iterative solver has been designed for multicore computing architectures with a Graphics Processing Unit (GPU). In the present work the proposed algorithm has been extended for high performance computing environments consisting of multiprocessor machines with multiple GPUs. Since this is a distributed GPU and shared CPU memory parallel architecture, a hybrid memory treatment is needed for the development of the parallel algorithm. The realization of the algorithm took place on a multiprocessor machine HP SL390 with Tesla M2070 GPUs using the OpenMP and OpenACC standards. Execution time measurements reveal the efficiency of the parallel implementation

An analytical investigation on unsteady motion of vertically falling spherical particles in non-Newtonian fluid by Collocation Method

Directory of Open Access Journals (Sweden)

M. Rahimi-Gorji

2015-06-01

Full Text Available An analytical investigation is applied for unsteady motion of a rigid spherical particle in a quiescent shear-thinning power-law fluid. The results were compared with those obtained from Collocation Method (CM and the established Numerical Method (Fourth order Runge–Kutta scheme. It was shown that CM gave accurate results. Collocation Method (CM and Numerical Method are used to solve the present problem. We obtained that the CM which was used to solve such nonlinear differential equation with fractional power is simpler and more accurate than series method such as HPM which was used in some previous works by others but the new method named Akbari-Ganji’s Method (AGM is an accurate and simple method which is slower than CM for solving such problems. The terminal settling velocity—that is the velocity at which the net forces on a falling particle eliminate—for three different spherical particles (made of plastic, glass and steel and three flow behavior index n, in three sets of power-law non-Newtonian fluids was investigated, based on polynomial solution (CM. Analytical results obtained indicated that the time of reaching the terminal velocity in a falling procedure is significantly increased with growing of the particle size that validated with Numerical Method. Further, with approaching flow behavior to Newtonian behavior from shear-thinning properties of flow (n → 1, the transient time to achieving the terminal settling velocity is decreased.

An efficient approach to numerical study of the coupled-BBM system with B-spline collocation method

Directory of Open Access Journals (Sweden)

khalid ali

2016-11-01

Full Text Available In the present paper, a numerical method is proposed for the numerical solution of a coupled-BBM system with appropriate initial and boundary conditions by using collocation method with cubic trigonometric B-spline on the uniform mesh points. The method is shown to be unconditionally stable using von-Neumann technique. To test accuracy the error norms2L, ?L are computed. Furthermore, interaction of two and three solitary waves are used to discuss the effect of the behavior of the solitary waves after the interaction. These results show that the technique introduced here is easy to apply. We make linearization for the nonlinear term.

Finite Volume Methods for Incompressible Navier-Stokes Equations on Collocated Grids with Nonconformal Interfaces

DEFF Research Database (Denmark)

Kolmogorov, Dmitry

turbine computations, collocated grid-based SIMPLE-like algorithms are developed for computations on block-structured grids with nonconformal interfaces. A technique to enhance both the convergence speed and the solution accuracy of the SIMPLE-like algorithms is presented. The erroneous behavior, which...... versions of the SIMPLE algorithm. The new technique is implemented in an existing conservative 2nd order finite-volume scheme flow solver (EllipSys), which is extended to cope with grids with nonconformal interfaces. The behavior of the discrete Navier-Stokes equations is discussed in detail...... Block LU relaxation scheme is shown to possess several optimal conditions, which enables to preserve high efficiency of the multigrid solver on both conformal and nonconformal grids. The developments are done using a parallel MPI algorithm, which can handle multiple numbers of interfaces with multiple...

A Fourier Collocation Approach for Transit-Time Ultrasonic Flowmeter Under Multi-Phase Flow Conditions

DEFF Research Database (Denmark)

Simurda, Matej; Lassen, Benny; Duggen, Lars

2017-01-01

A numerical model for a clamp-on transit-time ultrasonic flowmeter (TTUF) under multi-phase flow conditions is presented. The method solves equations of linear elasticity for isotropic heterogeneous materials with background flow where acoustic media are modeled by setting shear modulus to zero....... Spatial derivatives are calculated by a Fourier collocation method allowing the use of the fast Fourier transform (FFT) and time derivatives are approximated by a finite difference (FD) scheme. This approach is sometimes referred to as a pseudospectral time-domain method. Perfectly matched layers (PML......) are used to avoid wave-wrapping and staggered grids are implemented to improve stability and efficiency. The method is verified against exact analytical solutions and the effect of the time-staggering and associated lowest number of points per minimum wavelengths value is discussed. The method...

An Analysis of Peak Wind Speed Data from Collocated Mechanical and Ultrasonic Anemometers

Science.gov (United States)

Short, David A.; Wells, Leonard; Merceret, Francis J.; Roeder, William P.

2007-01-01

This study compared peak wind speeds reported by mechanical and ultrasonic anemometers at Cape Canaveral Air Force Station and Kennedy Space Center (CCAFS/KSC) on the east central coast of Florida and Vandenberg Air Force Base (VAFB) on the central coast of California. Launch Weather Officers, forecasters, and Range Safety analysts need to understand the performance of wind sensors at CCAFS/KSC and VAFB for weather warnings, watches, advisories, special ground processing operations, launch pad exposure forecasts, user Launch Commit Criteria (LCC) forecasts and evaluations, and toxic dispersion support. The legacy CCAFS/KSC and VAFB weather tower wind instruments are being changed from propeller-and-vane (CCAFS/KSC) and cup-and-vane (VAFB) sensors to ultrasonic sensors under the Range Standardization and Automation (RSA) program. Mechanical and ultrasonic wind measuring techniques are known to cause differences in the statistics of peak wind speed as shown in previous studies. The 45th Weather Squadron (45 WS) and the 30th Weather Squadron (30 WS) requested the Applied Meteorology Unit (AMU) to compare data between the RSA ultrasonic and legacy mechanical sensors to determine if there are significant differences. Note that the instruments were sited outdoors under naturally varying conditions and that this comparison was not designed to verify either technology. Approximately 3 weeks of mechanical and ultrasonic wind data from each range from May and June 2005 were used in this study. The CCAFS/KSC data spanned the full diurnal cycle, while the VAFB data were confined to 1000-1600 local time. The sample of 1-minute data from numerous levels on five different towers on each range totaled more than 500,000 minutes of data (482,979 minutes of data after quality control). The ten towers were instrumented at several levels, ranging from 12 ft to 492 ft above ground level. The ultrasonic sensors were collocated at the same vertical levels as the mechanical sensors and

Continuous Groundwater Monitoring Collocated at USGS Streamgages

Science.gov (United States)

Constantz, J. E.; Eddy-Miller, C.; Caldwell, R.; Wheeer, J.; Barlow, J.

2012-12-01

USGS Office of Groundwater funded a 2-year pilot study collocating groundwater wells for monitoring water level and temperature at several existing continuous streamgages in Montana and Wyoming, while U.S. Army Corps of Engineers funded enhancement to streamgages in Mississippi. To increase spatial relevance with in a given watershed, study sites were selected where near-stream groundwater was in connection with an appreciable aquifer, and where logistics and cost of well installations were considered representative. After each well installation and surveying, groundwater level and temperature were easily either radio-transmitted or hardwired to existing data acquisition system located in streamgaging shelter. Since USGS field personnel regularly visit streamgages during routine streamflow measurements and streamgage maintenance, the close proximity of observation wells resulted in minimum extra time to verify electronically transmitted measurements. After field protocol was tuned, stream and nearby groundwater information were concurrently acquired at streamgages and transmitted to satellite from seven pilot-study sites extending over nearly 2,000 miles (3,200 km) of the central US from October 2009 until October 2011, for evaluating the scientific and engineering add-on value of the enhanced streamgage design. Examination of the four-parameter transmission from the seven pilot study groundwater gaging stations reveals an internally consistent, dynamic data suite of continuous groundwater elevation and temperature in tandem with ongoing stream stage and temperature data. Qualitatively, the graphical information provides appreciation of seasonal trends in stream exchanges with shallow groundwater, as well as thermal issues of concern for topics ranging from ice hazards to suitability of fish refusia, while quantitatively this information provides a means for estimating flux exchanges through the streambed via heat-based inverse-type groundwater modeling. In June

Underground collocation of nuclear power plant reactors and repository to facilitate the post-renaissance expansion of nuclear power

Energy Technology Data Exchange (ETDEWEB)

Myers, Carl W [Los Alamos National Laboratory; Elkins, Ned Z [Los Alamos National Laboratory

2008-01-01

Underground collocation of nuclear power reactors and the nuclear waste management facilities supporting those reactors, termed an underground nuclear park (UNP), appears to have several advantages compared to the conventional approach to siting reactors and waste management facilities. These advantages include the potential to lower reactor capital and operating cost, lower nuclear waste management cost, and increase margins of physical security and safety. Envirorunental impacts related to worker health, facility accidents, waste transportation, and sabotage and terrorism appear to be lower for UNPs compared to the current approach. In-place decommissioning ofUNP reactors appears to have cost, safety, envirorunental and waste disposal advantages. The UNP approach has the potential to lead to greater public acceptance for the deployment of new power reactors. Use of the UNP during the post-nuclear renaissance time frame has the potential to enable a greater expansion of U.S. nuclear power generation than might otherwise result. Technical and economic aspects of the UNP concept need more study to determine the viability of the concept.

FRBRization of a Library Catalog: Better Collocation of Records, Leading to Enhanced Search, Retrieval, and Display

Directory of Open Access Journals (Sweden)

Timothy J. Dickey

2008-03-01

Full Text Available The Functional Requirements for Bibliographic Records (FRBR’s hierarchical system defines families of bibliographic relationship between records and collocates them better than most extant bibliographic systems. Certain library materials (especially audio-visual formats pose notable challenges to search and retrieval; the first benefits of a FRBRized system would be felt in music libraries, but research already has proven its advantages for fine arts, theology, and literature—the bulk of the non-science, technology, and mathematics collections. This report will summarize the benefits of FRBR to nextgeneration library catalogs and OPACs, and will review the handful of ILS and catalog systems currently operating with its theoretical structure.

Radiation budget studies using collocated observations from advanced Very High Resolution Radiometer, High-Resolution Infrared Sounder/2, and Earth Radiation Budget Experiment instruments

Science.gov (United States)

Ackerman, Steven A.; Frey, Richard A.; Smith, William L.

1992-01-01

Collocated observations from the Advanced Very High Resolution Radiometer (AVHRR), High-Resolution Infrared Sounder/2 (HIRS/2), and Earth Radiation Budget Experiment (ERBE) instruments onboard the NOAA 9 satellite are combined to describe the broadband and spectral radiative properties of the earth-atmosphere system. Broadband radiative properties are determined from the ERBE observations, while spectral properties are determined from the HIRS/2 and AVHRR observations. The presence of clouds, their areal coverage, and cloud top pressure are determined from a combination of the HIRS/2 and the AVHRR observations. The CO2 slicing method is applied to the HIRS/2 to determine the presence of upper level clouds and their effective emissivity. The AVHRR data collocated within the HIRS/2 field of view are utilized to determine the uniformity of the scene and retrieve sea surface temperature. Changes in the top of the atmosphere longwave and shortwave radiative energy budgets, and the spectral distribution of longwave radiation are presented as a function of cloud amount and cloud top pressure. The radiative characteristics of clear sky conditions over oceans are presented as a function of sea surface temperature and atmospheric water vapor structure.

Determination of processed animal proteins, including meat and bone meal, in animal feed

NARCIS (Netherlands)

Gizzi, G.; Holst, von C.; Baeten, V.; Berben, G.; Raamsdonk, van L.W.D.

2004-01-01

The presence of processed animal proteins (PAP), including meat and bone meal (MBM) from various species, in animal feed was investigated. It was demonstrated that microscopy is the most reliable method for enforcing the current total MBM ban in the European Uion (EU). It was shown that near

Feedback control of acoustic musical instruments: collocated control using physical analogs.

Science.gov (United States)

Berdahl, Edgar; Smith, Julius O; Niemeyer, Günter

2012-01-01

Traditionally, the average professional musician has owned numerous acoustic musical instruments, many of them having distinctive acoustic qualities. However, a modern musician could prefer to have a single musical instrument whose acoustics are programmable by feedback control, where acoustic variables are estimated from sensor measurements in real time and then fed back in order to influence the controlled variables. In this paper, theory is presented that describes stable feedback control of an acoustic musical instrument. The presentation should be accessible to members of the musical acoustics community who may have limited or no experience with feedback control. First, the only control strategy guaranteed to be stable subject to any musical instrument mobility is described: the sensors and actuators must be collocated, and the controller must emulate a physical analog system. Next, the most fundamental feedback controllers and the corresponding physical analog systems are presented. The effects that these controllers have on acoustic musical instruments are described. Finally, practical design challenges are discussed. A proof explains why changing the resonance frequency of a musical resonance requires much more control power than changing the decay time of the resonance. © 2012 Acoustical Society of America.

Multi-index Stochastic Collocation Convergence Rates for Random PDEs with Parametric Regularity

KAUST Repository

Haji Ali, Abdul Lateef; Nobile, Fabio; Tamellini, Lorenzo; Tempone, Raul

2016-01-01

We analyze the recent Multi-index Stochastic Collocation (MISC) method for computing statistics of the solution of a partial differential equation (PDE) with random data, where the random coefficient is parametrized by means of a countable sequence of terms in a suitable expansion. MISC is a combination technique based on mixed differences of spatial approximations and quadratures over the space of random data, and naturally, the error analysis uses the joint regularity of the solution with respect to both the variables in the physical domain and parametric variables. In MISC, the number of problem solutions performed at each discretization level is not determined by balancing the spatial and stochastic components of the error, but rather by suitably extending the knapsack-problem approach employed in the construction of the quasi-optimal sparse-grids and Multi-index Monte Carlo methods, i.e., we use a greedy optimization procedure to select the most effective mixed differences to include in the MISC estimator. We apply our theoretical estimates to a linear elliptic PDE in which the log-diffusion coefficient is modeled as a random field, with a covariance similar to a Matérn model, whose realizations have spatial regularity determined by a scalar parameter. We conduct a complexity analysis based on a summability argument showing algebraic rates of convergence with respect to the overall computational work. The rate of convergence depends on the smoothness parameter, the physical dimensionality and the efficiency of the linear solver. Numerical experiments show the effectiveness of MISC in this infinite dimensional setting compared with the Multi-index Monte Carlo method and compare the convergence rate against the rates predicted in our theoretical analysis. © 2016 SFoCM

Multi-index Stochastic Collocation Convergence Rates for Random PDEs with Parametric Regularity

KAUST Repository

Haji Ali, Abdul Lateef

2016-08-26

We analyze the recent Multi-index Stochastic Collocation (MISC) method for computing statistics of the solution of a partial differential equation (PDE) with random data, where the random coefficient is parametrized by means of a countable sequence of terms in a suitable expansion. MISC is a combination technique based on mixed differences of spatial approximations and quadratures over the space of random data, and naturally, the error analysis uses the joint regularity of the solution with respect to both the variables in the physical domain and parametric variables. In MISC, the number of problem solutions performed at each discretization level is not determined by balancing the spatial and stochastic components of the error, but rather by suitably extending the knapsack-problem approach employed in the construction of the quasi-optimal sparse-grids and Multi-index Monte Carlo methods, i.e., we use a greedy optimization procedure to select the most effective mixed differences to include in the MISC estimator. We apply our theoretical estimates to a linear elliptic PDE in which the log-diffusion coefficient is modeled as a random field, with a covariance similar to a Matérn model, whose realizations have spatial regularity determined by a scalar parameter. We conduct a complexity analysis based on a summability argument showing algebraic rates of convergence with respect to the overall computational work. The rate of convergence depends on the smoothness parameter, the physical dimensionality and the efficiency of the linear solver. Numerical experiments show the effectiveness of MISC in this infinite dimensional setting compared with the Multi-index Monte Carlo method and compare the convergence rate against the rates predicted in our theoretical analysis. © 2016 SFoCM

A method for stochastic constrained optimization using derivative-free surrogate pattern search and collocation

International Nuclear Information System (INIS)

Sankaran, Sethuraman; Audet, Charles; Marsden, Alison L.

2010-01-01

Recent advances in coupling novel optimization methods to large-scale computing problems have opened the door to tackling a diverse set of physically realistic engineering design problems. A large computational overhead is associated with computing the cost function for most practical problems involving complex physical phenomena. Such problems are also plagued with uncertainties in a diverse set of parameters. We present a novel stochastic derivative-free optimization approach for tackling such problems. Our method extends the previously developed surrogate management framework (SMF) to allow for uncertainties in both simulation parameters and design variables. The stochastic collocation scheme is employed for stochastic variables whereas Kriging based surrogate functions are employed for the cost function. This approach is tested on four numerical optimization problems and is shown to have significant improvement in efficiency over traditional Monte-Carlo schemes. Problems with multiple probabilistic constraints are also discussed.

A Protein Diet Score, Including Plant and Animal Protein, Investigating the Association with HbA1c and eGFR—The PREVIEW Project

Science.gov (United States)

Mikkilä, Vera; Raitakari, Olli T.; Hutri-Kähönen, Nina; Dragsted, Lars O.; Poppitt, Sally D.; Silvestre, Marta P.; Feskens, Edith J.M.

2017-01-01

Higher-protein diets have been advocated for body-weight regulation for the past few decades. However, the potential health risks of these diets are still uncertain. We aimed to develop a protein score based on the quantity and source of protein, and to examine the association of the score with glycated haemoglobin (HbA1c) and estimated glomerular filtration rate (eGFR). Analyses were based on three population studies included in the PREVIEW project (PREVention of diabetes through lifestyle Intervention and population studies in Europe and around the World): NQplus, Lifelines, and the Young Finns Study. Cross-sectional data from food-frequency questionnaires (n = 76,777 subjects) were used to develop a protein score consisting of two components: 1) percentage of energy from total protein, and 2) plant to animal protein ratio. An inverse association between protein score and HbA1c (slope −0.02 ± 0.01 mmol/mol, p < 0.001) was seen in Lifelines. We found a positive association between the protein score and eGFR in Lifelines (slope 0.17 ± 0.02 mL/min/1.73 m2, p < 0.0001). Protein scoring might be a useful tool to assess both the effect of quantity and source of protein on health parameters. Further studies are needed to validate this newly developed protein score. PMID:28714926

Fourier Collocation Approach With Mesh Refinement Method for Simulating Transit-Time Ultrasonic Flowmeters Under Multiphase Flow Conditions.

Science.gov (United States)

Simurda, Matej; Duggen, Lars; Basse, Nils T; Lassen, Benny

2018-02-01

A numerical model for transit-time ultrasonic flowmeters operating under multiphase flow conditions previously presented by us is extended by mesh refinement and grid point redistribution. The method solves modified first-order stress-velocity equations of elastodynamics with additional terms to account for the effect of the background flow. Spatial derivatives are calculated by a Fourier collocation scheme allowing the use of the fast Fourier transform, while the time integration is realized by the explicit third-order Runge-Kutta finite-difference scheme. The method is compared against analytical solutions and experimental measurements to verify the benefit of using mapped grids. Additionally, a study of clamp-on and in-line ultrasonic flowmeters operating under multiphase flow conditions is carried out.

Evolutionary optimization with data collocation for reverse engineering of biological networks.

Science.gov (United States)

Tsai, Kuan-Yao; Wang, Feng-Sheng

2005-04-01

Modern experimental biology is moving away from analyses of single elements to whole-organism measurements. Such measured time-course data contain a wealth of information about the structure and dynamic of the pathway or network. The dynamic modeling of the whole systems is formulated as a reverse problem that requires a well-suited mathematical model and a very efficient computational method to identify the model structure and parameters. Numerical integration for differential equations and finding global parameter values are still two major challenges in this field of the parameter estimation of nonlinear dynamic biological systems. We compare three techniques of parameter estimation for nonlinear dynamic biological systems. In the proposed scheme, the modified collocation method is applied to convert the differential equations to the system of algebraic equations. The observed time-course data are then substituted into the algebraic system equations to decouple system interactions in order to obtain the approximate model profiles. Hybrid differential evolution (HDE) with population size of five is able to find a global solution. The method is not only suited for parameter estimation but also can be applied for structure identification. The solution obtained by HDE is then used as the starting point for a local search method to yield the refined estimates.

Study of Anti-Fatigue Effect in Rats of Ferrous Chelates Including Hairtail Protein Hydrolysates

Directory of Open Access Journals (Sweden)

Saibo Huang

2015-12-01

Full Text Available The ability of ferrous chelates including hairtail protein hydrolysates to prevent and reduce fatigue was studied in rats. After hydrolysis of hairtail surimi with papain, the hairtail protein hydrolysates (HPH were separated into three groups by range of relative molecular weight using ultrafiltration membrane separation. Hairtail proteins were then chelated with ferrous ions, and the antioxidant activity, the amino acid composition and chelation rate of the three kinds of ferrous chelates including hairtail protein hydrolysates (Fe-HPH were determined. Among the three groups, the Fe-HPH chelate showing the best conditions was selected for the anti-fatigue animal experiment. For it, experimental rats were randomly divided into seven groups. Group A was designated as the negative control group given distilled water. Group B, the positive control group, was given glutathione. Groups C, D and E were designated as the Fe-HPH chelate treatment groups and given low, medium, and high doses, respectively. Group F was designated as HPH hydrolysate treatment group, and Group G was designated as FeCl2 treatment group. The different diets were orally administered to rats for 20 days. After that time, rats were subjected to forced swimming training after 1 h of gavage. Rats given Fe-FPH chelate had higher haemoglobin regeneration efficiency (HRE, longer exhaustive swimming time and higher SOD activity. Additionally, Fe-FPH chelate was found to significantly decrease the malondialdehyde content, visibly enhance the GSH-Px activity in liver and reduce blood lactic acid of rats. Fe-HPH chelate revealed an anti-fatigue effect, similar to or better than the positive control substance and superior to HPH or Fe when provided alone.

On the optimal polynomial approximation of stochastic PDEs by galerkin and collocation methods

KAUST Repository

Beck, Joakim; Tempone, Raul; Nobile, Fabio; Tamellini, Lorenzo

2012-01-01

In this work we focus on the numerical approximation of the solution u of a linear elliptic PDE with stochastic coefficients. The problem is rewritten as a parametric PDE and the functional dependence of the solution on the parameters is approximated by multivariate polynomials. We first consider the stochastic Galerkin method, and rely on sharp estimates for the decay of the Fourier coefficients of the spectral expansion of u on an orthogonal polynomial basis to build a sequence of polynomial subspaces that features better convergence properties, in terms of error versus number of degrees of freedom, than standard choices such as Total Degree or Tensor Product subspaces. We consider then the Stochastic Collocation method, and use the previous estimates to introduce a new class of Sparse Grids, based on the idea of selecting a priori the most profitable hierarchical surpluses, that, again, features better convergence properties compared to standard Smolyak or tensor product grids. Numerical results show the effectiveness of the newly introduced polynomial spaces and sparse grids. © 2012 World Scientific Publishing Company.

A Least Squares Collocation Method for Accuracy Improvement of Mobile LiDAR Systems

Directory of Open Access Journals (Sweden)

Qingzhou Mao

2015-06-01

Full Text Available In environments that are hostile to Global Navigation Satellites Systems (GNSS, the precision achieved by a mobile light detection and ranging (LiDAR system (MLS can deteriorate into the sub-meter or even the meter range due to errors in the positioning and orientation system (POS. This paper proposes a novel least squares collocation (LSC-based method to improve the accuracy of the MLS in these hostile environments. Through a thorough consideration of the characteristics of POS errors, the proposed LSC-based method effectively corrects these errors using LiDAR control points, thereby improving the accuracy of the MLS. This method is also applied to the calibration of misalignment between the laser scanner and the POS. Several datasets from different scenarios have been adopted in order to evaluate the effectiveness of the proposed method. The results from experiments indicate that this method would represent a significant improvement in terms of the accuracy of the MLS in environments that are essentially hostile to GNSS and is also effective regarding the calibration of misalignment.

On the optimal polynomial approximation of stochastic PDEs by galerkin and collocation methods

KAUST Repository

Beck, Joakim

2012-09-01

In this work we focus on the numerical approximation of the solution u of a linear elliptic PDE with stochastic coefficients. The problem is rewritten as a parametric PDE and the functional dependence of the solution on the parameters is approximated by multivariate polynomials. We first consider the stochastic Galerkin method, and rely on sharp estimates for the decay of the Fourier coefficients of the spectral expansion of u on an orthogonal polynomial basis to build a sequence of polynomial subspaces that features better convergence properties, in terms of error versus number of degrees of freedom, than standard choices such as Total Degree or Tensor Product subspaces. We consider then the Stochastic Collocation method, and use the previous estimates to introduce a new class of Sparse Grids, based on the idea of selecting a priori the most profitable hierarchical surpluses, that, again, features better convergence properties compared to standard Smolyak or tensor product grids. Numerical results show the effectiveness of the newly introduced polynomial spaces and sparse grids. © 2012 World Scientific Publishing Company.

A Simple Time Domain Collocation Method to Precisely Search for the Periodic Orbits of Satellite Relative Motion

Directory of Open Access Journals (Sweden)

Xiaokui Yue

2014-01-01

Full Text Available A numerical approach for obtaining periodic orbits of satellite relative motion is proposed, based on using the time domain collocation (TDC method to search for the periodic solutions of an exact J2 nonlinear relative model. The initial conditions for periodic relative orbits of the Clohessy-Wiltshire (C-W equations or Tschauner-Hempel (T-H equations can be refined with this approach to generate nearly bounded orbits. With these orbits, a method based on the least-squares principle is then proposed to generate projected closed orbit (PCO, which is a reference for the relative motion control. Numerical simulations reveal that the presented TDC searching scheme is effective and simple, and the projected closed orbit is very fuel saving.

Vs30 and spectral response from collocated shallow, active- and passive-source Vs data at 27 sites in Puerto Rico

Science.gov (United States)

Odum, Jack K.; Stephenson, William J.; Williams, Robert A.; von Hillebrandt-Andrade, Christa

2013-01-01

Shear‐wave velocity (VS) and time‐averaged shear‐wave velocity to 30 m depth (VS30) are the key parameters used in seismic site response modeling and earthquake engineering design. Where VS data are limited, available data are often used to develop and refine map‐based proxy models of VS30 for predicting ground‐motion intensities. In this paper, we present shallow VS data from 27 sites in Puerto Rico. These data were acquired using a multimethod acquisition approach consisting of noninvasive, collocated, active‐source body‐wave (refraction/reflection), active‐source surface wave at nine sites, and passive‐source surface‐wave refraction microtremor (ReMi) techniques. VS‐versus‐depth models are constructed and used to calculate spectral response plots for each site. Factors affecting method reliability are analyzed with respect to site‐specific differences in bedrock VS and spectral response. At many but not all sites, body‐ and surface‐wave methods generally determine similar depths to bedrock, and it is the difference in bedrock VS that influences site amplification. The predicted resonant frequencies for the majority of the sites are observed to be within a relatively narrow bandwidth of 1–3.5 Hz. For a first‐order comparison of peak frequency position, predictive spectral response plots from eight sites are plotted along with seismograph instrument spectra derived from the time series of the 16 May 2010 Puerto Rico earthquake. We show how a multimethod acquisition approach using collocated arrays compliments and corroborates VS results, thus adding confidence that reliable site characterization information has been obtained.

Proteomic identification of Drosophila melanogaster male accessory gland proteins, including a pro-cathepsin and a soluble γ-glutamyl transpeptidase

Directory of Open Access Journals (Sweden)

Sajid Mohammed

2006-05-01

Full Text Available Background In Drosophila melanogaster, the male seminal fluid contains proteins that are important for reproductive success. Many of these proteins are synthesised by the male accessory glands and are secreted into the accessory gland lumen, where they are stored until required. Previous studies on the identification of Drosophila accessory gland products have largely focused on characterisation of male-specific accessory gland cDNAs from D. melanogaster and, more recently, Drosophila simulans. In the present study, we have used a proteomics approach without any sex bias to identify proteins in D. melanogaster accessory gland secretions. Results Thirteen secreted accessory gland proteins, including seven new accessory gland proteins, were identified by 2D-gel electrophoresis combined with mass spectrometry of tryptic fragments. They included protein-folding and stress-response proteins, a hormone, a lipase, a serpin, a cysteine-rich protein and two peptidases, a pro-enzyme form of a cathepsin K-like cysteine peptidase and a γ-glutamyl transpeptidase. Enzymatic studies established that accessory gland secretions contain a cysteine peptidase zymogen that can be activated at low pH. This peptidase may have a role in the processing of female and other male-derived proteins, but is unlikely to be involved in the processing of the sex peptide. γ-Glutamyl transpeptidases are type II integral membrane proteins; however, the identified AG γ-glutamyl transpeptidase (GGT-1 is unusual in that it is predicted to be a soluble secreted protein, a prediction that is supported by biochemical evidence. GGT-1 is possibly involved in maintaining a protective redox environment for sperm. The strong γ-glutamyl transpeptidase activity found in the secretions provides an explanation for the observation that glutamic acid is the most abundant free amino acid in accessory gland secretions of D. melanogaster. Conclusion We have applied biochemical approaches, not used

Proteomic identification of Drosophila melanogaster male accessory gland proteins, including a pro-cathepsin and a soluble gamma-glutamyl transpeptidase.

Science.gov (United States)

Walker, Michael J; Rylett, Caroline M; Keen, Jeff N; Audsley, Neil; Sajid, Mohammed; Shirras, Alan D; Isaac, R Elwyn

2006-05-02

In Drosophila melanogaster, the male seminal fluid contains proteins that are important for reproductive success. Many of these proteins are synthesised by the male accessory glands and are secreted into the accessory gland lumen, where they are stored until required. Previous studies on the identification of Drosophila accessory gland products have largely focused on characterisation of male-specific accessory gland cDNAs from D. melanogaster and, more recently, Drosophila simulans. In the present study, we have used a proteomics approach without any sex bias to identify proteins in D. melanogaster accessory gland secretions. Thirteen secreted accessory gland proteins, including seven new accessory gland proteins, were identified by 2D-gel electrophoresis combined with mass spectrometry of tryptic fragments. They included protein-folding and stress-response proteins, a hormone, a lipase, a serpin, a cysteine-rich protein and two peptidases, a pro-enzyme form of a cathepsin K-like cysteine peptidase and a gamma-glutamyl transpeptidase. Enzymatic studies established that accessory gland secretions contain a cysteine peptidase zymogen that can be activated at low pH. This peptidase may have a role in the processing of female and other male-derived proteins, but is unlikely to be involved in the processing of the sex peptide. gamma-Glutamyl transpeptidases are type II integral membrane proteins; however, the identified AG gamma-glutamyl transpeptidase (GGT-1) is unusual in that it is predicted to be a soluble secreted protein, a prediction that is supported by biochemical evidence. GGT-1 is possibly involved in maintaining a protective redox environment for sperm. The strong gamma-glutamyl transpeptidase activity found in the secretions provides an explanation for the observation that glutamic acid is the most abundant free amino acid in accessory gland secretions of D. melanogaster. We have applied biochemical approaches, not used previously, to characterise

Seismic Noise Analysis and Reduction through Utilization of Collocated Seismic and Atmospheric Sensors at the GRO Chile Seismic Network

Science.gov (United States)

Farrell, M. E.; Russo, R. M.

2013-12-01

The installation of Earthscope Transportable Array-style geophysical observatories in Chile expands open data seismic recording capabilities in the southern hemisphere by nearly 30%, and has nearly tripled the number of seismic stations providing freely-available data in southern South America. Through the use of collocated seismic and atmospheric sensors at these stations we are able to analyze how local atmospheric conditions generate seismic noise, which can degrade data in seismic frequency bands at stations in the ';roaring forties' (S latitudes). Seismic vaults that are climate-controlled and insulated from the local environment are now employed throughout the world in an attempt to isolate seismometers from as many noise sources as possible. However, this is an expensive solution that is neither practical nor possible for all seismic deployments; and also, the increasing number and scope of temporary seismic deployments has resulted in the collection and archiving of terabytes of seismic data that is affected to some degree by natural seismic noise sources such as wind and atmospheric pressure changes. Changing air pressure can result in a depression and subsequent rebound of Earth's surface - which generates low frequency noise in seismic frequency bands - and even moderate winds can apply enough force to ground-coupled structures or to the surface above the seismometers themselves, resulting in significant noise. The 10 stations of the permanent Geophysical Reporting Observatories (GRO Chile), jointly installed during 2011-12 by IRIS and the Chilean Servicio Sismológico, include instrumentation in addition to the standard three seismic components. These stations, spaced approximately 300 km apart along the length of the country, continuously record a variety of atmospheric data including infrasound, air pressure, wind speed, and wind direction. The collocated seismic and atmospheric sensors at each station allow us to analyze both datasets together, to

Health effects of an increased protein intake on kidney function and colorectal cancer risk factors, including the role of animal and plant protein sources – the PREVIEW project

DEFF Research Database (Denmark)

Møller, Grith

intake, including the role of animal and plant protein in pre-diabetic, overweight or obese individuals on health outcomes: markers of kidney function and putative risk factors for colorectal cancer as well as insulin sensitivity and kidney function in healthy individuals. The thesis is based on PREVIEW......, especially plant protein, on insulin sensitivity and kidney function. In paper II, the aim of the study was to assess the effect after one year of a higher protein intake on kidney function, measured by in creatinine clearance. This was investigated in pre-diabetic older adults based on a sub-group of 310...... pre-diabetic individuals included in the PREVIEW RCT. We found that a higher protein intake was associated with a significant increase in urea to creatinine ratio and serum urea after one year. There were no associations between increased protein intake and creatinine clearance, estimated glomerular...

Thermoluminescence of SrAl_2O_4:Eu"2"+, Dy"3"+: dosimetric characteristics and evidence of glow-peak collocation

International Nuclear Information System (INIS)

Chithambo, M.L.

2016-01-01

The thermoluminescence of SrAl_2O_4:Eu"2"+, Dy"3"+ consists of collocated peaks whereby a dominant component subsumes subsidiary ones to such an extent that they appear as one; Qualitative and quantitative analysis of such cases will be described with suitable illustrative examples. The general features and qualitative kinetics properties of thermoluminescence from SrAl_2O_4:Eu"2"+, Dy"3"+ is reported. Measurements using X-ray excited optical luminescence show that stimulated luminescence from SrAl_2O_4:Eu"2"+, Dy"3"+ has two prominent emission bands, one at 475 nm and a more intense one near 575 nm, studied in this work. There are also weaker intensity emissions at 405, 510, 600 and 660 nm. The natural thermoluminescence measured at 1°C s"-"1 shows three peaks at 74, 170 and 340°C whereas 20 Gy beta-irradiation produces TL dominated by a single peak at 34°C. Analysis of this peak for its order of kinetics produces somewhat inconclusive results. The results of the partial heating procedure T_m - T_s_t_o_p are consistent with both first and second-order kinetics. On the other hand, the position of the peak is independent of dose for several ranges of doses implying that the apparently single peak consists of multiple first-order peaks. Complementary investigations using the fractional glow technique, resolution by isothermal heating and the effect of fading on the peak show that the glow-curve of SrAl_2O_4:Eu"2"+, Dy"3"+ comprises closely collocated thermoluminescence peaks. The implication of such complexity on kinetic analysis on this material and others that share this feature will be discussed. (author)

Closed-form solutions for linear regulator-design of mechanical systems including optimal weighting matrix selection

Science.gov (United States)

Hanks, Brantley R.; Skelton, Robert E.

1991-01-01

This paper addresses the restriction of Linear Quadratic Regulator (LQR) solutions to the algebraic Riccati Equation to design spaces which can be implemented as passive structural members and/or dampers. A general closed-form solution to the optimal free-decay control problem is presented which is tailored for structural-mechanical systems. The solution includes, as subsets, special cases such as the Rayleigh Dissipation Function and total energy. Weighting matrix selection is a constrained choice among several parameters to obtain desired physical relationships. The closed-form solution is also applicable to active control design for systems where perfect, collocated actuator-sensor pairs exist. Some examples of simple spring mass systems are shown to illustrate key points.

Protein folding includes oligomerization – examples from the endoplasmic reticulum and cytosol

NARCIS (Netherlands)

Christis, C.; Lubsen, N.H.; Braakman, I.

2008-01-01

A correct three-dimensional structure is a prerequisite for protein functionality, and therefore for life. Thus, it is not surprising that our cells are packed with proteins that assist protein folding, the process in which the native three-dimensional structure is formed. In general, plasma

ZP Domain Proteins in the Abalone Egg Coat Include a Paralog of VERL under Positive Selection That Binds Lysin and 18-kDa Sperm Proteins

Science.gov (United States)

Aagaard, Jan E.; Vacquier, Victor D.; MacCoss, Michael J.; Swanson, Willie J.

2010-01-01

Identifying fertilization molecules is key to our understanding of reproductive biology, yet only a few examples of interacting sperm and egg proteins are known. One of the best characterized comes from the invertebrate archeogastropod abalone (Haliotis spp.), where sperm lysin mediates passage through the protective egg vitelline envelope (VE) by binding to the VE protein vitelline envelope receptor for lysin (VERL). Rapid adaptive divergence of abalone lysin and VERL are an example of positive selection on interacting fertilization proteins contributing to reproductive isolation. Previously, we characterized a subset of the abalone VE proteins that share a structural feature, the zona pellucida (ZP) domain, which is common to VERL and the egg envelopes of vertebrates. Here, we use additional expressed sequence tag sequencing and shotgun proteomics to characterize this family of proteins in the abalone egg VE. We expand 3-fold the number of known ZP domain proteins present within the VE (now 30 in total) and identify a paralog of VERL (vitelline envelope zona pellucida domain protein [VEZP] 14) that contains a putative lysin-binding motif. We find that, like VERL, the divergence of VEZP14 among abalone species is driven by positive selection on the lysin-binding motif alone and that these paralogous egg VE proteins bind a similar set of sperm proteins including a rapidly evolving 18-kDa paralog of lysin, which may mediate sperm–egg fusion. This work identifies an egg coat paralog of VERL under positive selection and the candidate sperm proteins with which it may interact during abalone fertilization. PMID:19767347

Parametric study on a collocated PZT beam vibration absorber and power harvester

Energy Technology Data Exchange (ETDEWEB)

Huang, Shyh Chin [Mechanical Engineering, Ming Chi University of Technology, New Taipei (China); Tsai, Chao Yang [Mechanical Engineering Army Academy, R.O.C., Taoyuan (China); Liao, Hsiao Hui [LNG Construction and Project Division, CPC Corp., Taipei (China)

2016-11-15

The parametric effects of a PZT beam that is simultaneously used as a vibration absorber and a power harvester were investigated in this study. A cantilever beam paved with PZT layers and with added tip mass has been widely used as a harvester or sometimes as a Dynamic vibration absorber (DVA). However, the beam is rarely considered a collocated device. In this study, the first step was theoretical derivation of a distributed beam covered with bimorph PZT layers. Then, the beam was attached to a 1DOF vibratory main system. Two indicators for vibration absorption and power harvesting were defined. Numerical results demonstrated that the lumped mass ratio favored both of the abilities, but that the DVA mass ratio influenced these two abilities in exactly the opposite way. The conjunction of a harvester circuit into a DVA shifted its resonance frequency up to 5 % (an extreme case of open circuit R→∞). Simultaneous power harvesting diminished the absorption capability up to 35 % for each set of mass ratios. To achieve the maximum degree of power harvesting, a corresponding load resistance that somewhat increases with the lumped mass ratio is applied. Experimental results verified the existence of the best load resistance, but the measured harvested curve was lower than the theoretical calculation because of structure damping and deviations of PZT material properties.

Parametric study on a collocated PZT beam vibration absorber and power harvester

International Nuclear Information System (INIS)

Huang, Shyh Chin; Tsai, Chao Yang; Liao, Hsiao Hui

2016-01-01

The parametric effects of a PZT beam that is simultaneously used as a vibration absorber and a power harvester were investigated in this study. A cantilever beam paved with PZT layers and with added tip mass has been widely used as a harvester or sometimes as a Dynamic vibration absorber (DVA). However, the beam is rarely considered a collocated device. In this study, the first step was theoretical derivation of a distributed beam covered with bimorph PZT layers. Then, the beam was attached to a 1DOF vibratory main system. Two indicators for vibration absorption and power harvesting were defined. Numerical results demonstrated that the lumped mass ratio favored both of the abilities, but that the DVA mass ratio influenced these two abilities in exactly the opposite way. The conjunction of a harvester circuit into a DVA shifted its resonance frequency up to 5 % (an extreme case of open circuit R→∞). Simultaneous power harvesting diminished the absorption capability up to 35 % for each set of mass ratios. To achieve the maximum degree of power harvesting, a corresponding load resistance that somewhat increases with the lumped mass ratio is applied. Experimental results verified the existence of the best load resistance, but the measured harvested curve was lower than the theoretical calculation because of structure damping and deviations of PZT material properties

Structure soil structure interaction effects: Seismic analysis of safety related collocated concrete structures

International Nuclear Information System (INIS)

Joshi, J.R.

2000-01-01

The Process, Purification and Stack Buildings are collocated safety related concrete shear wall structures with plan dimensions in excess of 100 feet. An important aspect of their seismic analysis was the determination of structure soil structure interaction (SSSI) effects, if any. The SSSI analysis of the Process Building, with one other building at a time, was performed with the SASSI computer code for up to 50 frequencies. Each combined model had about 1500 interaction nodes. Results of the SSSI analysis were compared with those from soil structure interaction (SSI) analysis of the individual buildings, done with ABAQUS and SASSI codes, for three parameters: peak accelerations, seismic forces and the in-structure floor response spectra (FRS). The results may be of wider interest due to the model size and the potential applicability to other deep soil layered sites. Results obtained from the ABAQUS analysis were consistently higher, as expected, than those from the SSI and SSSI analyses using the SASSI. The SSSI effect between the Process and Purification Buildings was not significant. The Process and Stack Building results demonstrated that under certain conditions a massive structure can have an observable effect on the seismic response of a smaller and less stiff structure

Vibration suppression in cutting tools using collocated piezoelectric sensors/actuators with an adaptive control algorithm

Energy Technology Data Exchange (ETDEWEB)

Radecki, Peter P [Los Alamos National Laboratory; Farinholt, Kevin M [Los Alamos National Laboratory; Park, Gyuhae [Los Alamos National Laboratory; Bement, Matthew T [Los Alamos National Laboratory

2008-01-01

The machining process is very important in many engineering applications. In high precision machining, surface finish is strongly correlated with vibrations and the dynamic interactions between the part and the cutting tool. Parameters affecting these vibrations and dynamic interactions, such as spindle speed, cut depth, feed rate, and the part's material properties can vary in real-time, resulting in unexpected or undesirable effects on the surface finish of the machining product. The focus of this research is the development of an improved machining process through the use of active vibration damping. The tool holder employs a high bandwidth piezoelectric actuator with an adaptive positive position feedback control algorithm for vibration and chatter suppression. In addition, instead of using external sensors, the proposed approach investigates the use of a collocated piezoelectric sensor for measuring the dynamic responses from machining processes. The performance of this method is evaluated by comparing the surface finishes obtained with active vibration control versus baseline uncontrolled cuts. Considerable improvement in surface finish (up to 50%) was observed for applications in modern day machining.

Versions of the Collocation and Least Residuals Method for Solving Problems of Mathematical Physics in the Convex Quadrangular Domains

Directory of Open Access Journals (Sweden)

Vasily A. Belyaev

2017-01-01

Full Text Available The new versions of the collocations and least residuals (CLR method of high-order accuracy are proposed and implemented for the numerical solution of the boundary value problems for PDE in the convex quadrangular domains. Their implementation and numerical experiments are performed by the examples of solving the biharmonic and Poisson equations. The solution of the biharmonic equation is used for simulation of the stress-strain state of an isotropic plate under the action of the transverse load. Differential problems are projected into the space of fourth-degree polynomials by the CLR method. The boundary conditions for the approximate solution are put down exactly on the boundary of the computational domain. The versions of the CLR method are implemented on the grids, which are constructed by two different ways. In the first version, a “quasiregular” grid is constructed in the domain, the extreme lines of this grid coincide with the boundaries of the domain. In the second version, the domain is initially covered by a regular grid with rectangular cells. Herewith, the collocation and matching points that are situated outside the domain are used for approximation of the differential equations in the boundary cells that had been crossed by the boundary. In addition the “small” irregular triangular cells that had been cut off by the domain boundary from rectangular cells of the initial regular grid are joined to adjacent quadrangular cells. This technique allowed to essentially reduce the conditionality of the system of linear algebraic equations of the approximate problem in comparison with the case when small irregular cells together with other cells were used as independent ones for constructing an approximate solution of the problem. It is shown that the approximate solution of problems converges with high order and matches with high accuracy with the analytical solution of the test problems in the case of the known solution in

Nephrin regulates lamellipodia formation by assembling a protein complex that includes Ship2, filamin and lamellipodin.

Directory of Open Access Journals (Sweden)

Madhusudan Venkatareddy

Full Text Available Actin dynamics has emerged at the forefront of podocyte biology. Slit diaphragm junctional adhesion protein Nephrin is necessary for development of the podocyte morphology and transduces phosphorylation-dependent signals that regulate cytoskeletal dynamics. The present study extends our understanding of Nephrin function by showing in cultured podocytes that Nephrin activation induced actin dynamics is necessary for lamellipodia formation. Upon activation Nephrin recruits and regulates a protein complex that includes Ship2 (SH2 domain containing 5' inositol phosphatase, Filamin and Lamellipodin, proteins important in regulation of actin and focal adhesion dynamics, as well as lamellipodia formation. Using the previously described CD16-Nephrin clustering system, Nephrin ligation or activation resulted in phosphorylation of the actin crosslinking protein Filamin in a p21 activated kinase dependent manner. Nephrin activation in cell culture results in formation of lamellipodia, a process that requires specialized actin dynamics at the leading edge of the cell along with focal adhesion turnover. In the CD16-Nephrin clustering model, Nephrin ligation resulted in abnormal morphology of actin tails in human podocytes when Ship2, Filamin or Lamellipodin were individually knocked down. We also observed decreased lamellipodia formation and cell migration in these knock down cells. These data provide evidence that Nephrin not only initiates actin polymerization but also assembles a protein complex that is necessary to regulate the architecture of the generated actin filament network and focal adhesion dynamics.

CRISPRCasFinder, an update of CRISRFinder, includes a portable version, enhanced performance and integrates search for Cas proteins.

Science.gov (United States)

Couvin, David; Bernheim, Aude; Toffano-Nioche, Claire; Touchon, Marie; Michalik, Juraj; Néron, Bertrand; C Rocha, Eduardo P; Vergnaud, Gilles; Gautheret, Daniel; Pourcel, Christine

2018-05-22

CRISPR (clustered regularly interspaced short palindromic repeats) arrays and their associated (Cas) proteins confer bacteria and archaea adaptive immunity against exogenous mobile genetic elements, such as phages or plasmids. CRISPRCasFinder allows the identification of both CRISPR arrays and Cas proteins. The program includes: (i) an improved CRISPR array detection tool facilitating expert validation based on a rating system, (ii) prediction of CRISPR orientation and (iii) a Cas protein detection and typing tool updated to match the latest classification scheme of these systems. CRISPRCasFinder can either be used online or as a standalone tool compatible with Linux operating system. All third-party software packages employed by the program are freely available. CRISPRCasFinder is available at https://crisprcas.i2bc.paris-saclay.fr.

Hybrid motion sensing and experimental modal analysis using collocated smartphone camera and accelerometers

International Nuclear Information System (INIS)

Ozer, Ekin; Feng, Dongming; Feng, Maria Q

2017-01-01

State-of-the-art multisensory technologies and heterogeneous sensor networks propose a wide range of response measurement opportunities for structural health monitoring (SHM). Measuring and fusing different physical quantities in terms of structural vibrations can provide alternative acquisition methods and improve the quality of the modal testing results. In this study, a recently introduced SHM concept, SHM with smartphones, is focused to utilize multisensory smartphone features for a hybridized structural vibration response measurement framework. Based on vibration testing of a small-scale multistory laboratory model, displacement and acceleration responses are monitored using two different smartphone sensors, an embedded camera and accelerometer, respectively. Double-integration or differentiation among different measurement types is performed to combine multisensory measurements on a comparative basis. In addition, distributed sensor signals from collocated devices are processed for modal identification, and performance of smartphone-based sensing platforms are tested under different configuration scenarios and heterogeneity levels. The results of these tests show a novel and successful implementation of a hybrid motion sensing platform through multiple sensor type and device integration. Despite the heterogeneity of motion data obtained from different smartphone devices and technologies, it is shown that multisensory response measurements can be blended for experimental modal analysis. Getting benefit from the accessibility of smartphone technology, similar smartphone-based dynamic testing methodologies can provide innovative SHM solutions with mobile, programmable, and cost-free interfaces. (paper)

Hybrid motion sensing and experimental modal analysis using collocated smartphone camera and accelerometers

Science.gov (United States)

Ozer, Ekin; Feng, Dongming; Feng, Maria Q.

2017-10-01

State-of-the-art multisensory technologies and heterogeneous sensor networks propose a wide range of response measurement opportunities for structural health monitoring (SHM). Measuring and fusing different physical quantities in terms of structural vibrations can provide alternative acquisition methods and improve the quality of the modal testing results. In this study, a recently introduced SHM concept, SHM with smartphones, is focused to utilize multisensory smartphone features for a hybridized structural vibration response measurement framework. Based on vibration testing of a small-scale multistory laboratory model, displacement and acceleration responses are monitored using two different smartphone sensors, an embedded camera and accelerometer, respectively. Double-integration or differentiation among different measurement types is performed to combine multisensory measurements on a comparative basis. In addition, distributed sensor signals from collocated devices are processed for modal identification, and performance of smartphone-based sensing platforms are tested under different configuration scenarios and heterogeneity levels. The results of these tests show a novel and successful implementation of a hybrid motion sensing platform through multiple sensor type and device integration. Despite the heterogeneity of motion data obtained from different smartphone devices and technologies, it is shown that multisensory response measurements can be blended for experimental modal analysis. Getting benefit from the accessibility of smartphone technology, similar smartphone-based dynamic testing methodologies can provide innovative SHM solutions with mobile, programmable, and cost-free interfaces.

Discretisation of the non-linear heat transfer equation for food freezing processes using orthogonal collocation on finite elements

Directory of Open Access Journals (Sweden)

E. D. Resende

2007-09-01

Full Text Available The freezing process is considered as a propagation problem and mathematically classified as an "initial value problem." The mathematical formulation involves a complex situation of heat transfer with simultaneous changes of phase and abrupt variation in thermal properties. The objective of the present work is to solve the non-linear heat transfer equation for food freezing processes using orthogonal collocation on finite elements. This technique has not yet been applied to freezing processes and represents an alternative numerical approach in this area. The results obtained confirmed the good capability of the numerical method, which allows the simulation of the freezing process in approximately one minute of computer time, qualifying its application in a mathematical optimising procedure. The influence of the latent heat released during the crystallisation phenomena was identified by the significant increase in heat load in the early stages of the freezing process.

A unified pathogenesis for kidney diseases, including genetic diseases and cancers, by the protein-homeostasis-system hypothesis.

Science.gov (United States)

Lee, Kyung-Yil

2017-06-01

Every cell of an organism is separated and protected by a cell membrane. It is proposed that harmony between intercellular communication and the health of an organism is controlled by a system, designated the protein-homeostasis-system (PHS). Kidneys consist of a variety of types of renal cells, each with its own characteristic cell-receptor interactions and producing characteristic proteins. A functional union of these renal cells can be determined by various renal function tests, and harmonious intercellular communication is essential for the healthy state of the host. Injury to a kind of renal cells can impair renal function and induce an imbalance in total body health. Every acute or chronic renal disease has unknown etiologic substances that are responsible for renal cell injury at the molecular level. The immune/repair system of the host should control the etiologic substances acting against renal cells; if this system fails, the disease progresses to end stage renal disease. Each renal disease has its characteristic pathologic lesions where immune cells and immune proteins, such as immunoglobulins and complements, are infiltrated. These immune cells and immune proteins may control the etiologic substances involved in renal pathologic lesions. Also, genetic renal diseases and cancers may originate from a protein deficiency or malfunctioning protein under the PHS. A unified pathogenesis for renal diseases, including acute glomerulonephritis, idiopathic nephrotic syndrome, immunoglobulin A nephropathy, genetic renal diseases such as Alport syndrome, and malignancies such as Wilms tumor and renal cell carcinoma, is proposed using the PHS hypothesis.

Well-posedness and exact controllability of a fourth order Schrodinger equation with variable coefficients and Neumann boundary control and collocated observation

Directory of Open Access Journals (Sweden)

Ruili Wen

2016-08-01

Full Text Available We consider an open-loop system of a fourth order Schrodinger equation with variable coefficients and Neumann boundary control and collocated observation. Using the multiplier method on Riemannian manifold we show that that the system is well-posed in the sense of Salamon. This implies that the exponential stability of the closed-loop system under the direct proportional output feedback control and the exact controllability of open-loop system are equivalent. So in order to conclude feedback stabilization from well-posedness, we study the exact controllability under a uniqueness assumption by presenting the observability inequality for the dual system. In addition, we show that the system is regular in the sense of Weiss, and that the feedthrough operator is zero.

Fracture analysis of one-dimensional hexagonal quasicrystals: Researches of a finite dimension rectangular plate by boundary collocation method

Energy Technology Data Exchange (ETDEWEB)

Jiaxing, Cheng; Dongfa, Sheng [Southwest Forestry University, Yunnan (China)

2017-05-15

As an important supplement and development to crystallography, the applications about quasicrystal materials have played a core role in many fields, such as manufacturing and the space industry. Due to the sensitivity of quasicrystals to defects, the research on the fracture problem of quasicrystals has attracted a great deal of attention. We present a boundary collocation method to research fracture problems for a finite dimension rectangular one-dimensional hexagonal quasicrystal plate. Because mode I and mode II problems for one- dimensional hexagonal quasicrystals are like that for the classical elastic materials, only the anti-plane problem is discussed in this paper. The correctness of the present numerical method is verified through a comparison of the present results and the existing results. And then, the size effects on stress field, stress intensity factor and energy release rate are discussed in detail. The obtained results can provide valuable references for the fracture behavior of quasicrystals.

Spectral collocation method with a flexible angular discretization scheme for radiative transfer in multi-layer graded index medium

Science.gov (United States)

Wei, Linyang; Qi, Hong; Sun, Jianping; Ren, Yatao; Ruan, Liming

2017-05-01

The spectral collocation method (SCM) is employed to solve the radiative transfer in multi-layer semitransparent medium with graded index. A new flexible angular discretization scheme is employed to discretize the solid angle domain freely to overcome the limit of the number of discrete radiative direction when adopting traditional SN discrete ordinate scheme. Three radial basis function interpolation approaches, named as multi-quadric (MQ), inverse multi-quadric (IMQ) and inverse quadratic (IQ) interpolation, are employed to couple the radiative intensity at the interface between two adjacent layers and numerical experiments show that MQ interpolation has the highest accuracy and best stability. Variable radiative transfer problems in double-layer semitransparent media with different thermophysical properties are investigated and the influence of these thermophysical properties on the radiative transfer procedure in double-layer semitransparent media is also analyzed. All the simulated results show that the present SCM with the new angular discretization scheme can predict the radiative transfer in multi-layer semitransparent medium with graded index efficiently and accurately.

A fractional factorial probabilistic collocation method for uncertainty propagation of hydrologic model parameters in a reduced dimensional space

Science.gov (United States)

Wang, S.; Huang, G. H.; Huang, W.; Fan, Y. R.; Li, Z.

2015-10-01

In this study, a fractional factorial probabilistic collocation method is proposed to reveal statistical significance of hydrologic model parameters and their multi-level interactions affecting model outputs, facilitating uncertainty propagation in a reduced dimensional space. The proposed methodology is applied to the Xiangxi River watershed in China to demonstrate its validity and applicability, as well as its capability of revealing complex and dynamic parameter interactions. A set of reduced polynomial chaos expansions (PCEs) only with statistically significant terms can be obtained based on the results of factorial analysis of variance (ANOVA), achieving a reduction of uncertainty in hydrologic predictions. The predictive performance of reduced PCEs is verified by comparing against standard PCEs and the Monte Carlo with Latin hypercube sampling (MC-LHS) method in terms of reliability, sharpness, and Nash-Sutcliffe efficiency (NSE). Results reveal that the reduced PCEs are able to capture hydrologic behaviors of the Xiangxi River watershed, and they are efficient functional representations for propagating uncertainties in hydrologic predictions.

On the equivalence of spherical splines with least-squares collocation and Stokes's formula for regional geoid computation

Science.gov (United States)

Ophaug, Vegard; Gerlach, Christian

2017-11-01

This work is an investigation of three methods for regional geoid computation: Stokes's formula, least-squares collocation (LSC), and spherical radial base functions (RBFs) using the spline kernel (SK). It is a first attempt to compare the three methods theoretically and numerically in a unified framework. While Stokes integration and LSC may be regarded as classic methods for regional geoid computation, RBFs may still be regarded as a modern approach. All methods are theoretically equal when applied globally, and we therefore expect them to give comparable results in regional applications. However, it has been shown by de Min (Bull Géod 69:223-232, 1995. doi: 10.1007/BF00806734) that the equivalence of Stokes's formula and LSC does not hold in regional applications without modifying the cross-covariance function. In order to make all methods comparable in regional applications, the corresponding modification has been introduced also in the SK. Ultimately, we present numerical examples comparing Stokes's formula, LSC, and SKs in a closed-loop environment using synthetic noise-free data, to verify their equivalence. All agree on the millimeter level.

Ice particle production in mid-level stratiform mixed-phase clouds observed with collocated A-Train measurements

Directory of Open Access Journals (Sweden)

D. Zhang

2018-03-01

Full Text Available Collocated A-Train CloudSat radar and CALIPSO lidar measurements between 2006 and 2010 are analyzed to study primary ice particle production characteristics in mid-level stratiform mixed-phase clouds on a global scale. For similar clouds in terms of cloud top temperature and liquid water path, Northern Hemisphere latitude bands have layer-maximum radar reflectivity (ZL that is  ∼  1 to 8 dBZ larger than their counterparts in the Southern Hemisphere. The systematically larger ZL under similar cloud conditions suggests larger ice number concentrations in mid-level stratiform mixed-phase clouds over the Northern Hemisphere, which is possibly related to higher background aerosol loadings. Furthermore, we show that springtime northern mid- and high latitudes have ZL that is larger by up to 6 dBZ (a factor of 4 higher ice number concentration than other seasons, which might be related to more dust events that provide effective ice nucleating particles. Our study suggests that aerosol-dependent ice number concentration parameterizations are required in climate models to improve mixed-phase cloud simulations, especially over the Northern Hemisphere.

Kalman filter parameter estimation for a nonlinear diffusion model of epithelial cell migration using stochastic collocation and the Karhunen-Loeve expansion.

Science.gov (United States)

Barber, Jared; Tanase, Roxana; Yotov, Ivan

2016-06-01

Several Kalman filter algorithms are presented for data assimilation and parameter estimation for a nonlinear diffusion model of epithelial cell migration. These include the ensemble Kalman filter with Monte Carlo sampling and a stochastic collocation (SC) Kalman filter with structured sampling. Further, two types of noise are considered -uncorrelated noise resulting in one stochastic dimension for each element of the spatial grid and correlated noise parameterized by the Karhunen-Loeve (KL) expansion resulting in one stochastic dimension for each KL term. The efficiency and accuracy of the four methods are investigated for two cases with synthetic data with and without noise, as well as data from a laboratory experiment. While it is observed that all algorithms perform reasonably well in matching the target solution and estimating the diffusion coefficient and the growth rate, it is illustrated that the algorithms that employ SC and KL expansion are computationally more efficient, as they require fewer ensemble members for comparable accuracy. In the case of SC methods, this is due to improved approximation in stochastic space compared to Monte Carlo sampling. In the case of KL methods, the parameterization of the noise results in a stochastic space of smaller dimension. The most efficient method is the one combining SC and KL expansion. Copyright © 2016 Elsevier Inc. All rights reserved.

Collocation methods for uncertainty quanti cation in PDE models with random data

KAUST Repository

Nobile, Fabio

2014-01-06

In this talk we consider Partial Differential Equations (PDEs) whose input data are modeled as random fields to account for their intrinsic variability or our lack of knowledge. After parametrizing the input random fields by finitely many independent random variables, we exploit the high regularity of the solution of the PDE as a function of the input random variables and consider sparse polynomial approximations in probability (Polynomial Chaos expansion) by collocation methods. We first address interpolatory approximations where the PDE is solved on a sparse grid of Gauss points in the probability space and the solutions thus obtained interpolated by multivariate polynomials. We present recent results on optimized sparse grids in which the selection of points is based on a knapsack approach and relies on sharp estimates of the decay of the coefficients of the polynomial chaos expansion of the solution. Secondly, we consider regression approaches where the PDE is evaluated on randomly chosen points in the probability space and a polynomial approximation constructed by the least square method. We present recent theoretical results on the stability and optimality of the approximation under suitable conditions between the number of sampling points and the dimension of the polynomial space. In particular, we show that for uniform random variables, the number of sampling point has to scale quadratically with the dimension of the polynomial space to maintain the stability and optimality of the approximation. Numerical results show that such condition is sharp in the monovariate case but seems to be over-constraining in higher dimensions. The regression technique seems therefore to be attractive in higher dimensions.

Orbiting Carbon Observatory-2 (OCO-2) cloud screening algorithms; validation against collocated MODIS and CALIOP data

Science.gov (United States)

Taylor, T. E.; O'Dell, C. W.; Frankenberg, C.; Partain, P.; Cronk, H. Q.; Savtchenko, A.; Nelson, R. R.; Rosenthal, E. J.; Chang, A. Y.; Fisher, B.; Osterman, G.; Pollock, R. H.; Crisp, D.; Eldering, A.; Gunson, M. R.

2015-12-01

The objective of the National Aeronautics and Space Administration's (NASA) Orbiting Carbon Observatory-2 (OCO-2) mission is to retrieve the column-averaged carbon dioxide (CO2) dry air mole fraction (XCO2) from satellite measurements of reflected sunlight in the near-infrared. These estimates can be biased by clouds and aerosols within the instrument's field of view (FOV). Screening of the most contaminated soundings minimizes unnecessary calls to the computationally expensive Level 2 (L2) XCO2 retrieval algorithm. Hence, robust cloud screening methods have been an important focus of the OCO-2 algorithm development team. Two distinct, computationally inexpensive cloud screening algorithms have been developed for this application. The A-Band Preprocessor (ABP) retrieves the surface pressure using measurements in the 0.76 μm O2 A-band, neglecting scattering by clouds and aerosols, which introduce photon path-length (PPL) differences that can cause large deviations between the expected and retrieved surface pressure. The Iterative Maximum A-Posteriori (IMAP) Differential Optical Absorption Spectroscopy (DOAS) Preprocessor (IDP) retrieves independent estimates of the CO2 and H2O column abundances using observations taken at 1.61 μm (weak CO2 band) and 2.06 μm (strong CO2 band), while neglecting atmospheric scattering. The CO2 and H2O column abundances retrieved in these two spectral regions differ significantly in the presence of cloud and scattering aerosols. The combination of these two algorithms, which key off of different features in the spectra, provides the basis for cloud screening of the OCO-2 data set. To validate the OCO-2 cloud screening approach, collocated measurements from NASA's Moderate Resolution Imaging Spectrometer (MODIS), aboard the Aqua platform, were compared to results from the two OCO-2 cloud screening algorithms. With tuning to allow throughputs of ≃ 30 %, agreement between the OCO-2 and MODIS cloud screening methods is found to be

A Least Squares Collocation Approach with GOCE gravity gradients for regional Moho-estimation

Science.gov (United States)

Rieser, Daniel; Mayer-Guerr, Torsten

2014-05-01

The depth of the Moho discontinuity is commonly derived by either seismic observations, gravity measurements or combinations of both. In this study, we aim to use the gravity gradient measurements of the GOCE satellite mission in a Least Squares Collocation (LSC) approach for the estimation of the Moho depth on regional scale. Due to its mission configuration and measurement setup, GOCE is able to contribute valuable information in particular in the medium wavelengths of the gravity field spectrum, which is also of special interest for the crust-mantle boundary. In contrast to other studies we use the full information of the gradient tensor in all three dimensions. The problem outline is formulated as isostatically compensated topography according to the Airy-Heiskanen model. By using a topography model in spherical harmonics representation the topographic influences can be reduced from the gradient observations. Under the assumption of constant mantle and crustal densities, surface densities are directly derived by LSC on regional scale, which in turn are converted in Moho depths. First investigations proofed the ability of this method to resolve the gravity inversion problem already with a small amount of GOCE data and comparisons with other seismic and gravitmetric Moho models for the European region show promising results. With the recently reprocessed GOCE gradients, an improved data set shall be used for the derivation of the Moho depth. In this contribution the processing strategy will be introduced and the most recent developments and results using the currently available GOCE data shall be presented.

POD for Real-Time Simulation of Hyperelastic Soft Biological Tissue Using the Point Collocation Method of Finite Spheres

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Suleiman Banihani

2013-01-01

Full Text Available The point collocation method of finite spheres (PCMFS is used to model the hyperelastic response of soft biological tissue in real time within the framework of virtual surgery simulation. The proper orthogonal decomposition (POD model order reduction (MOR technique was used to achieve reduced-order model of the problem, minimizing computational cost. The PCMFS is a physics-based meshfree numerical technique for real-time simulation of surgical procedures where the approximation functions are applied directly on the strong form of the boundary value problem without the need for integration, increasing computational efficiency. Since computational speed has a significant role in simulation of surgical procedures, the proposed technique was able to model realistic nonlinear behavior of organs in real time. Numerical results are shown to demonstrate the effectiveness of the new methodology through a comparison between full and reduced analyses for several nonlinear problems. It is shown that the proposed technique was able to achieve good agreement with the full model; moreover, the computational and data storage costs were significantly reduced.

BioInfra.Prot: A comprehensive proteomics workflow including data standardization, protein inference, expression analysis and data publication.

Science.gov (United States)

Turewicz, Michael; Kohl, Michael; Ahrens, Maike; Mayer, Gerhard; Uszkoreit, Julian; Naboulsi, Wael; Bracht, Thilo; Megger, Dominik A; Sitek, Barbara; Marcus, Katrin; Eisenacher, Martin

2017-11-10

The analysis of high-throughput mass spectrometry-based proteomics data must address the specific challenges of this technology. To this end, the comprehensive proteomics workflow offered by the de.NBI service center BioInfra.Prot provides indispensable components for the computational and statistical analysis of this kind of data. These components include tools and methods for spectrum identification and protein inference, protein quantification, expression analysis as well as data standardization and data publication. All particular methods of the workflow which address these tasks are state-of-the-art or cutting edge. As has been shown in previous publications, each of these methods is adequate to solve its specific task and gives competitive results. However, the methods included in the workflow are continuously reviewed, updated and improved to adapt to new scientific developments. All of these particular components and methods are available as stand-alone BioInfra.Prot services or as a complete workflow. Since BioInfra.Prot provides manifold fast communication channels to get access to all components of the workflow (e.g., via the BioInfra.Prot ticket system: bioinfraprot@rub.de) users can easily benefit from this service and get support by experts. Copyright © 2017 The Authors. Published by Elsevier B.V. All rights reserved.

Towards ligand docking including explicit interface water molecules.

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Gordon Lemmon

Full Text Available Small molecule docking predicts the interaction of a small molecule ligand with a protein at atomic-detail accuracy including position and conformation the ligand but also conformational changes of the protein upon ligand binding. While successful in the majority of cases, docking algorithms including RosettaLigand fail in some cases to predict the correct protein/ligand complex structure. In this study we show that simultaneous docking of explicit interface water molecules greatly improves Rosetta's ability to distinguish correct from incorrect ligand poses. This result holds true for both protein-centric water docking wherein waters are located relative to the protein binding site and ligand-centric water docking wherein waters move with the ligand during docking. Protein-centric docking is used to model 99 HIV-1 protease/protease inhibitor structures. We find protease inhibitor placement improving at a ratio of 9:1 when one critical interface water molecule is included in the docking simulation. Ligand-centric docking is applied to 341 structures from the CSAR benchmark of diverse protein/ligand complexes [1]. Across this diverse dataset we see up to 56% recovery of failed docking studies, when waters are included in the docking simulation.

An efficient Bayesian inference approach to inverse problems based on an adaptive sparse grid collocation method

International Nuclear Information System (INIS)

Ma Xiang; Zabaras, Nicholas

2009-01-01

A new approach to modeling inverse problems using a Bayesian inference method is introduced. The Bayesian approach considers the unknown parameters as random variables and seeks the probabilistic distribution of the unknowns. By introducing the concept of the stochastic prior state space to the Bayesian formulation, we reformulate the deterministic forward problem as a stochastic one. The adaptive hierarchical sparse grid collocation (ASGC) method is used for constructing an interpolant to the solution of the forward model in this prior space which is large enough to capture all the variability/uncertainty in the posterior distribution of the unknown parameters. This solution can be considered as a function of the random unknowns and serves as a stochastic surrogate model for the likelihood calculation. Hierarchical Bayesian formulation is used to derive the posterior probability density function (PPDF). The spatial model is represented as a convolution of a smooth kernel and a Markov random field. The state space of the PPDF is explored using Markov chain Monte Carlo algorithms to obtain statistics of the unknowns. The likelihood calculation is performed by directly sampling the approximate stochastic solution obtained through the ASGC method. The technique is assessed on two nonlinear inverse problems: source inversion and permeability estimation in flow through porous media

Prediction of Navigation Satellite Clock Bias Considering Clock's Stochastic Variation Behavior with Robust Least Square Collocation

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WANG Yupu

2016-06-01

Full Text Available In order to better express the characteristic of satellite clock bias (SCB and further improve its prediction precision, a new SCB prediction model is proposed, which can take the physical feature, cyclic variation and stochastic variation behaviors of the space-borne atomic clock into consideration by using a robust least square collocation (LSC method. The proposed model firstly uses a quadratic polynomial model with periodic terms to fit and abstract the trend term and cyclic terms of SCB. Then for the residual stochastic variation part and possible gross errors hidden in SCB data, the model employs a robust LSC method to process them. The covariance function of the LSC is determined by selecting an empirical function and combining SCB prediction tests. Using the final precise IGS SCB products to conduct prediction tests, the results show that the proposed model can get better prediction performance. Specifically, the results' prediction accuracy can enhance 0.457 ns and 0.948 ns respectively, and the corresponding prediction stability can improve 0.445 ns and 1.233 ns, compared with the results of quadratic polynomial model and grey model. In addition, the results also show that the proposed covariance function corresponding to the new model is reasonable.

Temporal gravity field modeling based on least square collocation with short-arc approach

Science.gov (United States)

ran, jiangjun; Zhong, Min; Xu, Houze; Liu, Chengshu; Tangdamrongsub, Natthachet

2014-05-01

After the launch of the Gravity Recovery And Climate Experiment (GRACE) in 2002, several research centers have attempted to produce the finest gravity model based on different approaches. In this study, we present an alternative approach to derive the Earth's gravity field, and two main objectives are discussed. Firstly, we seek the optimal method to estimate the accelerometer parameters, and secondly, we intend to recover the monthly gravity model based on least square collocation method. The method has been paid less attention compared to the least square adjustment method because of the massive computational resource's requirement. The positions of twin satellites are treated as pseudo-observations and unknown parameters at the same time. The variance covariance matrices of the pseudo-observations and the unknown parameters are valuable information to improve the accuracy of the estimated gravity solutions. Our analyses showed that introducing a drift parameter as an additional accelerometer parameter, compared to using only a bias parameter, leads to a significant improvement of our estimated monthly gravity field. The gravity errors outside the continents are significantly reduced based on the selected set of the accelerometer parameters. We introduced the improved gravity model namely the second version of Institute of Geodesy and Geophysics, Chinese Academy of Sciences (IGG-CAS 02). The accuracy of IGG-CAS 02 model is comparable to the gravity solutions computed from the Geoforschungszentrum (GFZ), the Center for Space Research (CSR) and the NASA Jet Propulsion Laboratory (JPL). In term of the equivalent water height, the correlation coefficients over the study regions (the Yangtze River valley, the Sahara desert, and the Amazon) among four gravity models are greater than 0.80.

Orbiting Carbon Observatory-2 (OCO-2) cloud screening algorithms: validation against collocated MODIS and CALIOP data

Science.gov (United States)

Taylor, Thomas E.; O'Dell, Christopher W.; Frankenberg, Christian; Partain, Philip T.; Cronk, Heather Q.; Savtchenko, Andrey; Nelson, Robert R.; Rosenthal, Emily J.; Chang, Albert Y.; Fisher, Brenden; Osterman, Gregory B.; Pollock, Randy H.; Crisp, David; Eldering, Annmarie; Gunson, Michael R.

2016-03-01

The objective of the National Aeronautics and Space Administration's (NASA) Orbiting Carbon Observatory-2 (OCO-2) mission is to retrieve the column-averaged carbon dioxide (CO2) dry air mole fraction (XCO2) from satellite measurements of reflected sunlight in the near-infrared. These estimates can be biased by clouds and aerosols, i.e., contamination, within the instrument's field of view. Screening of the most contaminated soundings minimizes unnecessary calls to the computationally expensive Level 2 (L2) XCO2 retrieval algorithm. Hence, robust cloud screening methods have been an important focus of the OCO-2 algorithm development team. Two distinct, computationally inexpensive cloud screening algorithms have been developed for this application. The A-Band Preprocessor (ABP) retrieves the surface pressure using measurements in the 0.76 µm O2 A band, neglecting scattering by clouds and aerosols, which introduce photon path-length differences that can cause large deviations between the expected and retrieved surface pressure. The Iterative Maximum A Posteriori (IMAP) Differential Optical Absorption Spectroscopy (DOAS) Preprocessor (IDP) retrieves independent estimates of the CO2 and H2O column abundances using observations taken at 1.61 µm (weak CO2 band) and 2.06 µm (strong CO2 band), while neglecting atmospheric scattering. The CO2 and H2O column abundances retrieved in these two spectral regions differ significantly in the presence of cloud and scattering aerosols. The combination of these two algorithms, which are sensitive to different features in the spectra, provides the basis for cloud screening of the OCO-2 data set.To validate the OCO-2 cloud screening approach, collocated measurements from NASA's Moderate Resolution Imaging Spectrometer (MODIS), aboard the Aqua platform, were compared to results from the two OCO-2 cloud screening algorithms. With tuning of algorithmic threshold parameters that allows for processing of ≃ 20-25 % of all OCO-2 soundings

Reference frame access under the effects of great earthquakes: a least squares collocation approach for non-secular post-seismic evolution

Science.gov (United States)

Gómez, D. D.; Piñón, D. A.; Smalley, R.; Bevis, M.; Cimbaro, S. R.; Lenzano, L. E.; Barón, J.

2016-03-01

The 2010, (Mw 8.8) Maule, Chile, earthquake produced large co-seismic displacements and non-secular, post-seismic deformation, within latitudes 28°S-40°S extending from the Pacific to the Atlantic oceans. Although these effects are easily resolvable by fitting geodetic extended trajectory models (ETM) to continuous GPS (CGPS) time series, the co- and post-seismic deformation cannot be determined at locations without CGPS (e.g., on passive geodetic benchmarks). To estimate the trajectories of passive geodetic benchmarks, we used CGPS time series to fit an ETM that includes the secular South American plate motion and plate boundary deformation, the co-seismic discontinuity, and the non-secular, logarithmic post-seismic transient produced by the earthquake in the Posiciones Geodésicas Argentinas 2007 (POSGAR07) reference frame (RF). We then used least squares collocation (LSC) to model both the background secular inter-seismic and the non-secular post-seismic components of the ETM at the locations without CGPS. We tested the LSC modeled trajectories using campaign and CGPS data that was not used to generate the model and found standard deviations (95 % confidence level) for position estimates for the north and east components of 3.8 and 5.5 mm, respectively, indicating that the model predicts the post-seismic deformation field very well. Finally, we added the co-seismic displacement field, estimated using an elastic finite element model. The final, trajectory model allows accessing the POSGAR07 RF using post-Maule earthquake coordinates within 5 cm for ˜ 91 % of the passive test benchmarks.

Towards Improving the Efficiency of Bayesian Model Averaging Analysis for Flow in Porous Media via the Probabilistic Collocation Method

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Liang Xue

2018-04-01

Full Text Available The characterization of flow in subsurface porous media is associated with high uncertainty. To better quantify the uncertainty of groundwater systems, it is necessary to consider the model uncertainty. Multi-model uncertainty analysis can be performed in the Bayesian model averaging (BMA framework. However, the BMA analysis via Monte Carlo method is time consuming because it requires many forward model evaluations. A computationally efficient BMA analysis framework is proposed by using the probabilistic collocation method to construct a response surface model, where the log hydraulic conductivity field and hydraulic head are expanded into polynomials through Karhunen–Loeve and polynomial chaos methods. A synthetic test is designed to validate the proposed response surface analysis method. The results show that the posterior model weight and the key statistics in BMA framework can be accurately estimated. The relative errors of mean and total variance in the BMA analysis results are just approximately 0.013% and 1.18%, but the proposed method can be 16 times more computationally efficient than the traditional BMA method.

Multi-faceted proteomic characterization of host protein complement of Rift Valley fever virus virions and identification of specific heat shock proteins, including HSP90, as important viral host factors.

Science.gov (United States)

Nuss, Jonathan E; Kehn-Hall, Kylene; Benedict, Ashwini; Costantino, Julie; Ward, Michael; Peyser, Brian D; Retterer, Cary J; Tressler, Lyal E; Wanner, Laura M; McGovern, Hugh F; Zaidi, Anum; Anthony, Scott M; Kota, Krishna P; Bavari, Sina; Hakami, Ramin M

2014-01-01

Rift Valley fever is a potentially fatal disease of humans and domestic animals caused by Rift Valley fever virus (RVFV). Infection with RVFV in ruminants can cause near 100% abortion rates and recent outbreaks in naïve human populations have suggested case fatality rates of greater than thirty percent. To elucidate the roles that host proteins play during RVFV infection, proteomic analysis of RVFV virions was conducted using complementary analytical approaches, followed by functional validation studies of select identified host factors. Coupling the more traditional Gel LC/MS/MS approach (SDS PAGE followed by liquid chromatography tandem mass spectrometry) with an alternative technique that preserves protein complexes allowed the protein complement of these viral particles to be thoroughly examined. In addition to viral proteins present within the virions and virion-associated host proteins, multiple macromolecular complexes were identified. Bioinformatic analysis showed that host chaperones were among over-represented protein families associated with virions, and functional experiments using siRNA gene silencing and small molecule inhibitors identified several of these heat shock proteins, including heat shock protein 90 (HSP90), as important viral host factors. Further analysis indicated that HSP inhibition effects occur during the replication/transcription phase of the virus life cycle, leading to significant lowering of viral titers without compromising the functional capacity of released virions. Overall, these studies provide much needed further insight into interactions between RVFV and host cells, increasing our understanding of the infection process and suggesting novel strategies for anti-viral development. In particular, considering that several HSP90 inhibitors have been advancing through clinical trials for cancer treatment, these results also highlight the exciting potential of repurposing HSP90 inhibitors to treat RVF.

Multi-faceted proteomic characterization of host protein complement of Rift Valley fever virus virions and identification of specific heat shock proteins, including HSP90, as important viral host factors.

Directory of Open Access Journals (Sweden)

Jonathan E Nuss

Full Text Available Rift Valley fever is a potentially fatal disease of humans and domestic animals caused by Rift Valley fever virus (RVFV. Infection with RVFV in ruminants can cause near 100% abortion rates and recent outbreaks in naïve human populations have suggested case fatality rates of greater than thirty percent. To elucidate the roles that host proteins play during RVFV infection, proteomic analysis of RVFV virions was conducted using complementary analytical approaches, followed by functional validation studies of select identified host factors. Coupling the more traditional Gel LC/MS/MS approach (SDS PAGE followed by liquid chromatography tandem mass spectrometry with an alternative technique that preserves protein complexes allowed the protein complement of these viral particles to be thoroughly examined. In addition to viral proteins present within the virions and virion-associated host proteins, multiple macromolecular complexes were identified. Bioinformatic analysis showed that host chaperones were among over-represented protein families associated with virions, and functional experiments using siRNA gene silencing and small molecule inhibitors identified several of these heat shock proteins, including heat shock protein 90 (HSP90, as important viral host factors. Further analysis indicated that HSP inhibition effects occur during the replication/transcription phase of the virus life cycle, leading to significant lowering of viral titers without compromising the functional capacity of released virions. Overall, these studies provide much needed further insight into interactions between RVFV and host cells, increasing our understanding of the infection process and suggesting novel strategies for anti-viral development. In particular, considering that several HSP90 inhibitors have been advancing through clinical trials for cancer treatment, these results also highlight the exciting potential of repurposing HSP90 inhibitors to treat RVF.

An Improved Collocation Meshless Method Based on the Variable Shaped Radial Basis Function for the Solution of the Interior Acoustic Problems

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Shuang Wang

2012-01-01

Full Text Available As an efficient tool, radial basis function (RBF has been widely used for the multivariate approximation, interpolating continuous, and the solution of the particle differential equations. However, ill-conditioned interpolation matrix may be encountered when the interpolation points are very dense or irregularly arranged. To avert this problem, RBFs with variable shape parameters are introduced, and several new variation strategies are proposed. Comparison with the RBF with constant shape parameters are made, and the results show that the condition number of the interpolation matrix grows much slower with our strategies. As an application, an improved collocation meshless method is formulated by employing the new RBF. In addition, the Hermite-type interpolation is implemented to handle the Neumann boundary conditions and an additional sine/cosine basis is introduced for the Helmlholtz equation. Then, two interior acoustic problems are solved with the presented method; the results demonstrate the robustness and effectiveness of the method.

Triple collocation-based estimation of spatially correlated observation error covariance in remote sensing soil moisture data assimilation

Science.gov (United States)

Wu, Kai; Shu, Hong; Nie, Lei; Jiao, Zhenhang

2018-01-01

Spatially correlated errors are typically ignored in data assimilation, thus degenerating the observation error covariance R to a diagonal matrix. We argue that a nondiagonal R carries more observation information making assimilation results more accurate. A method, denoted TC_Cov, was proposed for soil moisture data assimilation to estimate spatially correlated observation error covariance based on triple collocation (TC). Assimilation experiments were carried out to test the performance of TC_Cov. AMSR-E soil moisture was assimilated with a diagonal R matrix computed using the TC and assimilated using a nondiagonal R matrix, as estimated by proposed TC_Cov. The ensemble Kalman filter was considered as the assimilation method. Our assimilation results were validated against climate change initiative data and ground-based soil moisture measurements using the Pearson correlation coefficient and unbiased root mean square difference metrics. These experiments confirmed that deterioration of diagonal R assimilation results occurred when model simulation is more accurate than observation data. Furthermore, nondiagonal R achieved higher correlation coefficient and lower ubRMSD values over diagonal R in experiments and demonstrated the effectiveness of TC_Cov to estimate richly structuralized R in data assimilation. In sum, compared with diagonal R, nondiagonal R may relieve the detrimental effects of assimilation when simulated model results outperform observation data.

Prediction of flexible/rigid regions from protein sequences using k-spaced amino acid pairs

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Ruan Jishou

2007-04-01

Full Text Available Abstract Background Traditionally, it is believed that the native structure of a protein corresponds to a global minimum of its free energy. However, with the growing number of known tertiary (3D protein structures, researchers have discovered that some proteins can alter their structures in response to a change in their surroundings or with the help of other proteins or ligands. Such structural shifts play a crucial role with respect to the protein function. To this end, we propose a machine learning method for the prediction of the flexible/rigid regions of proteins (referred to as FlexRP; the method is based on a novel sequence representation and feature selection. Knowledge of the flexible/rigid regions may provide insights into the protein folding process and the 3D structure prediction. Results The flexible/rigid regions were defined based on a dataset, which includes protein sequences that have multiple experimental structures, and which was previously used to study the structural conservation of proteins. Sequences drawn from this dataset were represented based on feature sets that were proposed in prior research, such as PSI-BLAST profiles, composition vector and binary sequence encoding, and a newly proposed representation based on frequencies of k-spaced amino acid pairs. These representations were processed by feature selection to reduce the dimensionality. Several machine learning methods for the prediction of flexible/rigid regions and two recently proposed methods for the prediction of conformational changes and unstructured regions were compared with the proposed method. The FlexRP method, which applies Logistic Regression and collocation-based representation with 95 features, obtained 79.5% accuracy. The two runner-up methods, which apply the same sequence representation and Support Vector Machines (SVM and Naïve Bayes classifiers, obtained 79.2% and 78.4% accuracy, respectively. The remaining considered methods are

Brine migration resulting from CO2 injection into saline aquifers – An approach to risk estimation including various levels of uncertainty

DEFF Research Database (Denmark)

Walter, Lena; Binning, Philip John; Oladyshkin, Sergey

2012-01-01

resulting from displaced brine. Quantifying risk on the basis of numerical simulations requires consideration of different kinds of uncertainties and this study considers both, scenario uncertainty and statistical uncertainty. Addressing scenario uncertainty involves expert opinion on relevant geological......Comprehensive risk assessment is a major task for large-scale projects such as geological storage of CO2. Basic hazards are damage to the integrity of caprocks, leakage of CO2, or reduction of groundwater quality due to intrusion of fluids. This study focuses on salinization of freshwater aquifers...... for large-scale 3D models including complex physics. Therefore, we apply a model reduction based on arbitrary polynomial chaos expansion combined with probabilistic collocation method. It is shown that, dependent on data availability, both types of uncertainty can be equally significant. The presented study...

Asymmetric free vibrations of laminated annular cross-ply circular plates including the effects of shear deformation and rotary inertia. Spline method

Energy Technology Data Exchange (ETDEWEB)

Viswanathan, K.K.; Kim, Kyung Su; Lee, Jang Hyun [Inha Univ., Incheon (Korea). Dept. of Naval Architecture and Ocean Engineering

2009-12-15

Asymmetric free vibrations of annular cross-ply circular plates are studied using spline function approximation. The governing equations are formulated including the effects of shear deformation and rotary inertia. Assumptions are made to study the cross-ply layered plates. A system of coupled differential equations are obtained in terms of displacement functions and rotational functions. These functions are approximated using Bickley- type spline functions of suitable order. Then the system is converted into the eigenvalue problem by applying the point collocation technique and suitable boundary conditions. Parametric studies have been made to investigate the effect of transverse shear deformation and rotary inertia on frequency parameter with respect to the circumferential node number, radii ratio and thickness to radius ratio for both symmetric and anti-symmetric cross-ply plates using various types of material properties. (orig.)

Closed-form solutions for linear regulator design of mechanical systems including optimal weighting matrix selection

Science.gov (United States)

Hanks, Brantley R.; Skelton, Robert E.

1991-01-01

Vibration in modern structural and mechanical systems can be reduced in amplitude by increasing stiffness, redistributing stiffness and mass, and/or adding damping if design techniques are available to do so. Linear Quadratic Regulator (LQR) theory in modern multivariable control design, attacks the general dissipative elastic system design problem in a global formulation. The optimal design, however, allows electronic connections and phase relations which are not physically practical or possible in passive structural-mechanical devices. The restriction of LQR solutions (to the Algebraic Riccati Equation) to design spaces which can be implemented as passive structural members and/or dampers is addressed. A general closed-form solution to the optimal free-decay control problem is presented which is tailored for structural-mechanical system. The solution includes, as subsets, special cases such as the Rayleigh Dissipation Function and total energy. Weighting matrix selection is a constrained choice among several parameters to obtain desired physical relationships. The closed-form solution is also applicable to active control design for systems where perfect, collocated actuator-sensor pairs exist.

Do we see what we should see? Describing non-covalent interactions in protein structures including precision

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Manickam Gurusaran

2014-01-01

Full Text Available The power of X-ray crystal structure analysis as a technique is to `see where the atoms are'. The results are extensively used by a wide variety of research communities. However, this `seeing where the atoms are' can give a false sense of security unless the precision of the placement of the atoms has been taken into account. Indeed, the presentation of bond distances and angles to a false precision (i.e. to too many decimal places is commonplace. This article has three themes. Firstly, a basis for a proper representation of protein crystal structure results is detailed and demonstrated with respect to analyses of Protein Data Bank entries. The basis for establishing the precision of placement of each atom in a protein crystal structure is non-trivial. Secondly, a knowledge base harnessing such a descriptor of precision is presented. It is applied here to the case of salt bridges, i.e. ion pairs, in protein structures; this is the most fundamental place to start with such structure-precision representations since salt bridges are one of the tenets of protein structure stability. Ion pairs also play a central role in protein oligomerization, molecular recognition of ligands and substrates, allosteric regulation, domain motion and α-helix capping. A new knowledge base, SBPS (Salt Bridges in Protein Structures, takes these structural precisions into account and is the first of its kind. The third theme of the article is to indicate natural extensions of the need for such a description of precision, such as those involving metalloproteins and the determination of the protonation states of ionizable amino acids. Overall, it is also noted that this work and these examples are also relevant to protein three-dimensional structure molecular graphics software.

NONLINEAR MODEL PREDICTIVE CONTROL OF CHEMICAL PROCESSES

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SILVA R. G.

1999-01-01

Full Text Available A new algorithm for model predictive control is presented. The algorithm utilizes a simultaneous solution and optimization strategy to solve the model's differential equations. The equations are discretized by equidistant collocation, and along with the algebraic model equations are included as constraints in a nonlinear programming (NLP problem. This algorithm is compared with the algorithm that uses orthogonal collocation on finite elements. The equidistant collocation algorithm results in simpler equations, providing a decrease in computation time for the control moves. Simulation results are presented and show a satisfactory performance of this algorithm.

Protein nanoparticles for therapeutic protein delivery.

Science.gov (United States)

Herrera Estrada, L P; Champion, J A

2015-06-01

Therapeutic proteins can face substantial challenges to their activity, requiring protein modification or use of a delivery vehicle. Nanoparticles can significantly enhance delivery of encapsulated cargo, but traditional small molecule carriers have some limitations in their use for protein delivery. Nanoparticles made from protein have been proposed as alternative carriers and have benefits specific to therapeutic protein delivery. This review describes protein nanoparticles made by self-assembly, including protein cages, protein polymers, and charged or amphipathic peptides, and by desolvation. It presents particle fabrication and delivery characterization for a variety of therapeutic and model proteins, as well as comparison of the features of different protein nanoparticles.

Kollokationsforschung und Kollokationsdidaktik

Directory of Open Access Journals (Sweden)

Reder, Anna

2006-01-01

Full Text Available Investigating and teaching collocations. The starting point of the paper is the observation that foreign language learners translate collocations literally from their L1. Collocations are conceived here as phrasal units which can be placed between free word groups and idioms. The paper focuses on metaphoric collocations, i.e. with polysemic collocator. In this type of collocation the collocator is used in a metaphoric meaning, while it appears in denotative meaning in free word groups. Contrasting types of collocation are presented in a model. Data from empirical research show that foreign language learners of a certain level regard metaphoric collocations as marked and transfer them less often than non-metaphoric collocations. The paper supports the need for pointing out the significance of collocations even for beginners.

Discretization of the induced-charge boundary integral equation.

Science.gov (United States)

Bardhan, Jaydeep P; Eisenberg, Robert S; Gillespie, Dirk

2009-07-01

Boundary-element methods (BEMs) for solving integral equations numerically have been used in many fields to compute the induced charges at dielectric boundaries. In this paper, we consider a more accurate implementation of BEM in the context of ions in aqueous solution near proteins, but our results are applicable more generally. The ions that modulate protein function are often within a few angstroms of the protein, which leads to the significant accumulation of polarization charge at the protein-solvent interface. Computing the induced charge accurately and quickly poses a numerical challenge in solving a popular integral equation using BEM. In particular, the accuracy of simulations can depend strongly on seemingly minor details of how the entries of the BEM matrix are calculated. We demonstrate that when the dielectric interface is discretized into flat tiles, the qualocation method of Tausch [IEEE Trans Comput.-Comput.-Aided Des. 20, 1398 (2001)] to compute the BEM matrix elements is always more accurate than the traditional centroid-collocation method. Qualocation is not more expensive to implement than collocation and can save significant computational time by reducing the number of boundary elements needed to discretize the dielectric interfaces.

Discretization of the induced-charge boundary integral equation.

Energy Technology Data Exchange (ETDEWEB)

Bardhan, J. P.; Eisenberg, R. S.; Gillespie, D.; Rush Univ. Medical Center

2009-07-01

Boundary-element methods (BEMs) for solving integral equations numerically have been used in many fields to compute the induced charges at dielectric boundaries. In this paper, we consider a more accurate implementation of BEM in the context of ions in aqueous solution near proteins, but our results are applicable more generally. The ions that modulate protein function are often within a few angstroms of the protein, which leads to the significant accumulation of polarization charge at the protein-solvent interface. Computing the induced charge accurately and quickly poses a numerical challenge in solving a popular integral equation using BEM. In particular, the accuracy of simulations can depend strongly on seemingly minor details of how the entries of the BEM matrix are calculated. We demonstrate that when the dielectric interface is discretized into flat tiles, the qualocation method of Tausch et al. [IEEE Trans Comput.-Comput.-Aided Des. 20, 1398 (2001)] to compute the BEM matrix elements is always more accurate than the traditional centroid-collocation method. Qualocation is not more expensive to implement than collocation and can save significant computational time by reducing the number of boundary elements needed to discretize the dielectric interfaces.

[Evaluation of ten fish species to be included as part of renal diet, due to their protein, phosphorus and fatty acids content].

Science.gov (United States)

Castro-González, Maria Isabel; Maafs-Rodríguez, Ana Gabriela; Pérez-Gil Romo, Fernando

2012-06-01

Because renal disease is highly complex, its nutritional treatment is complicated and many foods are restricted, including fish because its phosphorus content. The aim of the present study was to analyze ten fillet fish species, commonly consumed in Mexico (Cyprinus carpio carpio, Ophichthus rex, Symphurus elongatus, Eucinostomus entomelas, Chirostoma patzcuaro, Bairdiella chrysoura, Salmo salar Oreochromis urolepis hornorum, Sphyraena guachancho, Istiophorus albicans), to determine their phosphorus (P), protein (Pr), cholesterol, sodium, potassium, vitamins D3 and E, and n-3 PUFA (EPA+DHA) according to the AOAC techniques, in order to identify which species could be included in renal diet; particularly because of their risk:benefit relations (calculated with those results). Protein values ranged from 16.5 to 33.5g/100 g of fillet; the specie with the highest phosphorus contest was Salmo salar, and with the lowest, Symphurus elongatus. EPA+DHA quantity ranged from 79.64 mg/100 g to 1,381.53 mg/100 g. Considering de P/Pr relation recommended to renal patients, all analyzed species (except Salmo salar, Ophichthus rex and Istiophorus albicans) could be included in their diet. As for the P/EPA+DHA relation, the species most recommended to renal patients are Symphurus elongatus, Bairdiella chrysoura and Sphyraena guachancho.

Inverse Modeling Using Markov Chain Monte Carlo Aided by Adaptive Stochastic Collocation Method with Transformation

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Zhang, D.; Liao, Q.

2016-12-01

The Bayesian inference provides a convenient framework to solve statistical inverse problems. In this method, the parameters to be identified are treated as random variables. The prior knowledge, the system nonlinearity, and the measurement errors can be directly incorporated in the posterior probability density function (PDF) of the parameters. The Markov chain Monte Carlo (MCMC) method is a powerful tool to generate samples from the posterior PDF. However, since the MCMC usually requires thousands or even millions of forward simulations, it can be a computationally intensive endeavor, particularly when faced with large-scale flow and transport models. To address this issue, we construct a surrogate system for the model responses in the form of polynomials by the stochastic collocation method. In addition, we employ interpolation based on the nested sparse grids and takes into account the different importance of the parameters, under the condition of high random dimensions in the stochastic space. Furthermore, in case of low regularity such as discontinuous or unsmooth relation between the input parameters and the output responses, we introduce an additional transform process to improve the accuracy of the surrogate model. Once we build the surrogate system, we may evaluate the likelihood with very little computational cost. We analyzed the convergence rate of the forward solution and the surrogate posterior by Kullback-Leibler divergence, which quantifies the difference between probability distributions. The fast convergence of the forward solution implies fast convergence of the surrogate posterior to the true posterior. We also tested the proposed algorithm on water-flooding two-phase flow reservoir examples. The posterior PDF calculated from a very long chain with direct forward simulation is assumed to be accurate. The posterior PDF calculated using the surrogate model is in reasonable agreement with the reference, revealing a great improvement in terms of

Protein-Protein Docking in Drug Design and Discovery.

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Kaczor, Agnieszka A; Bartuzi, Damian; Stępniewski, Tomasz Maciej; Matosiuk, Dariusz; Selent, Jana

2018-01-01

Protein-protein interactions (PPIs) are responsible for a number of key physiological processes in the living cells and underlie the pathomechanism of many diseases. Nowadays, along with the concept of so-called "hot spots" in protein-protein interactions, which are well-defined interface regions responsible for most of the binding energy, these interfaces can be targeted with modulators. In order to apply structure-based design techniques to design PPIs modulators, a three-dimensional structure of protein complex has to be available. In this context in silico approaches, in particular protein-protein docking, are a valuable complement to experimental methods for elucidating 3D structure of protein complexes. Protein-protein docking is easy to use and does not require significant computer resources and time (in contrast to molecular dynamics) and it results in 3D structure of a protein complex (in contrast to sequence-based methods of predicting binding interfaces). However, protein-protein docking cannot address all the aspects of protein dynamics, in particular the global conformational changes during protein complex formation. In spite of this fact, protein-protein docking is widely used to model complexes of water-soluble proteins and less commonly to predict structures of transmembrane protein assemblies, including dimers and oligomers of G protein-coupled receptors (GPCRs). In this chapter we review the principles of protein-protein docking, available algorithms and software and discuss the recent examples, benefits, and drawbacks of protein-protein docking application to water-soluble proteins, membrane anchoring and transmembrane proteins, including GPCRs.

Molecular network including eIF1AX, RPS7, and 14-3-3γ regulates protein translation and cell proliferation in bovine mammary epithelial cells.

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Yu, Cuiping; Luo, Chaochao; Qu, Bo; Khudhair, Nagam; Gu, Xinyu; Zang, Yanli; Wang, Chunmei; Zhang, Na; Li, Qingzhang; Gao, Xuejun

2014-12-15

14-3-3γ, an isoform of the 14-3-3 protein family, was proved to be a positive regulator of mTOR pathway. Here, we analyzed the function of 14-3-3γ in protein synthesis using bovine mammary epithelial cells (BMECs). We found that 14-3-3γ interacted with eIF1AX and RPS7 by 14-3-3γ coimmunoprecipitation (CoIP) and matrix-assisted laser desorption/ionization-time-of-flight/time-of-flight (MALDI-TOF/TOF) peptide mass fingerprinting analysis. These interactions of 14-3-3γ with eIF1AX and RPS7 were further confirmed by colocalization and fluorescence resonance energy transfer (FRET) analysis. We also found that methionine could promote protein synthesis and trigger the protein expression levels of 14-3-3γ, eIF1AX and RPS7. Analysis of overexpression and inhibition of 14-3-3γ confirmed that it positively affected the protein expression levels of eIF1AX, RPS7, Stat5 and mTOR pathway to promote protein synthesis and cell proliferation in BMECs. We further showed that overexpression of eIF1AX and RPS7 also triggered protein translation and cell proliferation. From these results, we conclude that molecular network including eIF1AX, RPS7, and 14-3-3γ regulates protein translation and cell proliferation in BMECs. Copyright © 2014 Elsevier Inc. All rights reserved.

Integrated High-Speed Torque Control System for a Robotic Joint

Science.gov (United States)

Davis, Donald R. (Inventor); Radford, Nicolaus A. (Inventor); Permenter, Frank Noble (Inventor); Valvo, Michael C. (Inventor); Askew, R. Scott (Inventor)

2013-01-01

A control system for achieving high-speed torque for a joint of a robot includes a printed circuit board assembly (PCBA) having a collocated joint processor and high-speed communication bus. The PCBA may also include a power inverter module (PIM) and local sensor conditioning electronics (SCE) for processing sensor data from one or more motor position sensors. Torque control of a motor of the joint is provided via the PCBA as a high-speed torque loop. Each joint processor may be embedded within or collocated with the robotic joint being controlled. Collocation of the joint processor, PIM, and high-speed bus may increase noise immunity of the control system, and the localized processing of sensor data from the joint motor at the joint level may minimize bus cabling to and from each control node. The joint processor may include a field programmable gate array (FPGA).

Lack of Detection of Bt Sugarcane Cry1Ab and NptII DNA and Proteins in Sugarcane Processing Products Including Raw Sugar

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Adriana Cheavegatti-Gianotto

2018-03-01

Full Text Available Brazil is the largest sugarcane producer and the main sugar exporter in the world. The industrial processes applied by Brazilian mills are very efficient in producing highly purified sugar and ethanol. Literature presents evidence of lack of DNA/protein in these products, regardless of the nature of sugarcane used as raw material. Recently CTNBio, the Brazilian biosafety authority, has approved the first biotechnology-derived sugarcane variety for cultivation, event CTC175-A, which expresses the Cry1Ab protein to control the sugarcane borer (Diatraea saccharalis. The event also expresses neomycin-phosphotransferase type II (NptII protein used as selectable marker during the transformation process. Because of the high purity of sugar and ethanol produced from genetically modified sugarcane, these end-products should potentially be classified as “pure substances, chemically defined,” by Brazilian Biosafety Law No. 11.105. If this classification is to be adopted, these substances are not considered as “GMO derivatives” and fall out of the scope of Law No. 11.105. In order to assess sugar composition and quality, we evaluate Cry1Ab and NptII expression in several sugarcane tissues and in several fractions from laboratory-scale processing of event CTC175-A for the presence of these heterologous proteins as well as for the presence of traces of recombinant DNA. The results of these studies show that CTC175-A presents high expression of Cry1Ab in leaves and barely detectable expression of heterologous proteins in stalks. We also evaluated the presence of ribulose-1,5-bisphosphate carboxylase/oxygenase protein and DNA in the fractions of the industrial processing of conventional Brazilian sugarcane cultivars. Results from both laboratory and industrial processing were concordant, demonstrating that DNA and protein are not detected in the clarified juice and downstream processed fractions, including ethanol and raw sugar, indicating that protein

The TAL effector PthA4 interacts with nuclear factors involved in RNA-dependent processes including a HMG protein that selectively binds poly(U RNA.

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Tiago Antonio de Souza

Full Text Available Plant pathogenic bacteria utilize an array of effector proteins to cause disease. Among them, transcriptional activator-like (TAL effectors are unusual in the sense that they modulate transcription in the host. Although target genes and DNA specificity of TAL effectors have been elucidated, how TAL proteins control host transcription is poorly understood. Previously, we showed that the Xanthomonas citri TAL effectors, PthAs 2 and 3, preferentially targeted a citrus protein complex associated with transcription control and DNA repair. To extend our knowledge on the mode of action of PthAs, we have identified new protein targets of the PthA4 variant, required to elicit canker on citrus. Here we show that all the PthA4-interacting proteins are DNA and/or RNA-binding factors implicated in chromatin remodeling and repair, gene regulation and mRNA stabilization/modification. The majority of these proteins, including a structural maintenance of chromosomes protein (CsSMC, a translin-associated factor X (CsTRAX, a VirE2-interacting protein (CsVIP2, a high mobility group (CsHMG and two poly(A-binding proteins (CsPABP1 and 2, interacted with each other, suggesting that they assemble into a multiprotein complex. CsHMG was shown to bind DNA and to interact with the invariable leucine-rich repeat region of PthAs. Surprisingly, both CsHMG and PthA4 interacted with PABP1 and 2 and showed selective binding to poly(U RNA, a property that is novel among HMGs and TAL effectors. Given that homologs of CsHMG, CsPABP1, CsPABP2, CsSMC and CsTRAX in other organisms assemble into protein complexes to regulate mRNA stability and translation, we suggest a novel role of TAL effectors in mRNA processing and translational control.

Identification and characterization of novel ERC-55 interacting proteins: evidence for the existence of several ERC-55 splicing variants; including the cytosolic ERC-55-C.

Science.gov (United States)

Ludvigsen, Maja; Jacobsen, Christian; Maunsbach, Arvid B; Honoré, Bent

2009-12-01

ERC-55, encoded from RCN2, is localized in the ER and belongs to the CREC protein family. ERC-55 is involved in various diseases and abnormal cell behavior, however, the function is not well defined and it has controversially been reported to interact with a cytosolic protein, the vitamin D receptor. We have used a number of proteomic techniques to further our functional understanding of ERC-55. By affinity purification, we observed interaction with a large variety of proteins, including those secreted and localized outside of the secretory pathway, in the cytosol and also in various organelles. We confirm the existence of several ERC-55 splicing variants including ERC-55-C localized in the cytosol in association with the cytoskeleton. Localization was verified by immunoelectron microscopy and sub-cellular fractionation. Interaction of lactoferrin, S100P, calcyclin (S100A6), peroxiredoxin-6, kininogen and lysozyme with ERC-55 was further studied in vitro by SPR experiments. Interaction of S100P requires [Ca(2+)] of approximately 10(-7) M or greater, while calcyclin interaction requires [Ca(2+)] of >10(-5) M. Interaction with peroxiredoxin-6 is independent of Ca(2+). Co-localization of lactoferrin, S100P and calcyclin with ERC-55 in the perinuclear area was analyzed by fluorescence confocal microscopy. The functional variety of the interacting proteins indicates a broad spectrum of ERC-55 activities such as immunity, redox homeostasis, cell cycle regulation and coagulation.

Assigning Significance in Label-Free Quantitative Proteomics to Include Single-Peptide-Hit Proteins with Low Replicates

OpenAIRE

Li, Qingbo

2010-01-01

When sample replicates are limited in a label-free proteomics experiment, selecting differentially regulated proteins with an assignment of statistical significance remains difficult for proteins with a single-peptide hit or a small fold-change. This paper aims to address this issue. An important component of the approach employed here is to utilize the rule of Minimum number of Permuted Significant Pairings (MPSP) to reduce false positives. The MPSP rule generates permuted sample pairings fr...

[Renal patient's diet: Can fish be included?].

Science.gov (United States)

Castro González, M I; Maafs Rodríguez, A G; Galindo Gómez, C

2012-01-01

Medical and nutritional treatment for renal disease, now a major public health issue, is highly complicated. Nutritional therapy must seek to retard renal dysfunction, maintain an optimal nutritional status and prevent the development of underlying pathologies. To analyze ten fish species to identify those that, because of their low phosphorus content, high biological value protein and elevated n-3 fatty acids EPA and DHA, could be included in renal patient's diet. The following fish species (Litte tunny, Red drum, Spotted eagleray, Escolar, Swordfish, Big-scale pomfret, Cortez flounder, Largemouth blackbass, Periche mojarra, Florida Pompano) were analyzed according to the AOAC and Keller techniques to determine their protein, phosphorus, sodium, potassium, cholesterol, vitamins D(3) and E, and n-3 EPA+DHA content. These results were used to calculate relations between nutrients. The protein in the analyzed species ranged from 16.5 g/100 g of fillet (Largemouth black bass) to 27.2 g/100 g (Red drum); the lowest phosphorus value was 28.6 mg/100 g (Periche mojarra) and the highest 216.3 mg/100 g (Spotted eagle ray). 80% of the fish presented > 100 mg EPA + DHA in 100 g of fillet. By its Phosphorus/gProtein ratio, Escolar and Swordfish could not be included in the renal diet; Little tunny, Escolar, Big-scale pomfret, Largemouth black-bass, Periche mojarra and Florida Pompano presented a lower Phosphorus/EPA + DHA ratio. Florida pompano is the most recommended specie for renal patients, due to its optimal nutrient relations. However, all analyzed species, except Escolar and Swordfish, could be included in renal diets.

batman Interacts with polycomb and trithorax group genes and encodes a BTB/POZ protein that is included in a complex containing GAGA factor.

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Faucheux, M; Roignant, J-Y; Netter, S; Charollais, J; Antoniewski, C; Théodore, L

2003-02-01

Polycomb and trithorax group genes maintain the appropriate repressed or activated state of homeotic gene expression throughout Drosophila melanogaster development. We have previously identified the batman gene as a Polycomb group candidate since its function is necessary for the repression of Sex combs reduced. However, our present genetic analysis indicates functions of batman in both activation and repression of homeotic genes. The 127-amino-acid Batman protein is almost reduced to a BTB/POZ domain, an evolutionary conserved protein-protein interaction domain found in a large protein family. We show that this domain is involved in the interaction between Batman and the DNA binding GAGA factor encoded by the Trithorax-like gene. The GAGA factor and Batman codistribute on polytene chromosomes, coimmunoprecipitate from nuclear embryonic and larval extracts, and interact in the yeast two-hybrid assay. Batman, together with the GAGA factor, binds to MHS-70, a 70-bp fragment of the bithoraxoid Polycomb response element. This binding, like that of the GAGA factor, requires the presence of d(GA)n sequences. Together, our results suggest that batman belongs to a subset of the Polycomb/trithorax group of genes that includes Trithorax-like, whose products are involved in both activation and repression of homeotic genes.

Study on the Single Scattering of Elastic Waves by a Cylindrical Fiber with a Partially Imperfect Bonding Using the Collocation Point Method

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Jun Zhang

2018-01-01

Full Text Available The single scattering of P- and SV-waves by a cylindrical fiber with a partially imperfect bonding to the surrounding matrix is investigated, which benefits the characterization of the behavior of elastic waves in composite materials. The imperfect interface is modelled by the spring model. To solve the corresponding single scattering problem, a collocation point (CP method is introduced. Based on this method, influence of various aspects of the imperfect interface on the scattering of P- and SV-waves is studied. Results indicate that (i the total scattering cross section (SCS is almost symmetric about the axis α=π/2 with respect to the location (α of the imperfect interface, (ii imperfect interfaces located at α=0 and α=π highly reduce the total SCS under a P-wave incidence and imperfect interfaces located at α=π/2 reduce the total SCS most significantly under SV-incidence, and (iii under a P-wave incidence the SCS has a high sensitivity to the bonding level of imperfect interfaces when α is small, while it becomes more sensitive to the bonding level when α is larger under SV-wave incidence.

The Ser/Thr Protein Kinase Protein-Protein Interaction Map of M. tuberculosis.

Science.gov (United States)

Wu, Fan-Lin; Liu, Yin; Jiang, He-Wei; Luan, Yi-Zhao; Zhang, Hai-Nan; He, Xiang; Xu, Zhao-Wei; Hou, Jing-Li; Ji, Li-Yun; Xie, Zhi; Czajkowsky, Daniel M; Yan, Wei; Deng, Jiao-Yu; Bi, Li-Jun; Zhang, Xian-En; Tao, Sheng-Ce

2017-08-01

Mycobacterium tuberculosis (Mtb) is the causative agent of tuberculosis, the leading cause of death among all infectious diseases. There are 11 eukaryotic-like serine/threonine protein kinases (STPKs) in Mtb, which are thought to play pivotal roles in cell growth, signal transduction and pathogenesis. However, their underlying mechanisms of action remain largely uncharacterized. In this study, using a Mtb proteome microarray, we have globally identified the binding proteins in Mtb for all of the STPKs, and constructed the first STPK protein interaction (KPI) map that includes 492 binding proteins and 1,027 interactions. Bioinformatics analysis showed that the interacting proteins reflect diverse functions, including roles in two-component system, transcription, protein degradation, and cell wall integrity. Functional investigations confirmed that PknG regulates cell wall integrity through key components of peptidoglycan (PG) biosynthesis, e.g. MurC. The global STPK-KPIs network constructed here is expected to serve as a rich resource for understanding the key signaling pathways in Mtb, thus facilitating drug development and effective control of Mtb. © 2017 by The American Society for Biochemistry and Molecular Biology, Inc.

Occurrence of dead core in catalytic particles containing immobilized enzymes: analysis for the Michaelis-Menten kinetics and assessment of numerical methods.

Science.gov (United States)

Pereira, Félix Monteiro; Oliveira, Samuel Conceição

2016-11-01

In this article, the occurrence of dead core in catalytic particles containing immobilized enzymes is analyzed for the Michaelis-Menten kinetics. An assessment of numerical methods is performed to solve the boundary value problem generated by the mathematical modeling of diffusion and reaction processes under steady state and isothermal conditions. Two classes of numerical methods were employed: shooting and collocation. The shooting method used the ode function from Scilab software. The collocation methods included: that implemented by the bvode function of Scilab, the orthogonal collocation, and the orthogonal collocation on finite elements. The methods were validated for simplified forms of the Michaelis-Menten equation (zero-order and first-order kinetics), for which analytical solutions are available. Among the methods covered in this article, the orthogonal collocation on finite elements proved to be the most robust and efficient method to solve the boundary value problem concerning Michaelis-Menten kinetics. For this enzyme kinetics, it was found that the dead core can occur when verified certain conditions of diffusion-reaction within the catalytic particle. The application of the concepts and methods presented in this study will allow for a more generalized analysis and more accurate designs of heterogeneous enzymatic reactors.

The COG database: an updated version includes eukaryotes

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Sverdlov Alexander V

2003-09-01

Full Text Available Abstract Background The availability of multiple, essentially complete genome sequences of prokaryotes and eukaryotes spurred both the demand and the opportunity for the construction of an evolutionary classification of genes from these genomes. Such a classification system based on orthologous relationships between genes appears to be a natural framework for comparative genomics and should facilitate both functional annotation of genomes and large-scale evolutionary studies. Results We describe here a major update of the previously developed system for delineation of Clusters of Orthologous Groups of proteins (COGs from the sequenced genomes of prokaryotes and unicellular eukaryotes and the construction of clusters of predicted orthologs for 7 eukaryotic genomes, which we named KOGs after eukaryotic orthologous groups. The COG collection currently consists of 138,458 proteins, which form 4873 COGs and comprise 75% of the 185,505 (predicted proteins encoded in 66 genomes of unicellular organisms. The eukaryotic orthologous groups (KOGs include proteins from 7 eukaryotic genomes: three animals (the nematode Caenorhabditis elegans, the fruit fly Drosophila melanogaster and Homo sapiens, one plant, Arabidopsis thaliana, two fungi (Saccharomyces cerevisiae and Schizosaccharomyces pombe, and the intracellular microsporidian parasite Encephalitozoon cuniculi. The current KOG set consists of 4852 clusters of orthologs, which include 59,838 proteins, or ~54% of the analyzed eukaryotic 110,655 gene products. Compared to the coverage of the prokaryotic genomes with COGs, a considerably smaller fraction of eukaryotic genes could be included into the KOGs; addition of new eukaryotic genomes is expected to result in substantial increase in the coverage of eukaryotic genomes with KOGs. Examination of the phyletic patterns of KOGs reveals a conserved core represented in all analyzed species and consisting of ~20% of the KOG set. This conserved portion of the

Protein docking prediction using predicted protein-protein interface

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Li Bin

2012-01-01

Full Text Available Abstract Background Many important cellular processes are carried out by protein complexes. To provide physical pictures of interacting proteins, many computational protein-protein prediction methods have been developed in the past. However, it is still difficult to identify the correct docking complex structure within top ranks among alternative conformations. Results We present a novel protein docking algorithm that utilizes imperfect protein-protein binding interface prediction for guiding protein docking. Since the accuracy of protein binding site prediction varies depending on cases, the challenge is to develop a method which does not deteriorate but improves docking results by using a binding site prediction which may not be 100% accurate. The algorithm, named PI-LZerD (using Predicted Interface with Local 3D Zernike descriptor-based Docking algorithm, is based on a pair wise protein docking prediction algorithm, LZerD, which we have developed earlier. PI-LZerD starts from performing docking prediction using the provided protein-protein binding interface prediction as constraints, which is followed by the second round of docking with updated docking interface information to further improve docking conformation. Benchmark results on bound and unbound cases show that PI-LZerD consistently improves the docking prediction accuracy as compared with docking without using binding site prediction or using the binding site prediction as post-filtering. Conclusion We have developed PI-LZerD, a pairwise docking algorithm, which uses imperfect protein-protein binding interface prediction to improve docking accuracy. PI-LZerD consistently showed better prediction accuracy over alternative methods in the series of benchmark experiments including docking using actual docking interface site predictions as well as unbound docking cases.

Protein docking prediction using predicted protein-protein interface.

Science.gov (United States)

Li, Bin; Kihara, Daisuke

2012-01-10

Many important cellular processes are carried out by protein complexes. To provide physical pictures of interacting proteins, many computational protein-protein prediction methods have been developed in the past. However, it is still difficult to identify the correct docking complex structure within top ranks among alternative conformations. We present a novel protein docking algorithm that utilizes imperfect protein-protein binding interface prediction for guiding protein docking. Since the accuracy of protein binding site prediction varies depending on cases, the challenge is to develop a method which does not deteriorate but improves docking results by using a binding site prediction which may not be 100% accurate. The algorithm, named PI-LZerD (using Predicted Interface with Local 3D Zernike descriptor-based Docking algorithm), is based on a pair wise protein docking prediction algorithm, LZerD, which we have developed earlier. PI-LZerD starts from performing docking prediction using the provided protein-protein binding interface prediction as constraints, which is followed by the second round of docking with updated docking interface information to further improve docking conformation. Benchmark results on bound and unbound cases show that PI-LZerD consistently improves the docking prediction accuracy as compared with docking without using binding site prediction or using the binding site prediction as post-filtering. We have developed PI-LZerD, a pairwise docking algorithm, which uses imperfect protein-protein binding interface prediction to improve docking accuracy. PI-LZerD consistently showed better prediction accuracy over alternative methods in the series of benchmark experiments including docking using actual docking interface site predictions as well as unbound docking cases.

Slavic Phraseology: A View Through Corpora

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Zakharov Victor

2017-12-01

Full Text Available The study of word collocability is one of the main tasks of linguistics. The combinatory ability of language units, collocability, is one of the linguistic syntagmatic laws. This phenomenon is the main object of the phraseology and lexicography. The article deals with set phrases of different types in Russian, Czech and Slovak from the point of view of their quantitative evaluation. Corpus linguistics understand set phrases as statistically determined unities. This approach is the basic point of different automatic ways to extract idioms and collocations. The paper describes experiments which show how text corpora and corpus methods and tools can be used to expand the entries in existing dictionaries and how set phrases could be evaluated quantitatively. It is shown and maintained that corpus linguistics methods and tools allow to create dictionaries of new type which have to include a larger amount of set phrases and collocations than before.

Double demonstration of oncogenic high risk human papilloma virus DNA and HPV-E7 protein in oral cancers.

Science.gov (United States)

Pannone, G; Santoro, A; Carinci, F; Bufo, P; Papagerakis, S M; Rubini, C; Campisi, G; Giovannelli, L; Contaldo, M; Serpico, R; Mazzotta, M; Lo Muzio, L

2011-01-01

Oncogenic HPVs are necessarily involved in cervical cancer but their role in oral carcinogenesis is debated. To detect HPV in oral cancer, 38 cases of formalin fixed-paraffin embedded OSCC were studied by both DNA genotyping (MY09/11 L1 consensus primers in combination with GP5-GP6 primer pair followed by sequencing) and immunohistochemistry (monoclonal Abs against capsid protein and HPV-E7 protein, K1H8 DAKO and clone 8C9 INVITROGEN, respectively). HPV-16 tonsil cancer was used as positive control. The overall prevalence of HPV infection in OSCCs was 10.5%. Amplification of DNA samples showed single HPV DNA infection in 3 cases (HPV16; HPV53; HPV70) and double infection in one case of cheek cancer (HPV31/HPV44). The overall HR-HPV prevalence was 7.5%. E-7 antigen was immunohistochemically detected in all HPV-positive cases. HPV+ OSCC cases showed an overall better outcome than HPV negative oral cancers, as evaluated by Kaplan-Meier curves. HPVs exert their oncogenic role after DNA integration, gene expression of E5, E6 and E7 loci and p53/pRb host proteins suppression. This study showed that HPV-E7 protein inactivating pRb is expressed in oral cancer cells infected by oncogenic HPV other than classical HR-HPV-16/18. Interestingly HPV-70, considered a low risk virus with no definite collocation in oncogenic type category, gives rise to the expression of HPV-E7 protein and inactivate pRb in oral cancer. HPV-70, as proved in current literature, is able to inactivates also p53 protein, promoting cell immortalization. HPV-53, classified as a possible high risk virus, expresses E7 protein in OSCC, contributing to oral carcinogenesis. We have identified among OSCCs, a subgroup characterized by HPV infection (10.5%). Finally, we have proved the oncogenic potential of some HPV virus types, not well known in literature.

Application of Computer Algebra Systems to the Construction of the Collocations and Least Residuals Method for Solving the 3D Navier–Stokes Equations

Directory of Open Access Journals (Sweden)

V. P. Shapeev

2014-01-01

Full Text Available The method of collocations and least residuals (CLR, which was proposed previously for the numerical solution of two-dimensional Navier–Stokes equations governing the stationary flows of a viscous incompressible fluid, is extended here for the three-dimensional case. The solution is sought in the implemented version of the method in the form of an expansion in the basis solenoidal functions. At all stages of the CLR method construction, a computer algebra system (CAS is applied for the derivation and verification of the formulas of the method and for their translation into arithmetic operators of the Fortran language. For accelerating the convergence of iterations a sufficiently universal algorithm is proposed, which is simple in its implementation and is based on the use of the Krylov’s subspaces. The obtained computational formulas of the CLR method were verified on the exact analytic solution of a test problem. Comparisons with the published numerical results of solving the benchmark problem of the 3D driven cubic cavity flow show that the accuracy of the results obtained by the CLR method corresponds to the known high-accuracy solutions.

Bioinformatic Prediction of WSSV-Host Protein-Protein Interaction

Directory of Open Access Journals (Sweden)

Zheng Sun

2014-01-01

Full Text Available WSSV is one of the most dangerous pathogens in shrimp aquaculture. However, the molecular mechanism of how WSSV interacts with shrimp is still not very clear. In the present study, bioinformatic approaches were used to predict interactions between proteins from WSSV and shrimp. The genome data of WSSV (NC_003225.1 and the constructed transcriptome data of F. chinensis were used to screen potentially interacting proteins by searching in protein interaction databases, including STRING, Reactome, and DIP. Forty-four pairs of proteins were suggested to have interactions between WSSV and the shrimp. Gene ontology analysis revealed that 6 pairs of these interacting proteins were classified into “extracellular region” or “receptor complex” GO-terms. KEGG pathway analysis showed that they were involved in the “ECM-receptor interaction pathway.” In the 6 pairs of interacting proteins, an envelope protein called “collagen-like protein” (WSSV-CLP encoded by an early virus gene “wsv001” in WSSV interacted with 6 deduced proteins from the shrimp, including three integrin alpha (ITGA, two integrin beta (ITGB, and one syndecan (SDC. Sequence analysis on WSSV-CLP, ITGA, ITGB, and SDC revealed that they possessed the sequence features for protein-protein interactions. This study might provide new insights into the interaction mechanisms between WSSV and shrimp.

With Protein Foods, Variety Is Key: 10 Tips for Choosing Protein

Science.gov (United States)

... Dietary Guidelines Communicator’s Guide 10 Tips: Vary Your Protein Routine You are here Home 10 Tips: Vary ... Protein Routine Print Share 10 Tips: Vary Your Protein Routine Protein foods include both animal (meat, poultry, ...

Mapping Protein-Protein Interactions by Quantitative Proteomics

DEFF Research Database (Denmark)

Dengjel, Joern; Kratchmarova, Irina; Blagoev, Blagoy

2010-01-01

spectrometry (MS)-based proteomics in combination with affinity purification protocols has become the method of choice to map and track the dynamic changes in protein-protein interactions, including the ones occurring during cellular signaling events. Different quantitative MS strategies have been used...... to characterize protein interaction networks. In this chapter we describe in detail the use of stable isotope labeling by amino acids in cell culture (SILAC) for the quantitative analysis of stimulus-dependent dynamic protein interactions.......Proteins exert their function inside a cell generally in multiprotein complexes. These complexes are highly dynamic structures changing their composition over time and cell state. The same protein may thereby fulfill different functions depending on its binding partners. Quantitative mass...

The case of proverbs in Northern Sotho

African Journals Online (AJOL)

user

ferences in collocational preference of several words in a single diagram. ..... but the strongest collocation is made with fake (8 vs. 5 and 4). Another ... picture, it is possible to remove the collocations with lower collocation scores, as in Fig. 3.

On the analysis of protein-protein interactions via knowledge-based potentials for the prediction of protein-protein docking

DEFF Research Database (Denmark)

Feliu, Elisenda; Aloy, Patrick; Oliva, Baldo

2011-01-01

Development of effective methods to screen binary interactions obtained by rigid-body protein-protein docking is key for structure prediction of complexes and for elucidating physicochemical principles of protein-protein binding. We have derived empirical knowledge-based potential functions for s...... and with independence of the partner. This information is encoded at the residue level and could be easily incorporated in the initial grid scoring for Fast Fourier Transform rigid-body docking methods.......Development of effective methods to screen binary interactions obtained by rigid-body protein-protein docking is key for structure prediction of complexes and for elucidating physicochemical principles of protein-protein binding. We have derived empirical knowledge-based potential functions...... for selecting rigid-body docking poses. These potentials include the energetic component that provides the residues with a particular secondary structure and surface accessibility. These scoring functions have been tested on a state-of-art benchmark dataset and on a decoy dataset of permanent interactions. Our...

Non-interacting surface solvation and dynamics in protein-protein interactions

NARCIS (Netherlands)

Visscher, Koen M.; Kastritis, Panagiotis L.|info:eu-repo/dai/nl/315886668; Bonvin, Alexandre M J J|info:eu-repo/dai/nl/113691238

2015-01-01

Protein-protein interactions control a plethora of cellular processes, including cell proliferation, differentiation, apoptosis, and signal transduction. Understanding how and why proteins interact will inevitably lead to novel structure-based drug design methods, as well as design of de novo

Protein function prediction using neighbor relativity in protein-protein interaction network.

Science.gov (United States)

Moosavi, Sobhan; Rahgozar, Masoud; Rahimi, Amir

2013-04-01

There is a large gap between the number of discovered proteins and the number of functionally annotated ones. Due to the high cost of determining protein function by wet-lab research, function prediction has become a major task for computational biology and bioinformatics. Some researches utilize the proteins interaction information to predict function for un-annotated proteins. In this paper, we propose a novel approach called "Neighbor Relativity Coefficient" (NRC) based on interaction network topology which estimates the functional similarity between two proteins. NRC is calculated for each pair of proteins based on their graph-based features including distance, common neighbors and the number of paths between them. In order to ascribe function to an un-annotated protein, NRC estimates a weight for each neighbor to transfer its annotation to the unknown protein. Finally, the unknown protein will be annotated by the top score transferred functions. We also investigate the effect of using different coefficients for various types of functions. The proposed method has been evaluated on Saccharomyces cerevisiae and Homo sapiens interaction networks. The performance analysis demonstrates that NRC yields better results in comparison with previous protein function prediction approaches that utilize interaction network. Copyright © 2012 Elsevier Ltd. All rights reserved.

Comparison between two meshless methods based on collocation technique for the numerical solution of four-species tumor growth model

Science.gov (United States)

Dehghan, Mehdi; Mohammadi, Vahid

2017-03-01

As is said in [27], the tumor-growth model is the incorporation of nutrient within the mixture as opposed to being modeled with an auxiliary reaction-diffusion equation. The formulation involves systems of highly nonlinear partial differential equations of surface effects through diffuse-interface models [27]. Simulations of this practical model using numerical methods can be applied for evaluating it. The present paper investigates the solution of the tumor growth model with meshless techniques. Meshless methods are applied based on the collocation technique which employ multiquadrics (MQ) radial basis function (RBFs) and generalized moving least squares (GMLS) procedures. The main advantages of these choices come back to the natural behavior of meshless approaches. As well as, a method based on meshless approach can be applied easily for finding the solution of partial differential equations in high-dimension using any distributions of points on regular and irregular domains. The present paper involves a time-dependent system of partial differential equations that describes four-species tumor growth model. To overcome the time variable, two procedures will be used. One of them is a semi-implicit finite difference method based on Crank-Nicolson scheme and another one is based on explicit Runge-Kutta time integration. The first case gives a linear system of algebraic equations which will be solved at each time-step. The second case will be efficient but conditionally stable. The obtained numerical results are reported to confirm the ability of these techniques for solving the two and three-dimensional tumor-growth equations.

Protein supplementation with sports protein bars in renal patients.

Science.gov (United States)

Meade, Anthony

2007-05-01

Malnutrition prevalence in patients on dialysis is well established. The protein requirements for both hemodialysis and peritoneal dialysis have been documented elsewhere, including the Kidney Disease Outcomes Quality Initiative Clinical Practice Guidelines for Nutrition in Chronic Renal Failure. The clinical challenge is to assist patients in meeting these targets, especially in those with anorexia. Traditional supplements have included fluid, which is an issue for patients who are fluid restricted. The study objectives were to (1) investigate the range of sports protein supplements that may be suitable for patients on hemodialysis to use and (2) trial nonfluid protein supplements in patients on hemodialysis. Known manufacturers of sports protein bars and other sports supplements available in Australia were contacted for the nutrient breakdown of high-protein products, specifically potassium, protein, and phosphorus contents. As a result, selected high-protein sports bars (Protein FX, Aussie Bodies, Port Melbourne, Victoria, Australia) were used as an alternative to the more commonly used renal-specific fluid supplements (Nepro, Abbott Laboratories, Abbott Park, IL; Novasource Renal, Novartis Nutrition Corporation, Fremont, MI; and Renilon, Nutricia, Wiltshire, UK) in patients with poor nutritional status requiring supplementation. Patient satisfaction and clinical nutrition markers were investigated. The study took place at inpatient, in-center, and satellite hemodialysis settings in Adelaide, South Australia. A total of 32 patients (16 females and 16 males) with an average age of 62.9 years (range 32-86 years) undergoing hemodialysis (acute and maintenance) were included. Subjects were selected by the author as part of routine clinical nutrition care. Patients trialed sports protein bars as a protein supplement alone or in conjunction with other supplementary products. All patients were in favor of the trial, with 22 of 32 patients continuing with the protein

Synchronous and Asynchronous Multimedia and Iranian EFL Learners’ Learning of Collocations

Directory of Open Access Journals (Sweden)

Goudarz Alibakhshi

2016-07-01

Full Text Available The use of effective multimedia instructions such as mobiles, computers, and the internet in language learning has turned out to be useful since the last decades. The impact of multimedia and synchronous approaches of computer-assisted language learning (CALL on English as a foreign language (EFL learners' learning of language skills and components has been studied to some extent. However, the impact of computerized mediated instruction through multimedia (text and graphics on learning collocations requires further investigations. This study aimed at investigating whether synchronous and asynchronous multimedia components: text and text with added graphics had any effects on EFL learners' learning of collocations. In doing so, 150 male EFL learners at pre-intermediate proficiency level were selected through convenience sampling. They were divided into six groups. The results of the study showed that computerized mediated instruction was more effective than non-computerized instruction. Also, synchronous computerized instruction was more effective than asynchronous computerized instruction. The results also showed that presentation through text with added graphics was more effective than presentation through simple text. The results are discussed and some pedagogical implications are presented.   Persian Abstract: استفاده ازآموزش های چند رسانه ای مؤثر مانند موبایل، کامپیوتر، و اینترنت در آموزش زبان  از چند دهه قبل مرسوم شده است. تأثیر چند رسانه ای و روش های همزمان یادگیری  زبان به کمک کامپیوتر (CALL  بر  یادگیری مؤلفه ها و مهارتهای زبان انگلیسی به عنوان یک زبان خارجی (EFL توسط زبان آموزان  تا حدی مورد  مطالعه قرار گرفته است. بااین حال، تأثیر آموزش با کامپیوتر از طریق �

A Hydrological Tomography Collocated with Time-varying Gravimetry for Hydrogeology -An Example in Yun-Lin Alluvial Plain and Ming-Ju Basin in Taiwan

Science.gov (United States)

Chen, K. H.; Cheng, C. C.; Hwang, C.

2016-12-01

A new inversion technique featured by the collocation of hydrological modeling and gravimetry observation is presented in this report. Initially this study started from a project attempting to build a sequence of hydrodynamic models of ground water system, which was applied to identify the supplement areas of alluvial plains and basins along the west coast of Taiwan. To calibrate the decent hydro-geological parameters for the modeling, geological evolution were carefully investigated and absolute gravity observations, along with other on-site hydrological monitoring data were specially introduced. It was discovered in the data processing that the time-varying gravimetrical data are highly sensitive to certain boundary conditions in the hydrodynamic model, which are correspondent with respective geological features. A new inversion technique coined by the term "hydrological tomography" is therefore developed by reversing the boundary condition into the unknowns to be solved. An example of accurate estimate for water storage and precipitation infiltration of a costal alluvial plain Yun-Lin is presented. In the mean time, the study of an anticline structure of the upstream basin Ming-Ju is also presented to demonstrate how a geological formation is outlined when the gravimetrical data and hydrodynamic model are re-directed into an inversion.

A method for investigating protein-protein interactions related to Salmonella typhimurium pathogenesis

Energy Technology Data Exchange (ETDEWEB)

Chowdhury, Saiful M. [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Shi, Liang [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Yoon, Hyunjin [Dartmouth College, Hanover, NH (United States); Ansong, Charles [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Rommereim, Leah M. [Dartmouth College, Hanover, NH (United States); Norbeck, Angela D. [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Auberry, Kenneth J. [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Moore, R. J. [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Adkins, Joshua N. [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Heffron, Fred [Oregon Health and Science Univ., Portland, OR (United States); Smith, Richard D. [Pacific Northwest National Lab. (PNNL), Richland, WA (United States)

2009-02-10

We successfully modified an existing method to investigate protein-protein interactions in the pathogenic bacterium Salmonella typhimurium (STM). This method includes i) addition of a histidine-biotin-histidine tag to the bait proteins via recombinant DNA techniques; ii) in vivo cross-linking with formaldehyde; iii) tandem affinity purification of bait proteins under fully denaturing conditions; and iv) identification of the proteins cross-linked to the bait proteins by liquid-chromatography in conjunction with tandem mass-spectrometry. In vivo cross-linking stabilized protein interactions permitted the subsequent two-step purification step conducted under denaturing conditions. The two-step purification greatly reduced nonspecific binding of non-cross-linked proteins to bait proteins. Two different negative controls were employed to reduce false-positive identification. In an initial demonstration of this approach, we tagged three selected STM proteins- HimD, PduB and PhoP- with known binding partners that ranged from stable (e.g., HimD) to transient (i.e., PhoP). Distinct sets of interacting proteins were identified with each bait protein, including the known binding partners such as HimA for HimD, as well as anticipated and unexpected binding partners. Our results suggest that novel protein-protein interactions may be critical to pathogenesis by Salmonella typhimurium. .

Novel Technology for Protein-Protein Interaction-based Targeted Drug Discovery

Directory of Open Access Journals (Sweden)

Jung Me Hwang

2011-12-01

Full Text Available We have developed a simple but highly efficient in-cell protein-protein interaction (PPI discovery system based on the translocation properties of protein kinase C- and its C1a domain in live cells. This system allows the visual detection of trimeric and dimeric protein interactions including cytosolic, nuclear, and/or membrane proteins with their cognate ligands. In addition, this system can be used to identify pharmacological small compounds that inhibit specific PPIs. These properties make this PPI system an attractive tool for screening drug candidates and mapping the protein interactome.

Members of the HCMV US12 family of predicted heptaspanning membrane proteins have unique intracellular distributions, including association with the cytoplasmic virion assembly complex

International Nuclear Information System (INIS)

Das, Subhendu; Pellett, Philip E.

2007-01-01

The human cytomegalovirus (HCMV) US12 gene family is a group of 10 predicted seven-transmembrane domain proteins that have some features in common with G-protein-coupled receptors. Little is known of their patterns of expression, localization, or functional interactions. Here, we studied the intracellular localization of three US12 family members, US14, US17, and US18, with respect to various intracellular markers and the cytoplasmic virion assembly compartment (AC). The three proteins have distinct patterns of expression, which include associations with the AC. US14 is often distributed in a uniform granular manner throughout the cytoplasm, concentrating in the AC in some cells. US17 is expressed in a segmented manner, with its N-terminal domain localizing to the periphery of what we show here to be the AC and the C-terminal domain localizing to nuclei and the cytoplasm [Das, S., Skomorovska-Prokvolit, Y., Wang, F. Z., Pellett, P.E., 2006. Infection-dependent nuclear localization of US17, a member of the US12 family of human cytomegalovirus-encoded seven-transmembrane proteins. J. Virol. 80, 1191-1203]. Here, we show that the C-terminal domain is present at the center of the AC, in close association with markers of early endosomes; the N-terminal staining corresponds to an area stained by markers for the Golgi and trans-Golgi. US18 is distributed throughout the cytoplasm, concentrating in the AC at later stages of infection; it is localized more to the periphery of the AC than are US14 and US17C, in association with markers of the trans-Golgi. Although not detected in virions, their structures and localization in various zones within the AC suggest possible roles for these proteins in the process of virion maturation and egress

Cold and Heat Stress Diversely Alter Both Cauliflower Respiration and Distinct Mitochondrial Proteins Including OXPHOS Components and Matrix Enzymes

Science.gov (United States)

Rurek, Michał; Czołpińska, Magdalena; Pawłowski, Tomasz Andrzej; Krzesiński, Włodzimierz; Spiżewski, Tomasz

2018-01-01

Complex proteomic and physiological approaches for studying cold and heat stress responses in plant mitochondria are still limited. Variations in the mitochondrial proteome of cauliflower (Brassica oleracea var. botrytis) curds after cold and heat and after stress recovery were assayed by two-dimensional polyacrylamide gel electrophoresis (2D PAGE) in relation to mRNA abundance and respiratory parameters. Quantitative analysis of the mitochondrial proteome revealed numerous stress-affected protein spots. In cold, major downregulations in the level of photorespiratory enzymes, porine isoforms, oxidative phosphorylation (OXPHOS) and some low-abundant proteins were observed. In contrast, carbohydrate metabolism enzymes, heat-shock proteins, translation, protein import, and OXPHOS components were involved in heat response and recovery. Several transcriptomic and metabolic regulation mechanisms are also suggested. Cauliflower plants appeared less susceptible to heat; closed stomata in heat stress resulted in moderate photosynthetic, but only minor respiratory impairments, however, photosystem II performance was unaffected. Decreased photorespiration corresponded with proteomic alterations in cold. Our results show that cold and heat stress not only operate in diverse modes (exemplified by cold-specific accumulation of some heat shock proteins), but exert some associations at molecular and physiological levels. This implies a more complex model of action of investigated stresses on plant mitochondria. PMID:29547512

ProteinTracker: an application for managing protein production and purification.

Science.gov (United States)

Ponko, Stefan C; Bienvenue, David

2012-05-10

Laboratories that produce protein reagents for research and development face the challenge of deciding whether to track batch-related data using simple file based storage mechanisms (e.g. spreadsheets and notebooks), or commit the time and effort to install, configure and maintain a more complex laboratory information management system (LIMS). Managing reagent data stored in files is challenging because files are often copied, moved, and reformatted. Furthermore, there is no simple way to query the data if/when questions arise. Commercial LIMS often include additional modules that may be paid for but not actually used, and often require software expertise to truly customize them for a given environment. This web-application allows small to medium-sized protein production groups to track data related to plasmid DNA, conditioned media samples (supes), cell lines used for expression, and purified protein information, including method of purification and quality control results. In addition, a request system was added that includes a means of prioritizing requests to help manage the high demand of protein production resources at most organizations. ProteinTracker makes extensive use of existing open-source libraries and is designed to track essential data related to the production and purification of proteins. ProteinTracker is an open-source web-based application that provides organizations with the ability to track key data involved in the production and purification of proteins and may be modified to meet the specific needs of an organization. The source code and database setup script can be downloaded from http://sourceforge.net/projects/proteintracker. This site also contains installation instructions and a user guide. A demonstration version of the application can be viewed at http://www.proteintracker.org.

40 CFR 63.2334 - Am I subject to this subpart?

Science.gov (United States)

2010-07-01

... collocated with other industrial (e.g., manufacturing) operations at the same plant site. (b) Organic liquid... do not include the activities and equipment, including product loading racks, used to process, store...

Multiple protonation equilibria in electrostatics of protein-protein binding.

Science.gov (United States)

Piłat, Zofia; Antosiewicz, Jan M

2008-11-27

All proteins contain groups capable of exchanging protons with their environment. We present here an approach, based on a rigorous thermodynamic cycle and the partition functions for energy levels characterizing protonation states of the associating proteins and their complex, to compute the electrostatic pH-dependent contribution to the free energy of protein-protein binding. The computed electrostatic binding free energies include the pH of the solution as the variable of state, mutual "polarization" of associating proteins reflected as changes in the distribution of their protonation states upon binding and fluctuations between available protonation states. The only fixed property of both proteins is the conformation; the structure of the monomers is kept in the same conformation as they have in the complex structure. As a reference, we use the electrostatic binding free energies obtained from the traditional Poisson-Boltzmann model, computed for a single macromolecular conformation fixed in a given protonation state, appropriate for given solution conditions. The new approach was tested for 12 protein-protein complexes. It is shown that explicit inclusion of protonation degrees of freedom might lead to a substantially different estimation of the electrostatic contribution to the binding free energy than that based on the traditional Poisson-Boltzmann model. This has important implications for the balancing of different contributions to the energetics of protein-protein binding and other related problems, for example, the choice of protein models for Brownian dynamics simulations of their association. Our procedure can be generalized to include conformational degrees of freedom by combining it with molecular dynamics simulations at constant pH. Unfortunately, in practice, a prohibitive factor is an enormous requirement for computer time and power. However, there may be some hope for solving this problem by combining existing constant pH molecular dynamics

ANTIFREEZE PROTEINS IN PLANTS: AN OVERVIEW WITH AN INSIGHT INTO THE DETECTION TECHNIQUES INCLUDING NANOBIOTECHNOLOGY

Directory of Open Access Journals (Sweden)

Bhavana Sharma

2014-08-01

Full Text Available Antifreeze proteins (AFPs are a class of polypeptides which enables various organisms to survive subzero temperatures and have been found in vertebrates, invertebrates, plants, fungi and lichens. AFPs possess the characteristic thermal hysteresis (TH and ice recrystallization inhibition (IRI properties which allow them to adsorb the surface of ice crystals and inhibit their growth and recrystallization. AFPs are also known as ice restructuring proteins due to their ability to modify ice crystal morphology which leads to formation of hexagonal shape ice crystals in the presence of AFPs and disc shape AFPs in its absence. AFPs have various applications in medical, agricultural, industrial and biotechnological field. This review provides an overview of the AFPs, their TH and IRI properties and potential biotechnological applications of AFPs. Various conventional detection methods like Capillary assay and Differential Scanning Calorimetry (DSC with their advantages and disadvantages are discussed in detail along with the commonly used Splat assay and Nanoliter osmometer. Moreover, a novel, high-throughput and efficient nanobiotechnological method for AFP detection is also discussed. The method is based on colorimetric detection of freeze-labile gold nanoparticles and can provide an alternative to overcome the limitations of conventional methods by providing quick and easy way to screen AFPs in multiple systems simultaneously

ProteinTracker: an application for managing protein production and purification

Directory of Open Access Journals (Sweden)

Ponko Stefan C

2012-05-01

Full Text Available Abstract Background Laboratories that produce protein reagents for research and development face the challenge of deciding whether to track batch-related data using simple file based storage mechanisms (e.g. spreadsheets and notebooks, or commit the time and effort to install, configure and maintain a more complex laboratory information management system (LIMS. Managing reagent data stored in files is challenging because files are often copied, moved, and reformatted. Furthermore, there is no simple way to query the data if/when questions arise. Commercial LIMS often include additional modules that may be paid for but not actually used, and often require software expertise to truly customize them for a given environment. Findings This web-application allows small to medium-sized protein production groups to track data related to plasmid DNA, conditioned media samples (supes, cell lines used for expression, and purified protein information, including method of purification and quality control results. In addition, a request system was added that includes a means of prioritizing requests to help manage the high demand of protein production resources at most organizations. ProteinTracker makes extensive use of existing open-source libraries and is designed to track essential data related to the production and purification of proteins. Conclusions ProteinTracker is an open-source web-based application that provides organizations with the ability to track key data involved in the production and purification of proteins and may be modified to meet the specific needs of an organization. The source code and database setup script can be downloaded from http://sourceforge.net/projects/proteintracker. This site also contains installation instructions and a user guide. A demonstration version of the application can be viewed at http://www.proteintracker.org.

ProteinTracker: an application for managing protein production and purification

Science.gov (United States)

2012-01-01

Background Laboratories that produce protein reagents for research and development face the challenge of deciding whether to track batch-related data using simple file based storage mechanisms (e.g. spreadsheets and notebooks), or commit the time and effort to install, configure and maintain a more complex laboratory information management system (LIMS). Managing reagent data stored in files is challenging because files are often copied, moved, and reformatted. Furthermore, there is no simple way to query the data if/when questions arise. Commercial LIMS often include additional modules that may be paid for but not actually used, and often require software expertise to truly customize them for a given environment. Findings This web-application allows small to medium-sized protein production groups to track data related to plasmid DNA, conditioned media samples (supes), cell lines used for expression, and purified protein information, including method of purification and quality control results. In addition, a request system was added that includes a means of prioritizing requests to help manage the high demand of protein production resources at most organizations. ProteinTracker makes extensive use of existing open-source libraries and is designed to track essential data related to the production and purification of proteins. Conclusions ProteinTracker is an open-source web-based application that provides organizations with the ability to track key data involved in the production and purification of proteins and may be modified to meet the specific needs of an organization. The source code and database setup script can be downloaded from http://sourceforge.net/projects/proteintracker. This site also contains installation instructions and a user guide. A demonstration version of the application can be viewed at http://www.proteintracker.org. PMID:22574679

Accumulation of small heat shock proteins, including mitochondrial HSP22, induced by oxidative stress and adaptive response in tomato cells

International Nuclear Information System (INIS)

Banzet, N.; Richaud, C.; Deveaux, Y.; Kazmaier, M.; Gagnon, J.; Triantaphylides, C.

1998-01-01

Changes in gene expression, by application of H2O2, O2.- generating agents (methyl viologen, digitonin) and gamma irradiation to tomato suspension cultures, were investigated and compared to the well-described heat shock response. Two-dimensional gel protein mapping analyses gave the first indication that at least small heat shock proteins (smHSP) accumulated in response to application of H2O2 and gamma irradiation, but not to O2.- generating agents. While some proteins seemed to be induced specifically by each treatment, only part of the heat shock response was observed. On the basis of Northern hybridization experiments performed with four heterologous cDNA, corresponding to classes I-IV of pea smHSP, it could be concluded that significant amounts of class I and II smHSP mRNA are induced by H2O2 and by irradiation. Taken together, these results demonstrate that in plants some HSP genes are inducible by oxidative stresses, as in micro-organisms and other eukaryotic cells. HSP22, the main stress protein that accumulates following H2O2 action or gamma irradiation, was also purified. Sequence homology of amino terminal and internal sequences, and immunoreactivity with Chenopodium rubrum mitochondrial smHSP antibody, indicated that the protein belongs to the recently discovered class of plant mitochondrial smHSP. Heat shock or a mild H2O2 pretreatment was also shown to lead to plant cell protection against oxidative injury. Therefore, the synthesis of these stress proteins can be considered as an adaptive mechanism in which mitochondrial protection could be essential

Epigenetics targeted protein-vorinostat nanomedicine inducing apoptosis in heterogeneous population of primary acute myeloid leukemia cells including refractory and relapsed cases.

Science.gov (United States)

Chandran, Parwathy; Kavalakatt, Anu; Malarvizhi, Giridharan Loghanathan; Vasanthakumari, Divya Rani Vikraman Nair; Retnakumari, Archana Payickattu; Sidharthan, Neeraj; Pavithran, Keechilat; Nair, Shantikumar; Koyakutty, Manzoor

2014-05-01

Aberrant epigenetics play a key role in the onset and progression of acute myeloid leukemia (AML). Herein we report in silico modelling based development of a novel, protein-vorinostat nanomedicine exhibiting selective and superior anti-leukemic activity against heterogeneous population of AML patient samples (n=9), including refractory and relapsed cases, and three representative cell lines expressing CD34(+)/CD38(-) stem cell phenotype (KG-1a), promyelocytic phenotype (HL-60) and FLT3-ITD mutation (MV4-11). Nano-vorinostat having ~100nm size exhibited enhanced cellular uptake rendering significantly lower IC50 in AML cell lines and patient samples, and induced enhanced HDAC inhibition, oxidative injury, cell cycle arrest and apoptosis compared to free vorinostat. Most importantly, nanomedicine showed exceptional single-agent activity against the clonogenic proliferative capability of bone marrow derived leukemic progenitors, while remaining non-toxic to healthy bone marrow cells. Collectively, this epigenetics targeted nanomedicine appears to be a promising therapeutic strategy against various French-American-British (FAB) classes of AML. Through the use of a protein-vorinostat agent, exceptional single-agent activity was demonstrated against the clonogenic proliferative capability of bone marrow derived leukemic progenitors, while remaining non-toxic to healthy bone marrow cells. The studied epigenetics targeted nanomedicine approach is a promising therapeutic strategy against various French-American-British classes of acute myeloid leukemia. © 2014 Elsevier Inc. All rights reserved.

Collocated Interaction

DEFF Research Database (Denmark)

E. Fischer, Joel; Porcheron, Martin; Lucero, Andrés

2016-01-01

interactions. Yet, new challenges abound as people wear and carry more devices than ever, creating fragmented device ecologies at work, and changing the ways we socialise with each other. In this workshop we seek to start a dialogue to look back as well as forward, review best practices, discuss and design......In the 25 years since Ellis, Gibbs, and Rein proposed the time-space taxonomy, research in the ‘same time, same place’ quadrant has diversified, perhaps even fragmented. This one-day workshop will bring together researchers with diverse, yet convergent interests in tabletop, surface, mobile...

Protein-protein docking with dynamic residue protonation states.

Directory of Open Access Journals (Sweden)

Krishna Praneeth Kilambi

2014-12-01

Full Text Available Protein-protein interactions depend on a host of environmental factors. Local pH conditions influence the interactions through the protonation states of the ionizable residues that can change upon binding. In this work, we present a pH-sensitive docking approach, pHDock, that can sample side-chain protonation states of five ionizable residues (Asp, Glu, His, Tyr, Lys on-the-fly during the docking simulation. pHDock produces successful local docking funnels in approximately half (79/161 the protein complexes, including 19 cases where standard RosettaDock fails. pHDock also performs better than the two control cases comprising docking at pH 7.0 or using fixed, predetermined protonation states. On average, the top-ranked pHDock structures have lower interface RMSDs and recover more native interface residue-residue contacts and hydrogen bonds compared to RosettaDock. Addition of backbone flexibility using a computationally-generated conformational ensemble further improves native contact and hydrogen bond recovery in the top-ranked structures. Although pHDock is designed to improve docking, it also successfully predicts a large pH-dependent binding affinity change in the Fc-FcRn complex, suggesting that it can be exploited to improve affinity predictions. The approaches in the study contribute to the goal of structural simulations of whole-cell protein-protein interactions including all the environmental factors, and they can be further expanded for pH-sensitive protein design.

Subcellular localization of secondary lipid metabolites including fragrance volatiles in carnation petals

International Nuclear Information System (INIS)

Hudak, K.A.; Thompson, J.E.

1997-01-01

Pulse-chase labeling of carnation (Dianthus caryophyllus L. cv Improved White Sim) petals with [14C]acetate has provided evidence for a hydrophobic subcompartment of lipid-protein particles within the cytosol that resemble oil bodies, are formed by blebbing from membranes, and are enriched in lipid metabolites (including fragrance volatiles) derived from membrane fatty acids. Fractionation of the petals during pulse-chase labeling revealed that radiolabeled fatty acids appear first in microsomal membranes and subsequently in cytosolic lipid-protein particles, indicating that the particles originate from membranes. This interpretation is supported by the finding that the cytosolic lipid-protein particles contain phospholipid as well as the same fatty acids found in microsomal membranes. Radiolabeled polar lipid metabolites (methanol/ water-soluble) were detectable in both in situ lipid-protein particles isolated from the cytosol and those generated in vitro from isolated radiolabeled microsomal membranes. The lipid-protein particles were also enriched in hexanal, trans-2-hexenal, 1-hexanol, 3-hexen-1-ol, and 2-hexanol, volatiles of carnation flower fragrance that are derived from membrane fatty acids through the lipoxygenase pathway. Therefore, secondary lipid metabolites, including components of fragrance, appear to be formed within membranes of petal tissue and are subsequently released from the membrane bilayers into the cytosol by blebbing of lipid-protein particles

CDNA encoding a polypeptide including a hevein sequence

Science.gov (United States)

Raikhel, Natasha V.; Broekaert, Willem F.; Chua, Nam-Hai; Kush, Anil

1995-03-21

A cDNA clone (HEV1) encoding hevein was isolated via polymerase chain reaction (PCR) using mixed oligonucleotides corresponding to two regions of hevein as primers and a Hevea brasiliensis latex cDNA library as a template. HEV1 is 1018 nucleotides long and includes an open reading frame of 204 amino acids. The deduced amino acid sequence contains a putative signal sequence of 17 amino acid residues followed by a 187 amino acid polypeptide. The amino-terminal region (43 amino acids) is identical to hevein and shows homology to several chitin-binding proteins and to the amino-termini of wound-induced genes in potato and poplar. The carboxyl-terminal portion of the polypeptide (144 amino acids) is 74-79% homologous to the carboxyl-terminal region of wound-inducible genes of potato. Wounding, as well as application of the plant hormones abscisic acid and ethylene, resulted in accumulation of hevein transcripts in leaves, stems and latex, but not in roots, as shown by using the cDNA as a probe. A fusion protein was produced in E. coli from the protein of the present invention and maltose binding protein produced by the E. coli.

Polarizable protein packing

KAUST Repository

Ng, Albert H.; Snow, Christopher D.

2011-01-01

To incorporate protein polarization effects within a protein combinatorial optimization framework, we decompose the polarizable force field AMOEBA into low order terms. Including terms up to the third-order provides a fair approximation to the full

Quality control methodology for high-throughput protein-protein interaction screening.

Science.gov (United States)

Vazquez, Alexei; Rual, Jean-François; Venkatesan, Kavitha

2011-01-01

Protein-protein interactions are key to many aspects of the cell, including its cytoskeletal structure, the signaling processes in which it is involved, or its metabolism. Failure to form protein complexes or signaling cascades may sometimes translate into pathologic conditions such as cancer or neurodegenerative diseases. The set of all protein interactions between the proteins encoded by an organism constitutes its protein interaction network, representing a scaffold for biological function. Knowing the protein interaction network of an organism, combined with other sources of biological information, can unravel fundamental biological circuits and may help better understand the molecular basics of human diseases. The protein interaction network of an organism can be mapped by combining data obtained from both low-throughput screens, i.e., "one gene at a time" experiments and high-throughput screens, i.e., screens designed to interrogate large sets of proteins at once. In either case, quality controls are required to deal with the inherent imperfect nature of experimental assays. In this chapter, we discuss experimental and statistical methodologies to quantify error rates in high-throughput protein-protein interactions screens.

Alignment of non-covalent interactions at protein-protein interfaces.

Directory of Open Access Journals (Sweden)

Hongbo Zhu

Full Text Available BACKGROUND: The study and comparison of protein-protein interfaces is essential for the understanding of the mechanisms of interaction between proteins. While there are many methods for comparing protein structures and protein binding sites, so far no methods have been reported for comparing the geometry of non-covalent interactions occurring at protein-protein interfaces. METHODOLOGY/PRINCIPAL FINDINGS: Here we present a method for aligning non-covalent interactions between different protein-protein interfaces. The method aligns the vector representations of van der Waals interactions and hydrogen bonds based on their geometry. The method has been applied to a dataset which comprises a variety of protein-protein interfaces. The alignments are consistent to a large extent with the results obtained using two other complementary approaches. In addition, we apply the method to three examples of protein mimicry. The method successfully aligns respective interfaces and allows for recognizing conserved interface regions. CONCLUSIONS/SIGNIFICANCE: The Galinter method has been validated in the comparison of interfaces in which homologous subunits are involved, including cases of mimicry. The method is also applicable to comparing interfaces involving non-peptidic compounds. Galinter assists users in identifying local interface regions with similar patterns of non-covalent interactions. This is particularly relevant to the investigation of the molecular basis of interaction mimicry.

Gc protein (vitamin D-binding protein): Gc genotyping and GcMAF precursor activity.

Science.gov (United States)

Nagasawa, Hideko; Uto, Yoshihiro; Sasaki, Hideyuki; Okamura, Natsuko; Murakami, Aya; Kubo, Shinichi; Kirk, Kenneth L; Hori, Hitoshi

2005-01-01

The Gc protein (human group-specific component (Gc), a vitamin D-binding protein or Gc globulin), has important physiological functions that include involvement in vitamin D transport and storage, scavenging of extracellular G-actin, enhancement of the chemotactic activity of C5a for neutrophils in inflammation and macrophage activation (mediated by a GalNAc-modified Gc protein (GcMAF)). In this review, the structure and function of the Gc protein is focused on especially with regard to Gc genotyping and GcMAF precursor activity. A discussion of the research strategy "GcMAF as a target for drug discovery" is included, based on our own research.

An Online Spanish Learners’ Dictionary: The DAELE Project

Directory of Open Access Journals (Sweden)

Blanca Arias-Badia

2014-12-01

Full Text Available Current online dictionaries for learners of Spanish as a second language largely just reproduce their printed counterparts. This report summarizes the advances made in the DAELE, a prototype dictionary for learners of Spanish as a second language that has been designed solely for online publication. The purpose and main features of the macro- and microstructure of the dictionary are briefly described, as well as the methodology whereby the data are collected and the first steps taken to include the most significant collocations by applying a method based on collocational networks.

Computation of saddle-type slow manifolds using iterative methods

DEFF Research Database (Denmark)

Kristiansen, Kristian Uldall

2015-01-01

with respect to , appropriate estimates are directly attainable using the method of this paper. The method is applied to several examples, including a model for a pair of neurons coupled by reciprocal inhibition with two slow and two fast variables, and the computation of homoclinic connections in the Fitz......This paper presents an alternative approach for the computation of trajectory segments on slow manifolds of saddle type. This approach is based on iterative methods rather than collocation-type methods. Compared to collocation methods, which require mesh refinements to ensure uniform convergence...

Plant protein and animal proteins: do they differentially affect cardiovascular disease risk?

Science.gov (United States)

Richter, Chesney K; Skulas-Ray, Ann C; Champagne, Catherine M; Kris-Etherton, Penny M

2015-11-01

Proteins from plant-based compared with animal-based food sources may have different effects on cardiovascular disease (CVD) risk factors. Numerous epidemiologic and intervention studies have evaluated their respective health benefits; however, it is difficult to isolate the role of plant or animal protein on CVD risk. This review evaluates the current evidence from observational and intervention studies, focusing on the specific protein-providing foods and populations studied. Dietary protein is derived from many food sources, and each provides a different composite of nonprotein compounds that can also affect CVD risk factors. Increasing the consumption of protein-rich foods also typically results in lower intakes of other nutrients, which may simultaneously influence outcomes. Given these complexities, blanket statements about plant or animal protein may be too general, and greater consideration of the specific protein food sources and the background diet is required. The potential mechanisms responsible for any specific effects of plant and animal protein are similarly multifaceted and include the amino acid content of particular foods, contributions from other nonprotein compounds provided concomitantly by the whole food, and interactions with the gut microbiome. Evidence to date is inconclusive, and additional studies are needed to further advance our understanding of the complexity of plant protein vs. animal protein comparisons. Nonetheless, current evidence supports the idea that CVD risk can be reduced by a dietary pattern that provides more plant sources of protein compared with the typical American diet and also includes animal-based protein foods that are unprocessed and low in saturated fat. © 2015 American Society for Nutrition.

The interface of protein structure, protein biophysics, and molecular evolution

Science.gov (United States)

Liberles, David A; Teichmann, Sarah A; Bahar, Ivet; Bastolla, Ugo; Bloom, Jesse; Bornberg-Bauer, Erich; Colwell, Lucy J; de Koning, A P Jason; Dokholyan, Nikolay V; Echave, Julian; Elofsson, Arne; Gerloff, Dietlind L; Goldstein, Richard A; Grahnen, Johan A; Holder, Mark T; Lakner, Clemens; Lartillot, Nicholas; Lovell, Simon C; Naylor, Gavin; Perica, Tina; Pollock, David D; Pupko, Tal; Regan, Lynne; Roger, Andrew; Rubinstein, Nimrod; Shakhnovich, Eugene; Sjölander, Kimmen; Sunyaev, Shamil; Teufel, Ashley I; Thorne, Jeffrey L; Thornton, Joseph W; Weinreich, Daniel M; Whelan, Simon

2012-01-01

Abstract The interface of protein structural biology, protein biophysics, molecular evolution, and molecular population genetics forms the foundations for a mechanistic understanding of many aspects of protein biochemistry. Current efforts in interdisciplinary protein modeling are in their infancy and the state-of-the art of such models is described. Beyond the relationship between amino acid substitution and static protein structure, protein function, and corresponding organismal fitness, other considerations are also discussed. More complex mutational processes such as insertion and deletion and domain rearrangements and even circular permutations should be evaluated. The role of intrinsically disordered proteins is still controversial, but may be increasingly important to consider. Protein geometry and protein dynamics as a deviation from static considerations of protein structure are also important. Protein expression level is known to be a major determinant of evolutionary rate and several considerations including selection at the mRNA level and the role of interaction specificity are discussed. Lastly, the relationship between modeling and needed high-throughput experimental data as well as experimental examination of protein evolution using ancestral sequence resurrection and in vitro biochemistry are presented, towards an aim of ultimately generating better models for biological inference and prediction. PMID:22528593

Identification of structural protein-protein interactions of herpes simplex virus type 1.

Science.gov (United States)

Lee, Jin H; Vittone, Valerio; Diefenbach, Eve; Cunningham, Anthony L; Diefenbach, Russell J

2008-09-01

In this study we have defined protein-protein interactions between the structural proteins of herpes simplex virus type 1 (HSV-1) using a LexA yeast two-hybrid system. The majority of the capsid, tegument and envelope proteins of HSV-1 were screened in a matrix approach. A total of 40 binary interactions were detected including 9 out of 10 previously identified tegument-tegument interactions (Vittone, V., Diefenbach, E., Triffett, D., Douglas, M.W., Cunningham, A.L., and Diefenbach, R.J., 2005. Determination of interactions between tegument proteins of herpes simplex virus type 1. J. Virol. 79, 9566-9571). A total of 12 interactions involving the capsid protein pUL35 (VP26) and 11 interactions involving the tegument protein pUL46 (VP11/12) were identified. The most significant novel interactions detected in this study, which are likely to play a role in viral assembly, include pUL35-pUL37 (capsid-tegument), pUL46-pUL37 (tegument-tegument) and pUL49 (VP22)-pUS9 (tegument-envelope). This information will provide further insights into the pathways of HSV-1 assembly and the identified interactions are potential targets for new antiviral drugs.

Expression of multiple proteins in transgenic plants

Science.gov (United States)

Vierstra, Richard D.; Walker, Joseph M.

2002-01-01

A method is disclosed for the production of multiple proteins in transgenic plants. A DNA construct for introduction into plants includes a provision to express a fusion protein of two proteins of interest joined by a linking domain including plant ubiquitin. When the fusion protein is produced in the cells of a transgenic plant transformed with the DNA construction, native enzymes present in plant cells cleave the fusion protein to release both proteins of interest into the cells of the transgenic plant. Since the proteins are produced from the same fusion protein, the initial quantities of the proteins in the cells of the plant are approximately equal.

Annotating the protein-RNA interaction sites in proteins using evolutionary information and protein backbone structure.

Science.gov (United States)

Li, Tao; Li, Qian-Zhong

2012-11-07

RNA-protein interactions play important roles in various biological processes. The precise detection of RNA-protein interaction sites is very important for understanding essential biological processes and annotating the function of the proteins. In this study, based on various features from amino acid sequence and structure, including evolutionary information, solvent accessible surface area and torsion angles (φ, ψ) in the backbone structure of the polypeptide chain, a computational method for predicting RNA-binding sites in proteins is proposed. When the method is applied to predict RNA-binding sites in three datasets: RBP86 containing 86 protein chains, RBP107 containing 107 proteins chains and RBP109 containing 109 proteins chains, better sensitivities and specificities are obtained compared to previously published methods in five-fold cross-validation tests. In order to make further examination for the efficiency of our method, the RBP107 dataset is used as training set, RBP86 and RBP109 datasets are used as the independent test sets. In addition, as examples of our prediction, RNA-binding sites in a few proteins are presented. The annotated results are consistent with the PDB annotation. These results show that our method is useful for annotating RNA binding sites of novel proteins.

Canola/rapeseed protein-functionality and nutrition

Directory of Open Access Journals (Sweden)

Wanasundara Janitha P.D.

2016-07-01

Full Text Available Protein rich meal is a valuable co-product of canola/rapeseed oil extraction. Seed storage proteins that include cruciferin (11S and napin (2S dominate the protein complement of canola while oleosins, lipid transfer proteins and other minor proteins of non-storage nature are also found. Although oil-free canola meal contains 36–40% protein on a dry weight basis, non-protein components including fibre, polymeric phenolics, phytates and sinapine, etc. of the seed coat and cellular components make protein less suitable for food use. Separation of canola protein from non-protein components is a technical challenge but necessary to obtain full nutritional and functional potential of protein. Process conditions of raw material and protein preparation are critical of nutritional and functional value of the final protein product. The storage proteins of canola can satisfy many nutritional and functional requirements for food applications. Protein macromolecules of canola also provide functionalities required in applications beyond edible uses; there exists substantial potential as a source of plant protein and a renewable biopolymer. Available information at present is mostly based on the protein products that can be obtained as mixtures of storage protein types and other chemical constituents of the seed; therefore, full potential of canola storage proteins is yet to be revealed.

Tau protein

DEFF Research Database (Denmark)

Frederiksen, Jette Lautrup Battistini; Kristensen, Kim; Bahl, Jmc

2011-01-01

Background: Tau protein has been proposed as biomarker of axonal damage leading to irreversible neurological impairment in MS. CSF concentrations may be useful when determining risk of progression from ON to MS. Objective: To investigate the association between tau protein concentration and 14......-3-3 protein in the cerebrospinal fluid (CSF) of patients with monosymptomatic optic neuritis (ON) versus patients with monosymptomatic onset who progressed to multiple sclerosis (MS). To evaluate results against data found in a complete literature review. Methods: A total of 66 patients with MS and/or ON from...... the Department of Neurology of Glostrup Hospital, University of Copenhagen, Denmark, were included. CSF samples were analysed for tau protein and 14-3-3 protein, and clinical and paraclinical information was obtained from medical records. Results: The study shows a significantly increased concentration of tau...

Longitudinal changes in C-reactive protein, proform of eosinophil major basic protein, and pregnancy-associated plasma protein-A during weight changes in obese children

DEFF Research Database (Denmark)

Lausten-Thomsen, Ulrik; Gamborg, Michael; Bøjsøe, Christine

2015-01-01

BACKGROUND: Childhood obesity is associated with several complications, including cardiovascular comorbidity. Several biomarkers, such as high-sensitive C-reactive protein (hs-CRP), proform of eosinophil major basic protein (Pro-MBP) and pregnancy associated plasma protein-A (PAPP-A), have equally...

Scoring functions for protein-protein interactions.

Science.gov (United States)

Moal, Iain H; Moretti, Rocco; Baker, David; Fernández-Recio, Juan

2013-12-01

The computational evaluation of protein-protein interactions will play an important role in organising the wealth of data being generated by high-throughput initiatives. Here we discuss future applications, report recent developments and identify areas requiring further investigation. Many functions have been developed to quantify the structural and energetic properties of interacting proteins, finding use in interrelated challenges revolving around the relationship between sequence, structure and binding free energy. These include loop modelling, side-chain refinement, docking, multimer assembly, affinity prediction, affinity change upon mutation, hotspots location and interface design. Information derived from models optimised for one of these challenges can be used to benefit the others, and can be unified within the theoretical frameworks of multi-task learning and Pareto-optimal multi-objective learning. Copyright © 2013 Elsevier Ltd. All rights reserved.

Protein Correlation Profiles Identify Lipid Droplet Proteins with High Confidence*

Science.gov (United States)

Krahmer, Natalie; Hilger, Maximiliane; Kory, Nora; Wilfling, Florian; Stoehr, Gabriele; Mann, Matthias; Farese, Robert V.; Walther, Tobias C.

2013-01-01

Lipid droplets (LDs) are important organelles in energy metabolism and lipid storage. Their cores are composed of neutral lipids that form a hydrophobic phase and are surrounded by a phospholipid monolayer that harbors specific proteins. Most well-established LD proteins perform important functions, particularly in cellular lipid metabolism. Morphological studies show LDs in close proximity to and interacting with membrane-bound cellular organelles, including the endoplasmic reticulum, mitochondria, peroxisomes, and endosomes. Because of these close associations, it is difficult to purify LDs to homogeneity. Consequently, the confident identification of bona fide LD proteins via proteomics has been challenging. Here, we report a methodology for LD protein identification based on mass spectrometry and protein correlation profiles. Using LD purification and quantitative, high-resolution mass spectrometry, we identified LD proteins by correlating their purification profiles to those of known LD proteins. Application of the protein correlation profile strategy to LDs isolated from Drosophila S2 cells led to the identification of 111 LD proteins in a cellular LD fraction in which 1481 proteins were detected. LD localization was confirmed in a subset of identified proteins via microscopy of the expressed proteins, thereby validating the approach. Among the identified LD proteins were both well-characterized LD proteins and proteins not previously known to be localized to LDs. Our method provides a high-confidence LD proteome of Drosophila cells and a novel approach that can be applied to identify LD proteins of other cell types and tissues. PMID:23319140

Protein Data Bank (PDB)

Data.gov (United States)

U.S. Department of Health & Human Services — The Protein Data Bank (PDB) archive is the single worldwide repository of information about the 3D structures of large biological molecules, including proteins and...

A membrane protein / signaling protein interaction network for Arabidopsis version AMPv2

Directory of Open Access Journals (Sweden)

Sylvie Lalonde

2010-09-01

Full Text Available Interactions between membrane proteins and the soluble fraction are essential for signal transduction and for regulating nutrient transport. To gain insights into the membrane-based interactome, 3,852 open reading frames (ORFs out of a target list of 8,383 representing membrane and signaling proteins from Arabidopsis thaliana were cloned into a Gateway compatible vector. The mating-based split-ubiquitin system was used to screen for potential protein-protein interactions (pPPIs among 490 Arabidopsis ORFs. A binary robotic screen between 142 receptor-like kinases, 72 transporters, 57 soluble protein kinases and phosphatases, 40 glycosyltransferases, 95 proteins of various functions and 89 proteins with unknown function detected 387 out of 90,370 possible PPIs. A secondary screen confirmed 343 (of 387 pPPIs between 179 proteins, yielding a scale-free network (r2=0.863. Eighty of 142 transmembrane receptor-like kinases (RLK tested positive, identifying three homomers, 63 heteromers and 80 pPPIs with other proteins. Thirty-one out of 142 RLK interactors (including RLKs had previously been found to be phosphorylated; thus interactors may be substrates for respective RLKs. None of the pPPIs described here had been reported in the major interactome databases, including potential interactors of G protein-coupled receptors, phospholipase C, and AMT ammonium transporters. Two RLKs found as putative interactors of AMT1;1 were independently confirmed using a split luciferase assay in Arabidopsis protoplasts. These RLKs may be involved in ammonium-dependent phosphorylation of the C-terminus and regulation of ammonium uptake activity. The robotic screening method established here will enable a systematic analysis of membrane protein interactions in fungi, plants and metazoa.

Mitogen-activated protein kinase signaling in plants

DEFF Research Database (Denmark)

Rodriguez, Maria Cristina Suarez; Petersen, Morten; Mundy, John

2010-01-01

crossinhibition, feedback control, and scaffolding. Plant MAPK cascades regulate numerous processes, including stress and hormonal responses, innate immunity, and developmental programs. Genetic analyses have uncovered several predominant MAPK components shared by several of these processes including...... of substrate proteins, whose altered activities mediate a wide array of responses, including changes in gene expression. Cascades may share kinase components, but their signaling specificity is maintained by spaciotemporal constraints and dynamic protein-protein interactions and by mechanisms that include...

3DProIN: Protein-Protein Interaction Networks and Structure Visualization.

Science.gov (United States)

Li, Hui; Liu, Chunmei

2014-06-14

3DProIN is a computational tool to visualize protein-protein interaction networks in both two dimensional (2D) and three dimensional (3D) view. It models protein-protein interactions in a graph and explores the biologically relevant features of the tertiary structures of each protein in the network. Properties such as color, shape and name of each node (protein) of the network can be edited in either 2D or 3D views. 3DProIN is implemented using 3D Java and C programming languages. The internet crawl technique is also used to parse dynamically grasped protein interactions from protein data bank (PDB). It is a java applet component that is embedded in the web page and it can be used on different platforms including Linux, Mac and Window using web browsers such as Firefox, Internet Explorer, Chrome and Safari. It also was converted into a mac app and submitted to the App store as a free app. Mac users can also download the app from our website. 3DProIN is available for academic research at http://bicompute.appspot.com.

Adhesives from modified soy protein

Science.gov (United States)

Sun, Susan [Manhattan, KS; Wang, Donghai [Manhattan, KS; Zhong, Zhikai [Manhattan, KS; Yang, Guang [Shanghai, CN

2008-08-26

The present invention provides useful adhesive compositions having similar adhesive properties to conventional UF and PPF resins. The compositions generally include a protein portion and modifying ingredient portion selected from the group consisting of carboxyl-containing compounds, aldehyde-containing compounds, epoxy group-containing compounds, and mixtures thereof. The composition is preferably prepared at a pH level at or near the isoelectric point of the protein. In other preferred forms, the adhesive composition includes a protein portion and a carboxyl-containing group portion.

cDNA encoding a polypeptide including a hevein sequence

Energy Technology Data Exchange (ETDEWEB)

Raikhel, N.V.; Broekaert, W.F.; Chua, N.H.; Kush, A.

2000-07-04

A cDNA clone (HEV1) encoding hevein was isolated via polymerase chain reaction (PCR) using mixed oligonucleotides corresponding to two regions of hevein as primers and a Hevea brasiliensis latex cDNA library as a template. HEV1 is 1018 nucleotides long and includes an open reading frame of 204 amino acids. The deduced amino acid sequence contains a putative signal sequence of 17 amino acid residues followed by a 187 amino acid polypeptide. The amino-terminal region (43 amino acids) is identical to hevein and shows homology to several chitin-binding proteins and to the amino-termini of wound-induced genes in potato and poplar. The carboxyl-terminal portion of the polypeptide (144 amino acids) is 74--79% homologous to the carboxyl-terminal region of wound-inducible genes of potato. Wounding, as well as application of the plant hormones abscisic acid and ethylene, resulted in accumulation of hevein transcripts in leaves, stems and latex, but not in roots, as shown by using the cDNA as a probe. A fusion protein was produced in E. coli from the protein of the present invention and maltose binding protein produced by the E. coli.

cDNA encoding a polypeptide including a hevein sequence

Energy Technology Data Exchange (ETDEWEB)

Raikhel, N.V.; Broekaert, W.F.; Chua, N.H.; Kush, A.

1999-05-04

A cDNA clone (HEV1) encoding hevein was isolated via polymerase chain reaction (PCR) using mixed oligonucleotides corresponding to two regions of hevein as primers and a Hevea brasiliensis latex cDNA library as a template. HEV1 is 1018 nucleotides long and includes an open reading frame of 204 amino acids. The deduced amino acid sequence contains a putative signal sequence of 17 amino acid residues followed by a 187 amino acid polypeptide. The amino-terminal region (43 amino acids) is identical to hevein and shows homology to several chitin-binding proteins and to the amino-termini of wound-induced genes in potato and poplar. The carboxyl-terminal portion of the polypeptide (144 amino acids) is 74--79% homologous to the carboxyl-terminal region of wound-inducible genes of potato. Wounding, as well as application of the plant hormones abscisic acid and ethylene, resulted in accumulation of hevein transcripts in leaves, stems and latex, but not in roots, as shown by using the cDNA as a probe. A fusion protein was produced in E. coli from the protein of the present invention and maltose binding protein produced by the E. coli. 12 figs.

cDNA encoding a polypeptide including a hevein sequence

Energy Technology Data Exchange (ETDEWEB)

Raikhel, Natasha V. (Okemos, MI); Broekaert, Willem F. (Dilbeek, BE); Chua, Nam-Hai (Scarsdale, NY); Kush, Anil (New York, NY)

1999-05-04

A cDNA clone (HEV1) encoding hevein was isolated via polymerase chain reaction (PCR) using mixed oligonucleotides corresponding to two regions of hevein as primers and a Hevea brasiliensis latex cDNA library as a template. HEV1 is 1018 nucleotides long and includes an open reading frame of 204 amino acids. The deduced amino acid sequence contains a putative signal sequence of 17 amino acid residues followed by a 187 amino acid polypeptide. The amino-terminal region (43 amino acids) is identical to hevein and shows homology to several chitin-binding proteins and to the amino-termini of wound-induced genes in potato and poplar. The carboxyl-terminal portion of the polypeptide (144 amino acids) is 74-79% homologous to the carboxyl-terminal region of wound-inducible genes of potato. Wounding, as well as application of the plant hormones abscisic acid and ethylene, resulted in accumulation of hevein transcripts in leaves, stems and latex, but not in roots, as shown by using the cDNA as a probe. A fusion protein was produced in E. coli from the protein of the present invention and maltose binding protein produced by the E. coli.

cDNA encoding a polypeptide including a hevein sequence

Energy Technology Data Exchange (ETDEWEB)

Raikhel, N.V.; Broekaert, W.F.; Chua, N.H.; Kush, A.

1995-03-21

A cDNA clone (HEV1) encoding hevein was isolated via polymerase chain reaction (PCR) using mixed oligonucleotides corresponding to two regions of hevein as primers and a Hevea brasiliensis latex cDNA library as a template. HEV1 is 1,018 nucleotides long and includes an open reading frame of 204 amino acids. The deduced amino acid sequence contains a putative signal sequence of 17 amino acid residues followed by a 187 amino acid polypeptide. The amino-terminal region (43 amino acids) is identical to hevein and shows homology to several chitin-binding proteins and to the amino-termini of wound-induced genes in potato and poplar. The carboxyl-terminal portion of the polypeptide (144 amino acids) is 74--79% homologous to the carboxyl-terminal region of wound-inducible genes of potato. Wounding, as well as application of the plant hormones abscisic acid and ethylene, resulted in accumulation of hevein transcripts in leaves, stems and latex, but not in roots, as shown by using the cDNA as a probe. A fusion protein was produced in E. coli from the protein of the present invention and maltose binding protein produced by the E. coli. 11 figures.

Protein kinase substrate identification on functional protein arrays

Directory of Open Access Journals (Sweden)

Zhou Fang

2008-02-01

Full Text Available Abstract Background Over the last decade, kinases have emerged as attractive therapeutic targets for a number of different diseases, and numerous high throughput screening efforts in the pharmaceutical community are directed towards discovery of compounds that regulate kinase function. The emerging utility of systems biology approaches has necessitated the development of multiplex tools suitable for proteomic-scale experiments to replace lower throughput technologies such as mass spectroscopy for the study of protein phosphorylation. Recently, a new approach for identifying substrates of protein kinases has applied the miniaturized format of functional protein arrays to characterize phosphorylation for thousands of candidate protein substrates in a single experiment. This method involves the addition of protein kinases in solution to arrays of immobilized proteins to identify substrates using highly sensitive radioactive detection and hit identification algorithms. Results To date, the factors required for optimal performance of protein array-based kinase substrate identification have not been described. In the current study, we have carried out a detailed characterization of the protein array-based method for kinase substrate identification, including an examination of the effects of time, buffer compositions, and protein concentration on the results. The protein array approach was compared to standard solution-based assays for assessing substrate phosphorylation, and a correlation of greater than 80% was observed. The results presented here demonstrate how novel substrates for protein kinases can be quickly identified from arrays containing thousands of human proteins to provide new clues to protein kinase function. In addition, a pooling-deconvolution strategy was developed and applied that enhances characterization of specific kinase-substrate relationships and decreases reagent consumption. Conclusion Functional protein microarrays are an

Soldier use of dietary supplements, including protein and body building supplements, in a combat zone is different than use in garrison.

Science.gov (United States)

Austin, Krista G; McLellan, Tom M; Farina, Emily K; McGraw, Susan M; Lieberman, Harris R

2016-01-01

United States Army personnel in garrison who are not deployed to combat theater report using dietary supplements (DSs) to promote health, increase physical and mental strength, and improve energy levels. Given the substantial physical and cognitive demands of combat, DS use may increase during deployment. This study compared DS use by garrison soldiers with DS use by personnel deployed to a combat theater in Afghanistan. Prevalence and patterns of DS use, demographic factors, and health behaviors were assessed by survey (deployed n = 221; garrison n = 1001). Eighty-two percent of deployed and 74% of garrison soldiers used DSs ≥ 1 time·week(-1). Logistic regression analyses, adjusted for significant demographic and health predictors of DS use, showed deployed personnel were more likely than garrison soldiers to use protein, amino acids, and combination products. Deployed females were more likely to use protein supplements and deployed males were more likely to use multivitamins, combination products, protein, and body building supplements than garrison respondents. Significantly more deployed (17%) than garrison (10%) personnel spent more than $50∙month(-1) on DSs. Higher protein supplement use among deployed personnel was associated with higher frequency of strength training and lower amounts of aerobic exercise for males but similar amounts of strength training and aerobic exercise for females. Protein supplements and combination products are used more frequently by deployed than garrison soldiers with the intent of enhancing strength and energy.

Protein Polymers and Amyloids

DEFF Research Database (Denmark)

Risør, Michael Wulff

2014-01-01

Several human disorders are caused by a common general disease mechanism arising from abnormal folding and aggregation of the underlying protein. These include the prevalent dementias like Alzheimer’s and Parkinson’s, where accumulation of protein fibrillar structures, known as amyloid fibrils......, is a general hallmark. They also include the α1-antitrypsin deficiency, where disease-causing mutations in the serine protease inhibitor, α1-antitrypsin (α1AT), leads to accumulation of the aberrant protein in the liver of these patients. The native metastable structure of α1AT constitutes a molecular trap...... that inhibits its target protease through a large conformational change but mutations compromise this function and cause premature structural collapse into hyperstable polymers. Understanding the conformational disorders at a molecular level is not only important for our general knowledge on protein folding...

HIV protein sequence hotspots for crosstalk with host hub proteins.

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Mahdi Sarmady

Full Text Available HIV proteins target host hub proteins for transient binding interactions. The presence of viral proteins in the infected cell results in out-competition of host proteins in their interaction with hub proteins, drastically affecting cell physiology. Functional genomics and interactome datasets can be used to quantify the sequence hotspots on the HIV proteome mediating interactions with host hub proteins. In this study, we used the HIV and human interactome databases to identify HIV targeted host hub proteins and their host binding partners (H2. We developed a high throughput computational procedure utilizing motif discovery algorithms on sets of protein sequences, including sequences of HIV and H2 proteins. We identified as HIV sequence hotspots those linear motifs that are highly conserved on HIV sequences and at the same time have a statistically enriched presence on the sequences of H2 proteins. The HIV protein motifs discovered in this study are expressed by subsets of H2 host proteins potentially outcompeted by HIV proteins. A large subset of these motifs is involved in cleavage, nuclear localization, phosphorylation, and transcription factor binding events. Many such motifs are clustered on an HIV sequence in the form of hotspots. The sequential positions of these hotspots are consistent with the curated literature on phenotype altering residue mutations, as well as with existing binding site data. The hotspot map produced in this study is the first global portrayal of HIV motifs involved in altering the host protein network at highly connected hub nodes.

Bacterial Ice Crystal Controlling Proteins

Science.gov (United States)

Lorv, Janet S. H.; Rose, David R.; Glick, Bernard R.

2014-01-01

Across the world, many ice active bacteria utilize ice crystal controlling proteins for aid in freezing tolerance at subzero temperatures. Ice crystal controlling proteins include both antifreeze and ice nucleation proteins. Antifreeze proteins minimize freezing damage by inhibiting growth of large ice crystals, while ice nucleation proteins induce formation of embryonic ice crystals. Although both protein classes have differing functions, these proteins use the same ice binding mechanisms. Rather than direct binding, it is probable that these protein classes create an ice surface prior to ice crystal surface adsorption. Function is differentiated by molecular size of the protein. This paper reviews the similar and different aspects of bacterial antifreeze and ice nucleation proteins, the role of these proteins in freezing tolerance, prevalence of these proteins in psychrophiles, and current mechanisms of protein-ice interactions. PMID:24579057

JNK Signaling: Regulation and Functions Based on Complex Protein-Protein Partnerships

Science.gov (United States)

Zeke, András; Misheva, Mariya

2016-01-01

SUMMARY The c-Jun N-terminal kinases (JNKs), as members of the mitogen-activated protein kinase (MAPK) family, mediate eukaryotic cell responses to a wide range of abiotic and biotic stress insults. JNKs also regulate important physiological processes, including neuronal functions, immunological actions, and embryonic development, via their impact on gene expression, cytoskeletal protein dynamics, and cell death/survival pathways. Although the JNK pathway has been under study for >20 years, its complexity is still perplexing, with multiple protein partners of JNKs underlying the diversity of actions. Here we review the current knowledge of JNK structure and isoforms as well as the partnerships of JNKs with a range of intracellular proteins. Many of these proteins are direct substrates of the JNKs. We analyzed almost 100 of these target proteins in detail within a framework of their classification based on their regulation by JNKs. Examples of these JNK substrates include a diverse assortment of nuclear transcription factors (Jun, ATF2, Myc, Elk1), cytoplasmic proteins involved in cytoskeleton regulation (DCX, Tau, WDR62) or vesicular transport (JIP1, JIP3), cell membrane receptors (BMPR2), and mitochondrial proteins (Mcl1, Bim). In addition, because upstream signaling components impact JNK activity, we critically assessed the involvement of signaling scaffolds and the roles of feedback mechanisms in the JNK pathway. Despite a clarification of many regulatory events in JNK-dependent signaling during the past decade, many other structural and mechanistic insights are just beginning to be revealed. These advances open new opportunities to understand the role of JNK signaling in diverse physiological and pathophysiological states. PMID:27466283

Genome-wide analysis of protein-protein interactions and involvement of viral proteins in SARS-CoV replication.

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Ji'an Pan

Full Text Available Analyses of viral protein-protein interactions are an important step to understand viral protein functions and their underlying molecular mechanisms. In this study, we adopted a mammalian two-hybrid system to screen the genome-wide intraviral protein-protein interactions of SARS coronavirus (SARS-CoV and therefrom revealed a number of novel interactions which could be partly confirmed by in vitro biochemical assays. Three pairs of the interactions identified were detected in both directions: non-structural protein (nsp 10 and nsp14, nsp10 and nsp16, and nsp7 and nsp8. The interactions between the multifunctional nsp10 and nsp14 or nsp16, which are the unique proteins found in the members of Nidovirales with large RNA genomes including coronaviruses and toroviruses, may have important implication for the mechanisms of replication/transcription complex assembly and functions of these viruses. Using a SARS-CoV replicon expressing a luciferase reporter under the control of a transcription regulating sequence, it has been shown that several viral proteins (N, X and SUD domains of nsp3, and nsp12 provided in trans stimulated the replicon reporter activity, indicating that these proteins may regulate coronavirus replication and transcription. Collectively, our findings provide a basis and platform for further characterization of the functions and mechanisms of coronavirus proteins.

Mean protein evolutionary distance: a method for comparative protein evolution and its application.

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Michael J Wise

Full Text Available Proteins are under tight evolutionary constraints, so if a protein changes it can only do so in ways that do not compromise its function. In addition, the proteins in an organism evolve at different rates. Leveraging the history of patristic distance methods, a new method for analysing comparative protein evolution, called Mean Protein Evolutionary Distance (MeaPED, measures differential resistance to evolutionary pressure across viral proteomes and is thereby able to point to the proteins' roles. Different species' proteomes can also be compared because the results, consistent across virus subtypes, concisely reflect the very different lifestyles of the viruses. The MeaPED method is here applied to influenza A virus, hepatitis C virus, human immunodeficiency virus (HIV, dengue virus, rotavirus A, polyomavirus BK and measles, which span the positive and negative single-stranded, doubled-stranded and reverse transcribing RNA viruses, and double-stranded DNA viruses. From this analysis, host interaction proteins including hemagglutinin (influenza, and viroporins agnoprotein (polyomavirus, p7 (hepatitis C and VPU (HIV emerge as evolutionary hot-spots. By contrast, RNA-directed RNA polymerase proteins including L (measles, PB1/PB2 (influenza and VP1 (rotavirus, and internal serine proteases such as NS3 (dengue and hepatitis C virus emerge as evolutionary cold-spots. The hot spot influenza hemagglutinin protein is contrasted with the related cold spot H protein from measles. It is proposed that evolutionary cold-spot proteins can become significant targets for second-line anti-viral therapeutics, in cases where front-line vaccines are not available or have become ineffective due to mutations in the hot-spot, generally more antigenically exposed proteins. The MeaPED package is available from www.pam1.bcs.uwa.edu.au/~michaelw/ftp/src/meaped.tar.gz.

Mean protein evolutionary distance: a method for comparative protein evolution and its application.

Science.gov (United States)

Wise, Michael J

2013-01-01

Proteins are under tight evolutionary constraints, so if a protein changes it can only do so in ways that do not compromise its function. In addition, the proteins in an organism evolve at different rates. Leveraging the history of patristic distance methods, a new method for analysing comparative protein evolution, called Mean Protein Evolutionary Distance (MeaPED), measures differential resistance to evolutionary pressure across viral proteomes and is thereby able to point to the proteins' roles. Different species' proteomes can also be compared because the results, consistent across virus subtypes, concisely reflect the very different lifestyles of the viruses. The MeaPED method is here applied to influenza A virus, hepatitis C virus, human immunodeficiency virus (HIV), dengue virus, rotavirus A, polyomavirus BK and measles, which span the positive and negative single-stranded, doubled-stranded and reverse transcribing RNA viruses, and double-stranded DNA viruses. From this analysis, host interaction proteins including hemagglutinin (influenza), and viroporins agnoprotein (polyomavirus), p7 (hepatitis C) and VPU (HIV) emerge as evolutionary hot-spots. By contrast, RNA-directed RNA polymerase proteins including L (measles), PB1/PB2 (influenza) and VP1 (rotavirus), and internal serine proteases such as NS3 (dengue and hepatitis C virus) emerge as evolutionary cold-spots. The hot spot influenza hemagglutinin protein is contrasted with the related cold spot H protein from measles. It is proposed that evolutionary cold-spot proteins can become significant targets for second-line anti-viral therapeutics, in cases where front-line vaccines are not available or have become ineffective due to mutations in the hot-spot, generally more antigenically exposed proteins. The MeaPED package is available from www.pam1.bcs.uwa.edu.au/~michaelw/ftp/src/meaped.tar.gz.

ProteinHistorian: tools for the comparative analysis of eukaryote protein origin.

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John A Capra

Full Text Available The evolutionary history of a protein reflects the functional history of its ancestors. Recent phylogenetic studies identified distinct evolutionary signatures that characterize proteins involved in cancer, Mendelian disease, and different ontogenic stages. Despite the potential to yield insight into the cellular functions and interactions of proteins, such comparative phylogenetic analyses are rarely performed, because they require custom algorithms. We developed ProteinHistorian to make tools for performing analyses of protein origins widely available. Given a list of proteins of interest, ProteinHistorian estimates the phylogenetic age of each protein, quantifies enrichment for proteins of specific ages, and compares variation in protein age with other protein attributes. ProteinHistorian allows flexibility in the definition of protein age by including several algorithms for estimating ages from different databases of evolutionary relationships. We illustrate the use of ProteinHistorian with three example analyses. First, we demonstrate that proteins with high expression in human, compared to chimpanzee and rhesus macaque, are significantly younger than those with human-specific low expression. Next, we show that human proteins with annotated regulatory functions are significantly younger than proteins with catalytic functions. Finally, we compare protein length and age in many eukaryotic species and, as expected from previous studies, find a positive, though often weak, correlation between protein age and length. ProteinHistorian is available through a web server with an intuitive interface and as a set of command line tools; this allows biologists and bioinformaticians alike to integrate these approaches into their analysis pipelines. ProteinHistorian's modular, extensible design facilitates the integration of new datasets and algorithms. The ProteinHistorian web server, source code, and pre-computed ages for 32 eukaryotic genomes are

Cloud prediction of protein structure and function with PredictProtein for Debian.

Science.gov (United States)

Kaján, László; Yachdav, Guy; Vicedo, Esmeralda; Steinegger, Martin; Mirdita, Milot; Angermüller, Christof; Böhm, Ariane; Domke, Simon; Ertl, Julia; Mertes, Christian; Reisinger, Eva; Staniewski, Cedric; Rost, Burkhard

2013-01-01

We report the release of PredictProtein for the Debian operating system and derivatives, such as Ubuntu, Bio-Linux, and Cloud BioLinux. The PredictProtein suite is available as a standard set of open source Debian packages. The release covers the most popular prediction methods from the Rost Lab, including methods for the prediction of secondary structure and solvent accessibility (profphd), nuclear localization signals (predictnls), and intrinsically disordered regions (norsnet). We also present two case studies that successfully utilize PredictProtein packages for high performance computing in the cloud: the first analyzes protein disorder for whole organisms, and the second analyzes the effect of all possible single sequence variants in protein coding regions of the human genome.

HomPPI: a class of sequence homology based protein-protein interface prediction methods

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Dobbs Drena

2011-06-01

Full Text Available Abstract Background Although homology-based methods are among the most widely used methods for predicting the structure and function of proteins, the question as to whether interface sequence conservation can be effectively exploited in predicting protein-protein interfaces has been a subject of debate. Results We studied more than 300,000 pair-wise alignments of protein sequences from structurally characterized protein complexes, including both obligate and transient complexes. We identified sequence similarity criteria required for accurate homology-based inference of interface residues in a query protein sequence. Based on these analyses, we developed HomPPI, a class of sequence homology-based methods for predicting protein-protein interface residues. We present two variants of HomPPI: (i NPS-HomPPI (Non partner-specific HomPPI, which can be used to predict interface residues of a query protein in the absence of knowledge of the interaction partner; and (ii PS-HomPPI (Partner-specific HomPPI, which can be used to predict the interface residues of a query protein with a specific target protein. Our experiments on a benchmark dataset of obligate homodimeric complexes show that NPS-HomPPI can reliably predict protein-protein interface residues in a given protein, with an average correlation coefficient (CC of 0.76, sensitivity of 0.83, and specificity of 0.78, when sequence homologs of the query protein can be reliably identified. NPS-HomPPI also reliably predicts the interface residues of intrinsically disordered proteins. Our experiments suggest that NPS-HomPPI is competitive with several state-of-the-art interface prediction servers including those that exploit the structure of the query proteins. The partner-specific classifier, PS-HomPPI can, on a large dataset of transient complexes, predict the interface residues of a query protein with a specific target, with a CC of 0.65, sensitivity of 0.69, and specificity of 0.70, when homologs of

Designing proteins for therapeutic applications.

Science.gov (United States)

Lazar, Greg A; Marshall, Shannon A; Plecs, Joseph J; Mayo, Stephen L; Desjarlais, John R

2003-08-01

Protein design is becoming an increasingly useful tool for optimizing protein drugs and creating novel biotherapeutics. Recent progress includes the engineering of monoclonal antibodies, cytokines, enzymes and viral fusion inhibitors.

Highly thermostable fluorescent proteins

Science.gov (United States)

Bradbury, Andrew M [Santa Fe, NM; Waldo, Geoffrey S [Santa Fe, NM; Kiss, Csaba [Los Alamos, NM

2011-03-22

Thermostable fluorescent proteins (TSFPs), methods for generating these and other stability-enhanced proteins, polynucleotides encoding such proteins, and assays and method for using the TSFPs and TSFP-encoding nucleic acid molecules are provided. The TSFPs of the invention show extremely enhanced levels of stability and thermotolerance. In one case, for example, a TSFP of the invention is so stable it can be heated to 99.degree. C. for short periods of time without denaturing, and retains 85% of its fluorescence when heated to 80.degree. C. for several minutes. The invention also provides a method for generating stability-enhanced variants of a protein, including but not limited to fluorescent proteins.

Solving the Schroedinger equation using Smolyak interpolants

International Nuclear Information System (INIS)

Avila, Gustavo; Carrington, Tucker Jr.

2013-01-01

In this paper, we present a new collocation method for solving the Schroedinger equation. Collocation has the advantage that it obviates integrals. All previous collocation methods have, however, the crucial disadvantage that they require solving a generalized eigenvalue problem. By combining Lagrange-like functions with a Smolyak interpolant, we device a collocation method that does not require solving a generalized eigenvalue problem. We exploit the structure of the grid to develop an efficient algorithm for evaluating the matrix-vector products required to compute energy levels and wavefunctions. Energies systematically converge as the number of points and basis functions are increased

Dryland Agrivoltaics: A novel approach to collocating food production and solar renewable energy to maximize food production, water savings, and energy generation

Science.gov (United States)

Barron-Gafford, G.; Escobedo, E. B.; Smith, J.; Raub, H.; Jimenez, J. R.; Sutter, L., Jr.; Barnett-Moreno, I.; Blackett, D. T.; Thompson, M. S.; Minor, R. L.; Pavao-Zuckerman, M.

2017-12-01

Conventional understanding of land use asserts an inherent "zero-sum-game" of competition between renewable energy and agricultural food production. This discourse is so fundamentally entrenched that it drives most current policy around conservation practices, land and water allotments for agriculture, and permitting for large-scale renewable energy installations. We are investigating a novel approach to solve a problem key to our environment and economy in drylands by creating a hybrid of collocated "green" agriculture and "grey" solar photovoltaic (PV) infrastructure to maximize agricultural production while improving renewable energy production. We are monitoring atmospheric microclimatic conditions, soil moisture, plant ecophysiological function, and biomass production within both this novel "agrivoltaics" ecosystem and in traditional PV installations and agricultural settings (control plot) to quantify tradeoffs associated with this approach. We have found that levels of soil moisture remained higher after each irrigation event within the soils under the agrivoltaics installation than the traditional agricultural setting due to the shading provided by the PV panels overhead. We initiated a drought treatment, which underscored the water-savings under the agrivoltaics installation and increased water use efficiency in this system. We hypothesized that we will see more temperature and drought stresses on photosynthetic capacity and water use efficiency in the control plants relative to the agrivoltaic installation, and we found that several food crops either experienced significantly more production within the agrivoltaics area, whereas others resulted in nearly equal production but at significant water savings. Combined with localized cooling of the PV panels resulting from the transpiration from the vegetative "understory", we are finding a win-win-win at the food-water-energy nexus. photo credit: Bob Demers/UANews

Comparative transcriptional analysis of Bacillus subtilis cells overproducing either secreted proteins, lipoproteins or membrane proteins

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Marciniak Bogumiła C

2012-05-01

Full Text Available Abstract Background Bacillus subtilis is a favorable host for the production of industrially relevant proteins because of its capacity of secreting proteins into the medium to high levels, its GRAS (Generally Recognized As Safe status, its genetic accessibility and its capacity to grow in large fermentations. However, production of heterologous proteins still faces limitations. Results This study aimed at the identification of bottlenecks in secretory protein production by analyzing the response of B. subtilis at the transcriptome level to overproduction of eight secretory proteins of endogenous and heterologous origin and with different subcellular or extracellular destination: secreted proteins (NprE and XynA of B. subtilis, Usp45 of Lactococcus lactis, TEM-1 β-lactamase of Escherichia coli, membrane proteins (LmrA of L. lactis and XylP of Lactobacillus pentosus and lipoproteins (MntA and YcdH of B. subtilis. Responses specific for proteins with a common localization as well as more general stress responses were observed. The latter include upregulation of genes encoding intracellular stress proteins (groES/EL, CtsR regulated genes. Specific responses include upregulation of the liaIHGFSR operon under Usp45 and TEM-1 β-lactamase overproduction; cssRS, htrA and htrB under all secreted proteins overproduction; sigW and SigW-regulated genes mainly under membrane proteins overproduction; and ykrL (encoding an HtpX homologue specifically under membrane proteins overproduction. Conclusions The results give better insights into B. subtilis responses to protein overproduction stress and provide potential targets for genetic engineering in order to further improve B. subtilis as a protein production host.

Detecting annual and seasonal variations of CO2, CO and N2O from a multi-year collocated satellite-radiosonde data-set using the new Rapid Radiance Reconstruction (3R-N) model

International Nuclear Information System (INIS)

Chedin, A.; Serrar, S.; Hollingsworth, A.; Armante, R.; Scott, N.A.

2003-01-01

The NOAA polar meteorological satellites have embarked the TIROS-N operational vertical sounder (TOVS) since 1979. Using radiosondes and NOAA-10 TOVS measurements which are collocated within a narrow space and time window, we have studied the differences between the TOVS measurements and simulated measurements from a new fast, Rapid Radiance Reconstruction Network (3R-N), non-linear radiative transfer model with up to date spectroscopy. Simulations use radiosonde temperature and humidity measurements as the prime input. The radiative transfer model also uses fixed greenhouse gas absorber amounts (CO 2 ,CO,N 2 O) and reasonable estimates of O 3 and of surface temperature. The 3R-N model is first presented and validated. Then, a study of the differences between the simulated and measured radiances shows annual trends and seasonal variations consistent with independent measurements of variations in CO 2 and other greenhouse gases atmospheric concentrations. The improved accuracy of 3R-N and a better handling of its deviations with respect to observations allow most of difficulties met in a previous study (J. Climate 15 (2002) 95) to be resolved

Human cancer protein-protein interaction network: a structural perspective.

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Gozde Kar

2009-12-01

Full Text Available Protein-protein interaction networks provide a global picture of cellular function and biological processes. Some proteins act as hub proteins, highly connected to others, whereas some others have few interactions. The dysfunction of some interactions causes many diseases, including cancer. Proteins interact through their interfaces. Therefore, studying the interface properties of cancer-related proteins will help explain their role in the interaction networks. Similar or overlapping binding sites should be used repeatedly in single interface hub proteins, making them promiscuous. Alternatively, multi-interface hub proteins make use of several distinct binding sites to bind to different partners. We propose a methodology to integrate protein interfaces into cancer interaction networks (ciSPIN, cancer structural protein interface network. The interactions in the human protein interaction network are replaced by interfaces, coming from either known or predicted complexes. We provide a detailed analysis of cancer related human protein-protein interfaces and the topological properties of the cancer network. The results reveal that cancer-related proteins have smaller, more planar, more charged and less hydrophobic binding sites than non-cancer proteins, which may indicate low affinity and high specificity of the cancer-related interactions. We also classified the genes in ciSPIN according to phenotypes. Within phenotypes, for breast cancer, colorectal cancer and leukemia, interface properties were found to be discriminating from non-cancer interfaces with an accuracy of 71%, 67%, 61%, respectively. In addition, cancer-related proteins tend to interact with their partners through distinct interfaces, corresponding mostly to multi-interface hubs, which comprise 56% of cancer-related proteins, and constituting the nodes with higher essentiality in the network (76%. We illustrate the interface related affinity properties of two cancer-related hub

BLAST-based structural annotation of protein residues using Protein Data Bank.

Science.gov (United States)

Singh, Harinder; Raghava, Gajendra P S

2016-01-25

In the era of next-generation sequencing where thousands of genomes have been already sequenced; size of protein databases is growing with exponential rate. Structural annotation of these proteins is one of the biggest challenges for the computational biologist. Although, it is easy to perform BLAST search against Protein Data Bank (PDB) but it is difficult for a biologist to annotate protein residues from BLAST search. A web-server StarPDB has been developed for structural annotation of a protein based on its similarity with known protein structures. It uses standard BLAST software for performing similarity search of a query protein against protein structures in PDB. This server integrates wide range modules for assigning different types of annotation that includes, Secondary-structure, Accessible surface area, Tight-turns, DNA-RNA and Ligand modules. Secondary structure module allows users to predict regular secondary structure states to each residue in a protein. Accessible surface area predict the exposed or buried residues in a protein. Tight-turns module is designed to predict tight turns like beta-turns in a protein. DNA-RNA module developed for predicting DNA and RNA interacting residues in a protein. Similarly, Ligand module of server allows one to predicted ligands, metal and nucleotides ligand interacting residues in a protein. In summary, this manuscript presents a web server for comprehensive annotation of a protein based on similarity search. It integrates number of visualization tools that facilitate users to understand structure and function of protein residues. This web server is available freely for scientific community from URL http://crdd.osdd.net/raghava/starpdb .

Amino acids and proteins

NARCIS (Netherlands)

van Goudoever, Johannes B.; Vlaardingerbroek, Hester; van den Akker, Chris H.; de Groof, Femke; van der Schoor, Sophie R. D.

2014-01-01

Amino acids and protein are key factors for growth. The neonatal period requires the highest intake in life to meet the demands. Those demands include amino acids for growth, but proteins and amino acids also function as signalling molecules and function as neurotransmitters. Often the nutritional

Chitin and stress induced protein kinase activation

DEFF Research Database (Denmark)

Kenchappa, Chandra Shekar; Azevedo da Silva, Raquel; Bressendorff, Simon

2017-01-01

The assays described here are pertinent to protein kinase studies in any plant. They include an immunoblot phosphorylation/activation assay and an in-gel activity assay for MAP kinases (MPKs) using the general protein kinase substrate myelin basic protein. They also include a novel in-gel peptide...... substrate assay for Snf1-related kinase family 2 members (SnRK2s). This kinase family-specific assay overcomes some limitations of in-gel assays and permits the identification of different types of kinase activities in total protein extracts....

Functionality of system components: Conservation of protein function in protein feature space

DEFF Research Database (Denmark)

Jensen, Lars Juhl; Ussery, David; Brunak, Søren

2003-01-01

well on organisms other than the one on which it was trained. We evaluate the performance of such a method, ProtFun, which relies on protein features as its sole input, and show that the method gives similar performance for most eukaryotes and performs much better than anticipated on archaea......Many protein features useful for prediction of protein function can be predicted from sequence, including posttranslational modifications, subcellular localization, and physical/chemical properties. We show here that such protein features are more conserved among orthologs than paralogs, indicating...... they are crucial for protein function and thus subject to selective pressure. This means that a function prediction method based on sequence-derived features may be able to discriminate between proteins with different function even when they have highly similar structure. Also, such a method is likely to perform...

The HTLV-1 Tax protein binding domain of cyclin-dependent kinase 4 (CDK4 includes the regulatory PSTAIRE helix

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Grassmann Ralph

2005-09-01

Full Text Available Abstract Background The Tax oncoprotein of human T-cell leukemia virus type 1 (HTLV-1 is leukemogenic in transgenic mice and induces permanent T-cell growth in vitro. It is found in active CDK holoenzyme complexes from adult T-cell leukemia-derived cultures and stimulates the G1- to-S phase transition by activating the cyclin-dependent kinase (CDK CDK4. The Tax protein directly and specifically interacts with CDK4 and cyclin D2 and binding is required for enhanced CDK4 kinase activity. The protein-protein contact between Tax and the components of the cyclin D/CDK complexes increases the association of CDK4 and its positive regulatory subunit cyclin D and renders the complex resistant to p21CIP inhibition. Tax mutants affecting the N-terminus cannot bind cyclin D and CDK4. Results To analyze, whether the N-terminus of Tax is capable of CDK4-binding, in vitro binding -, pull down -, and mammalian two-hybrid analyses were performed. These experiments revealed that a segment of 40 amino acids is sufficient to interact with CDK4 and cyclin D2. To define a Tax-binding domain and analyze how Tax influences the kinase activity, a series of CDK4 deletion mutants was tested. Different assays revealed two regions which upon deletion consistently result in reduced binding activity. These were isolated and subjected to mammalian two-hybrid analysis to test their potential to interact with the Tax N-terminus. These experiments concurrently revealed binding at the N- and C-terminus of CDK4. The N-terminal segment contains the PSTAIRE helix, which is known to control the access of substrate to the active cleft of CDK4 and thus the kinase activity. Conclusion Since the N- and C-terminus of CDK4 are neighboring in the predicted three-dimensional protein structure, it is conceivable that they comprise a single binding domain, which interacts with the Tax N-terminus.

Synthesis of milligram quantities of proteins using a reconstituted in vitro protein synthesis system.

Science.gov (United States)

Kazuta, Yasuaki; Matsuura, Tomoaki; Ichihashi, Norikazu; Yomo, Tetsuya

2014-11-01

In this study, the amount of protein synthesized using an in vitro protein synthesis system composed of only highly purified components (the PURE system) was optimized. By varying the concentrations of each system component, we determined the component concentrations that result in the synthesis of 0.38 mg/mL green fluorescent protein (GFP) in batch mode and 3.8 mg/mL GFP in dialysis mode. In dialysis mode, protein concentrations of 4.3 and 4.4 mg/mL were synthesized for dihydrofolate reductase and β-galactosidase, respectively. Using the optimized system, the synthesized protein represented 30% (w/w) of the total protein, which is comparable to the level of overexpressed protein in Escherichia coli cells. This optimized reconstituted in vitro protein synthesis system may potentially be useful for various applications, including in vitro directed evolution of proteins, artificial cell assembly, and protein structural studies. Copyright © 2014 The Society for Biotechnology, Japan. Published by Elsevier B.V. All rights reserved.

cDNA encoding a polypeptide including a hev ein sequence

Energy Technology Data Exchange (ETDEWEB)

Raikhel, Natasha V. (Okemos, MI); Broekaert, Willem F. (Dilbeek, BE); Chua, Nam-Hai (Scarsdale, NY); Kush, Anil (New York, NY)

2000-07-04

A cDNA clone (HEV1) encoding hevein was isolated via polymerase chain reaction (PCR) using mixed oligonucleotides corresponding to two regions of hevein as primers and a Hevea brasiliensis latex cDNA library as a template. HEV1 is 1018 nucleotides long and includes an open reading frame of 204 amino acids. The deduced amino acid sequence contains a putative signal sequence of 17 amino acid residues followed by a 187 amino acid polypeptide. The amino-terminal region (43 amino acids) is identical to hevein and shows homology to several chitin-binding proteins and to the amino-termini of wound-induced genes in potato and poplar. The carboxyl-terminal portion of the polypeptide (144 amino acids) is 74-79% homologous to the carboxyl-terminal region of wound-inducible genes of potato. Wounding, as well as application of the plant hormones abscisic acid and ethylene, resulted in accumulation of hevein transcripts in leaves, stems and latex, but not in roots, as shown by using the cDNA as a probe. A fusion protein was produced in E. coli from the protein of the present invention and maltose binding protein produced by the E. coli.

Extracting knowledge from protein structure geometry

DEFF Research Database (Denmark)

Røgen, Peter; Koehl, Patrice

2013-01-01

potential from geometric knowledge extracted from native and misfolded conformers of protein structures. This new potential, Metric Protein Potential (MPP), has two main features that are key to its success. Firstly, it is composite in that it includes local and nonlocal geometric information on proteins...

Topological characteristics of helical repeat proteins

NARCIS (Netherlands)

Groves, M R; Barford, D

The recent elucidation of protein structures based upon repeating amino acid motifs, including the armadillo motif, the HEAT motif and tetratricopeptide repeats, reveals that they belong to the class of helical repeat proteins. These proteins share the common property of being assembled from tandem

Kinetics of protein unfolding at interfaces

International Nuclear Information System (INIS)

Yano, Yohko F

2012-01-01

The conformation of protein molecules is determined by a balance of various forces, including van der Waals attraction, electrostatic interaction, hydrogen bonding, and conformational entropy. When protein molecules encounter an interface, they are often adsorbed on the interface. The conformation of an adsorbed protein molecule strongly depends on the interaction between the protein and the interface. Recent time-resolved investigations have revealed that protein conformation changes during the adsorption process due to the protein-protein interaction increasing with increasing interface coverage. External conditions also affect the protein conformation. This review considers recent dynamic observations of protein adsorption at various interfaces and their implications for the kinetics of protein unfolding at interfaces. (topical review)

NMR Studies of Protein Hydration and Protein-Ligand Interactions

Science.gov (United States)

Chong, Yuan

Water on the surface of a protein is called hydration water. Hydration water is known to play a crucial role in a variety of biological processes including protein folding, enzymatic activation, and drug binding. Although the significance of hydration water has been recognized, the underlying mechanism remains far from being understood. This dissertation employs a unique in-situ nuclear magnetic resonance (NMR) technique to study the mechanism of protein hydration and the role of hydration in alcohol-protein interactions. Water isotherms in proteins are measured at different temperatures via the in-situ NMR technique. Water is found to interact differently with hydrophilic and hydrophobic groups on the protein. Water adsorption on hydrophilic groups is hardly affected by the temperature, while water adsorption on hydrophobic groups strongly depends on the temperature around 10 C, below which the adsorption is substantially reduced. This effect is induced by the dramatic decrease in the protein flexibility below 10 C. Furthermore, nanosecond to microsecond protein dynamics and the free energy, enthalpy, and entropy of protein hydration are studied as a function of hydration level and temperature. A crossover at 10 C in protein dynamics and thermodynamics is revealed. The effect of water at hydrophilic groups on protein dynamics and thermodynamics shows little temperature dependence, whereas water at hydrophobic groups has stronger effect above 10 C. In addition, I investigate the role of water in alcohol binding to the protein using the in-situ NMR detection. The isotherms of alcohols are first measured on dry proteins, then on proteins with a series of controlled hydration levels. The free energy, enthalpy, and entropy of alcohol binding are also determined. Two distinct types of alcohol binding are identified. On the one hand, alcohols can directly bind to a few specific sites on the protein. This type of binding is independent of temperature and can be

Propuesta para una didáctica de las colocaciones en la enseñanza del español como lengua materna

Directory of Open Access Journals (Sweden)

César Pascual Romero Casanova

2016-06-01

Full Text Available The collocation research on teaching the subject of Spanish as a first language has been practically ignored, in contrast with the attention paid to the Spanish as a second language. This paper presents a first approach to the collocations teaching directed to the native speakers starting on a experience with students in the first year of Compulsory Secondary Education. After reviewing the concept of collocation, we present the type of collocations with higher didactic performance and the reasons for its choice, as well as the more suitable teaching and learning metodology, where the inference role is mainly in developing lexical skills.

MM-ISMSA: An Ultrafast and Accurate Scoring Function for Protein-Protein Docking.

Science.gov (United States)

Klett, Javier; Núñez-Salgado, Alfonso; Dos Santos, Helena G; Cortés-Cabrera, Álvaro; Perona, Almudena; Gil-Redondo, Rubén; Abia, David; Gago, Federico; Morreale, Antonio

2012-09-11

An ultrafast and accurate scoring function for protein-protein docking is presented. It includes (1) a molecular mechanics (MM) part based on a 12-6 Lennard-Jones potential; (2) an electrostatic component based on an implicit solvent model (ISM) with individual desolvation penalties for each partner in the protein-protein complex plus a hydrogen bonding term; and (3) a surface area (SA) contribution to account for the loss of water contacts upon protein-protein complex formation. The accuracy and performance of the scoring function, termed MM-ISMSA, have been assessed by (1) comparing the total binding energies, the electrostatic term, and its components (charge-charge and individual desolvation energies), as well as the per residue contributions, to results obtained with well-established methods such as APBSA or MM-PB(GB)SA for a set of 1242 decoy protein-protein complexes and (2) testing its ability to recognize the docking solution closest to the experimental structure as that providing the most favorable total binding energy. For this purpose, a test set consisting of 15 protein-protein complexes with known 3D structure mixed with 10 decoys for each complex was used. The correlation between the values afforded by MM-ISMSA and those from the other methods is quite remarkable (r(2) ∼ 0.9), and only 0.2-5.0 s (depending on the number of residues) are spent on a single calculation including an all vs all pairwise energy decomposition. On the other hand, MM-ISMSA correctly identifies the best docking solution as that closest to the experimental structure in 80% of the cases. Finally, MM-ISMSA can process molecular dynamics trajectories and reports the results as averaged values with their standard deviations. MM-ISMSA has been implemented as a plugin to the widely used molecular graphics program PyMOL, although it can also be executed in command-line mode. MM-ISMSA is distributed free of charge to nonprofit organizations.

Functional structural motifs for protein-ligand, protein-protein, and protein-nucleic acid interactions and their connection to supersecondary structures.

Science.gov (United States)

Kinjo, Akira R; Nakamura, Haruki

2013-01-01

Protein functions are mediated by interactions between proteins and other molecules. One useful approach to analyze protein functions is to compare and classify the structures of interaction interfaces of proteins. Here, we describe the procedures for compiling a database of interface structures and efficiently comparing the interface structures. To do so requires a good understanding of the data structures of the Protein Data Bank (PDB). Therefore, we also provide a detailed account of the PDB exchange dictionary necessary for extracting data that are relevant for analyzing interaction interfaces and secondary structures. We identify recurring structural motifs by classifying similar interface structures, and we define a coarse-grained representation of supersecondary structures (SSS) which represents a sequence of two or three secondary structure elements including their relative orientations as a string of four to seven letters. By examining the correspondence between structural motifs and SSS strings, we show that no SSS string has particularly high propensity to be found interaction interfaces in general, indicating any SSS can be used as a binding interface. When individual structural motifs are examined, there are some SSS strings that have high propensity for particular groups of structural motifs. In addition, it is shown that while the SSS strings found in particular structural motifs for nonpolymer and protein interfaces are as abundant as in other structural motifs that belong to the same subunit, structural motifs for nucleic acid interfaces exhibit somewhat stronger preference for SSS strings. In regard to protein folds, many motif-specific SSS strings were found across many folds, suggesting that SSS may be a useful description to investigate the universality of ligand binding modes.

In silico modeling of the yeast protein and protein family interaction network

Science.gov (United States)

Goh, K.-I.; Kahng, B.; Kim, D.

2004-03-01

Understanding of how protein interaction networks of living organisms have evolved or are organized can be the first stepping stone in unveiling how life works on a fundamental ground. Here we introduce an in silico ``coevolutionary'' model for the protein interaction network and the protein family network. The essential ingredient of the model includes the protein family identity and its robustness under evolution, as well as the three previously proposed: gene duplication, divergence, and mutation. This model produces a prototypical feature of complex networks in a wide range of parameter space, following the generalized Pareto distribution in connectivity. Moreover, we investigate other structural properties of our model in detail with some specific values of parameters relevant to the yeast Saccharomyces cerevisiae, showing excellent agreement with the empirical data. Our model indicates that the physical constraints encoded via the domain structure of proteins play a crucial role in protein interactions.

Analysis and computation of the elastic wave equation with random coefficients

KAUST Repository

Motamed, Mohammad

2015-10-21

We consider the stochastic initial-boundary value problem for the elastic wave equation with random coefficients and deterministic data. We propose a stochastic collocation method for computing statistical moments of the solution or statistics of some given quantities of interest. We study the convergence rate of the error in the stochastic collocation method. In particular, we show that, the rate of convergence depends on the regularity of the solution or the quantity of interest in the stochastic space, which is in turn related to the regularity of the deterministic data in the physical space and the type of the quantity of interest. We demonstrate that a fast rate of convergence is possible in two cases: for the elastic wave solutions with high regular data; and for some high regular quantities of interest even in the presence of low regular data. We perform numerical examples, including a simplified earthquake, which confirm the analysis and show that the collocation method is a valid alternative to the more traditional Monte Carlo sampling method for approximating quantities with high stochastic regularity.

English Writing Teaching Model Dependent on Computer Network Corpus Drive Model

Directory of Open Access Journals (Sweden)

Shi Lei

2018-03-01

Full Text Available At present, the mainstream lexicalized English writing methods take only the corpus dependence between words into consideration, without introducing the corpus collocation and other issues. “Drive” is a relatively essential feature of words. And once the drive structure of a word is determined, it will be relatively clear what kinds of words to collocate with, hence the structure of the sentence can be derived relatively directly. In this paper, the English writing model that relies on the computer network corpus drive model is put forward. In this model, rich English corpus is introduced in the decomposition of the rules and the calculation of the probability, which includes not only the corpus dependence information, but also the drive structure and other corpus collocation information. Improved computer network corpus drive model is used to carry out the English writing teaching experiment. The experimental results show that the precision and the recall rate are 88.76% and 87.43%, respectively. The F value of the comprehensive index is improved by 6.65% compared with the Collins headword driven English modes of writing.

cDNA cloning of the basement membrane chondroitin sulfate proteoglycan core protein, bamacan: a five domain structure including coiled-coil motifs

DEFF Research Database (Denmark)

Wu, R R; Couchman, J R

1997-01-01

Basement membranes contain several proteoglycans, and those bearing heparan sulfate glycosaminoglycans such as perlecan and agrin usually predominate. Most mammalian basement membranes also contain chondroitin sulfate, and a core protein, bamacan, has been partially characterized. We have now....... The protein sequence has low overall homology, apart from very small NH2- and COOH-terminal motifs. At the junctions between the distal globular domains and the coiled-coil regions lie glycosylation sites, with up to three N-linked oligosaccharides and probably three chondroitin chains. Three other Ser...

Web-accessible molecular modeling with Rosetta: The Rosetta Online Server that Includes Everyone (ROSIE).

Science.gov (United States)

Moretti, Rocco; Lyskov, Sergey; Das, Rhiju; Meiler, Jens; Gray, Jeffrey J

2018-01-01

The Rosetta molecular modeling software package provides a large number of experimentally validated tools for modeling and designing proteins, nucleic acids, and other biopolymers, with new protocols being added continually. While freely available to academic users, external usage is limited by the need for expertise in the Unix command line environment. To make Rosetta protocols available to a wider audience, we previously created a web server called Rosetta Online Server that Includes Everyone (ROSIE), which provides a common environment for hosting web-accessible Rosetta protocols. Here we describe a simplification of the ROSIE protocol specification format, one that permits easier implementation of Rosetta protocols. Whereas the previous format required creating multiple separate files in different locations, the new format allows specification of the protocol in a single file. This new, simplified protocol specification has more than doubled the number of Rosetta protocols available under ROSIE. These new applications include pK a determination, lipid accessibility calculation, ribonucleic acid redesign, protein-protein docking, protein-small molecule docking, symmetric docking, antibody docking, cyclic toxin docking, critical binding peptide determination, and mapping small molecule binding sites. ROSIE is freely available to academic users at http://rosie.rosettacommons.org. © 2017 The Protein Society.

ASP53, a thermostable protein from Acacia erioloba seeds that protects target proteins against thermal denaturation

CSIR Research Space (South Africa)

Mtwisha, L

2007-02-01

Full Text Available ) and the Typha pollen D7 protein was found to stabilise sugar glasses in an in vitro system (Wolkers et al. 2001). The cupin family of proteins comprises a wide variety of proteins from both prokaryotes and eukaryotes and includes the seed storage proteins...–268. Garay-Arroyo A, Colmenero-Flores JM, Garciarrubio A, Covarrubias AA (2000) Highly hydrophilic proteins in prokaryotes and eukaryotes are common during conditions of water deficit. Journal of Biological Chemistry 275, 5668–5674. doi: 10.1074/jbc.275...

Gene expression profiling in the stress control brain region hypothalamic paraventricular nucleus reveals a novel gene network including Amyloid beta Precursor Protein

Directory of Open Access Journals (Sweden)

Deussing Jan M

2010-10-01

Full Text Available Abstract Background The pivotal role of stress in the precipitation of psychiatric diseases such as depression is generally accepted. This study aims at the identification of genes that are directly or indirectly responding to stress. Inbred mouse strains that had been evidenced to differ in their stress response as well as in their response to antidepressant treatment were chosen for RNA profiling after stress exposure. Gene expression and regulation was determined by microarray analyses and further evaluated by bioinformatics tools including pathway and cluster analyses. Results Forced swimming as acute stressor was applied to C57BL/6J and DBA/2J mice and resulted in sets of regulated genes in the paraventricular nucleus of the hypothalamus (PVN, 4 h or 8 h after stress. Although the expression changes between the mouse strains were quite different, they unfolded in phases over time in both strains. Our search for connections between the regulated genes resulted in potential novel signalling pathways in stress. In particular, Guanine nucleotide binding protein, alpha inhibiting 2 (GNAi2 and Amyloid β (A4 precursor protein (APP were detected as stress-regulated genes, and together with other genes, seem to be integrated into stress-responsive pathways and gene networks in the PVN. Conclusions This search for stress-regulated genes in the PVN revealed its impact on interesting genes (GNAi2 and APP and a novel gene network. In particular the expression of APP in the PVN that is governing stress hormone balance, is of great interest. The reported neuroprotective role of this molecule in the CNS supports the idea that a short acute stress can elicit positive adaptational effects in the brain.

Towards a rigorous network of protein-protein interactions of the model sulfate reducer Desulfovibrio vulgaris Hildenborough.

Directory of Open Access Journals (Sweden)

Swapnil R Chhabra

Full Text Available Protein-protein interactions offer an insight into cellular processes beyond what may be obtained by the quantitative functional genomics tools of proteomics and transcriptomics. The aforementioned tools have been extensively applied to study Escherichia coli and other aerobes and more recently to study the stress response behavior of Desulfovibrio vulgaris Hildenborough, a model obligate anaerobe and sulfate reducer and the subject of this study. Here we carried out affinity purification followed by mass spectrometry to reconstruct an interaction network among 12 chromosomally encoded bait and 90 prey proteins based on 134 bait-prey interactions identified to be of high confidence. Protein-protein interaction data are often plagued by the lack of adequate controls and replication analyses necessary to assess confidence in the results, including identification of potential false positives. We addressed these issues through the use of biological replication, exponentially modified protein abundance indices, results from an experimental negative control, and a statistical test to assign confidence to each putative interacting pair applicable to small interaction data studies. We discuss the biological significance of metabolic features of D. vulgaris revealed by these protein-protein interaction data and the observed protein modifications. These include the distinct role of the putative carbon monoxide-induced hydrogenase, unique electron transfer routes associated with different oxidoreductases, and the possible role of methylation in regulating sulfate reduction.

A Bacillus megaterium System for the Production of Recombinant Proteins and Protein Complexes.

Science.gov (United States)

Biedendieck, Rebekka

2016-01-01

For many years the Gram-positive bacterium Bacillus megaterium has been used for the production and secretion of recombinant proteins. For this purpose it was systematically optimized. Plasmids with different inducible promoter systems, with different compatible origins, with small tags for protein purification and with various specific signals for protein secretion were combined with genetically improved host strains. Finally, the development of appropriate cultivation conditions for the production strains established this organism as a bacterial cell factory even for large proteins. Along with the overproduction of individual proteins the organism is now also used for the simultaneous coproduction of up to 14 recombinant proteins, multiple subsequently interacting or forming protein complexes. Some of these recombinant strains are successfully used for bioconversion or the biosynthesis of valuable components including vitamins. The titers in the g per liter scale for the intra- and extracellular recombinant protein production prove the high potential of B. megaterium for industrial applications. It is currently further enhanced for the production of recombinant proteins and multi-subunit protein complexes using directed genetic engineering approaches based on transcriptome, proteome, metabolome and fluxome data.

Synthesis of Lipidated Proteins.

Science.gov (United States)

Mejuch, Tom; Waldmann, Herbert

2016-08-17

Protein lipidation is one of the major post-translational modifications (PTM) of proteins. The attachment of the lipid moiety frequently determines the localization and the function of the lipoproteins. Lipidated proteins participate in many essential biological processes in eukaryotic cells, including vesicular trafficking, signal transduction, and regulation of the immune response. Malfunction of these cellular processes usually leads to various diseases such as cancer. Understanding the mechanism of cellular signaling and identifying the protein-protein and protein-lipid interactions in which the lipoproteins are involved is a crucial task. To achieve these goals, fully functional lipidated proteins are required. However, access to lipoproteins by means of standard expression is often rather limited. Therefore, semisynthetic methods, involving the synthesis of lipidated peptides and their subsequent chemoselective ligation to yield full-length lipoproteins, were developed. In this Review we summarize the commonly used methods for lipoprotein synthesis and the development of the corresponding chemoselective ligation techniques. Several key studies involving full-length semisynthetic lipidated Ras, Rheb, and LC3 proteins are presented.

High throughput protein production screening

Science.gov (United States)

Beernink, Peter T [Walnut Creek, CA; Coleman, Matthew A [Oakland, CA; Segelke, Brent W [San Ramon, CA

2009-09-08

Methods, compositions, and kits for the cell-free production and analysis of proteins are provided. The invention allows for the production of proteins from prokaryotic sequences or eukaryotic sequences, including human cDNAs using PCR and IVT methods and detecting the proteins through fluorescence or immunoblot techniques. This invention can be used to identify optimized PCR and WT conditions, codon usages and mutations. The methods are readily automated and can be used for high throughput analysis of protein expression levels, interactions, and functional states.

PDZ Protein Regulation of G Protein-Coupled Receptor Trafficking and Signaling Pathways.

Science.gov (United States)

Dunn, Henry A; Ferguson, Stephen S G

2015-10-01

G protein-coupled receptors (GPCRs) contribute to the regulation of every aspect of human physiology and are therapeutic targets for the treatment of numerous diseases. As a consequence, understanding the myriad of mechanisms controlling GPCR signaling and trafficking is essential for the development of new pharmacological strategies for the treatment of human pathologies. Of the many GPCR-interacting proteins, postsynaptic density protein of 95 kilodaltons, disc large, zona occludens-1 (PDZ) domain-containing proteins appear most abundant and have similarly been implicated in disease mechanisms. PDZ proteins play an important role in regulating receptor and channel protein localization within synapses and tight junctions and function to scaffold intracellular signaling protein complexes. In the current study, we review the known functional interactions between PDZ domain-containing proteins and GPCRs and provide insight into the potential mechanisms of action. These PDZ domain-containing proteins include the membrane-associated guanylate-like kinases [postsynaptic density protein of 95 kilodaltons; synapse-associated protein of 97 kilodaltons; postsynaptic density protein of 93 kilodaltons; synapse-associated protein of 102 kilodaltons; discs, large homolog 5; caspase activation and recruitment domain and membrane-associated guanylate-like kinase domain-containing protein 3; membrane protein, palmitoylated 3; calcium/calmodulin-dependent serine protein kinase; membrane-associated guanylate kinase protein (MAGI)-1, MAGI-2, and MAGI-3], Na(+)/H(+) exchanger regulatory factor proteins (NHERFs) (NHERF1, NHERF2, PDZ domain-containing kidney protein 1, and PDZ domain-containing kidney protein 2), Golgi-associated PDZ proteins (Gα-binding protein interacting protein, C-terminus and CFTR-associated ligand), PDZ domain-containing guanine nucleotide exchange factors (GEFs) 1 and 2, regulator of G protein signaling (RGS)-homology-RhoGEFs (PDZ domain-containing RhoGEF and

Uncovering Viral Protein-Protein Interactions and their Role in Arenavirus Life Cycle

Directory of Open Access Journals (Sweden)

Nora López

2012-09-01

Full Text Available The Arenaviridae family includes widely distributed pathogens that cause severe hemorrhagic fever in humans. Replication and packaging of their single-stranded RNA genome involve RNA recognition by viral proteins and a number of key protein-protein interactions. Viral RNA synthesis is directed by the virus-encoded RNA dependent-RNA polymerase (L protein and requires viral RNA encapsidation by the Nucleoprotein. In addition to the role that the interaction between L and the Nucleoprotein may have in the replication process, polymerase activity appears to be modulated by the association between L and the small multifunctional Z protein. Z is also a structural component of the virions that plays an essential role in viral morphogenesis. Indeed, interaction of the Z protein with the Nucleoprotein is critical for genome packaging. Furthermore, current evidence suggests that binding between Z and the viral envelope glycoprotein complex is required for virion infectivity, and that Z homo-oligomerization is an essential step for particle assembly and budding. Efforts to understand the molecular basis of arenavirus life cycle have revealed important details on these viral protein-protein interactions that will be reviewed in this article.

Metagenomics and the protein universe

Science.gov (United States)

Godzik, Adam

2011-01-01

Metagenomics sequencing projects have dramatically increased our knowledge of the protein universe and provided over one-half of currently known protein sequences; they have also introduced a much broader phylogenetic diversity into the protein databases. The full analysis of metagenomic datasets is only beginning, but it has already led to the discovery of thousands of new protein families, likely representing novel functions specific to given environments. At the same time, a deeper analysis of such novel families, including experimental structure determination of some representatives, suggests that most of them represent distant homologs of already characterized protein families, and thus most of the protein diversity present in the new environments are due to functional divergence of the known protein families rather than the emergence of new ones. PMID:21497084

Solid-state NMR analysis of membrane proteins and protein aggregates by proton detected spectroscopy

International Nuclear Information System (INIS)

Zhou, Donghua H.; Nieuwkoop, Andrew J.; Berthold, Deborah A.; Comellas, Gemma; Sperling, Lindsay J.; Tang, Ming; Shah, Gautam J.; Brea, Elliott J.; Lemkau, Luisel R.; Rienstra, Chad M.

2012-01-01

Solid-state NMR has emerged as an important tool for structural biology and chemistry, capable of solving atomic-resolution structures for proteins in membrane-bound and aggregated states. Proton detection methods have been recently realized under fast magic-angle spinning conditions, providing large sensitivity enhancements for efficient examination of uniformly labeled proteins. The first and often most challenging step of protein structure determination by NMR is the site-specific resonance assignment. Here we demonstrate resonance assignments based on high-sensitivity proton-detected three-dimensional experiments for samples of different physical states, including a fully-protonated small protein (GB1, 6 kDa), a deuterated microcrystalline protein (DsbA, 21 kDa), a membrane protein (DsbB, 20 kDa) prepared in a lipid environment, and the extended core of a fibrillar protein (α-synuclein, 14 kDa). In our implementation of these experiments, including CONH, CO(CA)NH, CANH, CA(CO)NH, CBCANH, and CBCA(CO)NH, dipolar-based polarization transfer methods have been chosen for optimal efficiency for relatively high protonation levels (full protonation or 100 % amide proton), fast magic-angle spinning conditions (40 kHz) and moderate proton decoupling power levels. Each H–N pair correlates exclusively to either intra- or inter-residue carbons, but not both, to maximize spectral resolution. Experiment time can be reduced by at least a factor of 10 by using proton detection in comparison to carbon detection. These high-sensitivity experiments are especially important for membrane proteins, which often have rather low expression yield. Proton-detection based experiments are expected to play an important role in accelerating protein structure elucidation by solid-state NMR with the improved sensitivity and resolution.

Comments on the comparison of global methods for linear two-point boundary value problems

International Nuclear Information System (INIS)

de Boor, C.; Swartz, B.

1977-01-01

A more careful count of the operations involved in solving the linear system associated with collocation of a two-point boundary value problem using a rough splines reverses results recently reported by others in this journal. In addition, it is observed that the use of the technique of ''condensation of parameters'' can decrease the computer storage required. Furthermore, the use of a particular highly localized basis can also reduce the setup time when the mesh is irregular. Finally, operation counts are roughly estimated for the solution of certain linear system associated with two competing collocation methods; namely, collocation with smooth splines and collocation of the equivalent first order system with continuous piecewise polynomials

Cellular strategies to cope with protein aggregation

NARCIS (Netherlands)

Scior, Annika; Juenemann, Katrin; Kirstein, Janine

2016-01-01

Nature has evolved several mechanisms to detoxify intracellular protein aggregates that arise upon proteotoxic challenges. These include the controlled deposition of misfolded proteins at distinct cellular sites, the protein disaggregation and refolding by molecular chaperones and/or degradation of

The caveolin proteins

OpenAIRE

Williams, Terence M; Lisanti, Michael P

2004-01-01

The caveolin gene family has three members in vertebrates: caveolin-1, caveolin-2, and caveolin-3. So far, most caveolin-related research has been conducted in mammals, but the proteins have also been found in other animals, including Xenopus laevis, Fugu rubripes, and Caenorhabditis elegans. Caveolins can serve as protein markers of caveolae ('little caves'), invaginations in the plasma membrane 50-100 nanometers in diameter. Caveolins are found predominantly at the plasma membrane but also ...

Conformational dynamics data bank: a database for conformational dynamics of proteins and supramolecular protein assemblies.

Science.gov (United States)

Kim, Do-Nyun; Altschuler, Josiah; Strong, Campbell; McGill, Gaël; Bathe, Mark

2011-01-01

The conformational dynamics data bank (CDDB, http://www.cdyn.org) is a database that aims to provide comprehensive results on the conformational dynamics of high molecular weight proteins and protein assemblies. Analysis is performed using a recently introduced coarse-grained computational approach that is applied to the majority of structures present in the electron microscopy data bank (EMDB). Results include equilibrium thermal fluctuations and elastic strain energy distributions that identify rigid versus flexible protein domains generally, as well as those associated with specific functional transitions, and correlations in molecular motions that identify molecular regions that are highly coupled dynamically, with implications for allosteric mechanisms. A practical web-based search interface enables users to easily collect conformational dynamics data in various formats. The data bank is maintained and updated automatically to include conformational dynamics results for new structural entries as they become available in the EMDB. The CDDB complements static structural information to facilitate the investigation and interpretation of the biological function of proteins and protein assemblies essential to cell function.

Protein Design Using Unnatural Amino Acids

Science.gov (United States)

Bilgiçer, Basar; Kumar, Krishna

2003-11-01

With the increasing availability of whole organism genome sequences, understanding protein structure and function is of capital importance. Recent developments in the methodology of incorporation of unnatural amino acids into proteins allow the exploration of proteins at a very detailed level. Furthermore, de novo design of novel protein structures and function is feasible with unprecedented sophistication. Using examples from the literature, this article describes the available methods for unnatural amino acid incorporation and highlights some recent applications including the design of hyperstable protein folds.

Identification of membrane proteins by tandem mass spectrometry of protein ions

Science.gov (United States)

Carroll, Joe; Altman, Matthew C.; Fearnley, Ian M.; Walker, John E.

2007-01-01

The most common way of identifying proteins in proteomic analyses is to use short segments of sequence (“tags”) determined by mass spectrometric analysis of proteolytic fragments. The approach is effective with globular proteins and with membrane proteins with significant polar segments between membrane-spanning α-helices, but it is ineffective with other hydrophobic proteins where protease cleavage sites are either infrequent or absent. By developing methods to purify hydrophobic proteins in organic solvents and by fragmenting ions of these proteins by collision induced dissociation with argon, we have shown that partial sequences of many membrane proteins can be deduced easily by manual inspection. The spectra from small proteolipids (1–4 transmembrane α-helices) are dominated usually by fragment ions arising from internal amide cleavages, from which internal sequences can be obtained, whereas the spectra from larger membrane proteins (5–18 transmembrane α-helices) often contain fragment ions from N- and/or C-terminal parts yielding sequences in those regions. With these techniques, we have, for example, identified an abundant protein of unknown function from inner membranes of mitochondria that to our knowledge has escaped detection in proteomic studies, and we have produced sequences from 10 of 13 proteins encoded in mitochondrial DNA. They include the ND6 subunit of complex I, the last of its 45 subunits to be analyzed. The procedures have the potential to be developed further, for example by using newly introduced methods for protein ion dissociation to induce fragmentation of internal regions of large membrane proteins, which may remain partially folded in the gas phase. PMID:17720804

A Library of Plasmodium vivax Recombinant Merozoite Proteins Reveals New Vaccine Candidates and Protein-Protein Interactions

Science.gov (United States)

Hostetler, Jessica B.; Sharma, Sumana; Bartholdson, S. Josefin; Wright, Gavin J.; Fairhurst, Rick M.; Rayner, Julian C.

2015-01-01

Background A vaccine targeting Plasmodium vivax will be an essential component of any comprehensive malaria elimination program, but major gaps in our understanding of P. vivax biology, including the protein-protein interactions that mediate merozoite invasion of reticulocytes, hinder the search for candidate antigens. Only one ligand-receptor interaction has been identified, that between P. vivax Duffy Binding Protein (PvDBP) and the erythrocyte Duffy Antigen Receptor for Chemokines (DARC), and strain-specific immune responses to PvDBP make it a complex vaccine target. To broaden the repertoire of potential P. vivax merozoite-stage vaccine targets, we exploited a recent breakthrough in expressing full-length ectodomains of Plasmodium proteins in a functionally-active form in mammalian cells and initiated a large-scale study of P. vivax merozoite proteins that are potentially involved in reticulocyte binding and invasion. Methodology/Principal Findings We selected 39 P. vivax proteins that are predicted to localize to the merozoite surface or invasive secretory organelles, some of which show homology to P. falciparum vaccine candidates. Of these, we were able to express 37 full-length protein ectodomains in a mammalian expression system, which has been previously used to express P. falciparum invasion ligands such as PfRH5. To establish whether the expressed proteins were correctly folded, we assessed whether they were recognized by antibodies from Cambodian patients with acute vivax malaria. IgG from these samples showed at least a two-fold change in reactivity over naïve controls in 27 of 34 antigens tested, and the majority showed heat-labile IgG immunoreactivity, suggesting the presence of conformation-sensitive epitopes and native tertiary protein structures. Using a method specifically designed to detect low-affinity, extracellular protein-protein interactions, we confirmed a predicted interaction between P. vivax 6-cysteine proteins P12 and P41, further

Preparation of ubiquitin-conjugated proteins using an insect cell-free protein synthesis system.

Science.gov (United States)

Suzuki, Takashi; Ezure, Toru; Ando, Eiji; Nishimura, Osamu; Utsumi, Toshihiko; Tsunasawa, Susumu

2010-01-01

Ubiquitination is one of the most significant posttranslational modifications (PTMs). To evaluate the ability of an insect cell-free protein synthesis system to carry out ubiquitin (Ub) conjugation to in vitro translated proteins, poly-Ub chain formation was studied in an insect cell-free protein synthesis system. Poly-Ub was generated in the presence of Ub aldehyde (UA), a de-ubiquitinating enzyme inhibitor. In vitro ubiquitination of the p53 tumor suppressor protein was also analyzed, and p53 was poly-ubiquitinated when Ub, UA, and Mdm2, an E3 Ub ligase (E3) for p53, were added to the in vitro reaction mixture. These results suggest that the insect cell-free protein synthesis system contains enzymatic activities capable of carrying out ubiquitination. CBB-detectable ubiquitinated p53 was easily purified from the insect cell-free protein synthesis system, allowing analysis of the Ub-conjugated proteins by mass spectrometry (MS). Lys 305 of p53 was identified as one of the Ub acceptor sites using this strategy. Thus, we conclude that the insect cell-free protein synthesis system is a powerful tool for studying various PTMs of eukaryotic proteins including ubiqutination presented here.

The presentation and treatment

African Journals Online (AJOL)

user

tion of single collocations proposals are made for an implicit presentation of complex ... function lexicographers often include items to illustrate the typical use of the ... they have no items explicitly addressed at them to elevate them to treatment.

A Structural Perspective on the Modulation of Protein-Protein Interactions with Small Molecules.

Science.gov (United States)

Demirel, Habibe Cansu; Dogan, Tunca; Tuncbag, Nurcan

2018-05-31

Protein-protein interactions (PPIs) are the key components in many cellular processes including signaling pathways, enzymatic reactions and epigenetic regulation. Abnormal interactions of some proteins may be pathogenic and cause various disorders including cancer and neurodegenerative diseases. Although inhibiting PPIs with small molecules is a challenging task, it gained an increasing interest because of its strong potential for drug discovery and design. The knowledge of the interface as well as the structural and chemical characteristics of the PPIs and their roles in the cellular pathways are necessary for a rational design of small molecules to modulate PPIs. In this study, we review the recent progress in the field and detail the physicochemical properties of PPIs including binding hot spots with a focus on structural methods. Then, we review recent approaches for structural prediction of PPIs. Finally, we revisit the concept of targeting PPIs in a systems biology perspective and we refer to the non-structural approaches, usually employed when the structural information is not present. Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.org.

The 'tubulin-like' S1 protein of Spirochaeta is a member of the hsp65 stress protein family

Science.gov (United States)

Munson, D.; Obar, R.; Tzertzinis, G.; Margulis, L.

1993-01-01

A 65-kDa protein (called S1) from Spirochaeta bajacaliforniensis was identified as 'tubulin-like' because it cross-reacted with at least four different antisera raised against tubulin and was isolated, with a co-polymerizing 45-kDa protein, by warm-cold cycling procedures used to purify tubulin from mammalian brain. Furthermore, at least three genera of non-cultivable symbiotic spirochetes (Pillotina, Diplocalyx, and Hollandina) that contain conspicuous 24-nm cytoplasmic tubules displayed a strong fluorescence in situ when treated with polyclonal antisera raised against tubulin. Here we summarize results that lead to the conclusion that this 65-kDa protein has no homology to tubulin. S1 is an hsp65 stress protein homologue. Hsp65 is a highly immunogenic family of hsp60 proteins which includes the 65-kDa antigens of Mycobacterium tuberculosis (an active component of Freund's complete adjuvant), Borrelia, Treponema, Chlamydia, Legionella, and Salmonella. The hsp60s, also known as chaperonins, include E. coli GroEL, mitochondrial and chloroplast chaperonins, the pea aphid 'symbionin' and many other proteins involved in protein folding and the stress response.

Electron transfer in proteins

DEFF Research Database (Denmark)

Farver, O; Pecht, I

1991-01-01

Electron migration between and within proteins is one of the most prevalent forms of biological energy conversion processes. Electron transfer reactions take place between active centers such as transition metal ions or organic cofactors over considerable distances at fast rates and with remarkable...... specificity. The electron transfer is attained through weak electronic interaction between the active sites, so that considerable research efforts are centered on resolving the factors that control the rates of long-distance electron transfer reactions in proteins. These factors include (in addition......-containing proteins. These proteins serve almost exclusively in electron transfer reactions, and as it turns out, their metal coordination sites are endowed with properties uniquely optimized for their function....

Safety of protein hydrolysates, fractions thereof and

NARCIS (Netherlands)

Gertjan Schaafsma

2009-01-01

This paper evaluates the safety for humans with regard to consumption of protein hydrolysates and fractions thereof, including bioactive peptides. The available literature on the safety of protein, protein hydrolysates, fractions thereof and free amino acids on relevant food legislation is reviewed

Comparing side chain packing in soluble proteins, protein-protein interfaces, and transmembrane proteins.

Science.gov (United States)

Gaines, J C; Acebes, S; Virrueta, A; Butler, M; Regan, L; O'Hern, C S

2018-05-01

We compare side chain prediction and packing of core and non-core regions of soluble proteins, protein-protein interfaces, and transmembrane proteins. We first identified or created comparable databases of high-resolution crystal structures of these 3 protein classes. We show that the solvent-inaccessible cores of the 3 classes of proteins are equally densely packed. As a result, the side chains of core residues at protein-protein interfaces and in the membrane-exposed regions of transmembrane proteins can be predicted by the hard-sphere plus stereochemical constraint model with the same high prediction accuracies (>90%) as core residues in soluble proteins. We also find that for all 3 classes of proteins, as one moves away from the solvent-inaccessible core, the packing fraction decreases as the solvent accessibility increases. However, the side chain predictability remains high (80% within 30°) up to a relative solvent accessibility, rSASA≲0.3, for all 3 protein classes. Our results show that ≈40% of the interface regions in protein complexes are "core", that is, densely packed with side chain conformations that can be accurately predicted using the hard-sphere model. We propose packing fraction as a metric that can be used to distinguish real protein-protein interactions from designed, non-binding, decoys. Our results also show that cores of membrane proteins are the same as cores of soluble proteins. Thus, the computational methods we are developing for the analysis of the effect of hydrophobic core mutations in soluble proteins will be equally applicable to analyses of mutations in membrane proteins. © 2018 Wiley Periodicals, Inc.

Molecular imaging of drug-modulated protein-protein interactions in living subjects.

Science.gov (United States)

Paulmurugan, Ramasamy; Massoud, Tarik F; Huang, Jing; Gambhir, Sanjiv S

2004-03-15

Networks of protein interactions mediate cellular responses to environmental stimuli and direct the execution of many different cellular functional pathways. Small molecules synthesized within cells or recruited from the external environment mediate many protein interactions. The study of small molecule-mediated interactions of proteins is important to understand abnormal signal transduction pathways in cancer and in drug development and validation. In this study, we used split synthetic renilla luciferase (hRLUC) protein fragment-assisted complementation to evaluate heterodimerization of the human proteins FRB and FKBP12 mediated by the small molecule rapamycin. The concentration of rapamycin required for efficient dimerization and that of its competitive binder ascomycin required for dimerization inhibition were studied in cell lines. The system was dually modulated in cell culture at the transcription level, by controlling nuclear factor kappaB promoter/enhancer elements using tumor necrosis factor alpha, and at the interaction level, by controlling the concentration of the dimerizer rapamycin. The rapamycin-mediated dimerization of FRB and FKBP12 also was studied in living mice by locating, quantifying, and timing the hRLUC complementation-based bioluminescence imaging signal using a cooled charged coupled device camera. This split reporter system can be used to efficiently screen small molecule drugs that modulate protein-protein interactions and also to assess drugs in living animals. Both are essential steps in the preclinical evaluation of candidate pharmaceutical agents targeting protein-protein interactions, including signaling pathways in cancer cells.

Monoclonal protein reference change value as determined by gel-based serum protein electrophoresis.

Science.gov (United States)

Salamatmanesh, Mina; McCudden, Christopher R; McCurdy, Arleigh; Booth, Ronald A

2018-01-01

The International Myeloma Working Group recommendations for monitoring disease progression or response include quantitation of the involved monoclonal immunoglobulin. They have defined the minimum change criteria of ≧25% with an absolute change of no gel-based serum protein electrophoresis. Sixteen clinically stable MGUS patients were identified from our clinical hematology database. Individual biological variability (CVi) was determined and used to calculate a monoclonal protein reference change value (RCV). Analytical variability of the normal protein fractions (albumin, alpha-1, alpha-2, beta, total gamma) ranged from 1.3% for albumin to 5.8% for the alpha-1 globulins. CVa of low (5.6g/L) and high (32.2g/L) concentration monoclonal proteins were 3.1% and 22.2%, respectively. Individual CVi of stable patients ranged from 3.5% to 24.5% with a CVi of 12.9%. The reference change value (RCV) at a 95% probability was determined to be 36.7% (low) 39.6% (high) using our CVa and CVi. Serial monitoring of monoclonal protein concentration is important for MGUS and multiple myeloma patients. Accurate criteria for interpreting a change in monoclonal protein concentration are required for appropriate decision making. We used QC results and real-world conditions to assess imprecision of serum protein fractions including low and high monoclonal protein fractions and clinically stable MGUS patients to determine CVi and RCV. The calculated RCVs of 36.7% (low) and 39.6% (high) in this study were greater that reported previously and greater than the established criteria for relapse. Response criteria may be reassessed to increase sensitivity and specificity for detection of response. Copyright © 2017 The Canadian Society of Clinical Chemists. Published by Elsevier Inc. All rights reserved.

Dynamic Regulation of a Cell Adhesion Protein Complex Including CADM1 by Combinatorial Analysis of FRAP with Exponential Curve-Fitting

Science.gov (United States)

Sakurai-Yageta, Mika; Maruyama, Tomoko; Suzuki, Takashi; Ichikawa, Kazuhisa; Murakami, Yoshinori

2015-01-01

Protein components of cell adhesion machinery show continuous renewal even in the static state of epithelial cells and participate in the formation and maintenance of normal epithelial architecture and tumor suppression. CADM1 is a tumor suppressor belonging to the immunoglobulin superfamily of cell adhesion molecule and forms a cell adhesion complex with an actin-binding protein, 4.1B, and a scaffold protein, MPP3, in the cytoplasm. Here, we investigate dynamic regulation of the CADM1-4.1B-MPP3 complex in mature cell adhesion by fluorescence recovery after photobleaching (FRAP) analysis. Traditional FRAP analysis were performed for relatively short period of around 10min. Here, thanks to recent advances in the sensitive laser detector systems, we examine FRAP of CADM1 complex for longer period of 60 min and analyze the recovery with exponential curve-fitting to distinguish the fractions with different diffusion constants. This approach reveals that the fluorescence recovery of CADM1 is fitted to a single exponential function with a time constant (τ) of approximately 16 min, whereas 4.1B and MPP3 are fitted to a double exponential function with two τs of approximately 40-60 sec and 16 min. The longer τ is similar to that of CADM1, suggesting that 4.1B and MPP3 have two distinct fractions, one forming a complex with CADM1 and the other present as a free pool. Fluorescence loss in photobleaching analysis supports the presence of a free pool of these proteins near the plasma membrane. Furthermore, double exponential fitting makes it possible to estimate the ratio of 4.1B and MPP3 present as a free pool and as a complex with CADM1 as approximately 3:2 and 3:1, respectively. Our analyses reveal a central role of CADM1 in stabilizing the complex with 4.1B and MPP3 and provide insight in the dynamics of adhesion complex formation. PMID:25780926

Next-Generation Sequencing for Binary Protein-Protein Interactions

Directory of Open Access Journals (Sweden)

Bernhard eSuter

2015-12-01

Full Text Available The yeast two-hybrid (Y2H system exploits host cell genetics in order to display binary protein-protein interactions (PPIs via defined and selectable phenotypes. Numerous improvements have been made to this method, adapting the screening principle for diverse applications, including drug discovery and the scale-up for proteome wide interaction screens in human and other organisms. Here we discuss a systematic workflow and analysis scheme for screening data generated by Y2H and related assays that includes high-throughput selection procedures, readout of comprehensive results via next-generation sequencing (NGS, and the interpretation of interaction data via quantitative statistics. The novel assays and tools will serve the broader scientific community to harness the power of NGS technology to address PPI networks in health and disease. We discuss examples of how this next-generation platform can be applied to address specific questions in diverse fields of biology and medicine.

Promoters and proteins from Clostridium thermocellum and uses thereof

Science.gov (United States)

Wu, J. H. David; Newcomb, Michael

2012-11-13

The present invention relates to an inducible and a high expression nucleic acid promoter isolated from Clostridium thermocellum. These promoters are useful for directing expression of a protein or polypeptide encoded by a nucleic acid molecule operably associated with the nucleic acid promoters. The present invention also relates to nucleic acid constructs including the C. thermocellum promoters, and expression vectors and hosts containing such nucleic acid constructs. The present invention also relates to protein isolated from Clostridium thermocellum, including a repressor protein. The present invention also provides methods of using the isolated promoters and proteins from Clostridium thermocellum, including methods for directing inducible in vitro and in vivo expression of a protein or polypeptide in a host, and methods of producing ethanol from a cellulosic biomass.

Can understanding the packing of side chains improve the design of protein-protein interactions?

Science.gov (United States)

Zhou, Alice; O'Hern, Corey; Regan, Lynne

2011-03-01

With the long-term goal to improve the design of protein-protein interactions, we have begun extensive computational studies to understand how side-chains of key residues of binding partners geometrically fit together at protein-peptide interfaces, e.g. the tetratrico-peptide repeat protein and its cognate peptide). We describe simple atomic-scale models of hydrophobic dipeptides, which include hard-core repulsion, bond length and angle constraints, and Van der Waals attraction. By completely enumerating all minimal energy structures in these systems, we are able to reproduce important features of the probability distributions of side chain dihedral angles of hydrophic residues in the protein data bank. These results are the crucial first step in developing computational models that can predict the side chain conformations of residues at protein-peptide interfaces. CSO acknowledges support from NSF grant no. CMMT-1006527.

Short Toxin-like Proteins Abound in Cnidaria Genomes

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Michal Linial

2012-11-01

Full Text Available Cnidaria is a rich phylum that includes thousands of marine species. In this study, we focused on Anthozoa and Hydrozoa that are represented by the Nematostella vectensis (Sea anemone and Hydra magnipapillata genomes. We present a method for ranking the toxin-like candidates from complete proteomes of Cnidaria. Toxin-like functions were revealed using ClanTox, a statistical machine-learning predictor trained on ion channel inhibitors from venomous animals. Fundamental features that were emphasized in training ClanTox include cysteines and their spacing along the sequences. Among the 83,000 proteins derived from Cnidaria representatives, we found 170 candidates that fulfill the properties of toxin-like-proteins, the vast majority of which were previously unrecognized as toxins. An additional 394 short proteins exhibit characteristics of toxin-like proteins at a moderate degree of confidence. Remarkably, only 11% of the predicted toxin-like proteins were previously classified as toxins. Based on our prediction methodology and manual annotation, we inferred functions for over 400 of these proteins. Such functions include protease inhibitors, membrane pore formation, ion channel blockers and metal binding proteins. Many of the proteins belong to small families of paralogs. We conclude that the evolutionary expansion of toxin-like proteins in Cnidaria contributes to their fitness in the complex environment of the aquatic ecosystem.

Identification of FUSE-binding proteins as interacting partners of TIA proteins

International Nuclear Information System (INIS)

Rothe, Francoise; Gueydan, Cyril; Bellefroid, Eric; Huez, Georges; Kruys, Veronique

2006-01-01

TIA-1 and TIAR are closely related RNA-binding proteins involved in several mechanisms of RNA metabolism, including alternative hnRNA splicing and mRNA translation regulation. In particular, TIA-1 represses tumor necrosis factor (TNF) mRNA translation by binding to the AU-rich element (ARE) present in the mRNA 3' untranslated region. Here, we demonstrate that TIA proteins interact with FUSE-binding proteins (FBPs) and that fbp genes are co-expressed with tia genes during Xenopus embryogenesis. FBPs participate in various steps of RNA processing and degradation. In Cos cells, FBPs co-localize with TIA proteins in the nucleus and migrate into TIA-enriched cytoplasmic granules upon oxidative stress. Overexpression of FBP2-KH3 RNA-binding domain fused to EGFP induces the specific sequestration of TIA proteins in cytoplasmic foci, thereby precluding their nuclear accumulation. In cytosolic RAW 264.7 macrophage extracts, FBPs are found associated in EMSA to the TIA-1/TNF-ARE complex. Together, our results indicate that TIA and FBP proteins may thus be relevant biological involved in common events of RNA metabolism occurring both in the nucleus and the cytoplasm

Production of soluble mammalian proteins in Escherichia coli: identification of protein features that correlate with successful expression

Directory of Open Access Journals (Sweden)

Perera Rajika L

2004-12-01

Full Text Available Abstract Background In the search for generic expression strategies for mammalian protein families several bacterial expression vectors were examined for their ability to promote high yields of soluble protein. Proteins studied included cell surface receptors (Ephrins and Eph receptors, CD44, kinases (EGFR-cytoplasmic domain, CDK2 and 4, proteases (MMP1, CASP2, signal transduction proteins (GRB2, RAF1, HRAS and transcription factors (GATA2, Fli1, Trp53, Mdm2, JUN, FOS, MAD, MAX. Over 400 experiments were performed where expression of 30 full-length proteins and protein domains were evaluated with 6 different N-terminal and 8 C-terminal fusion partners. Expression of an additional set of 95 mammalian proteins was also performed to test the conclusions of this study. Results Several protein features correlated with soluble protein expression yield including molecular weight and the number of contiguous hydrophobic residues and low complexity regions. There was no relationship between successful expression and protein pI, grand average of hydropathicity (GRAVY, or sub-cellular location. Only small globular cytoplasmic proteins with an average molecular weight of 23 kDa did not require a solubility enhancing tag for high level soluble expression. Thioredoxin (Trx and maltose binding protein (MBP were the best N-terminal protein fusions to promote soluble expression, but MBP was most effective as a C-terminal fusion. 63 of 95 mammalian proteins expressed at soluble levels of greater than 1 mg/l as N-terminal H10-MBP fusions and those that failed possessed, on average, a higher molecular weight and greater number of contiguous hydrophobic amino acids and low complexity regions. Conclusions By analysis of the protein features identified here, this study will help predict which mammalian proteins and domains can be successfully expressed in E. coli as soluble product and also which are best targeted for a eukaryotic expression system. In some cases

Quantification of Protein Hydration, Glass Transitions, and Structural Relaxations of Aqueous Protein and Carbohydrate-Protein Systems.

Science.gov (United States)

Roos, Yrjö H; Potes, Naritchaya

2015-06-11

Water distribution and miscibility of carbohydrate and protein components in biological materials and their structural contributions in concentrated solids are poorly understood. In the present study, structural relaxations and a glass transition of protein hydration water and antiplasticization of the hydration water at low temperatures were measured using dynamic mechanical analysis (DMA) and differential scanning calorimetry (DSC) for bovine whey protein (BWP), aqueous glucose-fructose (GF), and their mixture. Thermal transitions of α-lactalbumin and β-lactoglobulin components of BWP included water-content-dependent endothermic but reversible dehydration and denaturation, and exothermic and irreversible aggregation. An α-relaxation assigned to hydration water in BWP appeared at water-content-dependent temperatures and increased to over the range of 150-200 K at decreasing water content and in the presence of GF. Two separate glass transitions and individual fractions of unfrozen water of ternary GF-BWP-water systems contributed to uncoupled α-relaxations, suggesting different roles of protein hydration water and carbohydrate vitrification in concentrated solids during freezing and dehydration. Hydration water in the BWP fraction of GF-BWP systems was derived from equilibrium water sorption and glass transition data of the GF fraction, which gave a significant universal method to quantify (i) protein hydration water and (ii) the unfrozen water in protein-carbohydrate systems for such applications as cryopreservation, freezing, lyophilization, and dehydration of biological materials. A ternary supplemented phase diagram (state diagram) established for the GF-BWP-water system can be used for the analysis of the water distribution across carbohydrate and protein components in such applications.

Simultaneous estimation of cross-validation errors in least squares collocation applied for statistical testing and evaluation of the noise variance components

Science.gov (United States)

Behnabian, Behzad; Mashhadi Hossainali, Masoud; Malekzadeh, Ahad

2018-02-01

The cross-validation technique is a popular method to assess and improve the quality of prediction by least squares collocation (LSC). We present a formula for direct estimation of the vector of cross-validation errors (CVEs) in LSC which is much faster than element-wise CVE computation. We show that a quadratic form of CVEs follows Chi-squared distribution. Furthermore, a posteriori noise variance factor is derived by the quadratic form of CVEs. In order to detect blunders in the observations, estimated standardized CVE is proposed as the test statistic which can be applied when noise variances are known or unknown. We use LSC together with the methods proposed in this research for interpolation of crustal subsidence in the northern coast of the Gulf of Mexico. The results show that after detection and removing outliers, the root mean square (RMS) of CVEs and estimated noise standard deviation are reduced about 51 and 59%, respectively. In addition, RMS of LSC prediction error at data points and RMS of estimated noise of observations are decreased by 39 and 67%, respectively. However, RMS of LSC prediction error on a regular grid of interpolation points covering the area is only reduced about 4% which is a consequence of sparse distribution of data points for this case study. The influence of gross errors on LSC prediction results is also investigated by lower cutoff CVEs. It is indicated that after elimination of outliers, RMS of this type of errors is also reduced by 19.5% for a 5 km radius of vicinity. We propose a method using standardized CVEs for classification of dataset into three groups with presumed different noise variances. The noise variance components for each of the groups are estimated using restricted maximum-likelihood method via Fisher scoring technique. Finally, LSC assessment measures were computed for the estimated heterogeneous noise variance model and compared with those of the homogeneous model. The advantage of the proposed method is the

IGF binding proteins.

Science.gov (United States)

Bach, Leon A

2017-12-18

Insulin-like growth factor binding proteins (IGFBPs) 1-6 bind IGFs but not insulin with high affinity. They were initially identified as serum carriers and passive inhibitors of IGF actions. However, subsequent studies showed that, although IGFBPs inhibit IGF actions in many circumstances, they may also potentiate these actions. IGFBPs are widely expressed in most tissues, and they are flexible endocrine and autocrine/paracrine regulators of IGF activity, which is essential for this important physiological system. More recently, individual IGFBPs have been shown to have IGF-independent actions. Mechanisms underlying these actions include (i) interaction with non-IGF proteins in compartments including the extracellular space and matrix, the cell surface and intracellularly; (ii) interaction with and modulation of other growth factor pathways including EGF, TGF- and VEGF; and (iii) direct or indirect transcriptional effects following nuclear entry of IGFBPs. Through these IGF-dependent and IGF-independent actions, IGFBPs modulate essential cellular processes including proliferation, survival, migration, senescence, autophagy and angiogenesis. They have been implicated in a range of disorders including malignant, metabolic, neurological and immune diseases. A more complete understanding of their cellular roles may lead to the development of novel IGFBP-based therapeutic opportunities.

PIPE: a protein-protein interaction prediction engine based on the re-occurring short polypeptide sequences between known interacting protein pairs

Directory of Open Access Journals (Sweden)

Greenblatt Jack

2006-07-01

included in genome-wide yeast TAP tagging projects. Conclusion PIPE analysis can predict yeast protein-protein interactions. Also, PIPE analysis can be used to study the internal architecture of yeast protein complexes. The data also suggests that a finite set of short polypeptide signals seem to be responsible for the majority of the yeast protein-protein interactions.

Protein Self-Assembly and Protein-Induced DNA Morphologies

Science.gov (United States)

Mawhinney, Matthew T.

The ability of biomolecules to associate into various structural configurations has a substantial impact on human physiology. The synthesis of protein polypeptide chains using the information encoded by DNA is mediated through the use of regulatory proteins, known as transcription factors. Some transcription factors perform function by inducing local curvature in deoxyribonucleic acid (DNA) strands, the mechanisms of which are not entirely known. An important architectural protein, eleven zinc finger CTCF (11 ZF CTCF) is involved in genome organization and hypothesized to mediate DNA loop formation. Direct evidence for these CTCF-induced DNA loops has yet to be observed. In this thesis, the effect of 11 ZF CTCF on DNA morphology is examined using atomic force microscopy, a powerful technique for visualizing biomolecules with nanometer resolution. The presence of CTCF is revealed to induce a variety of morphologies deviating from the relaxed state of control DNA samples, including compact circular complexes, meshes, and networks. Images reveal quasi-circular DNA/CTCF complexes consistent with a single DNA molecule twice wrapped around the protein. The structures of DNA and proteins are highly important for operations in the cell. Structural irregularities may lead to a variety of issues, including more than twenty human pathologies resulting from aberrant protein misfolding into amyloid aggregates of elongated fibrils. Insulin deficiency and resistance characterizing type 2 diabetes often requires administration of insulin. Injectable and inhalable delivery methods have been documented to result in the deposition of amyloid fibrils. Oligomers, soluble multiprotein assemblies, are believed to play an important role in this process. Insulin aggregation under physiological conditions is not well understood and oligomers have not yet been fully characterized. In this thesis, in vitro insulin aggregation at acidic and neutral pH is explored using a variety of techniques

Dietary protein restriction for renal patients: don't forget protein-free foods.

Science.gov (United States)

D'Alessandro, Claudia; Rossi, Andrea; Innocenti, Maurizio; Ricchiuti, Guido; Bozzoli, Laura; Sbragia, Giulietta; Meola, Mario; Cupisti, Adamasco

2013-09-01

The treatment of chronic kidney disease (CKD) consists of pharmacological, nutritional, and psychological-social approaches. The dietary therapy of CKD, namely a low-protein low-phosphorus diet, plays a crucial role in contributing to delay the onset of end-stage renal disease (ESRD) and to protect cardiovascular and nutritional status. The protein-free food products represent a very important tool for the implementation of a low-protein diet to ensure adequate energy supply, reducing the production of nitrogenous waste products. This survey included 100 consecutive CKD patients who were asked their opinion about the use of protein-free foods. Ninety-eight patients (98%) reported a regular daily intake of protein-free pasta (as macaroni, spaghetti, etc.), which was the preferred product consumed. Actually, the taste and texture of protein-free pasta were considered as "good" or "very good" by 70% of patients. Conversely, 43% of CKD patients perceived the taste and texture of protein-free bread as "bad" or "very bad", and 30% found it "acceptable". Therefore, the main concern for the implementation of low-protein diets is the use and palatability of the protein-free products, bread in particular. The use of these products may help in reducing protein, phosphorus, and sodium intake while supplying an adequate energy intake, which represents the basis for a nutritionally safe and successful dietary treatment of advanced CKD patients. Manufacturers and food technology should make more efforts to finding new solutions to improve the taste and texture of protein-free products. Copyright © 2013 National Kidney Foundation, Inc. Published by Elsevier Inc. All rights reserved.

Relative quantification of protein-protein interactions using a dual luciferase reporter pull-down assay system.

Directory of Open Access Journals (Sweden)

Shuaizheng Jia

Full Text Available The identification and quantitative analysis of protein-protein interactions are essential to the functional characterization of proteins in the post-proteomics era. The methods currently available are generally time-consuming, technically complicated, insensitive and/or semi-quantitative. The lack of simple, sensitive approaches to precisely quantify protein-protein interactions still prevents our understanding of the functions of many proteins. Here, we develop a novel dual luciferase reporter pull-down assay by combining a biotinylated Firefly luciferase pull-down assay with a dual luciferase reporter assay. The biotinylated Firefly luciferase-tagged protein enables rapid and efficient isolation of a putative Renilla luciferase-tagged binding protein from a relatively small amount of sample. Both of these proteins can be quantitatively detected using the dual luciferase reporter assay system. Protein-protein interactions, including Fos-Jun located in the nucleus; MAVS-TRAF3 in cytoplasm; inducible IRF3 dimerization; viral protein-regulated interactions, such as MAVS-MAVS and MAVS-TRAF3; IRF3 dimerization; and protein interaction domain mapping, are studied using this novel assay system. Herein, we demonstrate that this dual luciferase reporter pull-down assay enables the quantification of the relative amounts of interacting proteins that bind to streptavidin-coupled beads for protein purification. This study provides a simple, rapid, sensitive, and efficient approach to identify and quantify relative protein-protein interactions. Importantly, the dual luciferase reporter pull-down method will facilitate the functional determination of proteins.

Protein Enrichment of Familiar Foods as an Innovative Strategy to Increase Protein Intake in Institutionalized Elderly.

Science.gov (United States)

Beelen, J; de Roos, N M; de Groot, L C P G M

2017-01-01

To increase the protein intake of older adults, protein enrichment of familiar foods and drinks might be an effective and attractive alternative for oral nutritional supplements (ONS). We performed a pilot study to test whether these products could help institutionalized elderly to reach a protein intake of 1.2 gram per kg body weight per day (g/kg/d). Intervention study with one treatment group (no control group). Dietary assessment was done before and at the end of a 10-day intervention. Two care facilities in Gelderland, the Netherlands: a residential care home and a rehabilitation center. 22 elderly subjects (13 women, 9 men; mean age 83.0±9.4 years). We used a variety of newly developed protein enriched regular foods and drinks, including bread, soups, fruit juices, and instant mashed potatoes. Dietary intake was assessed on two consecutive days before and at the end of the intervention, using food records filled out by research assistants. Energy and macronutrient intake was calculated using the 2013 Dutch food composition database. Changes in protein intake were evaluated using paired t-tests. Protein intake increased by 11.8 g/d (P=0.003); from 0.96 to 1.14 g/kg/d (P=0.002). This increase is comparable to protein provided by one standard portion of ONS. The intake of energy and other macronutrients did not change significantly. At the end of the intervention more elderly reached a protein intake level of 1.2 g/kg/d than before (9 vs 4). Protein intake significantly increased during breakfast (+3.7 g) and during the evening (+2.2 g). Including familiar protein enriched foods and drinks in the menu helped to meet protein recommendations in institutionalized elderly.

Ultrafiltration of pegylated proteins

Science.gov (United States)

Molek, Jessica R.

There is considerable clinical interest in the use of "second-generation" therapeutics produced by conjugation of a native protein with various polymers including polyethylene glycol (PEG). PEG--protein conjugates, so-called PEGylated proteins, can exhibit enhanced stability, half-life, and bioavailability. One of the challenges in the commercial production of PEGylated proteins is the purification required to remove unreacted polymer, native protein, and in many cases PEGylated proteins with nonoptimal degrees of conjugation. The overall objective of this thesis was to examine the use of ultrafiltration for the purification of PEGylated proteins. This included: (1) analysis of size-based separation of PEGylated proteins using conventional ultrafiltration membranes, (2) use of electrically-charged membranes to exploit differences in electrostatic interactions, and (3) examination of the effects of PEGylation on protein fouling. The experimental results were analyzed using appropriate theoretical models, with the underlying physical properties of the PEGylated proteins evaluated using size exclusion chromatography, capillary electrophoresis, dynamic light scattering, and reverse phase chromatography. PEGylated proteins were produced by covalent attachment of activated PEG to a protein via primary amines on the lysine residues. A simple model was developed for the reaction kinetics, which was used to explore the effect of reaction conditions and mode of operation on the distribution of PEGylated products. The effective size of the PEGylated proteins was evaluated using size exclusion chromatography, with appropriate correlations developed for the size in terms of the molecular weight of the native protein and attached PEG. The electrophoretic mobility of the PEGylated proteins were evaluated by capillary electrophoresis with the data in good agreement with a simple model accounting for the increase in protein size and the reduction in the number of protonated amine

Protein stress and stress proteins: implications in aging and disease

Indian Academy of Sciences (India)

Madhu Sudhan

2007-04-02

Apr 2, 2007 ... (iii) modulating protein activity via stabilization and/or maturation to ... Resistance to any physical stress is correlated with longevity in many, if not all .... range of pathologies including cancer, diabetes, immune- problems and ...

Quantitative analysis of EGR proteins binding to DNA: assessing additivity in both the binding site and the protein

Directory of Open Access Journals (Sweden)

Stormo Gary D

2005-07-01

Full Text Available Abstract Background Recognition codes for protein-DNA interactions typically assume that the interacting positions contribute additively to the binding energy. While this is known to not be precisely true, an additive model over the DNA positions can be a good approximation, at least for some proteins. Much less information is available about whether the protein positions contribute additively to the interaction. Results Using EGR zinc finger proteins, we measure the binding affinity of six different variants of the protein to each of six different variants of the consensus binding site. Both the protein and binding site variants include single and double mutations that allow us to assess how well additive models can account for the data. For each protein and DNA alone we find that additive models are good approximations, but over the combined set of data there are context effects that limit their accuracy. However, a small modification to the purely additive model, with only three additional parameters, improves the fit significantly. Conclusion The additive model holds very well for every DNA site and every protein included in this study, but clear context dependence in the interactions was detected. A simple modification to the independent model provides a better fit to the complete data.

AIRS-AMSU variables-CloudSat cloud mask, radar reflectivities, and cloud classification matchups V3.2

Data.gov (United States)

National Aeronautics and Space Administration — This is AIRS-CloudSat collocated subset, in NetCDF 4 format. These data contain collocated: AIRS/AMSU retrievals at AMSU footprints, CloudSat radar reflectivities,...

Protein mislocalization: mechanisms, functions and clinical applications in cancer

Science.gov (United States)

Wang, Xiaohong; Li, Shulin

2014-01-01

The changes from normal cells to cancer cells are primarily regulated by genome instability, which foster hallmark functions of cancer through multiple mechanisms including protein mislocalization. Mislocalization of these proteins, including oncoproteins, tumor suppressors, and other cancer-related proteins, can interfere with normal cellular function and cooperatively drive tumor development and metastasis. This review describes the cancer-related effects of protein subcellular mislocalization, the related mislocalization mechanisms, and the potential application of this knowledge to cancer diagnosis, prognosis, and therapy. PMID:24709009

Prediction of Protein-Protein Interactions Related to Protein Complexes Based on Protein Interaction Networks

Directory of Open Access Journals (Sweden)

Peng Liu

2015-01-01

Full Text Available A method for predicting protein-protein interactions based on detected protein complexes is proposed to repair deficient interactions derived from high-throughput biological experiments. Protein complexes are pruned and decomposed into small parts based on the adaptive k-cores method to predict protein-protein interactions associated with the complexes. The proposed method is adaptive to protein complexes with different structure, number, and size of nodes in a protein-protein interaction network. Based on different complex sets detected by various algorithms, we can obtain different prediction sets of protein-protein interactions. The reliability of the predicted interaction sets is proved by using estimations with statistical tests and direct confirmation of the biological data. In comparison with the approaches which predict the interactions based on the cliques, the overlap of the predictions is small. Similarly, the overlaps among the predicted sets of interactions derived from various complex sets are also small. Thus, every predicted set of interactions may complement and improve the quality of the original network data. Meanwhile, the predictions from the proposed method replenish protein-protein interactions associated with protein complexes using only the network topology.

A meshless scheme for incompressible fluid flow using a velocity-pressure correction method

KAUST Repository

Bourantas, Georgios

2013-12-01

A meshless point collocation method is proposed for the numerical solution of the steady state, incompressible Navier-Stokes (NS) equations in their primitive u-v-p formulation. The flow equations are solved in their strong form using either a collocated or a semi-staggered "grid" configuration. The developed numerical scheme approximates the unknown field functions using the Moving Least Squares approximation. A velocity, along with a pressure correction scheme is applied in the context of the meshless point collocation method. The proposed meshless point collocation (MPC) scheme has the following characteristics: (i) it is a truly meshless method, (ii) there is no need for pressure boundary conditions since no pressure constitutive equation is solved, (iii) it incorporates simplicity and accuracy, (iv) results can be obtained using collocated or semi-staggered "grids", (v) there is no need for the usage of a curvilinear system of coordinates and (vi) it can solve steady and unsteady flows. The lid-driven cavity flow problem, for Reynolds numbers up to 5000, has been considered, by using both staggered and collocated grid configurations. Following, the Backward-Facing Step (BFS) flow problem was considered for Reynolds numbers up to 800 using a staggered grid. As a final example, the case of a laminar flow in a two-dimensional tube with an obstacle was examined. © 2013 Elsevier Ltd.

Maintaining protein composition in cilia.

Science.gov (United States)

Stephen, Louise A; Elmaghloob, Yasmin; Ismail, Shehab

2017-12-20

The primary cilium is a sensory organelle that is vital in regulating several signalling pathways. Unlike most organelles cilia are open to the rest of the cell, not enclosed by membranes. The distinct protein composition is crucial to the function of cilia and many signalling proteins and receptors are specifically concentrated within distinct compartments. To maintain this composition, a mechanism is required to deliver proteins to the cilium whilst another must counter the entropic tendency of proteins to distribute throughout the cell. The combination of the two mechanisms should result in the concentration of ciliary proteins to the cilium. In this review we will look at different cellular mechanisms that play a role in maintaining the distinct composition of cilia, including regulation of ciliary access and trafficking of ciliary proteins to, from and within the cilium.

FERM proteins in animal morphogenesis.

Science.gov (United States)

Tepass, Ulrich

2009-08-01

Proteins containing a FERM domain are ubiquitous components of the cytocortex of animal cells where they are engaged in structural, transport, and signaling functions. Recent years have seen a wealth of genetic studies in model organisms that explore FERM protein function in development and tissue organization. In addition, mutations in several FERM protein-encoding genes have been associated with human diseases. This review will provide a brief overview of the FERM domain structure and the FERM protein superfamily and then discuss recent advances in our understanding of the mechanism of function and developmental requirement of several FERM proteins including Moesin, Myosin-VIIA, Myosin-XV, Coracle/Band4.1 as well as Yurt and its vertebrate homologs Mosaic Eyes and EPB41L5/YMO1/Limulus.

Ion pairs in non-redundant protein structures

Indian Academy of Sciences (India)

Ion pairs contribute to several functions including the activity of catalytic triads, fusion of viral membranes, stability in thermophilic proteins and solvent–protein interactions. Furthermore, they have the ability to affect the stability of protein structures and are also a part of the forces that act to hold monomers together.

Mass spectrometric analysis of protein interactions

DEFF Research Database (Denmark)

Borch, Jonas; Jørgensen, Thomas J. D.; Roepstorff, Peter

2005-01-01

Mass spectrometry is a powerful tool for identification of interaction partners and structural characterization of protein interactions because of its high sensitivity, mass accuracy and tolerance towards sample heterogeneity. Several tools that allow studies of protein interaction are now...... available and recent developments that increase the confidence of studies of protein interaction by mass spectrometry include quantification of affinity-purified proteins by stable isotope labeling and reagents for surface topology studies that can be identified by mass-contributing reporters (e.g. isotope...... labels, cleavable cross-linkers or fragment ions. The use of mass spectrometers to study protein interactions using deuterium exchange and for analysis of intact protein complexes recently has progressed considerably....

Protein folding on a chip

CERN Multimedia

2004-01-01

"Scientists at the U.S. Department of Energy's Brookhaven National Laboratory are proposing to use a super- computer originally developed to simulate elementary particles in high- energy physics to help determine the structures and functions of proteins, including, for example, the 30,000 or so proteins encoded by the human genome" (1 page)

Vegetarian Choices in the Protein Foods Group

Science.gov (United States)

... foods selected are adequate. Protein sources from the Protein Foods Group for vegetarians include eggs (for ovo-vegetarians), beans and peas, nuts, nut butters, and soy products (tofu, tempeh, ...

In-house characterization of protein powder

DEFF Research Database (Denmark)

Hartmann, Christian Grundahl; Nielsen, Ole Faurskov; Ståhl, Kenny

2010-01-01

X-ray powder diffraction patterns of lysozyme and insulin were recorded on a standard in-house powder diffractometer. The experimental powder diffraction patterns were compared with patterns calculated from Protein Data Bank coordinate data. Good agreement was obtained by including straightforward...... to include calculated H-atom positions did not improve the overall fit and was abandoned. The method devised was shown to be a quick and convenient tool for distinguishing precipitates and polymorphs of proteins....

Specificity of molecular interactions in transient protein-protein interaction interfaces.

Science.gov (United States)

Cho, Kyu-il; Lee, KiYoung; Lee, Kwang H; Kim, Dongsup; Lee, Doheon

2006-11-15

In this study, we investigate what types of interactions are specific to their biological function, and what types of interactions are persistent regardless of their functional category in transient protein-protein heterocomplexes. This is the first approach to analyze protein-protein interfaces systematically at the molecular interaction level in the context of protein functions. We perform systematic analysis at the molecular interaction level using classification and feature subset selection technique prevalent in the field of pattern recognition. To represent the physicochemical properties of protein-protein interfaces, we design 18 molecular interaction types using canonical and noncanonical interactions. Then, we construct input vector using the frequency of each interaction type in protein-protein interface. We analyze the 131 interfaces of transient protein-protein heterocomplexes in PDB: 33 protease-inhibitors, 52 antibody-antigens, 46 signaling proteins including 4 cyclin dependent kinase and 26 G-protein. Using kNN classification and feature subset selection technique, we show that there are specific interaction types based on their functional category, and such interaction types are conserved through the common binding mechanism, rather than through the sequence or structure conservation. The extracted interaction types are C(alpha)-- H...O==C interaction, cation...anion interaction, amine...amine interaction, and amine...cation interaction. With these four interaction types, we achieve the classification success rate up to 83.2% with leave-one-out cross-validation at k = 15. Of these four interaction types, C(alpha)--H...O==C shows binding specificity for protease-inhibitor complexes, while cation-anion interaction is predominant in signaling complexes. The amine ... amine and amine...cation interaction give a minor contribution to the classification accuracy. When combined with these two interactions, they increase the accuracy by 3.8%. In the case of

Measurements of Protein Crystal Face Growth Rates

Science.gov (United States)

Gorti, S.

2014-01-01

Protein crystal growth rates will be determined for several hyperthermophile proteins.; The growth rates will be assessed using available theoretical models, including kinetic roughening.; If/when kinetic roughening supersaturations are established, determinations of protein crystal quality over a range of supersaturations will also be assessed.; The results of our ground based effort may well address the existence of a correlation between fundamental growth mechanisms and protein crystal quality.

DECK: Distance and environment-dependent, coarse-grained, knowledge-based potentials for protein-protein docking

Directory of Open Access Journals (Sweden)

Vakser Ilya A

2011-07-01

Full Text Available Abstract Background Computational approaches to protein-protein docking typically include scoring aimed at improving the rank of the near-native structure relative to the false-positive matches. Knowledge-based potentials improve modeling of protein complexes by taking advantage of the rapidly increasing amount of experimentally derived information on protein-protein association. An essential element of knowledge-based potentials is defining the reference state for an optimal description of the residue-residue (or atom-atom pairs in the non-interaction state. Results The study presents a new Distance- and Environment-dependent, Coarse-grained, Knowledge-based (DECK potential for scoring of protein-protein docking predictions. Training sets of protein-protein matches were generated based on bound and unbound forms of proteins taken from the DOCKGROUND resource. Each residue was represented by a pseudo-atom in the geometric center of the side chain. To capture the long-range and the multi-body interactions, residues in different secondary structure elements at protein-protein interfaces were considered as different residue types. Five reference states for the potentials were defined and tested. The optimal reference state was selected and the cutoff effect on the distance-dependent potentials investigated. The potentials were validated on the docking decoys sets, showing better performance than the existing potentials used in scoring of protein-protein docking results. Conclusions A novel residue-based statistical potential for protein-protein docking was developed and validated on docking decoy sets. The results show that the scoring function DECK can successfully identify near-native protein-protein matches and thus is useful in protein docking. In addition to the practical application of the potentials, the study provides insights into the relative utility of the reference states, the scope of the distance dependence, and the coarse-graining of

Comparison of protein degradation, protein oxidation, and μ-calpain activation between pale, soft, and exudative and red, firm, and nonexudative pork during postmortem aging.

Science.gov (United States)

Yin, Y; Zhang, W G; Zhou, G H; Guo, B

2014-08-01

The objective of this study was to investigate the differences in protein modifications between pale, soft, and exudative (PSE) and red, firm, and nonexudative (RFN) pork during postmortem (PM) aging. Longissimus dorsi (LD) including 8 PSE and 8 RFN muscles were individually removed from 16 carcasses. These 16 LD muscles were vacuum packaged at 24 h after slaughter and stored at 4°C for 1, 3, and 5 d. The centrifugation loss, drip loss, color, protein solubility, protein oxidation, protein degradation including desmin, troponin T, and integrin, and μ-calpain activation were determined. The pH of PSE samples was significantly lower than that of RFN samples at both 1 and 24 h PM (P 0.05). In addition, PSE pork presented a lower solubility of sarcoplasmic protein, myofibrillar protein, and total protein than RFN pork except the solubility of myofibrillar protein at d 1 (P firm, and nonexudative pork presented lower intensity of intact 80 kDa calpain and greater intensity of autolyzed 76 kDa product compared to PSE pork (P < 0.01). The results indicate that the degree of μ-calpain activation, the extent of protein degradation including desmin and integrin, and the level of protein solubility in PSE pork could contribute to its low water holding capacity during PM storage.

AIRS-CloudSat cloud mask, radar reflectivities, and cloud classification matchups V3.2

Data.gov (United States)

National Aeronautics and Space Administration — This is AIRS-CloudSat collocated subset, in NetCDF 4 format. These data contain collocated: AIRS Level 1b radiances spectra, CloudSat radar reflectivities, and MODIS...

Lexical Resources and Their Application.

Science.gov (United States)

Gellerstam, Martin

This paper discusses computer-based resources for lexical data and their uses. First, the kinds of lexical data available are described, including those related to form (spelling, pronunciation, inflection, word class), meaning (definition/equivalent, synonyms/antonyms/hyperonyms, thesaurus classification), context (grammatical collocations,…

Protein carriers of conjugate vaccines

Science.gov (United States)

Pichichero, Michael E

2013-01-01

The immunogenicity of polysaccharides as human vaccines was enhanced by coupling to protein carriers. Conjugation transformed the T cell-independent polysaccharide vaccines of the past to T cell-dependent antigenic vaccines that were much more immunogenic and launched a renaissance in vaccinology. This review discusses the conjugate vaccines for prevention of infections caused by Hemophilus influenzae type b, Streptococcus pneumoniae, and Neisseria meningitidis. Specifically, the characteristics of the proteins used in the construction of the vaccines including CRM, tetanus toxoid, diphtheria toxoid, Neisseria meningitidis outer membrane complex, and Hemophilus influenzae protein D are discussed. The studies that established differences among and key features of conjugate vaccines including immunologic memory induction, reduction of nasopharyngeal colonization and herd immunity, and antibody avidity and avidity maturation are presented. Studies of dose, schedule, response to boosters, of single protein carriers with single and multiple polysaccharides, of multiple protein carriers with multiple polysaccharides and conjugate vaccines administered concurrently with other vaccines are discussed along with undesirable consequences of conjugate vaccines. The clear benefits of conjugate vaccines in improving the protective responses of the immature immune systems of young infants and the senescent immune systems of the elderly have been made clear and opened the way to development of additional vaccines using this technology for future vaccine products. PMID:23955057

Folding 19 proteins to their native state and stability of large proteins from a coarse-grained model.

Science.gov (United States)

Kapoor, Abhijeet; Travesset, Alex

2014-03-01

We develop an intermediate resolution model, where the backbone is modeled with atomic resolution but the side chain with a single bead, by extending our previous model (Proteins (2013) DOI: 10.1002/prot.24269) to properly include proline, preproline residues and backbone rigidity. Starting from random configurations, the model properly folds 19 proteins (including a mutant 2A3D sequence) into native states containing β sheet, α helix, and mixed α/β. As a further test, the stability of H-RAS (a 169 residue protein, critical in many signaling pathways) is investigated: The protein is stable, with excellent agreement with experimental B-factors. Despite that proteins containing only α helices fold to their native state at lower backbone rigidity, and other limitations, which we discuss thoroughly, the model provides a reliable description of the dynamics as compared with all atom simulations, but does not constrain secondary structures as it is typically the case in more coarse-grained models. Further implications are described. Copyright © 2013 Wiley Periodicals, Inc.

Salvage of Failed Protein Targets by Reductive Alkylation

Science.gov (United States)

Tan, Kemin; Kim, Youngchang; Hatzos-Skintges, Catherine; Chang, Changsoo; Cuff, Marianne; Chhor, Gekleng; Osipiuk, Jerzy; Michalska, Karolina; Nocek, Boguslaw; An, Hao; Babnigg, Gyorgy; Bigelow, Lance; Joachimiak, Grazyna; Li, Hui; Mack, Jamey; Makowska-Grzyska, Magdalena; Maltseva, Natalia; Mulligan, Rory; Tesar, Christine; Zhou, Min; Joachimiak, Andrzej

2014-01-01

The growth of diffraction-quality single crystals is of primary importance in protein X-ray crystallography. Chemical modification of proteins can alter their surface properties and crystallization behavior. The Midwest Center for Structural Genomics (MCSG) has previously reported how reductive methylation of lysine residues in proteins can improve crystallization of unique proteins that initially failed to produce diffraction-quality crystals. Recently, this approach has been expanded to include ethylation and isopropylation in the MCSG protein crystallization pipeline. Applying standard methods, 180 unique proteins were alkylated and screened using standard crystallization procedures. Crystal structures of 12 new proteins were determined, including the first ethylated and the first isopropylated protein structures. In a few cases, the structures of native and methylated or ethylated states were obtained and the impact of reductive alkylation of lysine residues was assessed. Reductive methylation tends to be more efficient and produces the most alkylated protein structures. Structures of methylated proteins typically have higher resolution limits. A number of well-ordered alkylated lysine residues have been identified, which make both intermolecular and intramolecular contacts. The previous report is updated and complemented with the following new data; a description of a detailed alkylation protocol with results, structural features, and roles of alkylated lysine residues in protein crystals. These contribute to improved crystallization properties of some proteins. PMID:24590719

Salvage of failed protein targets by reductive alkylation.

Science.gov (United States)

Tan, Kemin; Kim, Youngchang; Hatzos-Skintges, Catherine; Chang, Changsoo; Cuff, Marianne; Chhor, Gekleng; Osipiuk, Jerzy; Michalska, Karolina; Nocek, Boguslaw; An, Hao; Babnigg, Gyorgy; Bigelow, Lance; Joachimiak, Grazyna; Li, Hui; Mack, Jamey; Makowska-Grzyska, Magdalena; Maltseva, Natalia; Mulligan, Rory; Tesar, Christine; Zhou, Min; Joachimiak, Andrzej

2014-01-01

The growth of diffraction-quality single crystals is of primary importance in protein X-ray crystallography. Chemical modification of proteins can alter their surface properties and crystallization behavior. The Midwest Center for Structural Genomics (MCSG) has previously reported how reductive methylation of lysine residues in proteins can improve crystallization of unique proteins that initially failed to produce diffraction-quality crystals. Recently, this approach has been expanded to include ethylation and isopropylation in the MCSG protein crystallization pipeline. Applying standard methods, 180 unique proteins were alkylated and screened using standard crystallization procedures. Crystal structures of 12 new proteins were determined, including the first ethylated and the first isopropylated protein structures. In a few cases, the structures of native and methylated or ethylated states were obtained and the impact of reductive alkylation of lysine residues was assessed. Reductive methylation tends to be more efficient and produces the most alkylated protein structures. Structures of methylated proteins typically have higher resolution limits. A number of well-ordered alkylated lysine residues have been identified, which make both intermolecular and intramolecular contacts. The previous report is updated and complemented with the following new data; a description of a detailed alkylation protocol with results, structural features, and roles of alkylated lysine residues in protein crystals. These contribute to improved crystallization properties of some proteins.

The point mutation process in proteins

Science.gov (United States)

Schwartz, R. M.; Dayhoff, M. O.

1978-01-01

An optimized scoring matrix for residue-by-residue comparisons of distantly related protein sequences has been developed. The scoring matrix is based on observed exchanges and mutabilities of amino acids in 1572 closely related sequences derived from a cross-section of protein groups. Very few superimposed or parallel mutations are included in the data. The scoring matrix is most useful for demonstrating the relatedness of proteins between 65 and 85% different.

Protein disulfide isomerase-like protein 1-1 controls endosperm development through regulation of the amount and composition of seed proteins in rice.

Directory of Open Access Journals (Sweden)

Yeon Jeong Kim

Full Text Available Protein disulfide isomerase (PDI is a chaperone protein involved in oxidative protein folding by acting as a catalyst and assisting folding in the endoplasmic reticulum (ER. A genome database search showed that rice contains 19 PDI-like genes. However, their functions are not clearly identified. This paper shows possible functions of rice PDI-like protein 1-1 (PDIL1-1 during seed development. Seeds of the T-DNA insertion PDIL1-1 mutant, PDIL1-1Δ, identified by genomic DNA PCR and western blot analysis, display a chalky phenotype and a thick aleurone layer. Protein content per seed was significantly lower and free sugar content higher in PDIL1-1Δ mutant seeds than in the wild type. Proteomic analysis of PDIL1-1Δ mutant seeds showed that PDIL1-1 is post-translationally regulated, and its loss causes accumulation of many types of seed proteins including glucose/starch metabolism- and ROS (reactive oxygen species scavenging-related proteins. In addition, PDIL1-1 strongly interacts with the cysteine protease OsCP1. Our data indicate that the opaque phenotype of PDIL1-1Δ mutant seeds results from production of irregular starch granules and protein body through loss of regulatory activity for various proteins involved in the synthesis of seed components.

Is a malleable protein necessarily highly dynamic?

DEFF Research Database (Denmark)

Kjærgaard, Magnus; Poulsen, Flemming Martin; Teilum, Kaare

2012-01-01

core of NCBD in the ligand-free state and in a well-folded complex with the ligand activator for thyroid hormone and retinoid receptors using multiple NMR methods including methyl chemical shifts, coupling constants, and methyl order parameters. From all NMR measures, the aliphatic side chains...... in the hydrophobic core are slightly more dynamic in the free protein than in the complex, but have mobility comparable to the hydrophobic cores of average folded proteins. Urea titration monitored by NMR reveals that all parts of the protein, including the side-chain packing in the hydrophobic core, denatures...

Analysis of Protein-Membrane Interactions

DEFF Research Database (Denmark)

Kemmer, Gerdi Christine

Cellular membranes are complex structures, consisting of hundreds of different lipids and proteins. These membranes act as barriers between distinct environments, constituting hot spots for many essential functions of the cell, including signaling, energy conversion, and transport. These functions....... Discovered interactions were then probed on the level of the membrane using liposome-based assays. In the second part, a transmembrane protein was investigated. Assays to probe activity of the plasma membrane ATPase (Arabidopsis thaliana H+ -ATPase isoform 2 (AHA2)) in single liposomes using both giant...... are implemented by soluble proteins reversibly binding to, as well as by integral membrane proteins embedded in, cellular membranes. The activity and interaction of these proteins is furthermore modulated by the lipids of the membrane. Here, liposomes were used as model membrane systems to investigate...

Random copolymers that protect proteins

Science.gov (United States)

Alexander-Katz, Alfredo; Van Lehn, Reid C.

2018-03-01

Scientists have tried and in some limited cases succeeded to harness proteins to do chemistry (1) or use them in functional materials. However, most proteins only function correctly if they fold into specific conformations, which typically occurs with the assistance of other proteins (such as chaperones, translocons, or transporters) that mediate structure formation, membrane insertion, and intracellular trafficking (2, 3). Several methods have been used to improve protein stability in nonbiological environments—including micelle encapsulation, polymer conjugation, and sol-gel trapping (4)—but for most intended applications, they suffer from low levels of functionality, difficult chemical postfunctionalization, or the requirement of very specific solvent environments. On page 1239 of this issue, Panganiban et al. (5) introduce an approach for stabilizing proteins in disparate solvent environments that does not suffer from these drawbacks.

Nanochemistry of protein-based delivery agents

Science.gov (United States)

Rajendran, Subin; Udenigwe, Chibuike; Yada, Rickey

2016-07-01

The past decade has seen an increased interest in the conversion of food proteins into functional biomaterials, including their use for loading and delivery of physiologically active compounds such as nutraceuticals and pharmaceuticals. Proteins possess a competitive advantage over other platforms for the development of nanodelivery systems since they are biocompatible, amphipathic, and widely available. Proteins also have unique molecular structures and diverse functional groups that can be selectively modified to alter encapsulation and release properties. A number of physical and chemical methods have been used for preparing protein nanoformulations, each based on different underlying protein chemistry. This review focuses on the chemistry of the reorganization and/or modification of proteins into functional nanostructures for delivery, from the perspective of their preparation, functionality, stability and physiological behavior.

Bioinformatic prediction of G protein-coupled receptor encoding sequences from the transcriptome of the foreleg, including the Haller's organ, of the cattle tick, Rhipicephalus australis.

Directory of Open Access Journals (Sweden)

Sergio Munoz

Full Text Available The cattle tick of Australia, Rhipicephalus australis, is a vector for microbial parasites that cause serious bovine diseases. The Haller's organ, located in the tick's forelegs, is crucial for host detection and mating. To facilitate the development of new technologies for better control of this agricultural pest, we aimed to sequence and annotate the transcriptome of the R. australis forelegs and associated tissues, including the Haller's organ. As G protein-coupled receptors (GPCRs are an important family of eukaryotic proteins studied as pharmaceutical targets in humans, we prioritized the identification and classification of the GPCRs expressed in the foreleg tissues. The two forelegs from adult R. australis were excised, RNA extracted, and pyrosequenced with 454 technology. Reads were assembled into unigenes and annotated by sequence similarity. Python scripts were written to find open reading frames (ORFs from each unigene. These ORFs were analyzed by different GPCR prediction approaches based on sequence alignments, support vector machines, hidden Markov models, and principal component analysis. GPCRs consistently predicted by multiple methods were further studied by phylogenetic analysis and 3D homology modeling. From 4,782 assembled unigenes, 40,907 possible ORFs were predicted. Using Blastp, Pfam, GPCRpred, TMHMM, and PCA-GPCR, a basic set of 46 GPCR candidates were compiled and a phylogenetic tree was constructed. With further screening of tertiary structures predicted by RaptorX, 6 likely GPCRs emerged and the strongest candidate was classified by PCA-GPCR to be a GABAB receptor.

Calibration laboratories as a regional repair center: consolidate or collocate

OpenAIRE

Mitchell, Marquita A; Pasch, John E.

1996-01-01

The purpose of this thesis is to examine the integration of AIMDs Miramar and North Island, and NADEP North Island calibration laboratories. The expected benefits and weaknesses or problems resulting from integration are examined. The benefits analyzed include those in the areas of manpower, training, standards reduction, inventory reduction, streamlining facilities, and increased productivity. The problems analyzed include increased transportation costs, facilities modification costs, reduce...

A cytoplasmic serine protein kinase binds and may regulate the Fanconi anemia protein FANCA.

Science.gov (United States)

Yagasaki, H; Adachi, D; Oda, T; Garcia-Higuera, I; Tetteh, N; D'Andrea, A D; Futaki, M; Asano, S; Yamashita, T

2001-12-15

Fanconi anemia (FA) is an autosomal recessive disease with congenital anomalies, bone marrow failure, and susceptibility to leukemia. Patient cells show chromosome instability and hypersensitivity to DNA cross-linking agents. At least 8 complementation groups (A-G) have been identified and 6 FA genes (for subtypes A, C, D2, E, F, and G) have been cloned. Increasing evidence indicates that a protein complex assembly of multiple FA proteins, including FANCA and FANCG, plays a crucial role in the FA pathway. Previously, it was reported that FANCA was phosphorylated in lymphoblasts from normal controls, whereas the phosphorylation was defective in those derived from patients with FA of multiple complementation groups. The present study examined phosphorylation of FANCA ectopically expressed in FANCA(-) cells. Several patient-derived mutations abrogated in vivo phosphorylation of FANCA in this system, suggesting that FANCA phosphorylation is associated with its function. In vitro phosphorylation studies indicated that a physiologic protein kinase for FANCA (FANCA-PK) forms a complex with the substrate. Furthermore, at least a part of FANCA-PK as well as phosphorylated FANCA were included in the FANCA/FANCG complex. Thus, FANCA-PK appears to be another component of the FA protein complex and may regulate function of FANCA. FANCA-PK was characterized as a cytoplasmic serine kinase sensitive to wortmannin. Identification of the protein kinase is expected to elucidate regulatory mechanisms that control the FA pathway.

The master two-dimensional gel database of human AMA cell proteins: towards linking protein and genome sequence and mapping information (update 1991)

DEFF Research Database (Denmark)

Celis, J E; Leffers, H; Rasmussen, H H

1991-01-01

autoantigens" and "cDNAs". For convenience we have included an alphabetical list of all known proteins recorded in this database. In the long run, the main goal of this database is to link protein and DNA sequencing and mapping information (Human Genome Program) and to provide an integrated picture......The master two-dimensional gel database of human AMA cells currently lists 3801 cellular and secreted proteins, of which 371 cellular polypeptides (306 IEF; 65 NEPHGE) were added to the master images during the last 10 months. These include: (i) very basic and acidic proteins that do not focus...

Processing and characteristics of canola protein-based biodegradable packaging: A review.

Science.gov (United States)

Zhang, Yachuan; Liu, Qiang; Rempel, Curtis

2018-02-11

Interest increased recently in manufacturing food packaging, such as films and coatings, from protein-based biopolymers. Among various protein sources, canola protein is a novel source for manufacturing polymer films. It can be concentrated or isolated by aqueous extraction technology followed by protein precipitation. Using this procedure, it was claimed that more than 99% of protein was extracted from the defatted canola meal, and protein recovery was 87.5%. Canola protein exhibits thermoplastic properties when plasticizers are present, including water, glycerol, polyethylene glycol, and sorbitol. Addition of these plasticizers allows the canola protein to undergo glass transition and facilitates deformation and processability. Normally, canola protein-based bioplastics showed low mechanical properties, which had tensile strength (TS) of 1.19 to 4.31 MPa. So, various factors were explored to improve it, including blending with synthetic polymers, modifying protein functionality through controlled denaturation, and adding cross-linking agents. Canola protein-based bioplastics were reported to have glass transition temperature, T g , below -50°C but it highly depends on the plasticizer content. Canola protein-based bioplastics have demonstrated comparable mechanical and moisture barrier properties compared with other plant protein-based bioplastics. They have great potential in food packaging applications, including their use as wraps, sacks, sachets, or pouches.

Overcoming barriers to membrane protein structure determination.