previously solved structures: Topics by Science.gov

Sample records for previously solved structures

Structure of the sporulation histidine kinase inhibitor Sda from Bacillus subtilis and insights into its solution state

DOE Office of Scientific and Technical Information (OSTI.GOV)

Jacques, David A.; Streamer, Margaret; Rowland, Susan L.

2009-06-01

The crystal structure of Sda, a DNA-replication/damage checkpoint inhibitor of sporulation in B. subtilis, has been solved via the MAD method. The subunit arrangement in the crystal has enabled a reappraisal of previous biophysical data, resulting in a new model for the behaviour of the protein in solution. The crystal structure of the DNA-damage checkpoint inhibitor of sporulation, Sda, from Bacillus subtilis, has been solved by the MAD technique using selenomethionine-substituted protein. The structure closely resembles that previously solved by NMR, as well as the structure of a homologue from Geobacillus stearothermophilus solved in complex with the histidine kinase KinB.more » The structure contains three molecules in the asymmetric unit. The unusual trimeric arrangement, which lacks simple internal symmetry, appears to be preserved in solution based on an essentially ideal fit to previously acquired scattering data for Sda in solution. This interpretation contradicts previous findings that Sda was monomeric or dimeric in solution. This study demonstrates the difficulties that can be associated with the characterization of small proteins and the value of combining multiple biophysical techniques. It also emphasizes the importance of understanding the physical principles behind these techniques and therefore their limitations.« less
How Instructional Design Experts Use Knowledge and Experience to Solve Ill-Structured Problems

ERIC Educational Resources Information Center

Ertmer, Peggy A.; Stepich, Donald A.; York, Cindy S.; Stickman, Ann; Wu, Xuemei (Lily); Zurek, Stacey; Goktas, Yuksel

2008-01-01

This study examined how instructional design (ID) experts used their prior knowledge and previous experiences to solve an ill-structured instructional design problem. Seven experienced designers used a think-aloud procedure to articulate their problem-solving processes while reading a case narrative. Results, presented in the form of four…
Structure of the sporulation histidine kinase inhibitor Sda from Bacillus subtilis and insights into its solution state

DOE Office of Scientific and Technical Information (OSTI.GOV)

Jacques, David A.; Streamer, Margaret; Rowland, Susan L.

2009-09-02

The crystal structure of the DNA-damage checkpoint inhibitor of sporulation, Sda, from Bacillus subtilis, has been solved by the MAD technique using selenomethionine-substituted protein. The structure closely resembles that previously solved by NMR, as well as the structure of a homologue from Geobacillus stearothermophilus solved in complex with the histidine kinase KinB. The structure contains three molecules in the asymmetric unit. The unusual trimeric arrangement, which lacks simple internal symmetry, appears to be preserved in solution based on an essentially ideal fit to previously acquired scattering data for Sda in solution. This interpretation contradicts previous findings that Sda was monomericmore » or dimeric in solution. This study demonstrates the difficulties that can be associated with the characterization of small proteins and the value of combining multiple biophysical techniques. It also emphasizes the importance of understanding the physical principles behind these techniques and therefore their limitations.« less
Proteins Are the Body's Worker Molecules

MedlinePlus

... molecular structures. Many of these new technologies are robots that automate previously labor-intensive steps in structure determination. Thanks to these robots, it is possible to solve structures faster than ...
The Effects of Successful versus Failure-Based Cases on Argumentation while Solving Decision-Making Problems

ERIC Educational Resources Information Center

Tawfik, Andrew; Jonassen, David

2013-01-01

Solving complex, ill-structured problems may be effectively supported by case-based reasoning through case libraries that provide just-in-time domain-specific principles in the form of stories. The cases not only articulate previous experiences of practitioners, but also serve as problem-solving narratives from which learners can acquire meaning.…
Representational Task Formats and Problem Solving Strategies in Kinematics and Work

ERIC Educational Resources Information Center

Ibrahim, Bashirah; Rebello, N. Sanjay

2012-01-01

Previous studies have reported that students employed different problem solving approaches when presented with the same task structured with different representations. In this study, we explored and compared students' strategies as they attempted tasks from two topical areas, kinematics and work. Our participants were 19 engineering students…
Lattice enumeration for inverse molecular design using the signature descriptor.

PubMed

Martin, Shawn

2012-07-23

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

NASA Astrophysics Data System (ADS)

Keller, William Cotesworth

A multifaceted protocol for solving ill-structured community problems has been developed. It embodies the lessons learned from the past by refining and extending features of previous models from the systems thinkers, and the fields of behavioral decision making and creative problem solving. The protocol also embraces additional features needed to address the unique aspects of community decision situations. The essential elements of the protocol are participants from the community, a problem-solving process, a systems picture, a facilitator, a modified Delphi method of communications, and technical expertise. This interdisciplinary framework has been tested by a quasi experiment with a real world community problem (the high cost of electrical power on Long Island, NY). Results indicate the protocol can enable members of the community to understand a complicated, ill-structured problem and guide them to action to solve the issue. However, the framework takes time (over one year in the test case) and will be inappropriate for crises where quick action is needed.
Exploring the speed and performance of molecular replacement with AMPLE using QUARK ab initio protein models.

PubMed

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

2015-02-01

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

PubMed

Zhang, Haonan; Qiao, Anna; Yang, Linlin; Van Eps, Ned; Frederiksen, Klaus S; Yang, Dehua; Dai, Antao; Cai, Xiaoqing; Zhang, Hui; Yi, Cuiying; Cao, Can; He, Lingli; Yang, Huaiyu; Lau, Jesper; Ernst, Oliver P; Hanson, Michael A; Stevens, Raymond C; Wang, Ming-Wei; Reedtz-Runge, Steffen; Jiang, Hualiang; Zhao, Qiang; Wu, Beili

2018-01-03

Class B G-protein-coupled receptors (GPCRs), which consist of an extracellular domain (ECD) and a transmembrane domain (TMD), respond to secretin peptides to play a key part in hormonal homeostasis, and are important therapeutic targets for a variety of diseases. Previous work has suggested that peptide ligands bind to class B GPCRs according to a two-domain binding model, in which the C-terminal region of the peptide targets the ECD and the N-terminal region of the peptide binds to the TMD binding pocket. Recently, three structures of class B GPCRs in complex with peptide ligands have been solved. These structures provide essential insights into peptide ligand recognition by class B GPCRs. However, owing to resolution limitations, the specific molecular interactions for peptide binding to class B GPCRs remain ambiguous. Moreover, these previously solved structures have different ECD conformations relative to the TMD, which introduces questions regarding inter-domain conformational flexibility and the changes required for receptor activation. Here we report the 3.0 Å-resolution crystal structure of the full-length human glucagon receptor (GCGR) in complex with a glucagon analogue and partial agonist, NNC1702. This structure provides molecular details of the interactions between GCGR and the peptide ligand. It reveals a marked change in the relative orientation between the ECD and TMD of GCGR compared to the previously solved structure of the inactive GCGR-NNC0640-mAb1 complex. Notably, the stalk region and the first extracellular loop undergo major conformational changes in secondary structure during peptide binding, forming key interactions with the peptide. We further propose a dual-binding-site trigger model for GCGR activation-which requires conformational changes of the stalk, first extracellular loop and TMD-that extends our understanding of the previously established two-domain peptide-binding model of class B GPCRs.
The Role of Previous Mother-Child Scaffolding in Head Start Children's Structuring of Problem-Solving Tasks with a Peer

ERIC Educational Resources Information Center

Hustedt, Jason T.

2015-01-01

This study further extends scaffolding research to mother-child dyads (N = 51) in poverty, examining relationships between maternal scaffolding and 4-year-old Head Start children's own later scaffolding behaviors. At Time 1, experimental group children received maternal scaffolding during problem-solving tasks, whereas control group children…
Exploring the speed and performance of molecular replacement with AMPLE using QUARK ab initio protein models

PubMed Central

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

2015-01-01

AMPLE clusters and truncates ab initio protein structure predictions, producing search models for molecular replacement. Here, an interesting degree of complementarity is shown between targets solved using the different ab initio modelling programs QUARK and ROSETTA. Search models derived from either program collectively solve almost all of the all-helical targets in the test set. Initial solutions produced by Phaser after only 5 min perform surprisingly well, improving the prospects for in situ structure solution by AMPLE during synchrotron visits. Taken together, the results show the potential for AMPLE to run more quickly and successfully solve more targets than previously suspected. PMID:25664744
Comparison of Types of Generalizations and Problem-Solving Schemas Used to Solve a Mathematical Problem

ERIC Educational Resources Information Center

Hodnik Cadež, Tatjana; Manfreda Kolar, Vida

2015-01-01

A cognitive schema is a mechanism which allows an individual to organize her/his experiences in such a way that a new similar experience can easily be recognised and dealt with successfully. Well-structured schemas provide for the knowledge base for subsequent mathematical activities. A new experience can be assimilated into a previously existing…
NMR crystallography of zeolites: How far can we go without diffraction data?

PubMed

Brouwer, Darren H; Van Huizen, Jared

2018-05-10

Nuclear magnetic resonance (NMR) crystallography-an approach to structure determination that seeks to integrate solid-state NMR spectroscopy, diffraction, and computation methods-has emerged as an effective strategy to determine structures of difficult-to-characterize materials, including zeolites and related network materials. This paper explores how far it is possible to go in determining the structure of a zeolite framework from a minimal amount of input information derived only from solid-state NMR spectroscopy. It is shown that the framework structure of the fluoride-containing and tetramethylammonium-templated octadecasil clathrasil material can be solved from the 1D 29 Si NMR spectrum and a single 2D 29 Si NMR correlation spectrum alone, without the space group and unit cell parameters normally obtained from diffraction data. The resulting NMR-solved structure is in excellent agreement with the structures determined previously by diffraction methods. It is anticipated that NMR crystallography strategies like this will be useful for structure determination of other materials, which cannot be solved from diffraction methods alone. Copyright © 2018 John Wiley & Sons, Ltd.
An approximate Riemann solver for magnetohydrodynamics (that works in more than one dimension)

NASA Technical Reports Server (NTRS)

Powell, Kenneth G.

1994-01-01

An approximate Riemann solver is developed for the governing equations of ideal magnetohydrodynamics (MHD). The Riemann solver has an eight-wave structure, where seven of the waves are those used in previous work on upwind schemes for MHD, and the eighth wave is related to the divergence of the magnetic field. The structure of the eighth wave is not immediately obvious from the governing equations as they are usually written, but arises from a modification of the equations that is presented in this paper. The addition of the eighth wave allows multidimensional MHD problems to be solved without the use of staggered grids or a projection scheme, one or the other of which was necessary in previous work on upwind schemes for MHD. A test problem made up of a shock tube with rotated initial conditions is solved to show that the two-dimensional code yields answers consistent with the one-dimensional methods developed previously.
Solving the crystal structure of human calcium-free S100Z: the siege and conquer of one of the last S100 family strongholds.

PubMed

Calderone, V; Fragai, M; Gallo, G; Luchinat, C

2017-06-01

The X-ray structure of human apo-S100Z has been solved and compared with that of the zebrafish calcium-bound S100Z, which is the closest in sequence. Human apo-S100A12, which shows only 43% sequence identity to human S100Z, has been used as template model to solve the crystallographic phase problem. Although a significant buried surface area between the two physiological dimers is present in the asymmetric unit of human apo-S100Z, the protein does not form the superhelical arrangement in the crystal as observed for the zebrafish calcium-bound S100Z and human calcium-bound S100A4. These findings further demonstrate that calcium plays a fundamental role in triggering quaternary structure formation in several S100s. Solving the X-ray structure of human apo-S100Z by standard molecular replacement procedures turned out to be a challenge and required trying different models and different software tools among which only one was successful. The model that allowed structure solution was that with one of the lowest sequence identity with the target protein among the S100 family in the apo state. Based on the previously solved zebrafish holo-S100Z, a putative human holo-S100Z structure has been then calculated through homology modeling; the differences between the experimental human apo and calculated holo structure have been compared to those existing for other members of the family.
Reproducing the Ensemble Average Polar Solvation Energy of a Protein from a Single Structure: Gaussian-Based Smooth Dielectric Function for Macromolecular Modeling.

PubMed

Chakravorty, Arghya; Jia, Zhe; Li, Lin; Zhao, Shan; Alexov, Emil

2018-02-13

Typically, the ensemble average polar component of solvation energy (ΔG polar solv ) of a macromolecule is computed using molecular dynamics (MD) or Monte Carlo (MC) simulations to generate conformational ensemble and then single/rigid conformation solvation energy calculation is performed on each snapshot. The primary objective of this work is to demonstrate that Poisson-Boltzmann (PB)-based approach using a Gaussian-based smooth dielectric function for macromolecular modeling previously developed by us (Li et al. J. Chem. Theory Comput. 2013, 9 (4), 2126-2136) can reproduce that ensemble average (ΔG polar solv ) of a protein from a single structure. We show that the Gaussian-based dielectric model reproduces the ensemble average ΔG polar solv (⟨ΔG polar solv ⟩) from an energy-minimized structure of a protein regardless of the minimization environment (structure minimized in vacuo, implicit or explicit waters, or crystal structure); the best case, however, is when it is paired with an in vacuo-minimized structure. In other minimization environments (implicit or explicit waters or crystal structure), the traditional two-dielectric model can still be selected with which the model produces correct solvation energies. Our observations from this work reflect how the ability to appropriately mimic the motion of residues, especially the salt bridge residues, influences a dielectric model's ability to reproduce the ensemble average value of polar solvation free energy from a single in vacuo-minimized structure.
Matrix Methods for Solving Hartree-Fock Equations in Atomic Structure Calculations and Line Broadening

DOE Office of Scientific and Technical Information (OSTI.GOV)

Gomez, Thomas; Nagayama, Taisuke; Fontes, Chris

Atomic structure of N-electron atoms is often determined by solving the Hartree-Fock equations, which are a set of integro-differential equations. The integral part of the Hartree-Fock equations treats electron exchange, but the Hartree-Fock equations are not often treated as an integro-differential equation. The exchange term is often approximated as an inhomogeneous or an effective potential so that the Hartree-Fock equations become a set of ordinary differential equations (which can be solved using the usual shooting methods). Because the Hartree-Fock equations are an iterative-refinement method, the inhomogeneous term relies on the previous guess of the wavefunction. In addition, there are numericalmore » complications associated with solving inhomogeneous differential equations. This work uses matrix methods to solve the Hartree-Fock equations as an integro-differential equation. It is well known that a derivative operator can be expressed as a matrix made of finite-difference coefficients; energy eigenvalues and eigenvectors can be obtained by using linear-algebra packages. The integral (exchange) part of the Hartree-Fock equation can be approximated as a sum and written as a matrix. The Hartree-Fock equations can be solved as a matrix that is the sum of the differential and integral matrices. We compare calculations using this method against experiment and standard atomic structure calculations. This matrix method can also be used to solve for free-electron wavefunctions, thus improving how the atoms and free electrons interact. Here, this technique is important for spectral line broadening in two ways: it improves the atomic structure calculations, and it improves the motion of the plasma electrons that collide with the atom.« less
Matrix Methods for Solving Hartree-Fock Equations in Atomic Structure Calculations and Line Broadening

DOE PAGES

Gomez, Thomas; Nagayama, Taisuke; Fontes, Chris; ...

2018-04-23

Atomic structure of N-electron atoms is often determined by solving the Hartree-Fock equations, which are a set of integro-differential equations. The integral part of the Hartree-Fock equations treats electron exchange, but the Hartree-Fock equations are not often treated as an integro-differential equation. The exchange term is often approximated as an inhomogeneous or an effective potential so that the Hartree-Fock equations become a set of ordinary differential equations (which can be solved using the usual shooting methods). Because the Hartree-Fock equations are an iterative-refinement method, the inhomogeneous term relies on the previous guess of the wavefunction. In addition, there are numericalmore » complications associated with solving inhomogeneous differential equations. This work uses matrix methods to solve the Hartree-Fock equations as an integro-differential equation. It is well known that a derivative operator can be expressed as a matrix made of finite-difference coefficients; energy eigenvalues and eigenvectors can be obtained by using linear-algebra packages. The integral (exchange) part of the Hartree-Fock equation can be approximated as a sum and written as a matrix. The Hartree-Fock equations can be solved as a matrix that is the sum of the differential and integral matrices. We compare calculations using this method against experiment and standard atomic structure calculations. This matrix method can also be used to solve for free-electron wavefunctions, thus improving how the atoms and free electrons interact. Here, this technique is important for spectral line broadening in two ways: it improves the atomic structure calculations, and it improves the motion of the plasma electrons that collide with the atom.« less
Near-Atomic Resolution Structure of a Highly Neutralizing Fab Bound to Canine Parvovirus.

PubMed

Organtini, Lindsey J; Lee, Hyunwook; Iketani, Sho; Huang, Kai; Ashley, Robert E; Makhov, Alexander M; Conway, James F; Parrish, Colin R; Hafenstein, Susan

2016-11-01

Canine parvovirus (CPV) is a highly contagious pathogen that causes severe disease in dogs and wildlife. Previously, a panel of neutralizing monoclonal antibodies (MAb) raised against CPV was characterized. An antibody fragment (Fab) of MAb E was found to neutralize the virus at low molar ratios. Using recent advances in cryo-electron microscopy (cryo-EM), we determined the structure of CPV in complex with Fab E to 4.1 Å resolution, which allowed de novo building of the Fab structure. The footprint identified was significantly different from the footprint obtained previously from models fitted into lower-resolution maps. Using single-chain variable fragments, we tested antibody residues that control capsid binding. The near-atomic structure also revealed that Fab binding had caused capsid destabilization in regions containing key residues conferring receptor binding and tropism, which suggests a mechanism for efficient virus neutralization by antibody. Furthermore, a general technical approach to solving the structures of small molecules is demonstrated, as binding the Fab to the capsid allowed us to determine the 50-kDa Fab structure by cryo-EM. Using cryo-electron microscopy and new direct electron detector technology, we have solved the 4 Å resolution structure of a Fab molecule bound to a picornavirus capsid. The Fab induced conformational changes in regions of the virus capsid that control receptor binding. The antibody footprint is markedly different from the previous one identified by using a 12 Å structure. This work emphasizes the need for a high-resolution structure to guide mutational analysis and cautions against relying on older low-resolution structures even though they were interpreted with the best methodology available at the time. Copyright © 2016, American Society for Microbiology. All Rights Reserved.

Near-Atomic Resolution Structure of a Highly Neutralizing Fab Bound to Canine Parvovirus

PubMed Central

Organtini, Lindsey J.; Lee, Hyunwook; Iketani, Sho; Huang, Kai; Ashley, Robert E.; Makhov, Alexander M.; Conway, James F.

2016-01-01

ABSTRACT Canine parvovirus (CPV) is a highly contagious pathogen that causes severe disease in dogs and wildlife. Previously, a panel of neutralizing monoclonal antibodies (MAb) raised against CPV was characterized. An antibody fragment (Fab) of MAb E was found to neutralize the virus at low molar ratios. Using recent advances in cryo-electron microscopy (cryo-EM), we determined the structure of CPV in complex with Fab E to 4.1 Å resolution, which allowed de novo building of the Fab structure. The footprint identified was significantly different from the footprint obtained previously from models fitted into lower-resolution maps. Using single-chain variable fragments, we tested antibody residues that control capsid binding. The near-atomic structure also revealed that Fab binding had caused capsid destabilization in regions containing key residues conferring receptor binding and tropism, which suggests a mechanism for efficient virus neutralization by antibody. Furthermore, a general technical approach to solving the structures of small molecules is demonstrated, as binding the Fab to the capsid allowed us to determine the 50-kDa Fab structure by cryo-EM. IMPORTANCE Using cryo-electron microscopy and new direct electron detector technology, we have solved the 4 Å resolution structure of a Fab molecule bound to a picornavirus capsid. The Fab induced conformational changes in regions of the virus capsid that control receptor binding. The antibody footprint is markedly different from the previous one identified by using a 12 Å structure. This work emphasizes the need for a high-resolution structure to guide mutational analysis and cautions against relying on older low-resolution structures even though they were interpreted with the best methodology available at the time. PMID:27535057
Social problem solving among depressed adolescents is enhanced by structured psychotherapies.

PubMed

Dietz, Laura J; Marshal, Michael P; Burton, Chad M; Bridge, Jeffrey A; Birmaher, Boris; Kolko, David; Duffy, Jamira N; Brent, David A

2014-04-01

Changes in adolescent interpersonal behavior before and after an acute course of psychotherapy were investigated as outcomes and mediators of remission status in a previously described treatment study of depressed adolescents. Maternal depressive symptoms were examined as moderators of the association between psychotherapy condition and changes in adolescents' interpersonal behavior. Adolescents (n = 63, mean age = 15.6 years, 77.8% female, 84.1% White) engaged in videotaped interactions with their mothers before randomization to cognitive behavior therapy (CBT), systemic behavior family therapy (SBFT), or nondirective supportive therapy (NST) and after 12-16 weeks of treatment. Adolescent involvement, problem solving, and dyadic conflict were examined. Improvements in adolescent problem solving were significantly associated with CBT and SBFT. Maternal depressive symptoms moderated the effect of CBT, but not SBFT, on adolescents' problem solving; adolescents experienced increases in problem solving only when their mothers had low or moderate levels of depressive symptoms. Improvements in adolescents' problem solving were associated with higher rates of remission across treatment conditions, but there were no significant indirect effects of SBFT on remission status through problem solving. Exploratory analyses revealed a significant indirect effect of CBT on remission status through changes in adolescent problem solving, but only when maternal depressive symptoms at study entry were low. Findings provide preliminary support for problem solving as an active treatment component of structured psychotherapies for depressed adolescents and suggest one pathway by which maternal depression may disrupt treatment efficacy for depressed adolescents treated with CBT.
Social problem solving among depressed adolescents is enhanced by structured psychotherapies

PubMed Central

Dietz, Laura J.; Marshal, Michael P.; Burton, Chad M.; Bridge, Jeffrey A.; Birmaher, Boris; Kolko, David; Duffy, Jamira N.; Brent, David A.

2014-01-01

Objective Changes in adolescent interpersonal behavior before and after an acute course of psychotherapy were investigated as outcomes and mediators of remission status in a previously described treatment study of depressed adolescents. Maternal depressive symptoms were examined as moderators of the association between psychotherapy condition and changes in adolescents’ interpersonal behavior. Method Adolescents (n = 63, mean age = 15.6 years, 77.8% female, 84.1% Caucasian) engaged in videotaped interactions with their mothers before randomization to cognitive behavior therapy (CBT), systemic behavior family therapy (SBFT), or nondirective supportive therapy (NST), and after 12–16 weeks of treatment. Adolescent involvement, problem solving and dyadic conflict were examined. Results Improvements in adolescent problem solving were significantly associated with CBT and SBFT. Maternal depressive symptoms moderated the effect of CBT, but not SBFT, on adolescents’ problem solving; adolescents experienced increases in problem solving only when their mothers had low or moderate levels of depressive symptoms. Improvements in adolescents’ problem solving were associated with higher rates of remission across treatment conditions, but there were no significant indirect effects of SBFT on remission status through problem solving. Exploratory analyses revealed a significant indirect effect of CBT on remission status through changes in adolescent problem solving, but only when maternal depressive symptoms at study entry were low. Conclusions Findings provide preliminary support for problem solving as an active treatment component of structured psychotherapies for depressed adolescents and suggest one Pathway by which maternal depression may disrupt treatment efficacy for depressed adolescents treated with CBT. PMID:24491077
The post-rigor structure of myosin VI and implications for the recovery stroke

PubMed Central

Ménétrey, Julie; Llinas, Paola; Cicolari, Jérome; Squires, Gaëlle; Liu, Xiaoyan; Li, Anna; Sweeney, H Lee; Houdusse, Anne

2008-01-01

Myosin VI has an unexpectedly large swing of its lever arm (powerstroke) that optimizes its unique reverse direction movement. The basis for this is an unprecedented rearrangement of the subdomain to which the lever arm is attached, referred to as the converter. It is unclear at what point(s) in the myosin VI ATPase cycle rearrangements in the converter occur, and how this would effect lever arm position. We solved the structure of myosin VI with an ATP analogue (ADP.BeF3) bound in its nucleotide-binding pocket. The structure reveals that no rearrangement in the converter occur upon ATP binding. Based on previously solved myosin structures, our structure suggests that no reversal of the powerstroke occurs during detachment of myosin VI from actin. The structure also reveals novel features of the myosin VI motor that may be important in maintaining the converter conformation during detachment from actin, and other features that may promote rapid rearrangements in the structure following actin detachment that enable hydrolysis of ATP. PMID:18046460
Redetermination of 2-methyl-4-nitropyridine N-oxide

PubMed Central

Peukert, Max; Seichter, Wilhelm; Weber, Edwin

2014-01-01

An improved crystal structure of the title compound, C6H6N2O3, is reported. The structure, previously solved [Li et al. (1987 ▶). Jiegou Huaxue (Chin. J. Struct. Chem.), 6, 20–24] in the orthorhombic space group Pca21 and refined to R = 0.067, has been solved in the orthorhombic space group Pbcm with data of enhanced quality, giving an improved structure (R = 0.0485). The molecule adopts a planar conformation with all atoms lying on a mirror plane. The crystal structure is composed of molecular sheets extending parallel to the ab plane and connected via C—H⋯O contacts involving ring H atoms and O atoms of the N-oxide and nitro groups, while van der Waals forces consolidate the stacking of the layers. PMID:24826136
Representational Flexibility and Problem-Solving Ability in Fraction and Decimal Number Addition: A Structural Model

ERIC Educational Resources Information Center

Deliyianni, Eleni; Gagatsis, Athanasios; Elia, Iliada; Panaoura, Areti

2016-01-01

The aim of this study was to propose and validate a structural model in fraction and decimal number addition, which is founded primarily on a synthesis of major theoretical approaches in the field of representations in Mathematics and also on previous research on the learning of fractions and decimals. The study was conducted among 1,701 primary…
A new crystal form of Aspergillus oryzae catechol oxidase and evaluation of copper site structures in coupled binuclear copper enzymes.

PubMed

Penttinen, Leena; Rutanen, Chiara; Saloheimo, Markku; Kruus, Kristiina; Rouvinen, Juha; Hakulinen, Nina

2018-01-01

Coupled binuclear copper (CBC) enzymes have a conserved type 3 copper site that binds molecular oxygen to oxidize various mono- and diphenolic compounds. In this study, we found a new crystal form of catechol oxidase from Aspergillus oryzae (AoCO4) and solved two new structures from two different crystals at 1.8-Å and at 2.5-Å resolutions. These structures showed different copper site forms (met/deoxy and deoxy) and also differed from the copper site observed in the previously solved structure of AoCO4. We also analysed the electron density maps of all of the 56 CBC enzyme structures available in the protein data bank (PDB) and found that many of the published structures have vague copper sites. Some of the copper sites were then re-refined to find a better fit to the observed electron density. General problems in the refinement of metalloproteins and metal centres are discussed.
Collection of solved problems in physics

NASA Astrophysics Data System (ADS)

Koupilová, ZdeÅka; Mandíková, Dana; Snětinová, Marie

2017-01-01

To solve physics problems is a key ability which students should reach during their physics education. Ten years ago we started to develop a Collection of fully solved problems. The structure of problems' solutions is specially designed to substitute tutor's help during lesson and encourage students to solve at least some parts of a problem independently. Nowadays the database contains about 770 fully solved problems in physics in Czech, more than 100 problems in Polish and more than 140 problems in English. Other problems are still being translated. Except for physics problems, the Collection has also a mathematical part, which contains more than 300 fully solved problems in mathematics. This paper follows the presentation of the Collection of solved problems from previous years and introduces a new interface of the Collection, its enhanced functionality, new topics, newly created interface for teachers, user feedback and plans for future development. The database is placed at the website of the Department of Physics Education, Faculty of Mathematics and Physics, Charles University in Prague, the links are: http://reseneulohy.cz/fyzika (Czech version); http://www.physicstasks.eu/ (English version).
Inhibition of Fatty Acid Synthase in Prostate Cancer by Olristat, a Novel Therapeutic

DTIC Science & Technology

2006-11-01

previous crystallography studies by solving the crystal structure of FAS bound to a cleaved orlistat . These data will provide valuable insight into...timeline of XBP-1 15 processing following orlistat treatment (Figure 3A). Previous studies have demonstrated that inhibition of protein translation with...future drug discovery and design within the FAS pathway. In total, we have made great strides toward understanding the anti-tumor effects of orlistat
Epistemic Game for Answer Making in Learning about Hydrostatics

ERIC Educational Resources Information Center

Chen, Ying; Irving, Paul W.; Sayre, Eleanor C.

2013-01-01

Previous research into problem solving in physics resulted in researchers introducing six epistemic games to describe the organizational structures of locally coherent resources. We present a new epistemic game--the "answer-making epistemic game"--which was identified in this paper through the analysis of interviews carried out to validate a…
Crystal structure of new AsS{sub 2} compound

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bolotina, N. B., E-mail: bolotina@ns.crys.ras.ru; Brazhkin, V. V.; Dyuzheva, T. I.

2013-01-15

AsS{sub 2} single crystals have been obtained for the first time from an As{sub 2}S{sub 3} melt at pressures above 6 GPa and temperatures above 800 K in the As{sub 2}S{sub 3} {yields} AsS + AsS{sub 2} reaction. The monoclinic structure of the new high-pressure phase is solved by X-ray diffraction analysis and compared to the structure of high-pressure AsS phase, which was studied previously.
Nickel binding to NikA: an additional binding site reconciles spectroscopy, calorimetry and crystallography.

PubMed

Addy, Christine; Ohara, Masato; Kawai, Fumihiro; Kidera, Akinori; Ikeguchi, Mitsunori; Fuchigami, Sotaro; Osawa, Masanori; Shimada, Ichio; Park, Sam-Yong; Tame, Jeremy R H; Heddle, Jonathan G

2007-02-01

Intracellular nickel is required by Escherichia coli as a cofactor for a number of enzymes and is necessary for anaerobic respiration. However, high concentrations of nickel are toxic, so both import and export systems have evolved to control the cellular level of the metal. The nik operon in E. coli encodes a nickel-uptake system that includes the periplasmic nickel-binding protein NikA. The crystal structures of wild-type NikA both bound to nickel and in the apo form have been solved previously. The liganded structure appeared to show an unusual interaction between the nickel and the protein in which no direct bonds are formed. The highly unusual nickel coordination suggested by the crystal structure contrasted strongly with earlier X-ray spectroscopic studies. The known nickel-binding site has been probed by extensive mutagenesis and isothermal titration calorimetry and it has been found that even large numbers of disruptive mutations appear to have little effect on the nickel affinity. The crystal structure of a binding-site mutant with nickel bound has been solved and it is found that nickel is bound to two histidine residues at a position distant from the previously characterized binding site. This novel site immediately resolves the conflict between the crystal structures and other biophysical analyses. The physiological relevance of the two binding sites is discussed.
Educating for Creativity and Innovation

ERIC Educational Resources Information Center

Treffinger, Donald J.; Schoonover, Patricia F.; Selby, Edwin C.

2012-01-01

Today, more than ever before, we must all be able to think creatively, manage change, and solve complex, open-ended problems. Education today is different in its structure and practice than it was in any previous generation, not just because of the impact of technology and the Internet, but also because, across the lifespan, every person studies,…
Stress mediates the relationship between past drug addiction and current risky sexual behavior among low income women

PubMed Central

Wu, Z. Helen; Tennen, Howard; Hosain, Monawar; Coman, Emil; Cullum, Jerry; Berenson, Abbey B.

2014-01-01

This study examined the role of stress as a mediator of the relationship between prior drug addiction and current high risk sexual behavior. Eight hundred twenty women aged 18 to 30 years, who received care at community-based family planning clinics were interviewed using the Composite International Diagnostic Interview and the Sexual Risk Behavior Assessment Schedule. They also completed the brief version of the Self-Control Scale as a measure of problem-solving strategies, and measures of recent stressful events, daily hassles, and ongoing chronic stress. Regardless of addiction history, stress exposure during the previous 12 months was associated with risky sexual behavior during the previous 12 months. Structural equation modeling revealed that 12-month stress levels mediated the relationship between past drug addiction and 12-month high risk sexual behaviors, as well as the negative relationship between problem-solving strategies and high risk sexual behaviors. Problem-solving strategies did not moderate the relationship between drug addiction and high risk sexual behaviors. These findings suggest that stress management training may help reduce risky behavior among young, low-income women PMID:24985341
Calculation and word problem-solving skills in primary grades - Impact of cognitive abilities and longitudinal interrelations with task-persistent behaviour.

PubMed

Jõgi, Anna-Liisa; Kikas, Eve

2016-06-01

Primary school math skills form a basis for academic success down the road. Different math skills have different antecedents and there is a reason to believe that more complex math tasks require better self-regulation. The study aimed to investigate longitudinal interrelations of calculation and problem-solving skills, and task-persistent behaviour in Grade 1 and Grade 3, and the effect of non-verbal intelligence, linguistic abilities, and executive functioning on math skills and task persistence. Participants were 864 students (52.3% boys) from 33 different schools in Estonia. Students were tested twice - at the end of Grade1 and at the end of Grade 3. Calculation and problem-solving skills, and teacher-rated task-persistent behaviour were measured at both time points. Non-verbal intelligence, linguistic abilities, and executive functioning were measured in Grade 1. Cross-lagged structural equation modelling indicated that calculation skills depend on previous math skills and linguistic abilities, while problem-solving skills require also non-verbal intelligence, executive functioning, and task persistence. Task-persistent behaviour in Grade 3 was predicted by previous problem-solving skills, linguistic abilities, and executive functioning. Gender and mother's educational level were added as covariates. The findings indicate that math skills and self-regulation are strongly related in primary grades and that solving complex tasks requires executive functioning and task persistence from children. Findings support the idea that instructional practices might benefit from supporting self-regulation in order to gain domain-specific, complex skill achievement. © 2015 The British Psychological Society.
Theoretical thermal conductivity equation for uniform density wood cells

Treesearch

John F. Hunt; Hongmei Gu; Patricia Lebow

2008-01-01

The anisotropy of wood creates a complex problem requiring that analyses be based on fundamental material properties and characteristics of the wood structure to solve heat transfer problems. A two-dimensional finite element model that evaluates the effective thermal conductivity of a wood cell over the full range of moisture contents and porosities was previously...
Solving Fluid Structure Interaction Problems with an Immersed Boundary Method

NASA Technical Reports Server (NTRS)

Barad, Michael F.; Brehm, Christoph; Kiris, Cetin C.

2016-01-01

An immersed boundary method for the compressible Navier-Stokes equations can be used for moving boundary problems as well as fully coupled fluid-structure interaction is presented. The underlying Cartesian immersed boundary method of the Launch Ascent and Vehicle Aerodynamics (LAVA) framework, based on the locally stabilized immersed boundary method previously presented by the authors, is extended to account for unsteady boundary motion and coupled to linear and geometrically nonlinear structural finite element solvers. The approach is validated for moving boundary problems with prescribed body motion and fully coupled fluid structure interaction problems. Keywords: Immersed Boundary Method, Higher-Order Finite Difference Method, Fluid Structure Interaction.
Structural insights into the interaction of human IgG1 with FcγRI: no direct role of glycans in binding

DOE Office of Scientific and Technical Information (OSTI.GOV)

Oganesyan, Vaheh, E-mail: oganesyanv@medimmune.com; Mazor, Yariv; Yang, Chunning

In an effort to identify the critical structural features responsible for the high-affinity interaction of IgG1 Fc with FcγRI, the structure of the corresponding complex was solved at a resolution of 2.4 Å. The three-dimensional structure of a human IgG1 Fc fragment bound to wild-type human FcγRI is reported. The structure of the corresponding complex was solved at a resolution of 2.4 Å using molecular replacement; this is the highest resolution achieved for an unmutated FcγRI molecule. This study highlights the critical structural and functional role played by the second extracellular subdomain of FcγRI. It also explains the long-known majormore » energetic contribution of the Fc ‘LLGG’ motif at positions 234–237, and particularly of Leu235, via a ‘lock-and-key’ mechanism. Finally, a previously held belief is corrected and a differing view is offered on the recently proposed direct role of Fc carbohydrates in the corresponding interaction. Structural evidence is provided that such glycan-related effects are strictly indirect.« less
Varying Use of Conceptual Metaphors across Levels of Expertise in Thermodynamics

NASA Astrophysics Data System (ADS)

Jeppsson, Fredrik; Haglund, Jesper; Amin, Tamer G.

2015-04-01

Many studies have previously focused on how people with different levels of expertise solve physics problems. In early work, focus was on characterising differences between experts and novices and a key finding was the central role that propositionally expressed principles and laws play in expert, but not novice, problem-solving. A more recent line of research has focused on characterising continuity between experts and novices at the level of non-propositional knowledge structures and processes such as image-schemas, imagistic simulation and analogical reasoning. This study contributes to an emerging literature addressing the coordination of both propositional and non-propositional knowledge structures and processes in the development of expertise. Specifically, in this paper, we compare problem-solving across two levels of expertise-undergraduate students of chemistry and Ph.D. students in physical chemistry-identifying differences in how conceptual metaphors (CMs) are used (or not) to coordinate propositional and non-propositional knowledge structures in the context of solving problems on entropy. It is hypothesised that the acquisition of expertise involves learning to coordinate the use of CMs to interpret propositional (linguistic and mathematical) knowledge and apply it to specific problem situations. Moreover, we suggest that with increasing expertise, the use of CMs involves a greater degree of subjective engagement with physical entities and processes. Implications for research on learning and instructional practice are discussed. Third contribution to special issue entitled: Conceptual metaphor and embodied cognition in science learning
An Immersed Boundary Method for Solving the Compressible Navier-Stokes Equations with Fluid Structure Interaction

NASA Technical Reports Server (NTRS)

Brehm, Christoph; Barad, Michael F.; Kiris, Cetin C.

2016-01-01

An immersed boundary method for the compressible Navier-Stokes equation and the additional infrastructure that is needed to solve moving boundary problems and fully coupled fluid-structure interaction is described. All the methods described in this paper were implemented in NASA's LAVA solver framework. The underlying immersed boundary method is based on the locally stabilized immersed boundary method that was previously introduced by the authors. In the present paper this method is extended to account for all aspects that are involved for fluid structure interaction simulations, such as fast geometry queries and stencil computations, the treatment of freshly cleared cells, and the coupling of the computational fluid dynamics solver with a linear structural finite element method. The current approach is validated for moving boundary problems with prescribed body motion and fully coupled fluid structure interaction problems in 2D and 3D. As part of the validation procedure, results from the second AIAA aeroelastic prediction workshop are also presented. The current paper is regarded as a proof of concept study, while more advanced methods for fluid structure interaction are currently being investigated, such as geometric and material nonlinearities, and advanced coupling approaches.

Crystal Structure of Toxoplasma gondii Porphobilinogen Synthase

PubMed Central

Jaffe, Eileen K.; Shanmugam, Dhanasekaran; Gardberg, Anna; Dieterich, Shellie; Sankaran, Banumathi; Stewart, Lance J.; Myler, Peter J.; Roos, David S.

2011-01-01

Porphobilinogen synthase (PBGS) is essential for heme biosynthesis, but the enzyme of the protozoan parasite Toxoplasma gondii (TgPBGS) differs from that of its human host in several important respects, including subcellular localization, metal ion dependence, and quaternary structural dynamics. We have solved the crystal structure of TgPBGS, which contains an octamer in the crystallographic asymmetric unit. Crystallized in the presence of substrate, each active site contains one molecule of the product porphobilinogen. Unlike prior structures containing a substrate-derived heterocycle directly bound to an active site zinc ion, the product-bound TgPBGS active site contains neither zinc nor magnesium, placing in question the common notion that all PBGS enzymes require an active site metal ion. Unlike human PBGS, the TgPBGS octamer contains magnesium ions at the intersections between pro-octamer dimers, which are presumed to function in allosteric regulation. TgPBGS includes N- and C-terminal regions that differ considerably from previously solved crystal structures. In particular, the C-terminal extension found in all apicomplexan PBGS enzymes forms an intersubunit β-sheet, stabilizing a pro-octamer dimer and preventing formation of hexamers that can form in human PBGS. The TgPBGS structure suggests strategies for the development of parasite-selective PBGS inhibitors. PMID:21383008
Stress Mediates the Relationship Between Past Drug Addiction and Current Risky Sexual Behaviour Among Low-income Women.

PubMed

Wu, Z Helen; Tennen, Howard; Hosain, G M Monawar; Coman, Emil; Cullum, Jerry; Berenson, Abbey B

2016-04-01

This study examined the role of stress as a mediator of the relationship between prior drug addiction and current high-risk sexual behaviour. Eight hundred twenty women aged 18 to 30 years, who received care at community-based family planning clinics, were interviewed using the Composite International Diagnostic Interview and the Sexual Risk Behavior Assessment Schedule. They also completed the brief version of the Self-Control Scale as a measure of problem-solving strategies and measures of recent stressful events, daily hassles and ongoing chronic stress. Regardless of addiction history, stress exposure during the previous 12 months was associated with risky sexual behaviour during the previous 12 months. Structural equation modelling revealed that 12-month stress levels mediated the relationship between past drug addiction and 12-month high-risk sexual behaviours, as well as the negative relationship between problem-solving strategies and high-risk sexual behaviours. Problem-solving strategies did not moderate the relationship between drug addiction and high-risk sexual behaviours. These findings suggest that stress management training may help reduce risky behaviour among young, low-income women. Copyright © 2014 John Wiley & Sons, Ltd.
Use of NASTRAN as a teaching aid

NASA Technical Reports Server (NTRS)

Wilkinson, M. T.

1972-01-01

Recent experiences with incorporating NASTRAN as a teaching tool in undergraduate courses was found pedagogically sound. Students with no previous computerized structures background are able to readily grasp the program's logic and begin solving realistic problems rapidly. The educational benefit is significantly enhanced by NASTRAN's plotting feature. However, the cost of operating the level 12 version makes the program difficult to justify.
Fluid-structure interaction with pipe-wall viscoelasticity during water hammer

NASA Astrophysics Data System (ADS)

Keramat, A.; Tijsseling, A. S.; Hou, Q.; Ahmadi, A.

2012-01-01

Fluid-structure interaction (FSI) due to water hammer in a pipeline which has viscoelastic wall behaviour is studied. Appropriate governing equations are derived and numerically solved. In the numerical implementation of the hydraulic and structural equations, viscoelasticity is incorporated using the Kelvin-Voigt mechanical model. The equations are solved by two different approaches, namely the Method of Characteristics-Finite Element Method (MOC-FEM) and full MOC. In both approaches two important effects of FSI in fluid-filled pipes, namely Poisson and junction coupling, are taken into account. The study proposes a more comprehensive model for studying fluid transients in pipelines as compared to previous works, which take into account either FSI or viscoelasticity. To verify the proposed mathematical model and its numerical solutions, the following problems are investigated: axial vibration of a viscoelastic bar subjected to a step uniaxial loading, FSI in an elastic pipe, and hydraulic transients in a pressurised polyethylene pipe without FSI. The results of each case are checked with available exact and experimental results. Then, to study the simultaneous effects of FSI and viscoelasticity, which is the new element of the present research, one problem is solved by the two different numerical approaches. Both numerical methods give the same results, thus confirming the correctness of the solutions.
Graphical models for optimal power flow

DOE PAGES

Dvijotham, Krishnamurthy; Chertkov, Michael; Van Hentenryck, Pascal; ...

2016-09-13

Optimal power flow (OPF) is the central optimization problem in electric power grids. Although solved routinely in the course of power grid operations, it is known to be strongly NP-hard in general, and weakly NP-hard over tree networks. In this paper, we formulate the optimal power flow problem over tree networks as an inference problem over a tree-structured graphical model where the nodal variables are low-dimensional vectors. We adapt the standard dynamic programming algorithm for inference over a tree-structured graphical model to the OPF problem. Combining this with an interval discretization of the nodal variables, we develop an approximation algorithmmore » for the OPF problem. Further, we use techniques from constraint programming (CP) to perform interval computations and adaptive bound propagation to obtain practically efficient algorithms. Compared to previous algorithms that solve OPF with optimality guarantees using convex relaxations, our approach is able to work for arbitrary tree-structured distribution networks and handle mixed-integer optimization problems. Further, it can be implemented in a distributed message-passing fashion that is scalable and is suitable for “smart grid” applications like control of distributed energy resources. In conclusion, numerical evaluations on several benchmark networks show that practical OPF problems can be solved effectively using this approach.« less
Crystal structures of a halophilic archaeal malate synthase from Haloferax volcanii and comparisons with isoforms A and G

PubMed Central

2011-01-01

Background Malate synthase, one of the two enzymes unique to the glyoxylate cycle, is found in all three domains of life, and is crucial to the utilization of two-carbon compounds for net biosynthetic pathways such as gluconeogenesis. In addition to the main isoforms A and G, so named because of their differential expression in E. coli grown on either acetate or glycolate respectively, a third distinct isoform has been identified. These three isoforms differ considerably in size and sequence conservation. The A isoform (MSA) comprises ~530 residues, the G isoform (MSG) is ~730 residues, and this third isoform (MSH-halophilic) is ~430 residues in length. Both isoforms A and G have been structurally characterized in detail, but no structures have been reported for the H isoform which has been found thus far only in members of the halophilic Archaea. Results We have solved the structure of a malate synthase H (MSH) isoform member from Haloferax volcanii in complex with glyoxylate at 2.51 Å resolution, and also as a ternary complex with acetyl-coenzyme A and pyruvate at 1.95 Å. Like the A and G isoforms, MSH is based on a β8/α8 (TIM) barrel. Unlike previously solved malate synthase structures which are all monomeric, this enzyme is found in the native state as a trimer/hexamer equilibrium. Compared to isoforms A and G, MSH displays deletion of an N-terminal domain and a smaller deletion at the C-terminus. The MSH active site is closely superimposable with those of MSA and MSG, with the ternary complex indicating a nucleophilic attack on pyruvate by the enolate intermediate of acetyl-coenzyme A. Conclusions The reported structures of MSH from Haloferax volcanii allow a detailed analysis and comparison with previously solved structures of isoforms A and G. These structural comparisons provide insight into evolutionary relationships among these isoforms, and also indicate that despite the size and sequence variation, and the truncated C-terminal domain of the H isoform, the catalytic mechanism is conserved. Sequence analysis in light of the structure indicates that additional members of isoform H likely exist in the databases but have been misannotated. PMID:21569248
Automated de novo phasing and model building of coiled-coil proteins.

PubMed

Rämisch, Sebastian; Lizatović, Robert; André, Ingemar

2015-03-01

Models generated by de novo structure prediction can be very useful starting points for molecular replacement for systems where suitable structural homologues cannot be readily identified. Protein-protein complexes and de novo-designed proteins are examples of systems that can be challenging to phase. In this study, the potential of de novo models of protein complexes for use as starting points for molecular replacement is investigated. The approach is demonstrated using homomeric coiled-coil proteins, which are excellent model systems for oligomeric systems. Despite the stereotypical fold of coiled coils, initial phase estimation can be difficult and many structures have to be solved with experimental phasing. A method was developed for automatic structure determination of homomeric coiled coils from X-ray diffraction data. In a benchmark set of 24 coiled coils, ranging from dimers to pentamers with resolutions down to 2.5 Å, 22 systems were automatically solved, 11 of which had previously been solved by experimental phasing. The generated models contained 71-103% of the residues present in the deposited structures, had the correct sequence and had free R values that deviated on average by 0.01 from those of the respective reference structures. The electron-density maps were of sufficient quality that only minor manual editing was necessary to produce final structures. The method, named CCsolve, combines methods for de novo structure prediction, initial phase estimation and automated model building into one pipeline. CCsolve is robust against errors in the initial models and can readily be modified to make use of alternative crystallographic software. The results demonstrate the feasibility of de novo phasing of protein-protein complexes, an approach that could also be employed for other small systems beyond coiled coils.
When Best Intentions Go Awry: The Failures of Concrete Representations to Help Solve Probability Word Problems

ERIC Educational Resources Information Center

Beitzel, Brian D.; Staley, Richard K.; DuBois, Nelson F.

2011-01-01

Previous research has cast doubt on the efficacy of utilizing external representations as an aid to solving word problems. The present study replicates previous findings that concrete representations hinder college students' ability to solve probability word problems, and extends those findings to apply to a multimedia instructional context. Our…
Solution structure of a GAAA tetraloop receptor RNA.

PubMed Central

Butcher, S E; Dieckmann, T; Feigon, J

1997-01-01

The GAAA tetraloop receptor is an 11-nucleotide RNA sequence that participates in the tertiary folding of a variety of large catalytic RNAs by providing a specific binding site for GAAA tetraloops. Here we report the solution structure of the isolated tetraloop receptor as solved by multidimensional, heteronuclear magnetic resonance spectroscopy. The internal loop of the tetraloop receptor has three adenosines stacked in a cross-strand or zipper-like fashion. This arrangement produces a high degree of base stacking within the asymmetric internal loop without extrahelical bases or kinking the helix. Additional interactions within the internal loop include a U. U mismatch pair and a G.U wobble pair. A comparison with the crystal structure of the receptor RNA bound to its tetraloop shows that a conformational change has to occur upon tetraloop binding, which is in good agreement with previous biochemical data. A model for an alternative binding site within the receptor is proposed based on the NMR structure, phylogenetic data and previous crystallographic structures of tetraloop interactions. PMID:9405377
Efecto de la difusión y la velocidad en la ionización del átomo de Carbono

NASA Astrophysics Data System (ADS)

Rovira, M. G.; Fontenla, J. M.

The equations of statistical equilibrium for all ionization states of the atom are solved. The effects of diffusion and center of mass velocity are included. In order to estimate the modifications of the ionization curves, they were applied to the Carbon atom. To solve these equations, solar prominences' models obtained in a previous paper were adopted. They were extended to reach a temperature of 1.5 × 106 K and the complete model of the prominence was calculated. Ionization curves for different values of velocity, diffusion and medium models were obtained. The different models represent structures with different densities. Considerable modifications due to these effects are found.
Structure-based discovery and binding site analysis of histamine receptor ligands.

PubMed

Kiss, Róbert; Keserű, György M

2016-12-01

The application of structure-based drug discovery in histamine receptor projects was previously hampered by the lack of experimental structures. The publication of the first X-ray structure of the histamine H1 receptor has been followed by several successful virtual screens and binding site analysis studies of H1-antihistamines. This structure together with several other recently solved aminergic G-protein coupled receptors (GPCRs) enabled the development of more realistic homology models for H2, H3 and H4 receptors. Areas covered: In this paper, the authors review the development of histamine receptor models and their application in drug discovery. Expert opinion: In the authors' opinion, the application of atomistic histamine receptor models has played a significant role in understanding key ligand-receptor interactions as well as in the discovery of novel chemical starting points. The recently solved H1 receptor structure is a major milestone in structure-based drug discovery; however, our analysis also demonstrates that for building H3 and H4 receptor homology models, other GPCRs may be more suitable as templates. For these receptors, the authors envisage that the development of higher quality homology models will significantly contribute to the discovery and optimization of novel H3 and H4 ligands.
The testing effect and analogical problem-solving.

PubMed

Peterson, Daniel J; Wissman, Kathryn T

2018-06-25

Researchers generally agree that retrieval practice of previously learned material facilitates subsequent recall of same material, a phenomenon known as the testing effect. There is debate, however, about when such benefits transfer to related (though not identical) material. The current study examines the phenomenon of transfer in the domain of analogical problem-solving. In Experiments 1 and 2, learners were presented a source text describing a problem and solution to read which was subsequently either restudied or recalled. Following a short (Experiment 1) or long (Experiment 2) delay, learners were given a new target text and asked to solve a problem. The two texts shared a common structure such that the provided solution for the source text could be applied to solve the problem in the target text. In a combined analysis of both experiments, learners in the retrieval practice condition were more successful at solving the problem than those in the restudy condition. Experiment 3 explored the degree to which retrieval practice promotes cued versus spontaneous transfer by manipulating whether participants were provided with an explicit hint that the source and target texts were related. Results revealed no effect of retrieval practice.
Solving large-scale dynamic systems using band Lanczos method in Rockwell NASTRAN on CRAY X-MP

NASA Technical Reports Server (NTRS)

Gupta, V. K.; Zillmer, S. D.; Allison, R. E.

1986-01-01

The improved cost effectiveness using better models, more accurate and faster algorithms and large scale computing offers more representative dynamic analyses. The band Lanczos eigen-solution method was implemented in Rockwell's version of 1984 COSMIC-released NASTRAN finite element structural analysis computer program to effectively solve for structural vibration modes including those of large complex systems exceeding 10,000 degrees of freedom. The Lanczos vectors were re-orthogonalized locally using the Lanczos Method and globally using the modified Gram-Schmidt method for sweeping rigid-body modes and previously generated modes and Lanczos vectors. The truncated band matrix was solved for vibration frequencies and mode shapes using Givens rotations. Numerical examples are included to demonstrate the cost effectiveness and accuracy of the method as implemented in ROCKWELL NASTRAN. The CRAY version is based on RPK's COSMIC/NASTRAN. The band Lanczos method was more reliable and accurate and converged faster than the single vector Lanczos Method. The band Lanczos method was comparable to the subspace iteration method which was a block version of the inverse power method. However, the subspace matrix tended to be fully populated in the case of subspace iteration and not as sparse as a band matrix.
Non-linear quantitative structure-activity relationship for adenine derivatives as competitive inhibitors of adenosine deaminase

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sadat Hayatshahi, Sayyed Hamed; Abdolmaleki, Parviz; Safarian, Shahrokh

2005-12-16

Logistic regression and artificial neural networks have been developed as two non-linear models to establish quantitative structure-activity relationships between structural descriptors and biochemical activity of adenosine based competitive inhibitors, toward adenosine deaminase. The training set included 24 compounds with known k {sub i} values. The models were trained to solve two-class problems. Unlike the previous work in which multiple linear regression was used, the highest of positive charge on the molecules was recognized to be in close relation with their inhibition activity, while the electric charge on atom N1 of adenosine was found to be a poor descriptor. Consequently, themore » previously developed equation was improved and the newly formed one could predict the class of 91.66% of compounds correctly. Also optimized 2-3-1 and 3-4-1 neural networks could increase this rate to 95.83%.« less
Development of a preprototype times wastewater recovery subsystem

NASA Technical Reports Server (NTRS)

Roebelen, G. J., Jr.; Dehner, G. F.

1982-01-01

A three-man wastewater recovery preprototype subsystem using a hollow fiber membrane evaporator with a thermoelectric heat pump to provide efficient potable water recovery from wastewater on extended duration space flights was designed, fabricated, and tested at one-gravity. Low power, compactness and gravity insensitive operation are featured in this vacuum distillation subsystem. The tubular hollow fiber elements provide positive liquid/gas phase control with no moving parts, and provide structural integrity, improving on previous flat sheet membrane designs. A thermoelectric heat pump provides latent energy recovery. Application and integration of these key elements solved problems inherent in all previous reclamation subsystem designs.
The crystal structure of dihydrodipicolinate synthase from Escherichia coli with bound pyruvate and succinic acid semialdehyde: unambiguous resolution of the stereochemistry of the condensation product.

PubMed

Boughton, Berin A; Dobson, Renwick C J; Hutton, Craig A

2012-08-01

The crystal structure of Escherichia coli dihydrodipicolinate synthase with pyruvate and substrate analogue succinic acid semialdehyde condensed with the active site lysine-161 was solved to a resolution of 2.3 Å. Comparative analysis to a previously reported structure both resolves the configuration at the aldol addition center, where the final addition product clearly displays the (S)-configuration, and the final conformation of the adduct within the active site. Direct comparison to two other crystal structures found in the Protein Data Bank, 1YXC, and 3DU0, demonstrates significant similarity between the active site residues of these structures. Copyright © 2012 Wiley Periodicals, Inc.
A weak-coupling immersed boundary method for fluid-structure interaction with low density ratio of solid to fluid

NASA Astrophysics Data System (ADS)

Kim, Woojin; Lee, Injae; Choi, Haecheon

2018-04-01

We present a weak-coupling approach for fluid-structure interaction with low density ratio (ρ) of solid to fluid. For accurate and stable solutions, we introduce predictors, an explicit two-step method and the implicit Euler method, to obtain provisional velocity and position of fluid-structure interface at each time step, respectively. The incompressible Navier-Stokes equations, together with these provisional velocity and position at the fluid-structure interface, are solved in an Eulerian coordinate using an immersed-boundary finite-volume method on a staggered mesh. The dynamic equation of an elastic solid-body motion, together with the hydrodynamic force at the provisional position of the interface, is solved in a Lagrangian coordinate using a finite element method. Each governing equation for fluid and structure is implicitly solved using second-order time integrators. The overall second-order temporal accuracy is preserved even with the use of lower-order predictors. A linear stability analysis is also conducted for an ideal case to find the optimal explicit two-step method that provides stable solutions down to the lowest density ratio. With the present weak coupling, three different fluid-structure interaction problems were simulated: flows around an elastically mounted rigid circular cylinder, an elastic beam attached to the base of a stationary circular cylinder, and a flexible plate, respectively. The lowest density ratios providing stable solutions are searched for the first two problems and they are much lower than 1 (ρmin = 0.21 and 0.31, respectively). The simulation results agree well with those from strong coupling suggested here and also from previous numerical and experimental studies, indicating the efficiency and accuracy of the present weak coupling.
Matrix metalloproteinase-10 (MMP-10) interaction with tissue inhibitors of metalloproteinases TIMP-1 and TIMP-2: binding studies and crystal structure.

PubMed

Batra, Jyotica; Robinson, Jessica; Soares, Alexei S; Fields, Alan P; Radisky, Derek C; Radisky, Evette S

2012-05-04

Matrix metalloproteinase 10 (MMP-10, stromelysin-2) is a secreted metalloproteinase with functions in skeletal development, wound healing, and vascular remodeling; its overexpression is also implicated in lung tumorigenesis and tumor progression. To understand the regulation of MMP-10 by tissue inhibitors of metalloproteinases (TIMPs), we have assessed equilibrium inhibition constants (K(i)) of putative physiological inhibitors TIMP-1 and TIMP-2 for the active catalytic domain of human MMP-10 (MMP-10cd) using multiple kinetic approaches. We find that TIMP-1 inhibits the MMP-10cd with a K(i) of 1.1 × 10(-9) M; this interaction is 10-fold weaker than the inhibition of the similar MMP-3 (stromelysin-1) catalytic domain (MMP-3cd) by TIMP-1. TIMP-2 inhibits the MMP-10cd with a K(i) of 5.8 × 10(-9) M, which is again 10-fold weaker than the inhibition of MMP-3cd by this inhibitor (K(i) = 5.5 × 10(-10) M). We solved the x-ray crystal structure of TIMP-1 bound to the MMP-10cd at 1.9 Å resolution; the structure was solved by molecular replacement and refined with an R-factor of 0.215 (R(free) = 0.266). Comparing our structure of MMP-10cd·TIMP-1 with the previously solved structure of MMP-3cd·TIMP-1 (Protein Data Bank entry 1UEA), we see substantial differences at the binding interface that provide insight into the differential binding of stromelysin family members to TIMP-1. This structural information may ultimately assist in the design of more selective TIMP-based inhibitors tailored for specificity toward individual members of the stromelysin family, with potential therapeutic applications.
Evaluation of Colorado Learning Attitudes about Science Survey

NASA Astrophysics Data System (ADS)

Douglas, K. A.; Yale, M. S.; Bennett, D. E.; Haugan, M. P.; Bryan, L. A.

2014-12-01

The Colorado Learning Attitudes about Science Survey (CLASS) is a widely used instrument designed to measure student attitudes toward physics and learning physics. Previous research revealed a fairly complex factor structure. In this study, exploratory and confirmatory factor analyses were conducted on data from an undergraduate introductory physics course (n =3844 ) to determine whether a more parsimonious factor structure exists. Exploratory factor analysis results indicate that many of the items from the original CLASS have poor psychometric properties and could not be used in a revised factor structure. The cross validation showed acceptable fit statistics for a three factor model found in the exploratory factor analysis. This research suggests that a more optimum measurement of students' attitudes about physics and learning physics is obtained with a 15-item instrument, which describes the factors of personal application, personal effort, and problem solving. The proposed revised version of the CLASS offers researchers the opportunity to test a shortened version of the instrument that may be able to provide information about students' attitudes in the areas of personal application of physics, personal effort in a physics course, and approaches to problem solving.
Alteration of the α1β2/α2β1 subunit interface contributes to the increased hemoglobin-oxygen affinity of high-altitude deer mice

PubMed Central

Inoguchi, Noriko; Mizuno, Nobuhiro; Baba, Seiki; Kumasaka, Takashi; Natarajan, Chandrasekhar; Storz, Jay F.

2017-01-01

Background Deer mice (Peromyscus maniculatus) that are native to high altitudes in the Rocky Mountains have evolved hemoglobins with an increased oxygen-binding affinity relative to those of lowland conspecifics. To elucidate the molecular mechanisms responsible for the evolved increase in hemoglobin-oxygen affinity, the crystal structure of the highland hemoglobin variant was solved and compared with the previously reported structure for the lowland variant. Results Highland hemoglobin yielded at least two crystal types, in which the longest axes were 507 and 230 Å. Using the smaller unit cell crystal, the structure was solved at 2.2 Å resolution. The asymmetric unit contained two tetrameric hemoglobin molecules. Conclusions The analyses revealed that αPro50 in the highland hemoglobin variant promoted a stable interaction between αHis45 and heme that was not seen in the αHis50 lowland variant. The αPro50 mutation also altered the nature of atomic contacts at the α1β2/α2β1 intersubunit interfaces. These results demonstrate how affinity-altering changes in intersubunit interactions can be produced by mutations at structurally remote sites. PMID:28362841

Alteration of the α1β2/α2β1 subunit interface contributes to the increased hemoglobin-oxygen affinity of high-altitude deer mice

DOE Office of Scientific and Technical Information (OSTI.GOV)

Inoguchi, Noriko; Mizuno, Nobuhiro; Baba, Seiki

2017-03-31

Deer mice (Peromyscus maniculatus) that are native to high altitudes in the Rocky Mountains have evolved hemoglobins with an increased oxygen-binding affinity relative to those of lowland conspecifics. To elucidate the molecular mechanisms responsible for the evolved increase in hemoglobin-oxygen affinity, the crystal structure of the highland hemoglobin variant was solved and compared with the previously reported structure for the lowland variant. Highland hemoglobin yielded at least two crystal types, in which the longest axes were 507 and 230 Å. Using the smaller unit cell crystal, the structure was solved at 2.2 Å resolution. The asymmetric unit contained two tetramericmore » hemoglobin molecules. The analyses revealed that αPro50 in the highland hemoglobin variant promoted a stable interaction between αHis45 and heme that was not seen in the αHis50 lowland variant. The αPro50 mutation also altered the nature of atomic contacts at the α1β2/α2β1 intersubunit interfaces. These results demonstrate how affinity-altering changes in intersubunit interactions can be produced by mutations at structurally remote sites.« less
Numerical simulation of two-dimensional heat transfer in composite bodies with application to de-icing of aircraft components. Ph.D. Thesis. Final Report

NASA Technical Reports Server (NTRS)

Chao, D. F. K.

1983-01-01

Transient, numerical simulations of the de-icing of composite aircraft components by electrothermal heating were performed for a two dimensional rectangular geometry. The implicit Crank-Nicolson formulation was used to insure stability of the finite-difference heat conduction equations and the phase change in the ice layer was simulated using the Enthalpy method. The Gauss-Seidel point iterative method was used to solve the system of difference equations. Numerical solutions illustrating de-icer performance for various composite aircraft structures and environmental conditions are presented. Comparisons are made with previous studies. The simulation can also be used to solve a variety of other heat conduction problems involving composite bodies.
Self-Affirmation Improves Problem-Solving under Stress

PubMed Central

Creswell, J. David; Dutcher, Janine M.; Klein, William M. P.; Harris, Peter R.; Levine, John M.

2013-01-01

High levels of acute and chronic stress are known to impair problem-solving and creativity on a broad range of tasks. Despite this evidence, we know little about protective factors for mitigating the deleterious effects of stress on problem-solving. Building on previous research showing that self-affirmation can buffer stress, we tested whether an experimental manipulation of self-affirmation improves problem-solving performance in chronically stressed participants. Eighty undergraduates indicated their perceived chronic stress over the previous month and were randomly assigned to either a self-affirmation or control condition. They then completed 30 difficult remote associate problem-solving items under time pressure in front of an evaluator. Results showed that self-affirmation improved problem-solving performance in underperforming chronically stressed individuals. This research suggests a novel means for boosting problem-solving under stress and may have important implications for understanding how self-affirmation boosts academic achievement in school settings. PMID:23658751
Self-affirmation improves problem-solving under stress.

PubMed

Creswell, J David; Dutcher, Janine M; Klein, William M P; Harris, Peter R; Levine, John M

2013-01-01

High levels of acute and chronic stress are known to impair problem-solving and creativity on a broad range of tasks. Despite this evidence, we know little about protective factors for mitigating the deleterious effects of stress on problem-solving. Building on previous research showing that self-affirmation can buffer stress, we tested whether an experimental manipulation of self-affirmation improves problem-solving performance in chronically stressed participants. Eighty undergraduates indicated their perceived chronic stress over the previous month and were randomly assigned to either a self-affirmation or control condition. They then completed 30 difficult remote associate problem-solving items under time pressure in front of an evaluator. Results showed that self-affirmation improved problem-solving performance in underperforming chronically stressed individuals. This research suggests a novel means for boosting problem-solving under stress and may have important implications for understanding how self-affirmation boosts academic achievement in school settings.
Transformations of the dislocation structure of nickel single crystals

NASA Astrophysics Data System (ADS)

Alfyorova, E. A.; Lychagin, D. V.; Lychagina, L. L.; Tsvetkov, N. A.

2017-12-01

A relationship between different-scale deformations of crystals has not been established yet. In order to solve this task, we investigate the development of a deformation relief and dislocation structure in nickel single crystals after deformation. The stress tensor, crystallography, and geometry of specimens affect the organization of some shear along corresponding systems of sliding. The organization of shear shows some features of self-organization. It is associated with the self-organization in the dislocation subsystem analyzed previously. The effectiveness of reducing external and internal stresses determines patterns of deformation processes at different scale levels.
Equilibrium structure of solar magnetic flux tubes: Energy transport with multistream radiative transfer

NASA Technical Reports Server (NTRS)

Hasan, S. S.; Kalkofen, W.

1994-01-01

We examine the equilibrium structure of vertical intense magnetic flux tubes on the Sun. Assuming cylindrical geometry, we solve the magnetohydrostatic equations in the thin flux-tube approximation, allowing for energy transport by radiation and convection. The radiative transfer equation is solved in the six-stream approximation, assuming gray opacity and local thermodynamic equilibrium. This constitutes a significant improvement over a previous study, in which the transfer was solved using the multidimensional generalization of the Eddington approximation. Convection in the flux tube is treated using mixing-length theory, with an additional parameter alpha, characterizing the suppression of convective energy transport in the tube by the strong magnetic field. The equations are solved using the method of partial linearization. We present results for tubes with different values of the magnetic field strength and radius at a fixed depth in the atmosphere. In general, we find that, at equal geometric heights, the temperature on the tube axis, compared to the ambient medium, is higher in the photosphere and lower in the convection zone, with the difference becoming larger for thicker tubes. At equal optical depths the tubes are generally hotter than their surroundings. The results are comparatively insensitive to alpha but depend upon whether radiative and convective energy transport operate simultaneously or in separate layers. A comparison of our results with semiempirical models shows that the temperature and intensity contrast are in broad agreement. However, the field strengths of the flux-tube models are somewhat lower than the values inferred from observations.
Gravitational field calculations on a dynamic lattice by distributed computing.

NASA Astrophysics Data System (ADS)

Mähönen, P.; Punkka, V.

A new method of calculating numerically time evolution of a gravitational field in general relativity is introduced. Vierbein (tetrad) formalism, dynamic lattice and massively parallelized computation are suggested as they are expected to speed up the calculations considerably and facilitate the solution of problems previously considered too hard to be solved, such as the time evolution of a system consisting of two or more black holes or the structure of worm holes.
Gravitation Field Calculations on a Dynamic Lattice by Distributed Computing

NASA Astrophysics Data System (ADS)

Mähönen, Petri; Punkka, Veikko

A new method of calculating numerically time evolution of a gravitational field in General Relatity is introduced. Vierbein (tetrad) formalism, dynamic lattice and massively parallelized computation are suggested as they are expected to speed up the calculations considerably and facilitate the solution of problems previously considered too hard to be solved, such as the time evolution of a system consisting of two or more black holes or the structure of worm holes.
The politics of insight

PubMed Central

Salvi, Carola; Cristofori, Irene; Grafman, Jordan; Beeman, Mark

2016-01-01

Previous studies showed that liberals and conservatives differ in cognitive style. Liberals are more flexible, and tolerant of complexity and novelty, whereas conservatives are more rigid, are more resistant to change, and prefer clear answers. We administered a set of compound remote associate problems, a task extensively used to differentiate problem-solving styles (via insight or analysis). Using this task, several researches have proven that self-reports, which differentiate between insight and analytic problem-solving, are reliable and are associated with two different neural circuits. In our research we found that participants self-identifying with distinct political orientations demonstrated differences in problem-solving strategy. Liberals solved significantly more problems via insight instead of in a step-by-step analytic fashion. Our findings extend previous observations that self-identified political orientations reflect differences in cognitive styles. More specifically, we show that type of political orientation is associated with problem-solving strategy. The data converge with previous neurobehavioural and cognitive studies indicating a link between cognitive style and the psychological mechanisms that mediate political beliefs. PMID:26810954
The politics of insight.

PubMed

Salvi, Carola; Cristofori, Irene; Grafman, Jordan; Beeman, Mark

2016-01-01

Previous studies showed that liberals and conservatives differ in cognitive style. Liberals are more flexible, and tolerant of complexity and novelty, whereas conservatives are more rigid, are more resistant to change, and prefer clear answers. We administered a set of compound remote associate problems, a task extensively used to differentiate problem-solving styles (via insight or analysis). Using this task, several researches have proven that self-reports, which differentiate between insight and analytic problem-solving, are reliable and are associated with two different neural circuits. In our research we found that participants self-identifying with distinct political orientations demonstrated differences in problem-solving strategy. Liberals solved significantly more problems via insight instead of in a step-by-step analytic fashion. Our findings extend previous observations that self-identified political orientations reflect differences in cognitive styles. More specifically, we show that type of political orientation is associated with problem-solving strategy. The data converge with previous neurobehavioural and cognitive studies indicating a link between cognitive style and the psychological mechanisms that mediate political beliefs.
Nonlinear calculations of the time evolution of black hole accretion disks

NASA Technical Reports Server (NTRS)

Luo, C.

1994-01-01

Based on previous works on black hole accretion disks, I continue to explore the disk dynamics using the finite difference method to solve the highly nonlinear problem of time-dependent alpha disk equations. Here a radially zoned model is used to develop a computational scheme in order to accommodate functional dependence of the viscosity parameter alpha on the disk scale height and/or surface density. This work is based on the author's previous work on the steady disk structure and the linear analysis of disk dynamics to try to apply to x-ray emissions from black candidates (i.e., multiple-state spectra, instabilities, QPO's, etc.).
Double-flow focused liquid injector for efficient serial femtosecond crystallography

DOE Office of Scientific and Technical Information (OSTI.GOV)

Oberthuer, Dominik; Knoška, Juraj; Wiedorn, Max O.

Serial femtosecond crystallography requires reliable and efficient delivery of fresh crystals across the beam of an X-ray free-electron laser over the course of an experiment. We introduce a double-flow focusing nozzle to meet this challenge, with significantly reduced sample consumption, while improving jet stability over previous generations of nozzles. We demonstrate its use to determine the first room-temperature structure of RNA polymerase II at high resolution, revealing new structural details. Furthermore, the double flow-focusing nozzles were successfully tested with three other protein samples and the first room temperature structure of an extradiol ring-cleaving dioxygenase was solved by utilizing the improvedmore » operation and characteristics of these devices.« less
Double-flow focused liquid injector for efficient serial femtosecond crystallography

PubMed Central

Oberthuer, Dominik; Knoška, Juraj; Wiedorn, Max O.; Beyerlein, Kenneth R.; Bushnell, David A.; Kovaleva, Elena G.; Heymann, Michael; Gumprecht, Lars; Kirian, Richard A.; Barty, Anton; Mariani, Valerio; Tolstikova, Aleksandra; Adriano, Luigi; Awel, Salah; Barthelmess, Miriam; Dörner, Katerina; Xavier, P. Lourdu; Yefanov, Oleksandr; James, Daniel R.; Nelson, Garrett; Wang, Dingjie; Calvey, George; Chen, Yujie; Schmidt, Andrea; Szczepek, Michael; Frielingsdorf, Stefan; Lenz, Oliver; Snell, Edward; Robinson, Philip J.; Šarler, Božidar; Belšak, Grega; Maček, Marjan; Wilde, Fabian; Aquila, Andrew; Boutet, Sébastien; Liang, Mengning; Hunter, Mark S.; Scheerer, Patrick; Lipscomb, John D.; Weierstall, Uwe; Kornberg, Roger D.; Spence, John C. H.; Pollack, Lois; Chapman, Henry N.; Bajt, Saša

2017-01-01

Serial femtosecond crystallography requires reliable and efficient delivery of fresh crystals across the beam of an X-ray free-electron laser over the course of an experiment. We introduce a double-flow focusing nozzle to meet this challenge, with significantly reduced sample consumption, while improving jet stability over previous generations of nozzles. We demonstrate its use to determine the first room-temperature structure of RNA polymerase II at high resolution, revealing new structural details. Moreover, the double flow-focusing nozzles were successfully tested with three other protein samples and the first room temperature structure of an extradiol ring-cleaving dioxygenase was solved by utilizing the improved operation and characteristics of these devices. PMID:28300169
Double-flow focused liquid injector for efficient serial femtosecond crystallography

DOE PAGES

Oberthuer, Dominik; Knoška, Juraj; Wiedorn, Max O.; ...

2017-03-16

Serial femtosecond crystallography requires reliable and efficient delivery of fresh crystals across the beam of an X-ray free-electron laser over the course of an experiment. We introduce a double-flow focusing nozzle to meet this challenge, with significantly reduced sample consumption, while improving jet stability over previous generations of nozzles. We demonstrate its use to determine the first room-temperature structure of RNA polymerase II at high resolution, revealing new structural details. Furthermore, the double flow-focusing nozzles were successfully tested with three other protein samples and the first room temperature structure of an extradiol ring-cleaving dioxygenase was solved by utilizing the improvedmore » operation and characteristics of these devices.« less
Use cases and DEMO: aligning functional features of ICT-infrastructure to business processes.

PubMed

Maij, E; Toussaint, P J; Kalshoven, M; Poerschke, M; Zwetsloot-Schonk, J H M

2002-11-12

The proper alignment of functional features of the ICT-infrastructure to business processes is a major challenge in health care organisations. This alignment takes into account that the organisational structure not only shapes the ICT-infrastructure, but that the inverse also holds. To solve the alignment problem, relevant features of the ICT-infrastructure should be derived from the organisational structure and the influence of this envisaged ICT to the work practices should be pointed out. The objective of our study was to develop a method to solve this alignment problem. In a previous study we demonstrated the appropriateness of the business process modelling methodology Dynamic Essential Modelling of Organizations (DEMO). A proven and widely used modelling language for expressing functional features is Unified Modelling Language (UML). In the context of a specific case study at the University Medical Centre Utrecht in the Netherlands we investigated if the combined use of DEMO and UML could solve the alignment problem. The study demonstrated that the DEMO models were suited as a starting point in deriving system functionality by using the use case concept of UML. Further, the case study demonstrated that in using this approach for the alignment problem, insight is gained into the mutual influence of ICT-infrastructure and organisation structure: (a) specification of independent, re-usable components-as a set of related functionalities-is realised, and (b) a helpful representation of the current and future work practice is provided for in relation to the envisaged ICT support.
Solving the inverse scattering problem in reflection-mode dynamic speckle-field phase microscopy (Conference Presentation)

NASA Astrophysics Data System (ADS)

Zhou, Renjie; So, Peter T. C.; Yaqoob, Zahid; Jin, Di; Hosseini, Poorya; Kuang, Cuifang; Singh, Vijay Raj; Kim, Yang-Hyo; Dasari, Ramachandra R.

2017-02-01

Most of the quantitative phase microscopy systems are unable to provide depth-resolved information for measuring complex biological structures. Optical diffraction tomography provides a non-trivial solution to it by 3D reconstructing the object with multiple measurements through different ways of realization. Previously, our lab developed a reflection-mode dynamic speckle-field phase microscopy (DSPM) technique, which can be used to perform depth resolved measurements in a single shot. Thus, this system is suitable for measuring dynamics in a layer of interest in the sample. DSPM can be also used for tomographic imaging, which promises to solve the long-existing "missing cone" problem in 3D imaging. However, the 3D imaging theory for this type of system has not been developed in the literature. Recently, we have developed an inverse scattering model to rigorously describe the imaging physics in DSPM. Our model is based on the diffraction tomography theory and the speckle statistics. Using our model, we first precisely calculated the defocus response and the depth resolution in our system. Then, we further calculated the 3D coherence transfer function to link the 3D object structural information with the axially scanned imaging data. From this transfer function, we found that in the reflection mode excellent sectioning effect exists in the low lateral spatial frequency region, thus allowing us to solve the "missing cone" problem. Currently, we are working on using this coherence transfer function to reconstruct layered structures and complex cells.
Effects of domain-specific exercise load on speed and accuracy of a domain-specific perceptual-cognitive task.

PubMed

Schapschröer, M; Baker, J; Schorer, J

2016-08-01

In the context of perceptual-cognitive expertise it is important to know whether physiological loads influence perceptual-cognitive performance. This study examined whether a handball specific physical exercise load influenced participants' speed and accuracy in a flicker task. At rest and during a specific interval exercise of 86.5-90% HRmax, 35 participants (experts: n=8, advanced: n=13, novices, n=14) performed a handball specific flicker task with two types of patterns (structured and unstructured). For reaction time, results revealed moderate effect sizes for group, with experts reacting faster than advanced and advanced reacting faster than novices, and for structure, with structured videos being performed faster than unstructured ones. A significant interaction for structure×group was also found, with experts and advanced players faster for structured videos, and novices faster for unstructured videos. For accuracy, significant main effects were found for structure with structured videos solved more accurately. A significant interaction for structure×group was revealed, with experts and advanced more accurate for structured scenes and novices more accurate for unstructured scenes. A significant interaction was also found for condition×structure; at rest, unstructured and structured scenes were performed with the same accuracy while under physical exercise, structured scenes were solved more accurately. No other interactions were found. These results were somewhat surprising given previous work in this area, although the impact of a specific physical exercise on a specific perceptual-cognitive task may be different from those tested generally. Copyright © 2016 Elsevier B.V. All rights reserved.
Exploiting Symmetry on Parallel Architectures.

NASA Astrophysics Data System (ADS)

Stiller, Lewis Benjamin

1995-01-01

This thesis describes techniques for the design of parallel programs that solve well-structured problems with inherent symmetry. Part I demonstrates the reduction of such problems to generalized matrix multiplication by a group-equivariant matrix. Fast techniques for this multiplication are described, including factorization, orbit decomposition, and Fourier transforms over finite groups. Our algorithms entail interaction between two symmetry groups: one arising at the software level from the problem's symmetry and the other arising at the hardware level from the processors' communication network. Part II illustrates the applicability of our symmetry -exploitation techniques by presenting a series of case studies of the design and implementation of parallel programs. First, a parallel program that solves chess endgames by factorization of an associated dihedral group-equivariant matrix is described. This code runs faster than previous serial programs, and discovered it a number of results. Second, parallel algorithms for Fourier transforms for finite groups are developed, and preliminary parallel implementations for group transforms of dihedral and of symmetric groups are described. Applications in learning, vision, pattern recognition, and statistics are proposed. Third, parallel implementations solving several computational science problems are described, including the direct n-body problem, convolutions arising from molecular biology, and some communication primitives such as broadcast and reduce. Some of our implementations ran orders of magnitude faster than previous techniques, and were used in the investigation of various physical phenomena.
Layout optimization using the homogenization method

NASA Technical Reports Server (NTRS)

Suzuki, Katsuyuki; Kikuchi, Noboru

1993-01-01

A generalized layout problem involving sizing, shape, and topology optimization is solved by using the homogenization method for three-dimensional linearly elastic shell structures in order to seek a possibility of establishment of an integrated design system of automotive car bodies, as an extension of the previous work by Bendsoe and Kikuchi. A formulation of a three-dimensional homogenized shell, a solution algorithm, and several examples of computing the optimum layout are presented in this first part of the two articles.
Unrewarded Object Combinations in Captive Parrots

PubMed Central

Auersperg, Alice Marie Isabel; Oswald, Natalie; Domanegg, Markus; Gajdon, Gyula Koppany; Bugnyar, Thomas

2015-01-01

In primates, complex object combinations during play are often regarded as precursors of functional behavior. Here we investigate combinatory behaviors during unrewarded object manipulation in seven parrot species, including kea, African grey parrots and Goffin cockatoos, three species previously used as model species for technical problem solving. We further examine a habitually tool using species, the black palm cockatoo. Moreover, we incorporate three neotropical species, the yellow- and the black-billed Amazon and the burrowing parakeet. Paralleling previous studies on primates and corvids, free object-object combinations and complex object-substrate combinations such as inserting objects into tubes/holes or stacking rings onto poles prevailed in the species previously linked to advanced physical cognition and tool use. In addition, free object-object combinations were intrinsically structured in Goffin cockatoos and in kea. PMID:25984564

Problem solving in great apes (Pan paniscus, Pan troglodytes, Gorilla gorilla, and Pongo abelii): the effect of visual feedback.

PubMed

Völter, Christoph J; Call, Josep

2012-09-01

What kind of information animals use when solving problems is a controversial topic. Previous research suggests that, in some situations, great apes prefer to use causally relevant cues over arbitrary ones. To further examine to what extent great apes are able to use information about causal relations, we presented three different puzzle box problems to the four nonhuman great ape species. Of primary interest here was a comparison between one group of apes that received visual access to the functional mechanisms of the puzzle boxes and one group that did not. Apes' performance in the first two, less complex puzzle boxes revealed that they are able to solve such problems by means of trial-and-error learning, requiring no information about the causal structure of the problem. However, visual inspection of the functional mechanisms of the puzzle boxes reduced the amount of time needed to solve the problems. In the case of the most complex problem, which required the use of a crank, visual feedback about what happened when the handle of the crank was turned was necessary for the apes to solve the task. Once the solution was acquired, however, visual feedback was no longer required. We conclude that visual feedback about the consequences of their actions helps great apes to solve complex problems. As the crank task matches the basic requirements of vertical string pulling in birds, the present results are discussed in light of recent findings with corvids.
X-ray crystallographic analysis of adipocyte fatty acid binding protein (aP2) modified with 4-hydroxy-2-nonenal

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hellberg, Kristina; Grimsrud, Paul A.; Kruse, Andrew C.

2012-07-11

Fatty acid binding proteins (FABP) have been characterized as facilitating the intracellular solubilization and transport of long-chain fatty acyl carboxylates via noncovalent interactions. More recent work has shown that the adipocyte FABP is also covalently modified in vivo on Cys117 with 4-hydroxy-2-nonenal (4-HNE), a bioactive aldehyde linked to oxidative stress and inflammation. To evaluate 4-HNE binding and modification, the crystal structures of adipocyte FABP covalently and noncovalently bound to 4-HNE have been solved to 1.9 {angstrom} and 2.3 {angstrom} resolution, respectively. While the 4-HNE in the noncovalently modified protein is coordinated similarly to a carboxylate of a fatty acid, themore » covalent form show a novel coordination through a water molecule at the polar end of the lipid. Other defining features between the two structures with 4-HNE and previously solved structures of the protein include a peptide flip between residues Ala36 and Lys37 and the rotation of the side chain of Phe57 into its closed conformation. Representing the first structure of an endogenous target protein covalently modified by 4-HNE, these results define a new class of in vivo ligands for FABPs and extend their physiological substrates to include bioactive aldehydes.« less
Crystallography of waxes - an electron diffraction study of refined and natural products

NASA Astrophysics Data System (ADS)

Dorset, Douglas L.

1997-02-01

The crystal structure of four waxes has been investigated by electron crystallography. Two of these waxes, including a refined petroleum product (Gulfwax) and a material from lignite (montan wax), form well ordered crystals and their structure could be solved quantitatively from the observed 0022-3727/30/3/018/img1 diffraction patterns. As also found previously for simpler binary n-paraffin solid solutions, the average structure resembles that of a pure paraffin (e.g. n-0022-3727/30/3/018/img2) but with a Gaussian distribution of atomic occupancies near the chain ends to account for the statistical distribution of chain lengths within a lamella. Two other waxes from living organisms, South African bee honeycomb and the leaves of the Brazilian carnauba palm, are much less ordered, even though they share the same methylene subcell packing of the most crystalline parts of the previous materials. It appears that these waxes cannot fully separate into distinct lamellae, perhaps due to the presence of very long `tie' molecules, and are therefore `frustrated' crystal structures.
A general strategy to solve the phase problem in RNA crystallography

PubMed Central

Keel, Amanda Y.; Rambo, Robert P.; Batey, Robert T.; Kieft, Jeffrey S.

2007-01-01

SUMMARY X-ray crystallography of biologically important RNA molecules has been hampered by technical challenges, including finding a heavy-atom derivative to obtain high-quality experimental phase information. Existing techniques have drawbacks, severely limiting the rate at which important new structures are solved. To address this need, we have developed a reliable means to localize heavy atoms specifically to virtually any RNA. By solving the crystal structures of thirteen variants of the G·U wobble pair cation binding motif we have identified an optimal version that when inserted into an RNA helix introduces a high-occupancy cation binding site suitable for phasing. This “directed soaking” strategy can be integrated fully into existing RNA and crystallography methods, potentially increasing the rate at which important structures are solved and facilitating routine solving of structures using Cu-Kα radiation. The success of this method has been proven in that it has already been used to solve several novel crystal structures. PMID:17637337
Effectiveness of multi tuned liquid dampers with slat screens for reducing dynamic responses of structures

NASA Astrophysics Data System (ADS)

Nguyen, T. P.; Pham, D. T.; Ngo, K. T.

2018-04-01

Reducing vibration in structures under lateral load always attracts many researchers in during pastime, hence the mainly purpose of paper analyzes effectiveness of multiple-tuned liquid dampers for reducing dynamic responses of structures under ground acceleration of earthquakes. In this study, the multi-tuned liquid damper with slat screens (M-TLDWSS) is considered in detail for analyzing dynamic response of multi-degrees of freedom structure due to earthquake, which is more different previous studies. Then, the general equation of motion of the structure and M-TLDWSS under ground acceleration of earthquake is established based on dynamic balance of principle and solved by numerical method in the time domain. The effects of characteristic parameters of M-TLDWSS on dynamic response of the structure are investigated. The results obtained in this study demonstrate that the M-TLDWSS has significantly effectiveness for reducing dynamic response of the structure.
Micro-crystallography comes of age

PubMed Central

Smith, Janet L.; Fischetti, Robert F.; Yamamoto, Masaki

2012-01-01

The latest revolution in macromolecular crystallography was incited by the development of dedicated, user friendly, micro-crystallography beamlines. Brilliant X-ray beams of diameter 20 microns or less, now available at most synchrotron sources, enable structure determination from samples that previously were inaccessible. Relative to traditional crystallography, crystals with one or more small dimensions have diffraction patterns with vastly improved signal-to-noise when recorded with an appropriately matched beam size. Structures can be solved from isolated, well diffracting regions within inhomogeneous samples. This review summarizes the technological requirements and approaches to producing micro-beams and how they continue to change the practice of crystallography. PMID:23021872
Functional and genomic analyses of alpha-solenoid proteins.

PubMed

Fournier, David; Palidwor, Gareth A; Shcherbinin, Sergey; Szengel, Angelika; Schaefer, Martin H; Perez-Iratxeta, Carol; Andrade-Navarro, Miguel A

2013-01-01

Alpha-solenoids are flexible protein structural domains formed by ensembles of alpha-helical repeats (Armadillo and HEAT repeats among others). While homology can be used to detect many of these repeats, some alpha-solenoids have very little sequence homology to proteins of known structure and we expect that many remain undetected. We previously developed a method for detection of alpha-helical repeats based on a neural network trained on a dataset of protein structures. Here we improved the detection algorithm and updated the training dataset using recently solved structures of alpha-solenoids. Unexpectedly, we identified occurrences of alpha-solenoids in solved protein structures that escaped attention, for example within the core of the catalytic subunit of PI3KC. Our results expand the current set of known alpha-solenoids. Application of our tool to the protein universe allowed us to detect their significant enrichment in proteins interacting with many proteins, confirming that alpha-solenoids are generally involved in protein-protein interactions. We then studied the taxonomic distribution of alpha-solenoids to discuss an evolutionary scenario for the emergence of this type of domain, speculating that alpha-solenoids have emerged in multiple taxa in independent events by convergent evolution. We observe a higher rate of alpha-solenoids in eukaryotic genomes and in some prokaryotic families, such as Cyanobacteria and Planctomycetes, which could be associated to increased cellular complexity. The method is available at http://cbdm.mdc-berlin.de/~ard2/.
Pre-Service Elementary Teachers' Motivation and Ill-Structured Problem Solving in Korea

ERIC Educational Resources Information Center

Kim, Min Kyeong; Cho, Mi Kyung

2016-01-01

This article examines the use and application of an ill-structured problem to pre-service elementary teachers in Korea in order to find implications of pre-service teacher education with regard to contextualized problem solving by analyzing experiences of ill-structured problem solving. Participants were divided into small groups depending on the…
Rosetta Structure Prediction as a Tool for Solving Difficult Molecular Replacement Problems.

PubMed

DiMaio, Frank

2017-01-01

Molecular replacement (MR), a method for solving the crystallographic phase problem using phases derived from a model of the target structure, has proven extremely valuable, accounting for the vast majority of structures solved by X-ray crystallography. However, when the resolution of data is low, or the starting model is very dissimilar to the target protein, solving structures via molecular replacement may be very challenging. In recent years, protein structure prediction methodology has emerged as a powerful tool in model building and model refinement for difficult molecular replacement problems. This chapter describes some of the tools available in Rosetta for model building and model refinement specifically geared toward difficult molecular replacement cases.
RNA-Puzzles Round II: assessment of RNA structure prediction programs applied to three large RNA structures

PubMed Central

Miao, Zhichao; Adamiak, Ryszard W.; Blanchet, Marc-Frédérick; Boniecki, Michal; Bujnicki, Janusz M.; Chen, Shi-Jie; Cheng, Clarence; Chojnowski, Grzegorz; Chou, Fang-Chieh; Cordero, Pablo; Cruz, José Almeida; Ferré-D'Amaré, Adrian R.; Das, Rhiju; Ding, Feng; Dokholyan, Nikolay V.; Dunin-Horkawicz, Stanislaw; Kladwang, Wipapat; Krokhotin, Andrey; Lach, Grzegorz; Magnus, Marcin; Major, François; Mann, Thomas H.; Masquida, Benoît; Matelska, Dorota; Meyer, Mélanie; Peselis, Alla; Popenda, Mariusz; Purzycka, Katarzyna J.; Serganov, Alexander; Stasiewicz, Juliusz; Szachniuk, Marta; Tandon, Arpit; Tian, Siqi; Wang, Jian; Xiao, Yi; Xu, Xiaojun; Zhang, Jinwei; Zhao, Peinan; Zok, Tomasz; Westhof, Eric

2015-01-01

This paper is a report of a second round of RNA-Puzzles, a collective and blind experiment in three-dimensional (3D) RNA structure prediction. Three puzzles, Puzzles 5, 6, and 10, represented sequences of three large RNA structures with limited or no homology with previously solved RNA molecules. A lariat-capping ribozyme, as well as riboswitches complexed to adenosylcobalamin and tRNA, were predicted by seven groups using RNAComposer, ModeRNA/SimRNA, Vfold, Rosetta, DMD, MC-Fold, 3dRNA, and AMBER refinement. Some groups derived models using data from state-of-the-art chemical-mapping methods (SHAPE, DMS, CMCT, and mutate-and-map). The comparisons between the predictions and the three subsequently released crystallographic structures, solved at diffraction resolutions of 2.5–3.2 Å, were carried out automatically using various sets of quality indicators. The comparisons clearly demonstrate the state of present-day de novo prediction abilities as well as the limitations of these state-of-the-art methods. All of the best prediction models have similar topologies to the native structures, which suggests that computational methods for RNA structure prediction can already provide useful structural information for biological problems. However, the prediction accuracy for non-Watson–Crick interactions, key to proper folding of RNAs, is low and some predicted models had high Clash Scores. These two difficulties point to some of the continuing bottlenecks in RNA structure prediction. All submitted models are available for download at http://ahsoka.u-strasbg.fr/rnapuzzles/. PMID:25883046
Crystal structures of tiotropium bromide and its monohydrate in view of combined solid-state nuclear magnetic resonance and gauge-including projector-augmented wave studies.

PubMed

Pindelska, Edyta; Szeleszczuk, Lukasz; Pisklak, Dariusz Maciej; Majka, Zbigniew; Kolodziejski, Waclaw

2015-07-01

Tiotropium bromide is an anticholinergic bronchodilator used in the management of chronic obstructive pulmonary disease. The crystal structures of this compound and its monohydrate have been previously solved and published. However, in this paper, we showed that those structures contain some major errors. Our methodology based on combination of the solid-state nuclear magnetic resonance (NMR) spectroscopy and quantum mechanical gauge-including projector-augmented wave (GIPAW) calculations of NMR shielding constants enabled us to correct those errors and obtain reliable structures of the studied compounds. It has been proved that such approach can be used not only to perform the structural analysis of a drug substance and to identify its polymorphs, but also to verify and optimize already existing crystal structures. © 2015 Wiley Periodicals, Inc. and the American Pharmacists Association.
A combined computational and structural model of the full-length human prolactin receptor

PubMed Central

Bugge, Katrine; Papaleo, Elena; Haxholm, Gitte W.; Hopper, Jonathan T. S.; Robinson, Carol V.; Olsen, Johan G.; Lindorff-Larsen, Kresten; Kragelund, Birthe B.

2016-01-01

The prolactin receptor is an archetype member of the class I cytokine receptor family, comprising receptors with fundamental functions in biology as well as key drug targets. Structurally, each of these receptors represent an intriguing diversity, providing an exceptionally challenging target for structural biology. Here, we access the molecular architecture of the monomeric human prolactin receptor by combining experimental and computational efforts. We solve the NMR structure of its transmembrane domain in micelles and collect structural data on overlapping fragments of the receptor with small-angle X-ray scattering, native mass spectrometry and NMR spectroscopy. Along with previously published data, these are integrated by molecular modelling to generate a full receptor structure. The result provides the first full view of a class I cytokine receptor, exemplifying the architecture of more than 40 different receptor chains, and reveals that the extracellular domain is merely the tip of a molecular iceberg. PMID:27174498
Pre-service mathematics teachers’ ability in solving well-structured problem

NASA Astrophysics Data System (ADS)

Paradesa, R.

2018-01-01

This study aimed to describe the mathematical problem-solving ability of undergraduate students of mathematics education in solving the well-structured problem. The type of this study was qualitative descriptive. The subjects in this study were 100 undergraduate students of Mathematics Education at one of the private universities in Palembang city. The data in this study was collected through two test items with essay form. The results of this study showed that, from the first problem, only 8% students can solve it, but do not check back again to validate the process. Based on a scoring rubric that follows Polya strategy, their answer satisfied 2 4 2 0 patterns. But, from the second problem, 45% students satisfied it. This is because the second problem imitated from the example that was given in learning process. The average score of undergraduate students mathematical problem-solving ability in solving well-structured problems showed 56.00 with standard deviation was 13.22. It means that, from 0 - 100 scale, undergraduate students mathematical problem-solving ability can be categorized low. From this result, the conclusion was undergraduate students of mathematics education in Palembang still have a problem in solving mathematics well-structured problem.
Characteristics of a Cognitive Tool That Helps Students Learn Diagnostic Problem Solving

ERIC Educational Resources Information Center

Danielson, Jared A.; Mills, Eric M.; Vermeer, Pamela J.; Preast, Vanessa A.; Young, Karen M.; Christopher, Mary M.; George, Jeanne W.; Wood, R. Darren; Bender, Holly S.

2007-01-01

Three related studies replicated and extended previous work (J.A. Danielson et al. (2003), "Educational Technology Research and Development," 51(3), 63-81) involving the Diagnostic Pathfinder (dP) (previously Problem List Generator [PLG]), a cognitive tool for learning diagnostic problem solving. In studies 1 and 2, groups of 126 and 113…
Goal specificity and knowledge acquisition in statistics problem solving: evidence for attentional focus.

PubMed

Trumpower, David L; Goldsmith, Timothy E; Guynn, Melissa J

2004-12-01

Solving training problems with nonspecific goals (NG; i.e., solving for all possible unknown values) often results in better transfer than solving training problems with standard goals (SG; i.e., solving for one particular unknown value). In this study, we evaluated an attentional focus explanation of the goal specificity effect. According to the attentional focus view, solving NG problems causes attention to be directed to local relations among successive problem states, whereas solving SG problems causes attention to be directed to relations between the various problem states and the goal state. Attention to the former is thought to enhance structural knowledge about the problem domain and thus promote transfer. Results supported this view because structurally different transfer problems were solved faster following NG training than following SG training. Moreover, structural knowledge representations revealed more links depicting local relations following NG training and more links to the training goal following SG training. As predicted, these effects were obtained only by domain novices.
Why do children lack the flexibility to innovate tools?

PubMed

Cutting, Nicola; Apperly, Ian A; Beck, Sarah R

2011-08-01

Despite being proficient tool users, young children have surprising difficulty in innovating tools (making novel tools to solve problems). Two experiments found that 4- to 7-year-olds had difficulty on two tool innovation problems and explored reasons for this inflexibility. Experiment 1 (N=51) showed that children's performance was unaffected by the need to switch away from previously correct strategies. Experiment 2 (N=92) suggested that children's difficulty could not easily be explained by task pragmatics or permission issues. Both experiments found evidence that some children perseverated on a single incorrect strategy, but such perseveration was insufficient to explain children's tendency not to innovate tools. We suggest that children's difficulty lies not with switching, task pragmatics, or behavioral perseveration but rather with solving the fundamentally "ill-structured" nature of tool innovation problems. Copyright © 2011 Elsevier Inc. All rights reserved.
The Use of a Bar Model Drawing to Teach Word Problem Solving to Students with Mathematics Difficulties

ERIC Educational Resources Information Center

Morin, Lisa L.; Watson, Silvana M. R.; Hester, Peggy; Raver, Sharon

2017-01-01

For students with mathematics difficulties (MD), math word problem solving is especially challenging. The purpose of this study was to examine the effects of a problem-solving strategy, bar model drawing, on the mathematical problem-solving skills of students with MD. The study extended previous research that suggested that schematic-based…
[Brain mapping in verbal and spatial thinking].

PubMed

Ivanitskiĭ, A M; Portnova, G V; Martynova, O V; Maĭorova, L A; Fedina, O N; Petrushevskiĭ, A G

2013-01-01

The goal of this study was to describe the topography of the active cortical areas and subcortical structuresin verbal and spatial thinking. The method of functional magnetic resonance imaging (fMRI) was used. 18 right-handed subjects participated in the study. Four types of tasks were presented: two experimental tasks--verbal (anagram) and spatial (search for a piece to complement a square), and two types of control tasks (written words and a spatial task, where all the pieces are identical). In solving verbal tasks the greater volume of activation was observed in the left hemisphere involving Broca's area, while the right middle frontal gyrus was activated in solving the spatial tasks. For occipital region an activation of the visual field 18 was more explicitin solving spatial problems, while the solution of anagrams caused an activation of the field 19 associated with higher levels of visual processing. The cerebellum was active bilaterally in both tasks with predominance in the second. The obtained fMRI data indicate that the verbal and spatial types of thinking are provided by an activation of narrow specific sets of brain structures, while the previous electrophysiological studies indicate the distributed nature of the brain processes in thinking. Combining these two approaches, it can be concluded that cognitive functions are supported by the systemic brain processes with a distinct location of the particular salient structures.
You Need to Know: There Is a Causal Relationship between Structural Knowledge and Control Performance in Complex Problem Solving Tasks

ERIC Educational Resources Information Center

Goode, Natassia; Beckmann, Jens F.

2010-01-01

This study investigates the relationships between structural knowledge, control performance and fluid intelligence in a complex problem solving (CPS) task. 75 participants received either complete, partial or no information regarding the underlying structure of a complex problem solving task, and controlled the task to reach specific goals.…
Asymmetrical reverse vortex flow due to induced-charge electro-osmosis around carbon stacking structures.

PubMed

Sugioka, Hideyuki

2011-05-01

Broken symmetry of vortices due to induced-charge electro-osmosis (ICEO) around stacking structures is important for the generation of a large net flow in a microchannel. Following theoretical predictions in our previous study, we herein report experimental observations of asymmetrical reverse vortex flows around stacking structures of carbon posts with a large height (~110 μm) in water, prepared by the pyrolysis of a photoresist film in a reducing gas. Further, by the use of a coupled calculation method that considers boundary effects precisely, the experimental results, except for the problem of anomalous flow reversal, are successfully explained. That is, unlike previous predictions, the precise calculations here show that stacking structures accelerate a reverse flow rather than suppressing it for a microfluidic channel because of the deformation of electric fields near the stacking portions; these structures can also generate a large net flow theoretically in the direction opposite that of a previous prediction for a standard vortex flow. Furthermore, by solving the one-dimensional Poisson-Nernst-Plank (PNP) equations in the presence of ac electric fields, we find that the anomalous flow reversal occurs by the phase retardation between the induced diffuse charge and the tangential electric field. In addition, we successfully explain the nonlinearity of the flow velocity on the applied voltage by the PNP analysis. In the future, we expect to improve the pumping performance significantly by using stacking structures of conductive posts along with a low-cost process. © 2011 American Physical Society

Crystal Structure of the Escherichia coli 23S rRNA: m{5}C Methyltransferase RlmI (YccW) Reveals Evolutionary Links Between RNA Modification Enzymes

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sunita, S.; Tkaczuk, K; Purta, E

2008-01-01

Methylation is the most common RNA modification in the three domains of life. Transfer of the methyl group from S-adenosyl-l-methionine (AdoMet) to specific atoms of RNA nucleotides is catalyzed by methyltransferase (MTase) enzymes. The rRNA MTase RlmI (rRNA large subunit methyltransferase gene I; previously known as YccW) specifically modifies Escherichia coli 23S rRNA at nucleotide C1962 to form 5-methylcytosine. Here, we report the crystal structure of RlmI refined at 2 {angstrom} to a final R-factor of 0.194 (R{sub free} = 0.242). The RlmI molecule comprises three domains: the N-terminal PUA domain; the central domain, which resembles a domain previously foundmore » in RNA:5-methyluridine MTases; and the C-terminal catalytic domain, which contains the AdoMet-binding site. The central and C-terminal domains are linked by a {Beta}-hairpin structure that has previously been observed in several MTases acting on nucleic acids or proteins. Based on bioinformatics analyses, we propose a model for the RlmI-AdoMet-RNA complex. Comparative structural analyses of RlmI and its homologs provide insight into the potential function of several structures that have been solved by structural genomics groups and furthermore indicate that the evolutionary paths of RNA and DNA 5-methyluridine and 5-methylcytosine MTases have been closely intertwined.« less
Scaffolding Online Argumentation during Problem Solving

ERIC Educational Resources Information Center

Oh, S.; Jonassen, D. H.

2007-01-01

In this study, constraint-based argumentation scaffolding was proposed to facilitate online argumentation performance and ill-structured problem solving during online discussions. In addition, epistemological beliefs were presumed to play a role in solving ill-structured diagnosis-solution problems. Constraint-based discussion boards were…
The Structure of Ill-Structured (and Well-Structured) Problems Revisited

ERIC Educational Resources Information Center

Reed, Stephen K.

2016-01-01

In his 1973 article "The Structure of ill structured problems", Herbert Simon proposed that solving ill-structured problems could be modeled within the same information-processing framework developed for solving well-structured problems. This claim is reexamined within the context of over 40 years of subsequent research and theoretical…
A complexity theory model in science education problem solving: random walks for working memory and mental capacity.

PubMed

Stamovlasis, Dimitrios; Tsaparlis, Georgios

2003-07-01

The present study examines the role of limited human channel capacity from a science education perspective. A model of science problem solving has been previously validated by applying concepts and tools of complexity theory (the working memory, random walk method). The method correlated the subjects' rank-order achievement scores in organic-synthesis chemistry problems with the subjects' working memory capacity. In this work, we apply the same nonlinear approach to a different data set, taken from chemical-equilibrium problem solving. In contrast to the organic-synthesis problems, these problems are algorithmic, require numerical calculations, and have a complex logical structure. As a result, these problems cause deviations from the model, and affect the pattern observed with the nonlinear method. In addition to Baddeley's working memory capacity, the Pascual-Leone's mental (M-) capacity is examined by the same random-walk method. As the complexity of the problem increases, the fractal dimension of the working memory random walk demonstrates a sudden drop, while the fractal dimension of the M-capacity random walk decreases in a linear fashion. A review of the basic features of the two capacities and their relation is included. The method and findings have consequences for problem solving not only in chemistry and science education, but also in other disciplines.
A FAST ITERATIVE METHOD FOR SOLVING THE EIKONAL EQUATION ON TETRAHEDRAL DOMAINS

PubMed Central

Fu, Zhisong; Kirby, Robert M.; Whitaker, Ross T.

2014-01-01

Generating numerical solutions to the eikonal equation and its many variations has a broad range of applications in both the natural and computational sciences. Efficient solvers on cutting-edge, parallel architectures require new algorithms that may not be theoretically optimal, but that are designed to allow asynchronous solution updates and have limited memory access patterns. This paper presents a parallel algorithm for solving the eikonal equation on fully unstructured tetrahedral meshes. The method is appropriate for the type of fine-grained parallelism found on modern massively-SIMD architectures such as graphics processors and takes into account the particular constraints and capabilities of these computing platforms. This work builds on previous work for solving these equations on triangle meshes; in this paper we adapt and extend previous two-dimensional strategies to accommodate three-dimensional, unstructured, tetrahedralized domains. These new developments include a local update strategy with data compaction for tetrahedral meshes that provides solutions on both serial and parallel architectures, with a generalization to inhomogeneous, anisotropic speed functions. We also propose two new update schemes, specialized to mitigate the natural data increase observed when moving to three dimensions, and the data structures necessary for efficiently mapping data to parallel SIMD processors in a way that maintains computational density. Finally, we present descriptions of the implementations for a single CPU, as well as multicore CPUs with shared memory and SIMD architectures, with comparative results against state-of-the-art eikonal solvers. PMID:25221418
A FAST ITERATIVE METHOD FOR SOLVING THE EIKONAL EQUATION ON TRIANGULATED SURFACES*

PubMed Central

Fu, Zhisong; Jeong, Won-Ki; Pan, Yongsheng; Kirby, Robert M.; Whitaker, Ross T.

2012-01-01

This paper presents an efficient, fine-grained parallel algorithm for solving the Eikonal equation on triangular meshes. The Eikonal equation, and the broader class of Hamilton–Jacobi equations to which it belongs, have a wide range of applications from geometric optics and seismology to biological modeling and analysis of geometry and images. The ability to solve such equations accurately and efficiently provides new capabilities for exploring and visualizing parameter spaces and for solving inverse problems that rely on such equations in the forward model. Efficient solvers on state-of-the-art, parallel architectures require new algorithms that are not, in many cases, optimal, but are better suited to synchronous updates of the solution. In previous work [W. K. Jeong and R. T. Whitaker, SIAM J. Sci. Comput., 30 (2008), pp. 2512–2534], the authors proposed the fast iterative method (FIM) to efficiently solve the Eikonal equation on regular grids. In this paper we extend the fast iterative method to solve Eikonal equations efficiently on triangulated domains on the CPU and on parallel architectures, including graphics processors. We propose a new local update scheme that provides solutions of first-order accuracy for both architectures. We also propose a novel triangle-based update scheme and its corresponding data structure for efficient irregular data mapping to parallel single-instruction multiple-data (SIMD) processors. We provide detailed descriptions of the implementations on a single CPU, a multicore CPU with shared memory, and SIMD architectures with comparative results against state-of-the-art Eikonal solvers. PMID:22641200
Parallel deterministic transport sweeps of structured and unstructured meshes with overloaded mesh decompositions

DOE Office of Scientific and Technical Information (OSTI.GOV)

Pautz, Shawn D.; Bailey, Teresa S.

Here, the efficiency of discrete ordinates transport sweeps depends on the scheduling algorithm, the domain decomposition, the problem to be solved, and the computational platform. Sweep scheduling algorithms may be categorized by their approach to several issues. In this paper we examine the strategy of domain overloading for mesh partitioning as one of the components of such algorithms. In particular, we extend the domain overloading strategy, previously defined and analyzed for structured meshes, to the general case of unstructured meshes. We also present computational results for both the structured and unstructured domain overloading cases. We find that an appropriate amountmore » of domain overloading can greatly improve the efficiency of parallel sweeps for both structured and unstructured partitionings of the test problems examined on up to 10 5 processor cores.« less
Parallel deterministic transport sweeps of structured and unstructured meshes with overloaded mesh decompositions

DOE PAGES

Pautz, Shawn D.; Bailey, Teresa S.

2016-11-29

Here, the efficiency of discrete ordinates transport sweeps depends on the scheduling algorithm, the domain decomposition, the problem to be solved, and the computational platform. Sweep scheduling algorithms may be categorized by their approach to several issues. In this paper we examine the strategy of domain overloading for mesh partitioning as one of the components of such algorithms. In particular, we extend the domain overloading strategy, previously defined and analyzed for structured meshes, to the general case of unstructured meshes. We also present computational results for both the structured and unstructured domain overloading cases. We find that an appropriate amountmore » of domain overloading can greatly improve the efficiency of parallel sweeps for both structured and unstructured partitionings of the test problems examined on up to 10 5 processor cores.« less
Sequence-dependent effects in drug-DNA interaction: the crystal structure of Hoechst 33258 bound to the d(CGCAAATTTGCG)2 duplex.

PubMed Central

Spink, N; Brown, D G; Skelly, J V; Neidle, S

1994-01-01

The bis-benzimidazole drug Hoechst 33258 has been co-crystallized with the dodecanucleotide sequence d(CGCAAATTTGCG)2. The structure has been solved by molecular replacement and refined to an R factor of 18.5% for 2125 reflections collected on a Xentronics area detector. The drug is bound in the minor groove, at the five base-pair site 5'-ATTTG and is in a unique orientation. This is displaced by one base pair in the 5' direction compared to previously-determined structures of this drug with the sequence d(CGCGAATTCGCG)2. Reasons for this difference in behaviour are discussed in terms of several sequence-dependent structural features of the DNA, with particular reference to differences in propeller twist and minor-groove width. Images PMID:7515488
DOE Office of Scientific and Technical Information (OSTI.GOV)

Wurzburg, Beth A.; Tarchevskaya, Svetlana S.; Jardetzky, Theodore S.

CD23, the low-affinity receptor for IgE (Fc{var_epsilon}RII), regulates IgE synthesis and also mediates IgE-dependent antigen transport and processing. CD23 is a unique Fc receptor belonging to the C-type lectin-like domain superfamily and binds IgE in an unusual, non-lectin-like manner, requiring calcium but not carbohydrate. We have solved the high-resolution crystal structures of the human CD23 lectin domain in the presence and absence of Ca{sup 2+}. The crystal structures differ significantly from a previously determined NMR structure and show that calcium binding occurs at the principal binding site, but not at an auxiliary site that appears to be absent in humanmore » CD23. Conformational differences between the apo and Ca{sup 2+} bound structures suggest how IgE-Fc binding can be both calcium-dependent and carbohydrate-independent.« less
Problem Solving Under Time-Constraints.

ERIC Educational Resources Information Center

Richardson, Michael; Hunt, Earl

A model of how automated and controlled processing can be mixed in computer simulations of problem solving is proposed. It is based on previous work by Hunt and Lansman (1983), who developed a model of problem solving that could reproduce the data obtained with several attention and performance paradigms, extending production-system notation to…
Research Projects in Physics: A Mechanism for Teaching Ill-Structured Problem Solving

NASA Astrophysics Data System (ADS)

Milbourne, Jeff; Bennett, Jonathan

2017-10-01

Physics education research has a tradition of studying problem solving, exploring themes such as physical intuition and differences between expert and novice problem solvers. However, most of this work has focused on traditional, or well-structured, problems, similar to what might appear in a textbook. Less work has been done with open-ended, or ill-structured, problems, similar to the types of problems students might face in their professional lives. Given the national discourse on educational system reform aligned with 21st century skills, including problem solving, it is critical to provide educational experiences that help students learn to solve all types of problems, including ill-structured problems.
Approaches to ab initio molecular replacement of α-helical transmembrane proteins.

PubMed

Thomas, Jens M H; Simkovic, Felix; Keegan, Ronan; Mayans, Olga; Zhang, Chengxin; Zhang, Yang; Rigden, Daniel J

2017-12-01

α-Helical transmembrane proteins are a ubiquitous and important class of proteins, but present difficulties for crystallographic structure solution. Here, the effectiveness of the AMPLE molecular replacement pipeline in solving α-helical transmembrane-protein structures is assessed using a small library of eight ideal helices, as well as search models derived from ab initio models generated both with and without evolutionary contact information. The ideal helices prove to be surprisingly effective at solving higher resolution structures, but ab initio-derived search models are able to solve structures that could not be solved with the ideal helices. The addition of evolutionary contact information results in a marked improvement in the modelling and makes additional solutions possible.
Factor Structure and Item Level Psychometrics of the Social Problem Solving Inventory Revised-Short Form in Traumatic Brain Injury

PubMed Central

Li, Chih-Ying; Waid-Ebbs, Julia; Velozo, Craig A.; Heaton, Shelley C.

2016-01-01

Primary Objective Social problem solving deficits characterize individuals with traumatic brain injury (TBI). Poor social problem solving interferes with daily functioning and productive lifestyles. Therefore, it is of vital importance to use the appropriate instrument to identify deficits in social problem solving for individuals with TBI. This study investigates factor structure and item-level psychometrics of the Social Problem Solving Inventory-Revised Short Form (SPSI-R:S), for adults with moderate and severe TBI. Research Design Secondary analysis of 90 adults with moderate and severe TBI who completed the SPSI-R:S. Methods and Procedures An exploratory factor analysis (EFA), principal components analysis (PCA) and Rasch analysis examined the factor structure and item-level psychometrics of the SPSI-R:S. Main Outcomes and Results The EFA showed three dominant factors, with positively worded items represented as the most definite factor. The other two factors are negative problem solving orientation and skills; and negative problem solving emotion. Rasch analyses confirmed the three factors are each unidimensional constructs. Conclusions The total score interpretability of the SPSI-R:S may be challenging due to the multidimensional structure of the total measure. Instead, we propose using three separate SPSI-R:S subscores to measure social problem solving for the TBI population. PMID:26052731
Factor structure and item level psychometrics of the Social Problem Solving Inventory-Revised: Short Form in traumatic brain injury.

PubMed

Li, Chih-Ying; Waid-Ebbs, Julia; Velozo, Craig A; Heaton, Shelley C

2016-01-01

Social problem-solving deficits characterise individuals with traumatic brain injury (TBI), and poor social problem solving interferes with daily functioning and productive lifestyles. Therefore, it is of vital importance to use the appropriate instrument to identify deficits in social problem solving for individuals with TBI. This study investigates factor structure and item-level psychometrics of the Social Problem Solving Inventory-Revised: Short Form (SPSI-R:S), for adults with moderate and severe TBI. Secondary analysis of 90 adults with moderate and severe TBI who completed the SPSI-R:S was performed. An exploratory factor analysis (EFA), principal components analysis (PCA) and Rasch analysis examined the factor structure and item-level psychometrics of the SPSI-R:S. The EFA showed three dominant factors, with positively worded items represented as the most definite factor. The other two factors are negative problem-solving orientation and skills; and negative problem-solving emotion. Rasch analyses confirmed the three factors are each unidimensional constructs. It was concluded that the total score interpretability of the SPSI-R:S may be challenging due to the multidimensional structure of the total measure. Instead, we propose using three separate SPSI-R:S subscores to measure social problem solving for the TBI population.
Structural characterization of metal binding to a cold-adapted frataxin.

PubMed

Noguera, Martín E; Roman, Ernesto A; Rigal, Juan B; Cousido-Siah, Alexandra; Mitschler, André; Podjarny, Alberto; Santos, Javier

2015-06-01

Frataxin is an evolutionary conserved protein that participates in iron metabolism. Deficiency of this small protein in humans causes a severe neurodegenerative disease known as Friedreich's ataxia. A number of studies indicate that frataxin binds iron and regulates Fe-S cluster biosynthesis. Previous structural studies showed that metal binding occurs mainly in a region of high density of negative charge. However, a comprehensive characterization of the binding sites is required to gain further insights into the mechanistic details of frataxin function. In this work, we have solved the X-ray crystal structures of a cold-adapted frataxin from a psychrophilic bacterium in the presence of cobalt or europium ions. We have identified a number of metal-binding sites, mainly solvent exposed, several of which had not been observed in previous studies on mesophilic homologues. No major structural changes were detected upon metal binding, although the structures exhibit significant changes in crystallographic B-factors. The analysis of these B-factors, in combination with crystal packing and RMSD among structures, suggests the existence of localized changes in the internal motions. Based on these results, we propose that bacterial frataxins possess binding sites of moderate affinity for a quick capture and transfer of iron to other proteins and for the regulation of Fe-S cluster biosynthesis, modulating interactions with partner proteins.
Is Trait Rumination Associated with the Ability to Generate Effective Problem Solving Strategies? Utilizing Two Versions of the Means-Ends Problem-Solving Test.

PubMed

Hasegawa, Akira; Nishimura, Haruki; Mastuda, Yuko; Kunisato, Yoshihiko; Morimoto, Hiroshi; Adachi, Masaki

This study examined the relationship between trait rumination and the effectiveness of problem solving strategies as assessed by the Means-Ends Problem-Solving Test (MEPS) in a nonclinical population. The present study extended previous studies in terms of using two instructions in the MEPS: the second-person, actual strategy instructions, which has been utilized in previous studies on rumination, and the third-person, ideal-strategy instructions, which is considered more suitable for assessing the effectiveness of problem solving strategies. We also replicated the association between rumination and each dimension of the Social Problem-Solving Inventory-Revised Short Version (SPSI-R:S). Japanese undergraduate students ( N = 223) completed the Beck Depression Inventory-Second Edition, Ruminative Responses Scale (RRS), MEPS, and SPSI-R:S. One half of the sample completed the MEPS with the second-person, actual strategy instructions. The other participants completed the MEPS with the third-person, ideal-strategy instructions. The results showed that neither total RRS score, nor its subscale scores were significantly correlated with MEPS scores under either of the two instructions. These findings taken together with previous findings indicate that in nonclinical populations, trait rumination is not related to the effectiveness of problem solving strategies, but that state rumination while responding to the MEPS deteriorates the quality of strategies. The correlations between RRS and SPSI-R:S scores indicated that trait rumination in general, and its brooding subcomponent in particular are parts of cognitive and behavioral responses that attempt to avoid negative environmental and negative private events. Results also showed that reflection is a part of active problem solving.
The Effect of an Extended Wilderness Education Experience on Ill-Structured Problem-Solving Skill Development in Emerging Adult Students

ERIC Educational Resources Information Center

Collins, Rachel H.

2014-01-01

In a society that is becoming more dynamic, complex, and diverse, the ability to solve ill-structured problems has become an increasingly critical skill. Emerging adults are at a critical life stage that is an ideal time to develop the skills needed to solve ill-structured problems (ISPs) as they are transitioning to adult roles and starting to…
Micro-crystallography comes of age.

PubMed

Smith, Janet L; Fischetti, Robert F; Yamamoto, Masaki

2012-10-01

The latest revolution in macromolecular crystallography was incited by the development of dedicated, user friendly, micro-crystallography beam lines. Brilliant X-ray beams of diameter 20 μm or less, now available at most synchrotron sources, enable structure determination from samples that previously were inaccessible. Relative to traditional crystallography, crystals with one or more small dimensions have diffraction patterns with vastly improved signal-to-noise when recorded with an appropriately matched beam size. Structures can be solved from isolated, well diffracting regions within inhomogeneous samples. This review summarizes the technological requirements and approaches to producing micro-beams and how they continue to change the practice of crystallography. Copyright © 2012 Elsevier Ltd. All rights reserved.
Electrode Build-Up of Reducible Metal Composites toward Achievable Electrochemical Conversion of Carbon Dioxide.

PubMed

Lee, Seunghwa; Lee, Jaeyoung

2016-02-19

At the beginning of the 21st century, our world is faced with a global-warming problem due to the continuous increase in carbon dioxide emission, and thus, the development of novel experimental techniques is needed. The electrochemical conversion of carbon dioxide into high-value organic compounds could be of vital importance to solve this issue. The biggest challenge has always been to develop an electrocatalyst that is chemically active and structurally stable. Herein, previous studies, recent approaches, and current points of view on the electrode structure of metal oxide composites for the advanced electrochemical conversion of carbon dioxide are reviewed. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Gentamicin Binds to the Megalin Receptor as a Competitive Inhibitor Using the Common Ligand Binding Motif of Complement Type Repeats

PubMed Central

Dagil, Robert; O'Shea, Charlotte; Nykjær, Anders; Bonvin, Alexandre M. J. J.; Kragelund, Birthe B.

2013-01-01

Gentamicin is an aminoglycoside widely used in treatments of, in particular, enterococcal, mycobacterial, and severe Gram-negative bacterial infections. Large doses of gentamicin cause nephrotoxicity and ototoxicity, entering the cell via the receptor megalin. Until now, no structural information has been available to describe the interaction with gentamicin in atomic detail, and neither have any three-dimensional structures of domains from the human megalin receptor been solved. To address this gap in our knowledge, we have solved the NMR structure of the 10th complement type repeat of human megalin and investigated its interaction with gentamicin. Using NMR titration data in HADDOCK, we have generated a three-dimensional model describing the complex between megalin and gentamicin. Gentamicin binds to megalin with low affinity and exploits the common ligand binding motif previously described (Jensen, G. A., Andersen, O. M., Bonvin, A. M., Bjerrum-Bohr, I., Etzerodt, M., Thogersen, H. C., O'Shea, C., Poulsen, F. M., and Kragelund, B. B. (2006) J. Mol. Biol. 362, 700–716) utilizing the indole side chain of Trp-1126 and the negatively charged residues Asp-1129, Asp-1131, and Asp-1133. Binding to megalin is highly similar to gentamicin binding to calreticulin. We discuss the impact of this novel insight for the future structure-based design of gentamicin antagonists. PMID:23275343
Computational structural mechanics for engine structures

NASA Technical Reports Server (NTRS)

Chamis, C. C.

1989-01-01

The computational structural mechanics (CSM) program at Lewis encompasses: (1) fundamental aspects for formulating and solving structural mechanics problems, and (2) development of integrated software systems to computationally simulate the performance/durability/life of engine structures. It is structured to mainly supplement, complement, and whenever possible replace, costly experimental efforts which are unavoidable during engineering research and development programs. Specific objectives include: investigate unique advantages of parallel and multiprocesses for: reformulating/solving structural mechanics and formulating/solving multidisciplinary mechanics and develop integrated structural system computational simulators for: predicting structural performances, evaluating newly developed methods, and for identifying and prioritizing improved/missing methods needed. Herein the CSM program is summarized with emphasis on the Engine Structures Computational Simulator (ESCS). Typical results obtained using ESCS are described to illustrate its versatility.
Improving the efficiency of molecular replacement by utilizing a new iterative transform phasing algorithm

DOE Office of Scientific and Technical Information (OSTI.GOV)

He, Hongxing; Fang, Hengrui; Miller, Mitchell D.

2016-07-15

An iterative transform algorithm is proposed to improve the conventional molecular-replacement method for solving the phase problem in X-ray crystallography. Several examples of successful trial calculations carried out with real diffraction data are presented. An iterative transform method proposed previously for direct phasing of high-solvent-content protein crystals is employed for enhancing the molecular-replacement (MR) algorithm in protein crystallography. Target structures that are resistant to conventional MR due to insufficient similarity between the template and target structures might be tractable with this modified phasing method. Trial calculations involving three different structures are described to test and illustrate the methodology. The relationshipmore » of the approach to PHENIX Phaser-MR and MR-Rosetta is discussed.« less
Structure of the Si(111)-(5×2)-Au Surface

NASA Astrophysics Data System (ADS)

Abukawa, Tadashi; Nishigaya, Yoshiki

2013-01-01

The structure of the Si(111)-(5×2)-Au surface, one of the long-standing problems in surface science, has been solved by means of Weissenberg reflection high-energy electron diffraction. The arrangement of the Au atoms and their positions with respect to the substrate were determined from a three-dimensional Patterson function with a lateral resolution of 0.3 Å based on a large amount of diffraction data. The new structural model consists of six Au atoms in a 5×2 unit, which agrees with the recently confirmed Au coverage of 0.6 ML [I. Barke , Phys. Rev. B 79, 155301 (2009).PRBMDO1098-0121]. The model has a distinct ×2 periodicity, and includes a Au dimer. The model is also compatible with previously obtained STM images.
Chroman-4-One Derivatives Targeting Pteridine Reductase 1 and Showing Anti-Parasitic Activity.

PubMed

Di Pisa, Flavio; Landi, Giacomo; Dello Iacono, Lucia; Pozzi, Cecilia; Borsari, Chiara; Ferrari, Stefania; Santucci, Matteo; Santarem, Nuno; Cordeiro-da-Silva, Anabela; Moraes, Carolina B; Alcantara, Laura M; Fontana, Vanessa; Freitas-Junior, Lucio H; Gul, Sheraz; Kuzikov, Maria; Behrens, Birte; Pöhner, Ina; Wade, Rebecca C; Costi, Maria Paola; Mangani, Stefano

2017-03-08

Flavonoids have previously been identified as antiparasitic agents and pteridine reductase 1 (PTR1) inhibitors. Herein, we focus our attention on the chroman-4-one scaffold. Three chroman-4-one analogues ( 1 - 3 ) of previously published chromen-4-one derivatives were synthesized and biologically evaluated against parasitic enzymes ( Trypanosoma brucei PTR1- Tb PTR1 and Leishmania major-Lm PTR1) and parasites ( Trypanosoma brucei and Leishmania infantum ). A crystal structure of Tb PTR1 in complex with compound 1 and the first crystal structures of Lm PTR1-flavanone complexes (compounds 1 and 3 ) were solved. The inhibitory activity of the chroman-4-one and chromen-4-one derivatives was explained by comparison of observed and predicted binding modes of the compounds. Compound 1 showed activity both against the targeted enzymes and the parasites with a selectivity index greater than 7 and a low toxicity. Our results provide a basis for further scaffold optimization and structure-based drug design aimed at the identification of potent anti-trypanosomatidic compounds targeting multiple PTR1 variants.
Learner-Centered Teaching and Improving Learning by Writing Down the Statement of Problems in an Introductory Physics Course

NASA Astrophysics Data System (ADS)

Aurora, Tarlok

2005-04-01

In a calculus-based introductory physics course, students were assigned to write the statements of word problems (along with the accompanying diagrams if any), analyze these, identify important concepts/equations and try to solve these end-of- chapter homework problems. They were required to bring to class their written assignment until the chapter was completed in lecture. These were quickly checked at the beginning of the class. In addition, re-doing selected solved examples in the textbook were assigned as homework. Where possible, students were asked to look for similarities between the solved-examples and the end-of-the-chapter problems, or occasionally these were brought to the students' attention. It was observed that many students were able to solve several of the solved-examples on the test even though the instructor had not solved these in class. This was seen as an improvement over the previous years. It made the students more responsible for their learning. Another benefit was that it alleviated the problems previously created by many students not bringing the textbooks to class. It allowed more time for problem solving/discussions in class.
Development of a preprototype thermoelectric integrated membrane evaporation subsystem for water recovery

NASA Technical Reports Server (NTRS)

Winkler, H. E.; Roebelen, G. J., Jr.

1980-01-01

A three-man urine water recovery preprototype subsystem using a new concept to provide efficient potable water recovery from waste fluids on extended duration space flights has been designed, fabricated, and tested. Low power, compactness, and gravity insensitive operation are featured in this vacuum distillation subsystem that combines a hollow fiber polysulfone membrane evaporator with a thermoelectric heat pump. Application and integration of these key elements have solved problems inherent in previous reclamation subsystem designs. The hollow fiber elements provide positive liquid/gas phase control with no moving parts other than a waste liquid recirculation pump and a product water withdrawal pump. Tubular membranes provide structural integrity, improving on previous flat sheet membrane designs. A thermoelectric heat pump provides latent energy recovery.
The structure of amylosucrase from Deinococcus radiodurans has an unusual open active-site topology.

PubMed

Skov, Lars K; Pizzut-Serin, Sandra; Remaud-Simeon, Magali; Ernst, Heidi A; Gajhede, Michael; Mirza, Osman

2013-09-01

Amylosucrases (ASes) catalyze the formation of an α-1,4-glucosidic linkage by transferring a glucosyl unit from sucrose onto an acceptor α-1,4-glucan. To date, several ligand-bound crystal structures of wild-type and mutant ASes from Neisseria polysaccharea and Deinococcus geothermalis have been solved. These structures all display a very similar overall conformation with a deep pocket leading to the site for transglucosylation, subsite -1. This has led to speculation on how sucrose enters the active site during glucan elongation. In contrast to previous studies, the AS structure from D. radiodurans presented here has a completely empty -1 subsite. This structure is strikingly different from other AS structures, as an active-site-lining loop comprising residues Leu214-Asn225 is found in a previously unobserved conformation. In addition, a large loop harbouring the conserved active-site residues Asp133 and Tyr136 is disordered. The result of the changed loop conformations is that the active-site topology is radically changed, leaving subsite -1 exposed and partially dismantled. This structure provides novel insights into the dynamics of ASes and comprises the first structural support for an elongation mechanism that involves considerable conformational changes to modulate accessibility to the sucrose-binding site and thereby allows successive cycles of glucosyl-moiety transfer to a growing glucan chain.
Maximum likelihood density modification by pattern recognition of structural motifs

DOEpatents

Terwilliger, Thomas C.

2004-04-13

An electron density for a crystallographic structure having protein regions and solvent regions is improved by maximizing the log likelihood of a set of structures factors {F.sub.h } using a local log-likelihood function: (x)+p(.rho.(x).vertline.SOLV)p.sub.SOLV (x)+p(.rho.(x).vertline.H)p.sub.H (x)], where p.sub.PROT (x) is the probability that x is in the protein region, p(.rho.(x).vertline.PROT) is the conditional probability for .rho.(x) given that x is in the protein region, and p.sub.SOLV (x) and p(.rho.(x).vertline.SOLV) are the corresponding quantities for the solvent region, p.sub.H (x) refers to the probability that there is a structural motif at a known location, with a known orientation, in the vicinity of the point x; and p(.rho.(x).vertline.H) is the probability distribution for electron density at this point given that the structural motif actually is present. One appropriate structural motif is a helical structure within the crystallographic structure.
A Simple Syllogism-Solving Test: Empirical Findings and Implications for "g" Research

ERIC Educational Resources Information Center

Shikishima, Chizuru; Yamagata, Shinji; Hiraishi, Kai; Sugimoto, Yutaro; Murayama, Kou; Ando, Juko

2011-01-01

It has been reported that the ability to solve syllogisms is highly "g"-loaded. In the present study, using a self-administered shortened version of a syllogism-solving test, the "BAROCO Short," we examined whether robust findings generated by previous research regarding IQ scores were also applicable to "BAROCO…
Students' Mathematical Reasoning and Beliefs in Non-Routine Task Solving

ERIC Educational Resources Information Center

Jäder, Jonas; Sidenvall, Johan; Sumpter, Lovisa

2017-01-01

Beliefs and problem solving are connected and have been studied in different contexts. One of the common results of previous research is that students tend to prefer algorithmic approaches to mathematical tasks. This study explores Swedish upper secondary school students' beliefs and reasoning when solving non-routine tasks. The results regarding…
Effects of Cognitive Strategy Interventions on Word Problem Solving and Working Memory in Children with Math Disabilities

ERIC Educational Resources Information Center

Swanson, H. Lee; Lussier, Catherine; Orosco, Michael

2011-01-01

Although current categories of learning disabilities include as specific disabilities calculation and mathematical problem solving [see IDEA reauthorization, 2004, Sec. 300.8(c)(10)], the majority of research focuses on calculation disabilities. Previous studies have shown, however, that deficits in word problem solving difficulties are persistent…
The Coffee-Milk Mixture Problem Revisited

ERIC Educational Resources Information Center

Marion, Charles F.

2015-01-01

This analysis of a problem that is frequently posed at professional development workshops, in print, and on the Web--the coffee-milk mixture riddle--illustrates the timeless advice of George Pólya's masterpiece on problem solving in mathematics, "How to Solve It." In his book, Pólya recommends that problems previously solved and put…
Structural and electronic snapshots during the transition from a Cu(II) to Cu(I) metal center of a lytic polysaccharide monooxygenase by X-ray photoreduction.

PubMed

Gudmundsson, Mikael; Kim, Seonah; Wu, Miao; Ishida, Takuya; Momeni, Majid Hadadd; Vaaje-Kolstad, Gustav; Lundberg, Daniel; Royant, Antoine; Ståhlberg, Jerry; Eijsink, Vincent G H; Beckham, Gregg T; Sandgren, Mats

2014-07-04

Lytic polysaccharide monooxygenases (LPMOs) are a recently discovered class of enzymes that employ a copper-mediated, oxidative mechanism to cleave glycosidic bonds. The LPMO catalytic mechanism likely requires that molecular oxygen first binds to Cu(I), but the oxidation state in many reported LPMO structures is ambiguous, and the changes in the LPMO active site required to accommodate both oxidation states of copper have not been fully elucidated. Here, a diffraction data collection strategy minimizing the deposited x-ray dose was used to solve the crystal structure of a chitin-specific LPMO from Enterococcus faecalis (EfaCBM33A) in the Cu(II)-bound form. Subsequently, the crystalline protein was photoreduced in the x-ray beam, which revealed structural changes associated with the conversion from the initial Cu(II)-oxidized form with two coordinated water molecules, which adopts a trigonal bipyramidal geometry, to a reduced Cu(I) form in a T-shaped geometry with no coordinated water molecules. A comprehensive survey of Cu(II) and Cu(I) structures in the Cambridge Structural Database unambiguously shows that the geometries observed in the least and most reduced structures reflect binding of Cu(II) and Cu(I), respectively. Quantum mechanical calculations of the oxidized and reduced active sites reveal little change in the electronic structure of the active site measured by the active site partial charges. Together with a previous theoretical investigation of a fungal LPMO, this suggests significant functional plasticity in LPMO active sites. Overall, this study provides molecular snapshots along the reduction process to activate the LPMO catalytic machinery and provides a general method for solving LPMO structures in both copper oxidation states. © 2014 by The American Society for Biochemistry and Molecular Biology, Inc.
Functional and Genomic Analyses of Alpha-Solenoid Proteins

PubMed Central

Fournier, David; Palidwor, Gareth A.; Shcherbinin, Sergey; Szengel, Angelika; Schaefer, Martin H.; Perez-Iratxeta, Carol; Andrade-Navarro, Miguel A.

2013-01-01

Alpha-solenoids are flexible protein structural domains formed by ensembles of alpha-helical repeats (Armadillo and HEAT repeats among others). While homology can be used to detect many of these repeats, some alpha-solenoids have very little sequence homology to proteins of known structure and we expect that many remain undetected. We previously developed a method for detection of alpha-helical repeats based on a neural network trained on a dataset of protein structures. Here we improved the detection algorithm and updated the training dataset using recently solved structures of alpha-solenoids. Unexpectedly, we identified occurrences of alpha-solenoids in solved protein structures that escaped attention, for example within the core of the catalytic subunit of PI3KC. Our results expand the current set of known alpha-solenoids. Application of our tool to the protein universe allowed us to detect their significant enrichment in proteins interacting with many proteins, confirming that alpha-solenoids are generally involved in protein-protein interactions. We then studied the taxonomic distribution of alpha-solenoids to discuss an evolutionary scenario for the emergence of this type of domain, speculating that alpha-solenoids have emerged in multiple taxa in independent events by convergent evolution. We observe a higher rate of alpha-solenoids in eukaryotic genomes and in some prokaryotic families, such as Cyanobacteria and Planctomycetes, which could be associated to increased cellular complexity. The method is available at http://cbdm.mdc-berlin.de/~ard2/. PMID:24278209
Jahn-Teller versus quantum effects in the spin-orbital material LuVO 3

DOE PAGES

Skoulatos, M.; Toth, S.; Roessli, B.; ...

2015-04-13

In this article, we report on combined neutron and resonant x-ray scattering results, identifying the nature of the spin-orbital ground state and magnetic excitations in LuVO 3 as driven by the orbital parameter. In particular, we distinguish between models based on orbital-Peierls dimerization, taken as a signature of quantum effects in orbitals, and Jahn-Teller distortions, in favor of the latter. In order to solve this long-standing puzzle, polarized neutron beams were employed as a prerequisite in order to solve details of the magnetic structure, which allowed quantitative intensity analysis of extended magnetic-excitation data sets. The results of this detailed studymore » enabled us to draw definite conclusions about the classical versus quantum behavior of orbitals in this system and to discard the previous claims about quantum effects dominating the orbital physics of LuVO 3 and similar systems.« less
Using Creative Problem Solving to Promote Students' Performance of Concept Mapping

ERIC Educational Resources Information Center

Tseng, Kuo-Hung; Chang, Chi-Cheng; Lou, Shi-Jer; Hsu, Pi-Shan

2013-01-01

The purpose of the study was to explore that using creative problem solving can promote students' performance of concept mapping (CMPING). Students were encouraged to use creative problem solving (CPS) in constructing nanometer knowledge structure, and then to promote the performance of CMPING. The knowledge structure was visualized through…
Solving coiled-coil protein structures

DOE PAGES

Dauter, Zbigniew

2015-02-26

With the availability of more than 100,000 entries stored in the Protein Data Bank (PDB) that can be used as search models, molecular replacement (MR) is currently the most popular method of solving crystal structures of macromolecules. Significant methodological efforts have been directed in recent years towards making this approach more powerful and practical. This resulted in the creation of several computer programs, highly automated and user friendly, that are able to successfully solve many structures even by researchers who, although interested in structures of biomolecules, are not very experienced in crystallography.
Thermomechanical Stresses Analysis of a Single Event Burnout Process

NASA Astrophysics Data System (ADS)

Tais, Carlos E.; Romero, Eduardo; Demarco, Gustavo L.

2009-06-01

This work analyzes the thermal and mechanical effects arising in a power Diffusion Metal Oxide Semiconductor (DMOS) during a Single Event Burnout (SEB) process. For studying these effects we propose a more detailed simulation structure than the previously used by other authors, solving the mathematical models by means of the Finite Element Method. We use a cylindrical heat generation region, with 5 W, 10 W, 50 W and 100 W for emulating the thermal phenomena occurring during SEB processes, avoiding the complexity of the mathematical treatment of the ion-semiconductor interaction.
Innovation and behavioral flexibility in wild redfronted lemurs (Eulemur rufifrons).

PubMed

Huebner, Franziska; Fichtel, Claudia

2015-05-01

Innovations and problem-solving abilities can provide animals with important ecological advantages as they allow individuals to deal with novel social and ecological challenges. Innovation is a solution to a novel problem or a novel solution to an old problem, with the latter being especially difficult. Finding a new solution to an old problem requires individuals to inhibit previously applied solutions to invent new strategies and to behave flexibly. We examined the role of experience on cognitive flexibility to innovate and to find new problem-solving solutions with an artificial feeding task in wild redfronted lemurs (Eulemur rufifrons). Four groups of lemurs were tested with feeding boxes, each offering three different techniques to extract food, with only one technique being available at a time. After the subjects learned a technique, this solution was no longer successful and subjects had to invent a new technique. For the first transition between task 1 and 2, subjects had to rely on their experience of the previous technique to solve task 2. For the second transition, subjects had to inhibit the previously learned technique to learn the new task 3. Tasks 1 and 2 were solved by most subjects, whereas task 3 was solved by only a few subjects. In this task, besides behavioral flexibility, especially persistence, i.e., constant trying, was important for individual success during innovation. Thus, wild strepsirrhine primates are able to innovate flexibly, suggesting a general ecological relevance of behavioral flexibility and persistence during innovation and problem solving across all primates.

Structure of the Ebola virus envelope protein MPER/TM domain and its interaction with the fusion loop explains their fusion activity.

PubMed

Lee, Jinwoo; Nyenhuis, David A; Nelson, Elizabeth A; Cafiso, David S; White, Judith M; Tamm, Lukas K

2017-09-19

Ebolavirus (EBOV), an enveloped filamentous RNA virus causing severe hemorrhagic fever, enters cells by macropinocytosis and membrane fusion in a late endosomal compartment. Fusion is mediated by the EBOV envelope glycoprotein GP, which consists of subunits GP1 and GP2. GP1 binds to cellular receptors, including Niemann-Pick C1 (NPC1) protein, and GP2 is responsible for low pH-induced membrane fusion. Proteolytic cleavage and NPC1 binding at endosomal pH lead to conformational rearrangements of GP2 that include exposing the hydrophobic fusion loop (FL) for insertion into the cellular target membrane and forming a six-helix bundle structure. Although major portions of the GP2 structure have been solved in pre- and postfusion states and although current models place the transmembrane (TM) and FL domains of GP2 in close proximity at critical steps of membrane fusion, their structures in membrane environments, and especially interactions between them, have not yet been characterized. Here, we present the structure of the membrane proximal external region (MPER) connected to the TM domain: i.e., the missing parts of the EBOV GP2 structure. The structure, solved by solution NMR and EPR spectroscopy in membrane-mimetic environments, consists of a helix-turn-helix architecture that is independent of pH. Moreover, the MPER region is shown to interact in the membrane interface with the previously determined structure of the EBOV FL through several critical aromatic residues. Mutation of aromatic and neighboring residues in both binding partners decreases fusion and viral entry, highlighting the functional importance of the MPER/TM-FL interaction in EBOV entry and fusion.
Structure of a CLC chloride ion channel by cryo-electron microscopy

PubMed Central

Park, Eunyong; Campbell, Ernest B.; MacKinnon, Roderick

2017-01-01

CLC proteins transport chloride (Cl−) ions across cellular membranes to regulate muscle excitability, electrolyte movement across epithelia, and acidification of intracellular organelles. Some CLC proteins are channels that conduct Cl− ions passively, whereas others are secondary active transporters that exchange two Cl− ions for one H+. The structural basis underlying these distinctive transport mechanisms is puzzling because CLC channels and transporters are expected to share the same architecture based on sequence homology. To solve this puzzle we determined the structure of a mammalian CLC channel (CLC-K) using cryo-electron microscopy. A conserved loop in the Cl− transport pathway shows a structure markedly different from that of CLC transporters. Consequently, the cytosolic constriction for Cl− passage is widened in CLC-K such that the kinetic barrier previously postulated for Cl−/H+ transporter function would be reduced. Thus, reduction of a kinetic barrier in CLC channels enables fast flow of Cl− down its electrochemical gradient. PMID:28002411
Crystal structure of the Entamoeba histolytica RNA lariat debranching enzyme EhDbr1 reveals a catalytic Zn 2+/Mn 2+ heterobinucleation

DOE PAGES

Ransey, Elizabeth; Paredes, Eduardo; Dey, Sourav K.; ...

2017-05-17

Here, the RNA lariat debranching enzyme, Dbr1, is a metallophosphoesterase that cleaves 2'-5' phosphodiester bonds within intronic lariats. Previous reports have indicated that Dbr1 enzymatic activity is supported by diverse metal ions including Ni 2+, Mn 2+, Mg 2+, Fe 2+, and Zn 2+. While in initial structures of the Entamoeba histolytica Dbr1 only one of the two catalytic metal-binding sites were observed to be occupied (with a Mn 2+ ion), recent structures determined a Zn 2+/Fe 2+ heterobinucleation. We solved a high-resolution X-ray crystal structure (1.8 Å) of the E. histolytica Dbr1 and determined a Zn 2+/Mn 2+ occupancy.more » ICP-AES corroborate this finding, and in vitro debranching assays with fluorescently labeled branched substrates confirm activity.« less
Crystal structure of the Entamoeba histolytica RNA lariat debranching enzyme EhDbr1 reveals a catalytic Zn 2+/Mn 2+ heterobinucleation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ransey, Elizabeth; Paredes, Eduardo; Dey, Sourav K.

Here, the RNA lariat debranching enzyme, Dbr1, is a metallophosphoesterase that cleaves 2'-5' phosphodiester bonds within intronic lariats. Previous reports have indicated that Dbr1 enzymatic activity is supported by diverse metal ions including Ni 2+, Mn 2+, Mg 2+, Fe 2+, and Zn 2+. While in initial structures of the Entamoeba histolytica Dbr1 only one of the two catalytic metal-binding sites were observed to be occupied (with a Mn 2+ ion), recent structures determined a Zn 2+/Fe 2+ heterobinucleation. We solved a high-resolution X-ray crystal structure (1.8 Å) of the E. histolytica Dbr1 and determined a Zn 2+/Mn 2+ occupancy.more » ICP-AES corroborate this finding, and in vitro debranching assays with fluorescently labeled branched substrates confirm activity.« less
The Self-Organization of Insight: Entropy and Power Laws in Problem Solving

ERIC Educational Resources Information Center

Stephen, Damian G.; Dixon, James A.

2008-01-01

Explaining emergent structure remains a challenge for all areas of cognitive science, and problem solving is no exception. The modern study of insight has drawn attention to the issue of emergent cognitive structure in problem solving research. We propose that the explanation of insight is beyond the scope of conventional approaches to cognitive…
Ill-Structured Problem Solving of Novice Reading Specialists and Expert Assessment Specialists: Learning and Expertise

ERIC Educational Resources Information Center

Currie-Rubin, Rachel

2012-01-01

This dissertation examines the problem-solving processes of seven graduate student novices enrolled in a course in educational assessment and ten educational assessment experts. Using Jonassen's (1997) ill- and well-structured problem-solving frameworks, I analyze think-aloud protocols of experts and novices as they examine ill-structured…
Predicting protein structures with a multiplayer online game.

PubMed

Cooper, Seth; Khatib, Firas; Treuille, Adrien; Barbero, Janos; Lee, Jeehyung; Beenen, Michael; Leaver-Fay, Andrew; Baker, David; Popović, Zoran; Players, Foldit

2010-08-05

People exert large amounts of problem-solving effort playing computer games. Simple image- and text-recognition tasks have been successfully 'crowd-sourced' through games, but it is not clear if more complex scientific problems can be solved with human-directed computing. Protein structure prediction is one such problem: locating the biologically relevant native conformation of a protein is a formidable computational challenge given the very large size of the search space. Here we describe Foldit, a multiplayer online game that engages non-scientists in solving hard prediction problems. Foldit players interact with protein structures using direct manipulation tools and user-friendly versions of algorithms from the Rosetta structure prediction methodology, while they compete and collaborate to optimize the computed energy. We show that top-ranked Foldit players excel at solving challenging structure refinement problems in which substantial backbone rearrangements are necessary to achieve the burial of hydrophobic residues. Players working collaboratively develop a rich assortment of new strategies and algorithms; unlike computational approaches, they explore not only the conformational space but also the space of possible search strategies. The integration of human visual problem-solving and strategy development capabilities with traditional computational algorithms through interactive multiplayer games is a powerful new approach to solving computationally-limited scientific problems.
Three-Dimensional RNA Structure of the Major HIV-1 Packaging Signal Region

PubMed Central

Stephenson, James D.; Li, Haitao; Kenyon, Julia C.; Symmons, Martyn; Klenerman, Dave; Lever, Andrew M.L.

2013-01-01

Summary HIV-1 genomic RNA has a noncoding 5′ region containing sequential conserved structural motifs that control many parts of the life cycle. Very limited data exist on their three-dimensional (3D) conformation and, hence, how they work structurally. To assemble a working model, we experimentally reassessed secondary structure elements of a 240-nt region and used single-molecule distances, derived from fluorescence resonance energy transfer, between defined locations in these elements as restraints to drive folding of the secondary structure into a 3D model with an estimated resolution below 10 Å. The folded 3D model satisfying the data is consensual with short nuclear-magnetic-resonance-solved regions and reveals previously unpredicted motifs, offering insight into earlier functional assays. It is a 3D representation of this entire region, with implications for RNA dimerization and protein binding during regulatory steps. The structural information of this highly conserved region of the virus has the potential to reveal promising therapeutic targets. PMID:23685210
Crystal structures of η''-Cu3+xSi and η'''-Cu3+xSi.

PubMed

Corrêa, Cinthia Antunes; Perez, Olivier; Kopeček, Jaromír; Brázda, Petr; Klementová, Mariana; Palatinus, Lukáš

2017-08-01

The binary phase diagram of Cu-Si is unexpectedly complex in the vicinity of Cu 3+x Si. The low-temperature region contains three closely related incommensurately modulated phases denoted, in order of increasing temperature of stability, η''', η'' and η'. The structure analysis of η' has been reported previously [Palatinus et al. (2011). Inorg. Chem. 50, 3743]. Here the structure model for the phases η'' and η''' is reported. The structures could be solved in superspace, but no superspace structure model could be constructed due to the complexity of the modulation functions. Therefore, the structures were described in a supercell approximation, which involved a 4 × 4 × 3 supercell for the η'' phase and a 14 × 14 × 3 supercell for the η''' phase. Both structures are very similar and differ only by a subtle symmetry lowering from η'' to η'''. A comparison of the structure models of η'' and η''' with the reported structure of η' suggests that the reported structure model of η' contains an incorrect assignment of atomic types.
Observed Parenting Behavior with Teens: Measurement Invariance and Predictive Validity Across Race

PubMed Central

Skinner, Martie L.; MacKenzie, Elizabeth P.; Haggerty, Kevin P.; Hill, Karl G.; Roberson, Kendra C.

2011-01-01

Previous reports supporting measurement equality between European American and African American families have often focused on self-reported risk factors or observed parent behavior with young children. This study examines equality of measurement of observer ratings of parenting behavior with adolescents during structured tasks; mean levels of observed parenting; and predictive validity of teen self-reports of antisocial behaviors and beliefs using a sample of 163 African American and 168 European American families. Multiple-group confirmatory factor analyses supported measurement invariance across ethnic groups for 4 measures of observed parenting behavior: prosocial rewards, psychological costs, antisocial rewards, and problem solving. Some mean-level differences were found: African American parents exhibited lower levels of prosocial rewards, higher levels of psychological costs, and lower problem solving when compared to European Americans. No significant mean difference was found in rewards for antisocial behavior. Multigroup structural equation models suggested comparable relationships across race (predictive validity) between parenting constructs and youth antisocial constructs (i.e., drug initiation, positive drug attitudes, antisocial attitudes, problem behaviors) in all but one of the tested relationships. This study adds to existing evidence that family-based interventions targeting parenting behaviors can be generalized to African American families. PMID:21787057
Residue contacts predicted by evolutionary covariance extend the application of ab initio molecular replacement to larger and more challenging protein folds.

PubMed

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

2016-07-01

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

PubMed Central

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

2016-01-01

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

PubMed Central

Nogly, Przemyslaw; James, Daniel; Wang, Dingjie; White, Thomas A.; Zatsepin, Nadia; Shilova, Anastasya; Nelson, Garrett; Liu, Haiguang; Johansson, Linda; Heymann, Michael; Jaeger, Kathrin; Metz, Markus; Wickstrand, Cecilia; Wu, Wenting; Båth, Petra; Berntsen, Peter; Oberthuer, Dominik; Panneels, Valerie; Cherezov, Vadim; Chapman, Henry; Schertler, Gebhard; Neutze, Richard; Spence, John; Moraes, Isabel; Burghammer, Manfred; Standfuss, Joerg; Weierstall, Uwe

2015-01-01

Lipidic cubic phases (LCPs) have emerged as successful matrixes for the crystallization of membrane proteins. Moreover, the viscous LCP also provides a highly effective delivery medium for serial femtosecond crystallography (SFX) at X-ray free-electron lasers (XFELs). Here, the adaptation of this technology to perform serial millisecond crystallography (SMX) at more widely available synchrotron microfocus beamlines is described. Compared with conventional microcrystallography, LCP-SMX eliminates the need for difficult handling of individual crystals and allows for data collection at room temperature. The technology is demonstrated by solving a structure of the light-driven proton-pump bacteriorhodopsin (bR) at a resolution of 2.4 Å. The room-temperature structure of bR is very similar to previous cryogenic structures but shows small yet distinct differences in the retinal ligand and proton-transfer pathway. PMID:25866654
Reshaping of large aeronautical structural parts: A simplified simulation approach

NASA Astrophysics Data System (ADS)

Mena, Ramiro; Aguado, José V.; Guinard, Stéphane; Huerta, Antonio

2018-05-01

Large aeronautical structural parts present important distortions after machining. This problem is caused by the presence of residual stresses, which are developed during previous manufacturing steps (quenching). Before being put into service, the nominal geometry is restored by means of mechanical methods. This operation is called reshaping and exclusively depends on the skills of a well-trained and experienced operator. Moreover, this procedure is time consuming and nowadays, it is only based on a trial and error approach. Therefore, there is a need at industrial level to solve this problem with the support of numerical simulation tools. By using a simplification hypothesis, it was found that the springback phenomenon behaves linearly and it allows developing a strategy to implement reshaping at an industrial level.
Activity Structures and the Unfolding of Problem-Solving Actions in High-School Chemistry Classrooms

NASA Astrophysics Data System (ADS)

Criswell, Brett A.; Rushton, Greg T.

2014-02-01

In this paper, we argue for a more systematic approach for studying the relationship between classroom practices and scientific practices—an approach that will likely better support the systemic reforms being promoted in the Next Generation Science Standards in the USA and similar efforts in other countries. One component of that approach is looking at how the nature of the activity structure may influence the relative alignment between classroom and scientific practices. To that end, we build on previously published research related to the practices utilized by five high-school chemistry teachers as they enacted problem-solving activities in which students were likely to generate proposals that were not aligned with normative scientific understandings. In that prior work, our analysis had emphasized micro-level features of the talk interactions and how they related to the way students' ideas were explored; in the current paper, the analysis zooms out to consider the macro-level nature of the enactments associated with the activity structure of each lesson examined. Our data show that there were two general patterns to the activity structure across the 14 lessons scrutinized, and that each pattern had associated with it a constellation of features that impinged on the way the problem space was navigated. A key finding is that both activity structures (the expansive and the open) had features that aligned with scientific practices espoused in the Next Generation Science Standards—and both had features that were not aligned with those practices. We discuss the nature of these two structures, evidence of the relationship of each structure to key features of how the lessons unfolded, and the implications of these findings for both future research and the training of teachers.
Structures of the Procapsid and Mature Virion of Enterovirus 71 Strain 1095

PubMed Central

Cifuente, Javier O.; Lee, Hyunwook; Yoder, Joshua D.; Shingler, Kristin L.; Carnegie, Michael S.; Yoder, Jennifer L.; Ashley, Robert E.; Makhov, Alexander M.; Conway, James F.

2013-01-01

Enterovirus 71 (EV71) is an important emerging human pathogen with a global distribution and presents a disease pattern resembling poliomyelitis with seasonal epidemics that include cases of severe neurological complications, such as acute flaccid paralysis. EV71 is a member of the Picornaviridae family, which consists of icosahedral, nonenveloped, single-stranded RNA viruses. Here we report structures derived from X-ray crystallography and cryoelectron microscopy (cryo-EM) for the 1095 strain of EV71, including a putative precursor in virus assembly, the procapsid, and the mature virus capsid. The cryo-EM map of the procapsid provides new structural information on portions of the capsid proteins VP0 and VP1 that are disordered in the higher-resolution crystal structures. Our structures solved from virus particles in solution are largely in agreement with those from prior X-ray crystallographic studies; however, we observe small but significant structural differences for the 1095 procapsid compared to a structure solved in a previous study (X. Wang, W. Peng, J. Ren, Z. Hu, J. Xu, Z. Lou, X. Li, W. Yin, X. Shen, C. Porta, T. S. Walter, G. Evans, D. Axford, R. Owen, D. J. Rowlands, J. Wang, D. I. Stuart, E. E. Fry, and Z. Rao, Nat. Struct. Mol. Biol. 19:424–429, 2012) for a different strain of EV71. For both EV71 strains, the procapsid is significantly larger in diameter than the mature capsid, unlike in any other picornavirus. Nonetheless, our results demonstrate that picornavirus capsid expansion is possible without RNA encapsidation and that picornavirus assembly may involve an inward radial collapse of the procapsid to yield the native virion. PMID:23637404
Solution structure of the c-terminal dimerization domain of SARS coronavirus nucleocapsid protein solved by the SAIL-NMR method.

PubMed

Takeda, Mitsuhiro; Chang, Chung-ke; Ikeya, Teppei; Güntert, Peter; Chang, Yuan-hsiang; Hsu, Yen-lan; Huang, Tai-huang; Kainosho, Masatsune

2008-07-18

The C-terminal domain (CTD) of the severe acute respiratory syndrome coronavirus (SARS-CoV) nucleocapsid protein (NP) contains a potential RNA-binding region in its N-terminal portion and also serves as a dimerization domain by forming a homodimer with a molecular mass of 28 kDa. So far, the structure determination of the SARS-CoV NP CTD in solution has been impeded by the poor quality of NMR spectra, especially for aromatic resonances. We have recently developed the stereo-array isotope labeling (SAIL) method to overcome the size problem of NMR structure determination by utilizing a protein exclusively composed of stereo- and regio-specifically isotope-labeled amino acids. Here, we employed the SAIL method to determine the high-quality solution structure of the SARS-CoV NP CTD by NMR. The SAIL protein yielded less crowded and better resolved spectra than uniform (13)C and (15)N labeling, and enabled the homodimeric solution structure of this protein to be determined. The NMR structure is almost identical with the previously solved crystal structure, except for a disordered putative RNA-binding domain at the N-terminus. Studies of the chemical shift perturbations caused by the binding of single-stranded DNA and mutational analyses have identified the disordered region at the N-termini as the prime site for nucleic acid binding. In addition, residues in the beta-sheet region also showed significant perturbations. Mapping of the locations of these residues onto the helical model observed in the crystal revealed that these two regions are parts of the interior lining of the positively charged helical groove, supporting the hypothesis that the helical oligomer may form in solution.
Normal Science Education and its Dangers: The Case of School Chemistry

NASA Astrophysics Data System (ADS)

Van Berkel, Berry; De Vos, Wobbe; Verdonk, Adri H.; Pilot, Albert

We started the Conceptual Structure of School Chemistry research project, a part of which is reported on here, with an attempt to solve the problem of the hidden structure in school chemistry. In order to solve that problem, and informed by previous research, we performed a content analysis of school chemistry textbooks and syllabi. This led us to the hypothesis that school chemistry curricula are based on an underlying, coherent structure of chemical concepts that students are supposed to learn for the purpose of explaining and predicting chemical phenomena. The elicited comments and criticisms of an International Forum of twenty-eight researchers of chemical education, though, refuted the central claims of this hypothesis. This led to a descriptive theory of the currently dominant school chemistry curriculum in terms of a rigid combination of a specific substantive structure, based on corpuscular theory, a specific philosophical structure, educational positivism, and a specific pedagogical structure, involving initiatory and preparatory training of future chemists. Secondly, it led to an explanatory theory of the structure of school chemistry - based on Kuhn's theory of normal science and scientific training - in which dominant school chemistry is interpreted as a form of normal science education. Since the former has almost all characteristics in common with the latter, dominant school chemistry must be regarded as normal chemistry education. Forum members also formulated a number of normative criticisms on dominant school chemistry, which we interpret as specific dangers of normal chemistry education, complementing Popper's discussion of the general dangers of normal science and its teaching. On the basis of these criticisms, it is argued that normal chemistry education is isolated from common sense, everyday life and society, history and philosophy of science, technology, school physics, and from chemical research.
DOE Office of Scientific and Technical Information (OSTI.GOV)

Bowley, S.; Okumura, N; Lord, S

'A:a' knob-hole interactions and D:D interfacial interactions are important for fibrin polymerization. Previous studies with recombinant ?N308K fibrinogen, a substitution at the D:D interface, showed impaired polymerization. We examined the molecular basis for this loss of function by solving the crystal structure of ?N308K fragment D. In contrast to previous fragment D crystals, the ?N308K crystals belonged to a tetragonal space group with an unusually long unit cell (a = b = 95 Angstroms, c = 448.3 Angstroms). Alignment of the normal and ?N308K structures showed the global structure of the variant was not changed and the knob 'A' peptidemore » GPRP was bound as usual to hole 'a'. The substitution introduced an elongated positively charged patch in the D:D region. The structure showed novel, symmetric D:D crystal contacts between ?N308K molecules, indicating the normal asymmetric D:D interface in fibrin would be unstable in this variant. We examined GPRP binding to ?N308K in solution by plasmin protection assay. The results showed weaker peptide binding, suggesting that 'A:a' interactions were altered. We examined fibrin network structures by scanning electron microscopy and found the variant fibers were thicker and more heterogeneous than normal fibers. Considered together, our structural and biochemical studies indicate both 'A:a' and D:D interactions are weaker. We conclude that stable protofibrils cannot assemble from ?N308K monomers, leading to impaired polymerization.« less
Structure of a Premicellar Complex of Alkyl Sulfates with the Interfacial Binding Surfaces of 4 Subunits of Phospholipase A2✰

PubMed Central

Pan, Ying H.; Bahnson, Brian J.

2010-01-01

The properties of three discrete premicellar complexes (E1#, E2#, E3#) of pig pancreatic group-IB secreted phospholipase A2 (sPLA2) with monodisperse alkyl sulfates has been characterized [Berg, O. G., et al., Biochemistry 43, 7999–8013, 2004]. Here we have solved the 2.7 Å crystal structure of group-IB sPLA2 complexed with 12 molecules of octyl sulfate (C8S) in a form consistent with a tetrameric oligomeric that exists during the E1# phase of premicellar complexes. The alkyl tails of the C8S molecules are centered in the middle of the tetrameric cluster of sPLA2 subunits. Three of the four sPLA2 subunits also contain a C8S molecule in the active site pocket. The sulfate oxygen of a C8S ligand is complexed to the active site calcium in 3 of the 4 protein active sites. The interactions of the alkyl sulfate head group with Arg-6 and Lys-10, as well as the backbone amide of Met-20, are analogous to those observed in the previously solved sPLA2 crystal structures with bound phosphate and sulfate anions. The cluster of three anions found in the present structure is postulated to be the site for nucleating the binding of anionic amphiphiles to the interfacial surface of the protein, and therefore this binding interaction has implications for interfacial activation of the enzyme. PMID:20302975

Rapid Structured Volume Grid Smoothing and Adaption Technique

NASA Technical Reports Server (NTRS)

Alter, Stephen J.

2006-01-01

A rapid, structured volume grid smoothing and adaption technique, based on signal processing methods, was developed and applied to the Shuttle Orbiter at hypervelocity flight conditions in support of the Columbia Accident Investigation. Because of the fast pace of the investigation, computational aerothermodynamicists, applying hypersonic viscous flow solving computational fluid dynamic (CFD) codes, refined and enhanced a grid for an undamaged baseline vehicle to assess a variety of damage scenarios. Of the many methods available to modify a structured grid, most are time-consuming and require significant user interaction. By casting the grid data into different coordinate systems, specifically two computational coordinates with arclength as the third coordinate, signal processing methods are used for filtering the data [Taubin, CG v/29 1995]. Using a reverse transformation, the processed data are used to smooth the Cartesian coordinates of the structured grids. By coupling the signal processing method with existing grid operations within the Volume Grid Manipulator tool, problems related to grid smoothing are solved efficiently and with minimal user interaction. Examples of these smoothing operations are illustrated for reductions in grid stretching and volume grid adaptation. In each of these examples, other techniques existed at the time of the Columbia accident, but the incorporation of signal processing techniques reduced the time to perform the corrections by nearly 60%. This reduction in time to perform the corrections therefore enabled the assessment of approximately twice the number of damage scenarios than previously possible during the allocated investigation time.
Rapid Structured Volume Grid Smoothing and Adaption Technique

NASA Technical Reports Server (NTRS)

Alter, Stephen J.

2004-01-01

A rapid, structured volume grid smoothing and adaption technique, based on signal processing methods, was developed and applied to the Shuttle Orbiter at hypervelocity flight conditions in support of the Columbia Accident Investigation. Because of the fast pace of the investigation, computational aerothermodynamicists, applying hypersonic viscous flow solving computational fluid dynamic (CFD) codes, refined and enhanced a grid for an undamaged baseline vehicle to assess a variety of damage scenarios. Of the many methods available to modify a structured grid, most are time-consuming and require significant user interaction. By casting the grid data into different coordinate systems, specifically two computational coordinates with arclength as the third coordinate, signal processing methods are used for filtering the data [Taubin, CG v/29 1995]. Using a reverse transformation, the processed data are used to smooth the Cartesian coordinates of the structured grids. By coupling the signal processing method with existing grid operations within the Volume Grid Manipulator tool, problems related to grid smoothing are solved efficiently and with minimal user interaction. Examples of these smoothing operations are illustrated for reduction in grid stretching and volume grid adaptation. In each of these examples, other techniques existed at the time of the Columbia accident, but the incorporation of signal processing techniques reduced the time to perform the corrections by nearly 60%. This reduction in time to perform the corrections therefore enabled the assessment of approximately twice the number of damage scenarios than previously possible during the allocated investigation time.
Structural basis for non-competitive product inhibition in human thymidine phosphorylase: implications for drug design

PubMed Central

Omari, Kamel EL; Bronckaers, Annelies; Liekens, Sandra; Pérez-Pérez, Maria-Jésus; Balzarini, Jan; Stammers, David K.

2006-01-01

HTP (human thymidine phosphorylase), also known as PD-ECGF (platelet-derived endothelial cell growth factor) or gliostatin, has an important role in nucleoside metabolism. HTP is implicated in angiogenesis and apoptosis and therefore is a prime target for drug design, including antitumour therapies. An HTP structure in a closed conformation complexed with an inhibitor has previously been solved. Earlier kinetic studies revealed an ordered release of thymine followed by ribose phosphate and product inhibition by both ligands. We have determined the structure of HTP from crystals grown in the presence of thymidine, which, surprisingly, resulted in bound thymine with HTP in a closed dead-end com-plex. Thus thymine appears to be able to reassociate with HTP after its initial ordered release before ribose phosphate and induces the closed conformation, hence explaining the mechanism of non-competitive product inhibition. In the active site in one of the four HTP molecules within the crystal asymmetric unit, additional electron density is present. This density has not been previously seen in any pyrimidine nucleoside phosphorylase and it defines a subsite that may be exploitable in drug design. Finally, because our crystals did not require proteolysed HTP to grow, the structure reveals a loop (residues 406–415), disordered in the previous HTP structure. This loop extends across the active-site cleft and appears to stabilize the dimer interface and the closed conformation by hydrogen-bonding. The present study will assist in the design of HTP inhibitors that could lead to drugs for anti-angiogenesis as well as for the potentiation of other nucleoside drugs. PMID:16803458
The 2-D magnetotelluric inverse problem solved with optimization

NASA Astrophysics Data System (ADS)

van Beusekom, Ashley E.; Parker, Robert L.; Bank, Randolph E.; Gill, Philip E.; Constable, Steven

2011-02-01

The practical 2-D magnetotelluric inverse problem seeks to determine the shallow-Earth conductivity structure using finite and uncertain data collected on the ground surface. We present an approach based on using PLTMG (Piecewise Linear Triangular MultiGrid), a special-purpose code for optimization with second-order partial differential equation (PDE) constraints. At each frequency, the electromagnetic field and conductivity are treated as unknowns in an optimization problem in which the data misfit is minimized subject to constraints that include Maxwell's equations and the boundary conditions. Within this framework it is straightforward to accommodate upper and lower bounds or other conditions on the conductivity. In addition, as the underlying inverse problem is ill-posed, constraints may be used to apply various kinds of regularization. We discuss some of the advantages and difficulties associated with using PDE-constrained optimization as the basis for solving large-scale nonlinear geophysical inverse problems. Combined transverse electric and transverse magnetic complex admittances from the COPROD2 data are inverted. First, we invert penalizing size and roughness giving solutions that are similar to those found previously. In a second example, conventional regularization is replaced by a technique that imposes upper and lower bounds on the model. In both examples the data misfit is better than that obtained previously, without any increase in model complexity.
Structure of the cyanobactin oxidase ThcOx from Cyanothece sp. PCC 7425, the first structure to be solved at Diamond Light Source beamline I23 by means of S-SAD.

PubMed

Bent, Andrew F; Mann, Greg; Houssen, Wael E; Mykhaylyk, Vitaliy; Duman, Ramona; Thomas, Louise; Jaspars, Marcel; Wagner, Armin; Naismith, James H

2016-11-01

Determination of protein crystal structures requires that the phases are derived independently of the observed measurement of diffraction intensities. Many techniques have been developed to obtain phases, including heavy-atom substitution, molecular replacement and substitution during protein expression of the amino acid methionine with selenomethionine. Although the use of selenium-containing methionine has transformed the experimental determination of phases it is not always possible, either because the variant protein cannot be produced or does not crystallize. Phasing of structures by measuring the anomalous diffraction from S atoms could in theory be almost universal since almost all proteins contain methionine or cysteine. Indeed, many structures have been solved by the so-called native sulfur single-wavelength anomalous diffraction (S-SAD) phasing method. However, the anomalous effect is weak at the wavelengths where data are normally recorded (between 1 and 2 Å) and this limits the potential of this method to well diffracting crystals. Longer wavelengths increase the strength of the anomalous signal but at the cost of increasing air absorption and scatter, which degrade the precision of the anomalous measurement, consequently hindering phase determination. A new instrument, the long-wavelength beamline I23 at Diamond Light Source, was designed to work at significantly longer wavelengths compared with standard synchrotron beamlines in order to open up the native S-SAD method to projects of increasing complexity. Here, the first novel structure, that of the oxidase domain involved in the production of the natural product patellamide, solved on this beamline is reported using data collected to a resolution of 3.15 Å at a wavelength of 3.1 Å. The oxidase is an example of a protein that does not crystallize as the selenium variant and for which no suitable homology model for molecular replacement was available. Initial attempts collecting anomalous diffraction data for native sulfur phasing on a standard macromolecular crystallography beamline using a wavelength of 1.77 Å did not yield a structure. The new beamline thus has the potential to facilitate structure determination by native S-SAD phasing for what would previously have been regarded as very challenging cases with modestly diffracting crystals and low sulfur content.
Third Structure Determination by Powder Diffractometery Round Robin (SDPDRR-3)

DOE Office of Scientific and Technical Information (OSTI.GOV)

Le Bail, A.; Cranswick, L; Adil, K

2009-01-01

The results from a third structure determination by powder diffractometry (SDPD) round robin are discussed. From the 175 potential participants having downloaded the powder data, nine sent a total of 12 solutions (8 and 4 for samples 1 and 2, respectively, a tetrahydrated calcium tartrate and a lanthanum tungstate). Participants used seven different computer programs for structure solution (ESPOIR, EXPO, FOX, PSSP, SHELXS, SUPERFLIP, and TOPAS), applying Patterson, direct methods, direct space methods, and charge flipping approach. It is concluded that solving a structure from powder data remains a challenge, at least one order of magnitude more difficult than solvingmore » a problem with similar complexity from single-crystal data. Nevertheless, a few more steps in the direction of increasing the SDPD rate of success were accomplished since the two previous round robins: this time, not only the computer program developers were successful but also some users. No result was obtained from crystal structure prediction experts.« less
Crystal structure of a Schistosoma mansoni septin reveals the phenomenon of strand slippage in septins dependent on the nature of the bound nucleotide.

PubMed

Zeraik, Ana E; Pereira, Humberto M; Santos, Yuri V; Brandão-Neto, José; Spoerner, Michael; Santos, Maiara S; Colnago, Luiz A; Garratt, Richard C; Araújo, Ana P U; DeMarco, Ricardo

2014-03-14

Septins are filament-forming GTP-binding proteins involved in important cellular events, such as cytokinesis, barrier formation, and membrane remodeling. Here, we present two crystal structures of the GTPase domain of a Schistosoma mansoni septin (SmSEPT10), one bound to GDP and the other to GTP. The structures have been solved at an unprecedented resolution for septins (1.93 and 2.1 Å, respectively), which has allowed for unambiguous structural assignment of regions previously poorly defined. Consequently, we provide a reliable model for functional interpretation and a solid foundation for future structural studies. Upon comparing the two complexes, we observe for the first time the phenomenon of a strand slippage in septins. Such slippage generates a front-back communication mechanism between the G and NC interfaces. These data provide a novel mechanistic framework for the influence of nucleotide binding to the GTPase domain, opening new possibilities for the study of the dynamics of septin filaments.
GPCR-I-TASSER: A hybrid approach to G protein-coupled receptor structure modeling and the application to the human genome

PubMed Central

Zhang, Jian; Yang, Jianyi; Jang, Richard; Zhang, Yang

2015-01-01

SUMMARY Experimental structure determination remains very difficult for G protein-coupled receptors (GPCRs). We propose a new hybrid protocol to construct GPCR structure models that integrates experimental mutagenesis data with ab initio transmembrane (TM) helix assembly simulations. The method was tested on 24 known GPCRs where the ab initio TM-helix assembly procedure constructed the correct fold for 20 cases. When combined with weak-homology and sparse mutagenesis restraints, the method generated correct folds for all the tested cases with an average C-alpha RMSD 2.4 Å in the TM-regions. The new hybrid protocol was applied to model all 1026 GPCRs in the human genome, where 923 have a high confidence score that are expected to have correct folds; these contain many pharmaceutically important families with no previously solved structures, including Trace amine, Prostanoids, Releasing hormones, Melanocortins, Vasopressin and Neuropeptide Y receptors. The results demonstrate new progress on genome-wide structure modeling of transmembrane proteins. PMID:26190572
Structure of the full-length glucagon class B G protein-coupled receptor

PubMed Central

Zhang, Haonan; Qiao, Anna; Yang, Dehua; Yang, Linlin; Dai, Antao; de Graaf, Chris; Reedtz-Runge, Steffen; Dharmarajan, Venkatasubramanian; Zhang, Hui; Han, Gye Won; Grant, Thomas D.; Sierra, Raymond G.; Weierstall, Uwe; Nelson, Garrett; Liu, Wei; Wu, Yanhong; Ma, Limin; Cai, Xiaoqing; Lin, Guangyao; Wu, Xiaoai; Geng, Zhi; Dong, Yuhui; Song, Gaojie; Griffin, Patrick R.; Lau, Jesper; Cherezov, Vadim; Yang, Huaiyu; Hanson, Michael A.; Stevens, Raymond C.; Zhao, Qiang; Jiang, Hualiang; Wang, Ming-Wei; Wu, Beili

2017-01-01

The human glucagon receptor (GCGR) belongs to the class B G protein-coupled receptor (GPCR) family and plays a key role in glucose homeostasis and the pathophysiology of type 2 diabetes. Here we report the 3.0 Å crystal structure of full-length GCGR containing both extracellular domain (ECD) and transmembrane domain (TMD) in an inactive conformation. The two domains are connected by a 12-residue segment termed the ‘stalk’, which adopts a β-strand conformation, instead of forming an α-helix as observed in the previously solved structure of GCGR-TMD. The first extracellular loop (ECL1) exhibits a β-hairpin conformation and interacts with the stalk to form a compact β-sheet structure. Hydrogen/deuterium exchange, disulfide cross-linking and molecular dynamics studies suggest that the stalk and ECL1 play critical roles in modulating peptide ligand binding and receptor activation. These insights into the full-length GCGR structure deepen our understanding about the signaling mechanisms of class B GPCRs. PMID:28514451
Mercury increases water permeability of a plant aquaporin through a non-cysteine-related mechanism.

PubMed

Frick, Anna; Järvå, Michael; Ekvall, Mikael; Uzdavinys, Povilas; Nyblom, Maria; Törnroth-Horsefield, Susanna

2013-09-15

Water transport across cellular membranes is mediated by a family of membrane proteins known as AQPs (aquaporins). AQPs were first discovered on the basis of their ability to be inhibited by mercurial compounds, an experiment which has followed the AQP field ever since. Although mercury inhibition is most common, many AQPs are mercury insensitive. In plants, regulation of AQPs is important in order to cope with environmental changes. Plant plasma membrane AQPs are known to be gated by phosphorylation, pH and Ca²⁺. We have previously solved the structure of the spinach AQP SoPIP2;1 (Spinacia oleracea plasma membrane intrinsic protein 2;1) in closed and open conformations and proposed a mechanism for how this gating can be achieved. To study the effect of mercury on SoPIP2;1 we solved the structure of the SoPIP2;1-mercury complex and characterized the water transport ability using proteoliposomes. The structure revealed mercury binding to three out of four cysteine residues. In contrast to what is normally seen for AQPs, mercury increased the water transport rate of SoPIP2;1, an effect which could not be attributed to any of the cysteine residues. This indicates that other factors might influence the effect of mercury on SoPIP2;1, one of which could be the properties of the lipid bilayer.
Interference thinking in constructing students’ knowledge to solve mathematical problems

NASA Astrophysics Data System (ADS)

Jayanti, W. E.; Usodo, B.; Subanti, S.

2018-04-01

This research aims to describe interference thinking in constructing students’ knowledge to solve mathematical problems. Interference thinking in solving problems occurs when students have two concepts that interfere with each other’s concept. Construction of problem-solving can be traced using Piaget’s assimilation and accommodation framework, helping to know the students’ thinking structures in solving the problems. The method of this research was a qualitative method with case research strategy. The data in this research involving problem-solving result and transcripts of interviews about students’ errors in solving the problem. The results of this research focus only on the student who experience proactive interference, where student in solving a problem using old information to interfere with the ability to recall new information. The student who experience interference thinking in constructing their knowledge occurs when the students’ thinking structures in the assimilation and accommodation process are incomplete. However, after being given reflection to the student, then the students’ thinking process has reached equilibrium condition even though the result obtained remains wrong.
Associations of Patient Health-Related Problem Solving with Disease Control, Emergency Department Visits, and Hospitalizations in HIV and Diabetes Clinic Samples

PubMed Central

Gemmell, Leigh; Kulkarni, Babul; Klick, Brendan; Brancati, Frederick L.

2007-01-01

Background Patient problem solving and decision making are recognized as essential to effective self-management across multiple chronic diseases. However, a health-related problem-solving instrument that demonstrates sensitivity to disease control parameters in multiple diseases has not been established. Objectives To determine, in two disease samples, internal consistency and associations with disease control of the Health Problem-Solving Scale (HPSS), a 50-item measure with 7 subscales assessing effective and ineffective problem-solving approaches, learning from past experiences, and motivation/orientation. Design Cross-sectional study. Participants Outpatients from university-affiliated medical center HIV (N = 111) and diabetes mellitus (DM, N = 78) clinics. Measurements HPSS, CD4, hemoglobin A1c (HbA1c), and number of hospitalizations in the previous year and Emergency Department (ED) visits in the previous 6 months. Results Administration time for the HPSS ranged from 5 to 10 minutes. Cronbach’s alpha for the total HPSS was 0.86 and 0.89 for HIV and DM, respectively. Higher total scores (better problem solving) were associated with higher CD4 and fewer hospitalizations in HIV and lower HbA1c and fewer ED visits in DM. Health Problem-Solving Scale subscales representing negative problem-solving approaches were consistently associated with more hospitalizations (HIV, DM) and ED visits (DM). Conclusions The HPSS may identify problem-solving difficulties with disease self-management and assess effectiveness of interventions targeting patient decision making in self-care. PMID:17443373
On sufficient statistics of least-squares superposition of vector sets.

PubMed

Konagurthu, Arun S; Kasarapu, Parthan; Allison, Lloyd; Collier, James H; Lesk, Arthur M

2015-06-01

The problem of superposition of two corresponding vector sets by minimizing their sum-of-squares error under orthogonal transformation is a fundamental task in many areas of science, notably structural molecular biology. This problem can be solved exactly using an algorithm whose time complexity grows linearly with the number of correspondences. This efficient solution has facilitated the widespread use of the superposition task, particularly in studies involving macromolecular structures. This article formally derives a set of sufficient statistics for the least-squares superposition problem. These statistics are additive. This permits a highly efficient (constant time) computation of superpositions (and sufficient statistics) of vector sets that are composed from its constituent vector sets under addition or deletion operation, where the sufficient statistics of the constituent sets are already known (that is, the constituent vector sets have been previously superposed). This results in a drastic improvement in the run time of the methods that commonly superpose vector sets under addition or deletion operations, where previously these operations were carried out ab initio (ignoring the sufficient statistics). We experimentally demonstrate the improvement our work offers in the context of protein structural alignment programs that assemble a reliable structural alignment from well-fitting (substructural) fragment pairs. A C++ library for this task is available online under an open-source license.
The relation of locus-of-control orientation and task structure to problem-solving performance of sixth-grade student pairs

NASA Astrophysics Data System (ADS)

Main, June Dewey; Budd Rowe, Mary

This study investigated the relationship of locus-of-control orientations and task structure to the science problem-solving performance of 100 same-sex, sixth-grade student pairs. Pairs performed a four-variable problem-solving task, racing cylinders down a ramp in a series of trials to determine the 3 fastest of 18 different cylinders. The task was completed in one of two treatment conditions: the structured condition with moderate cuing and the unstructured condition with minimal cuing. Pairs completed an after-task assessment, predicting the results of proposed cylinder races, to measure the ability to understand and apply task concepts. Overall conclusions were: (1) There was no relationship between locus-of-control orientation and effectiveness of problem-solving strategy; (2) internality was significantly related to higher accuracy on task solutions and on after-task predictions; (3) there was no significant relationship between task structure and effectiveness of problem-solving strategy; (4) solutions to the task were more accurate in the unstructured task condition; (5) internality related to more accurate solutions in the unstructured task condition.
Solution structure of the phosphoryl transfer complex between the cytoplasmic A domain of the mannitol transporter IIMannitol and HPr of the Escherichia coli phosphotransferase system.

PubMed

Cornilescu, Gabriel; Lee, Byeong Ryong; Cornilescu, Claudia C; Wang, Guangshun; Peterkofsky, Alan; Clore, G Marius

2002-11-01

The solution structure of the complex between the cytoplasmic A domain (IIA(Mtl)) of the mannitol transporter II(Mannitol) and the histidine-containing phosphocarrier protein (HPr) of the Escherichia coli phosphotransferase system has been solved by NMR, including the use of conjoined rigid body/torsion angle dynamics, and residual dipolar couplings, coupled with cross-validation, to permit accurate orientation of the two proteins. A convex surface on HPr, formed by helices 1 and 2, interacts with a complementary concave depression on the surface of IIA(Mtl) formed by helix 3, portions of helices 2 and 4, and beta-strands 2 and 3. The majority of intermolecular contacts are hydrophobic, with a small number of electrostatic interactions at the periphery of the interface. The active site histidines, His-15 of HPr and His-65 of IIA(Mtl), are in close spatial proximity, and a pentacoordinate phosphoryl transition state can be readily accommodated with no change in protein-protein orientation and only minimal perturbations of the backbone immediately adjacent to the histidines. Comparison with two previously solved structures of complexes of HPr with partner proteins of the phosphotransferase system, the N-terminal domain of enzyme I (EIN) and enzyme IIA(Glucose) (IIA(Glc)), reveals a number of common features despite the fact that EIN, IIA(Glc), and IIA(Mtl) bear no structural resemblance to one another. Thus, entirely different underlying structural elements can form binding surfaces for HPr that are similar in terms of both shape and residue composition. These structural comparisons illustrate the roles of surface and residue complementarity, redundancy, incremental build-up of specificity and conformational side chain plasticity in the formation of transient specific protein-protein complexes in signal transduction pathways.
A Coding Scheme for Analysing Problem-Solving Processes of First-Year Engineering Students

ERIC Educational Resources Information Center

Grigg, Sarah J.; Benson, Lisa C.

2014-01-01

This study describes the development and structure of a coding scheme for analysing solutions to well-structured problems in terms of cognitive processes and problem-solving deficiencies for first-year engineering students. A task analysis approach was used to assess students' problem solutions using the hierarchical structure from a…
Factors of Problem-Solving Competency in a Virtual Chemistry Environment: The Role of Metacognitive Knowledge about Strategies

ERIC Educational Resources Information Center

Scherer, Ronny; Tiemann, Rudiger

2012-01-01

The ability to solve complex scientific problems is regarded as one of the key competencies in science education. Until now, research on problem solving focused on the relationship between analytical and complex problem solving, but rarely took into account the structure of problem-solving processes and metacognitive aspects. This paper,…
High-resolution combined global gravity field modelling: Solving large kite systems using distributed computational algorithms

NASA Astrophysics Data System (ADS)

Zingerle, Philipp; Fecher, Thomas; Pail, Roland; Gruber, Thomas

2016-04-01

One of the major obstacles in modern global gravity field modelling is the seamless combination of lower degree inhomogeneous gravity field observations (e.g. data from satellite missions) with (very) high degree homogeneous information (e.g. gridded and reduced gravity anomalies, beyond d/o 1000). Actual approaches mostly combine such data only on the basis of the coefficients, meaning that previously for both observation classes (resp. models) a spherical harmonic analysis is done independently, solving dense normal equations (NEQ) for the inhomogeneous model and block-diagonal NEQs for the homogeneous. Obviously those methods are unable to identify or eliminate effects as spectral leakage due to band limitations of the models and non-orthogonality of the spherical harmonic base functions. To antagonize such problems a combination of both models on NEQ-basis is desirable. Theoretically this can be achieved using NEQ-stacking. Because of the higher maximum degree of the homogeneous model a reordering of the coefficient is needed which leads inevitably to the destruction of the block diagonal structure of the appropriate NEQ-matrix and therefore also to the destruction of simple sparsity. Hence, a special coefficient ordering is needed to create some new favorable sparsity pattern leading to a later efficient computational solving method. Such pattern can be found in the so called kite-structure (Bosch, 1993), achieving when applying the kite-ordering to the stacked NEQ-matrix. In a first step it is shown what is needed to attain the kite-(NEQ)system, how to solve it efficiently and also how to calculate the appropriate variance information from it. Further, because of the massive computational workload when operating on large kite-systems (theoretically possible up to about max. d/o 100.000), the main emphasis is put on to the presentation of special distributed algorithms which may solve those systems parallel on an indeterminate number of processes and are therefore suitable for the application on supercomputers (such as SuperMUC). Finally, (if time or space) some in-detail problems are shown that occur when dealing with high degree spherical harmonic base functions (mostly due to instabilities of Legendre polynomials), introducing also an appropriate solution for each.
Ensembles generated from crystal structures of single distant homologues solve challenging molecular-replacement cases in AMPLE.

PubMed

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

2018-03-01

Molecular replacement (MR) is the predominant route to solution of the phase problem in macromolecular crystallography. Although routine in many cases, it becomes more effortful and often impossible when the available experimental structures typically used as search models are only distantly homologous to the target. Nevertheless, with current powerful MR software, relatively small core structures shared between the target and known structure, of 20-40% of the overall structure for example, can succeed as search models where they can be isolated. Manual sculpting of such small structural cores is rarely attempted and is dependent on the crystallographer's expertise and understanding of the protein family in question. Automated search-model editing has previously been performed on the basis of sequence alignment, in order to eliminate, for example, side chains or loops that are not present in the target, or on the basis of structural features (e.g. solvent accessibility) or crystallographic parameters (e.g. B factors). Here, based on recent work demonstrating a correlation between evolutionary conservation and protein rigidity/packing, novel automated ways to derive edited search models from a given distant homologue over a range of sizes are presented. A variety of structure-based metrics, many readily obtained from online webservers, can be fed to the MR pipeline AMPLE to produce search models that succeed with a set of test cases where expertly manually edited comparators, further processed in diverse ways with MrBUMP, fail. Further significant performance gains result when the structure-based distance geometry method CONCOORD is used to generate ensembles from the distant homologue. To our knowledge, this is the first such approach whereby a single structure is meaningfully transformed into an ensemble for the purposes of MR. Additional cases further demonstrate the advantages of the approach. CONCOORD is freely available and computationally inexpensive, so these novel methods offer readily available new routes to solve difficult MR cases.
Ensembles generated from crystal structures of single distant homologues solve challenging molecular-replacement cases in AMPLE

PubMed Central

Simpkin, Adam; Mayans, Olga; Keegan, Ronan M.

2018-01-01

Molecular replacement (MR) is the predominant route to solution of the phase problem in macromolecular crystallography. Although routine in many cases, it becomes more effortful and often impossible when the available experimental structures typically used as search models are only distantly homologous to the target. Nevertheless, with current powerful MR software, relatively small core structures shared between the target and known structure, of 20–40% of the overall structure for example, can succeed as search models where they can be isolated. Manual sculpting of such small structural cores is rarely attempted and is dependent on the crystallographer’s expertise and understanding of the protein family in question. Automated search-model editing has previously been performed on the basis of sequence alignment, in order to eliminate, for example, side chains or loops that are not present in the target, or on the basis of structural features (e.g. solvent accessibility) or crystallographic parameters (e.g. B factors). Here, based on recent work demonstrating a correlation between evolutionary conservation and protein rigidity/packing, novel automated ways to derive edited search models from a given distant homologue over a range of sizes are presented. A variety of structure-based metrics, many readily obtained from online webservers, can be fed to the MR pipeline AMPLE to produce search models that succeed with a set of test cases where expertly manually edited comparators, further processed in diverse ways with MrBUMP, fail. Further significant performance gains result when the structure-based distance geometry method CONCOORD is used to generate ensembles from the distant homologue. To our knowledge, this is the first such approach whereby a single structure is meaningfully transformed into an ensemble for the purposes of MR. Additional cases further demonstrate the advantages of the approach. CONCOORD is freely available and computationally inexpensive, so these novel methods offer readily available new routes to solve difficult MR cases. PMID:29533226

Computational structural mechanics for engine structures

NASA Technical Reports Server (NTRS)

Chamis, Christos C.

1988-01-01

The computational structural mechanics (CSM) program at Lewis encompasses the formulation and solution of structural mechanics problems and the development of integrated software systems to computationally simulate the performance, durability, and life of engine structures. It is structured to supplement, complement, and, whenever possible, replace costly experimental efforts. Specific objectives are to investigate unique advantages of parallel and multiprocessing for reformulating and solving structural mechanics and formulating and solving multidisciplinary mechanics and to develop integrated structural system computational simulators for predicting structural performance, evaluating newly developed methods, and identifying and prioritizing improved or missing methods.
Computational structural mechanics for engine structures

NASA Technical Reports Server (NTRS)

Chamis, Christos C.

1989-01-01

The computational structural mechanics (CSM) program at Lewis encompasses the formulation and solution of structural mechanics problems and the development of integrated software systems to computationally simulate the performance, durability, and life of engine structures. It is structured to supplement, complement, and, whenever possible, replace costly experimental efforts. Specific objectives are to investigate unique advantages of parallel and multiprocessing for reformulating and solving structural mechanics and formulating and solving multidisciplinary mechanics and to develop integrated structural system computational simulators for predicting structural performance, evaluating newly developed methods, and identifying and prioritizing improved or missing methods.
Crystal structure of lactose permease in complex with an affinity inactivator yields unique insight into sugar recognition

DOE Office of Scientific and Technical Information (OSTI.GOV)

Chaptal, Vincent; Kwon, Seunghyug; Sawaya, Michael R.

Lactose permease of Escherichia coli (LacY) with a single-Cys residue in place of A122 (helix IV) transports galactopyranosides and is specifically inactivated by methanethiosulfonyl-galactopyranosides (MTS-gal), which behave as unique suicide substrates. In order to study the mechanism of inactivation more precisely, we solved the structure of single-Cys122 LacY in complex with covalently bound MTS-gal. This structure exhibits an inward-facing conformation similar to that observed previously with a slight narrowing of the cytoplasmic cavity. MTS-gal is bound covalently, forming a disulfide bond with C122 and positioned between R144 and W151. E269, a residue essential for binding, coordinates the C-4 hydroxyl ofmore » the galactopyranoside moiety. The location of the sugar is in accord with many biochemical studies.« less
GPU computing with Kaczmarz’s and other iterative algorithms for linear systems

PubMed Central

Elble, Joseph M.; Sahinidis, Nikolaos V.; Vouzis, Panagiotis

2009-01-01

The graphics processing unit (GPU) is used to solve large linear systems derived from partial differential equations. The differential equations studied are strongly convection-dominated, of various sizes, and common to many fields, including computational fluid dynamics, heat transfer, and structural mechanics. The paper presents comparisons between GPU and CPU implementations of several well-known iterative methods, including Kaczmarz’s, Cimmino’s, component averaging, conjugate gradient normal residual (CGNR), symmetric successive overrelaxation-preconditioned conjugate gradient, and conjugate-gradient-accelerated component-averaged row projections (CARP-CG). Computations are preformed with dense as well as general banded systems. The results demonstrate that our GPU implementation outperforms CPU implementations of these algorithms, as well as previously studied parallel implementations on Linux clusters and shared memory systems. While the CGNR method had begun to fall out of favor for solving such problems, for the problems studied in this paper, the CGNR method implemented on the GPU performed better than the other methods, including a cluster implementation of the CARP-CG method. PMID:20526446
Impulsivity as a mediator in the relationship between problem solving and suicidal ideation.

PubMed

Gonzalez, Vivian M; Neander, Lucía L

2018-03-15

This study examined whether three facets of impulsivity previously shown to be associated with suicidal ideation and attempts (negative urgency, lack of premeditation, and lack of perseverance) help to account for the established association between problem solving deficits and suicidal ideation. Emerging adult college student drinkers with a history of at least passive suicidal ideation (N = 387) completed measures of problem solving, impulsivity, and suicidal ideation. A path analysis was conducted to examine the mediating role of impulsivity variables in the association between problem solving (rational problem solving, positive and negative problem orientation, and avoidance style) and suicidal ideation. Direct and indirect associations through impulsivity, particularly negative urgency, were found between problem solving and severity of suicidal ideation. Interventions aimed at teaching problem solving skills, as well as self-efficacy and optimism for solving life problems, may help to reduce impulsivity and suicidal ideation. © 2018 Wiley Periodicals, Inc.
The Influence of Science Knowledge Structures on Children's Success in Solving Academic Problems.

ERIC Educational Resources Information Center

Champagne, Audrey B.; And Others

Presented is a study of eighth-grade students' academic problem-solving ability based on their knowledge structures, or their information stored in semantic or long-term memory. The authors describe a technique that they developed to probe knowledge structures with an extension of the card-sort method. The method, known as the Concept Structure…
Obstacles Related to Structuring for Mathematization Encountered by Students When Solving Physics Problems

ERIC Educational Resources Information Center

Niss, Martin

2017-01-01

This paper studies the cognitive obstacles related to one aspect of mathematization in physics problem-solving, namely, what might be called "structuring for mathematization," where the problem situation is structured in such a way that a translation to a mathematical universe can be done. We report the results of an analysis of four…
Introducing Algebraic Structures through Solving Equations: Vertical Content Knowledge for K-12 Mathematics Teachers

ERIC Educational Resources Information Center

Wasserman, Nicholas H.

2014-01-01

Algebraic structures are a necessary aspect of algebraic thinking for K-12 students and teachers. An approach for introducing the algebraic structure of groups and fields through the arithmetic properties required for solving simple equations is summarized; the collective (not individual) importance of these axioms as a foundation for algebraic…
Using a Semantic Diagram to Structure a Collaborative Problem Solving Process in the Classroom

ERIC Educational Resources Information Center

Cai, Huiying; Lin, Lin; Gu, Xiaoqing

2016-01-01

This study provides an in-depth look into the implementation process of visualization-based tools for structuring collaborative problem solving (CPS) in the classroom. A visualization-based learning platform--the semantic diagram for structuring CPS in a real classroom was designed and implemented. Metafora, the preliminary vehicle of the semantic…
The fundamentals behind solving for unknown molecular structures using computer-assisted structure elucidation: a free software package at the undergraduate and graduate levels.

PubMed

Moser, Arvin; Pautler, Brent G

2016-05-15

The successful elucidation of an unknown compound's molecular structure often requires an analyst with profound knowledge and experience of advanced spectroscopic techniques, such as Nuclear Magnetic Resonance (NMR) spectroscopy and mass spectrometry. The implementation of Computer-Assisted Structure Elucidation (CASE) software in solving for unknown structures, such as isolated natural products and/or reaction impurities, can serve both as elucidation and teaching tools. As such, the introduction of CASE software with 112 exercises to train students in conjunction with the traditional pen and paper approach will strengthen their overall understanding of solving unknowns and explore of various structural end points to determine the validity of the results quickly. Copyright © 2016 John Wiley & Sons, Ltd. Copyright © 2016 John Wiley & Sons, Ltd.
Investigation of the viscous reconnection phenomenon of two vortex tubes through spectral simulations

NASA Astrophysics Data System (ADS)

Beardsell, Guillaume; Dufresne, Louis; Dumas, Guy

2016-09-01

This paper aims to shed further light on the viscous reconnection phenomenon. To this end, we propose a robust and efficient method in order to quantify the degree of reconnection of two vortex tubes. This method is used to compare the evolutions of two simple initial vortex configurations: orthogonal and antiparallel. For the antiparallel configuration, the proposed method is compared with alternative estimators and it is found to improve accuracy since it can account properly for the formation of looping structures inside the domain. This observation being new, the physical mechanism for the formation of those looping structures is discussed. For the orthogonal configuration, we report results from simulations that were performed at a much higher vortex Reynolds number (ReΓ ≡ circulation/viscosity = 104) and finer resolution (N3 = 10243) than previously presented in the literature. The incompressible Navier-stokes equations are solved directly (Direct Numerical Simulation or DNS) using a Fourier pseudospectral algorithm with triply periodic boundary conditions. The associated zero-circulation constraint is circumvented by solving the governing equations in a proper rotating frame of reference. Using ideas similar to those behind our method to compute the degree of reconnection, we split the vorticity field into its reconnected and non-reconnected parts, which allows to create insightful visualizations of the evolving vortex topology. It also allows to detect regions in the vorticity field that are neither reconnected nor non-reconnected and thus must be associated to internal looping structures. Finally, the Reynolds number dependence of the reconnection time scale Trec is investigated in the range 500 ≤ ReΓ ≤ 10 000. For both initial configurations, the scaling is generally found to vary continuously as ReΓ is increased from T rec ˜ R eΓ - 1 to T rec ˜ R eΓ - 1 / 2 , thus providing quantitative support for previous claims that the reconnection physics of two vortices should be similar regardless of their spatial arrangement.
Ill-defined problem solving in amnestic mild cognitive impairment: linking episodic memory to effective solution generation.

PubMed

Sheldon, S; Vandermorris, S; Al-Haj, M; Cohen, S; Winocur, G; Moscovitch, M

2015-02-01

It is well accepted that the medial temporal lobes (MTL), and the hippocampus specifically, support episodic memory processes. Emerging evidence suggests that these processes also support the ability to effectively solve ill-defined problems which are those that do not have a set routine or solution. To test the relation between episodic memory and problem solving, we examined the ability of individuals with single domain amnestic mild cognitive impairment (aMCI), a condition characterized by episodic memory impairment, to solve ill-defined social problems. Participants with aMCI and age and education matched controls were given a battery of tests that included standardized neuropsychological measures, the Autobiographical Interview (Levine et al., 2002) that scored for episodic content in descriptions of past personal events, and a measure of ill-defined social problem solving. Corroborating previous findings, the aMCI group generated less episodically rich narratives when describing past events. Individuals with aMCI also generated less effective solutions when solving ill-defined problems compared to the control participants. Correlation analyses demonstrated that the ability to recall episodic elements from autobiographical memories was positively related to the ability to effectively solve ill-defined problems. The ability to solve these ill-defined problems was related to measures of activities of daily living. In conjunction with previous reports, the results of the present study point to a new functional role of episodic memory in ill-defined goal-directed behavior and other non-memory tasks that require flexible thinking. Our findings also have implications for the cognitive and behavioural profile of aMCI by suggesting that the ability to effectively solve ill-defined problems is related to sustained functional independence. Copyright © 2015 Elsevier Ltd. All rights reserved.
Using Digital Mapping Tool in Ill-Structured Problem Solving

ERIC Educational Resources Information Center

Bai, Hua

2013-01-01

Scaffolding students' problem solving and helping them to improve problem solving skills are critical in instructional design courses. This study investigated the effects of students' uses of a digital mapping tool on their problem solving performance in a design case study. It was found that the students who used the digital mapping tool…
A new modified conjugate gradient coefficient for solving system of linear equations

NASA Astrophysics Data System (ADS)

Hajar, N.; ‘Aini, N.; Shapiee, N.; Abidin, Z. Z.; Khadijah, W.; Rivaie, M.; Mamat, M.

2017-09-01

Conjugate gradient (CG) method is an evolution of computational method in solving unconstrained optimization problems. This approach is easy to implement due to its simplicity and has been proven to be effective in solving real-life application. Although this field has received copious amount of attentions in recent years, some of the new approaches of CG algorithm cannot surpass the efficiency of the previous versions. Therefore, in this paper, a new CG coefficient which retains the sufficient descent and global convergence properties of the original CG methods is proposed. This new CG is tested on a set of test functions under exact line search. Its performance is then compared to that of some of the well-known previous CG methods based on number of iterations and CPU time. The results show that the new CG algorithm has the best efficiency amongst all the methods tested. This paper also includes an application of the new CG algorithm for solving large system of linear equations
Student’s scheme in solving mathematics problems

NASA Astrophysics Data System (ADS)

Setyaningsih, Nining; Juniati, Dwi; Suwarsono

2018-03-01

The purpose of this study was to investigate students’ scheme in solving mathematics problems. Scheme are data structures for representing the concepts stored in memory. In this study, we used it in solving mathematics problems, especially ratio and proportion topics. Scheme is related to problem solving that assumes that a system is developed in the human mind by acquiring a structure in which problem solving procedures are integrated with some concepts. The data were collected by interview and students’ written works. The results of this study revealed are students’ scheme in solving the problem of ratio and proportion as follows: (1) the content scheme, where students can describe the selected components of the problem according to their prior knowledge, (2) the formal scheme, where students can explain in construct a mental model based on components that have been selected from the problem and can use existing schemes to build planning steps, create something that will be used to solve problems and (3) the language scheme, where students can identify terms, or symbols of the components of the problem.Therefore, by using the different strategies to solve the problems, the students’ scheme in solving the ratio and proportion problems will also differ.
Tertiary model of a plant cellulose synthase

PubMed Central

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

2013-01-01

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

NASA Astrophysics Data System (ADS)

Qiao, Baijie; Zhang, Xingwu; Gao, Jiawei; Liu, Ruonan; Chen, Xuefeng

2017-01-01

Most previous regularization methods for solving the inverse problem of force reconstruction are to minimize the l2-norm of the desired force. However, these traditional regularization methods such as Tikhonov regularization and truncated singular value decomposition, commonly fail to solve the large-scale ill-posed inverse problem in moderate computational cost. In this paper, taking into account the sparse characteristic of impact force, the idea of sparse deconvolution is first introduced to the field of impact force reconstruction and a general sparse deconvolution model of impact force is constructed. Second, a novel impact force reconstruction method based on the primal-dual interior point method (PDIPM) is proposed to solve such a large-scale sparse deconvolution model, where minimizing the l2-norm is replaced by minimizing the l1-norm. Meanwhile, the preconditioned conjugate gradient algorithm is used to compute the search direction of PDIPM with high computational efficiency. Finally, two experiments including the small-scale or medium-scale single impact force reconstruction and the relatively large-scale consecutive impact force reconstruction are conducted on a composite wind turbine blade and a shell structure to illustrate the advantage of PDIPM. Compared with Tikhonov regularization, PDIPM is more efficient, accurate and robust whether in the single impact force reconstruction or in the consecutive impact force reconstruction.
A poroplastic model of structural reorganisation in porous media of biomechanical interest

NASA Astrophysics Data System (ADS)

Grillo, Alfio; Prohl, Raphael; Wittum, Gabriel

2016-03-01

We present a poroplastic model of structural reorganisation in a binary mixture comprising a solid and a fluid phase. The solid phase is the macroscopic representation of a deformable porous medium, which exemplifies the matrix of a biological system (consisting e.g. of cells, extracellular matrix, collagen fibres). The fluid occupies the interstices of the porous medium and is allowed to move throughout it. The system reorganises its internal structure in response to mechanical stimuli. Such structural reorganisation, referred to as remodelling, is described in terms of "plastic" distortions, whose evolution is assumed to obey a phenomenological flow rule driven by stress. We study the influence of remodelling on the mechanical and hydraulic behaviour of the system, showing how the plastic distortions modulate the flow pattern of the fluid, and the distributions of pressure and stress inside it. To accomplish this task, we solve a highly nonlinear set of model equations by elaborating a previously developed numerical procedure, which is implemented in a non-commercial finite element solver.
Unravelling the molecular structure and packing of a planar molecule by combining nuclear magnetic resonance and scanning tunneling microscopy.

PubMed

Sáfar, Gustavo A M; Malachias, Angelo; Magalhães-Paniago, Rogério; Martins, Dayse C S; Idemori, Ynara M

2013-12-21

The determination of the molecular structure of a porphyrin is achieved by using nuclear magnetic resonance (NMR) and scanning tunneling microscopy (STM) techniques. Since macroscopic crystals cannot be obtained in this system, this combination of techniques is crucial to solve the molecular structure without the need for X-ray crystallography. For this purpose, previous knowledge of the flatness of the reagent molecules (a porphyrin and its functionalizing group, a naphthalimide) and the resulting molecular structure obtained by a force-field simulation are used. The exponents of the I-V curves obtained by scanning tunneling spectroscopy (STS) allow us to check whether the thickness of the film of molecules is greater than a monolayer, even when there is no direct access to the exposed surface of the metal substrate. Photoluminescence (PL), optical absorption, infrared (IR) reflectance and solubility tests are used to confirm the results obtained here with this NMR/STM/STS combination.
Social learning strategies modify the effect of network structure on group performance.

PubMed

Barkoczi, Daniel; Galesic, Mirta

2016-10-07

The structure of communication networks is an important determinant of the capacity of teams, organizations and societies to solve policy, business and science problems. Yet, previous studies reached contradictory results about the relationship between network structure and performance, finding support for the superiority of both well-connected efficient and poorly connected inefficient network structures. Here we argue that understanding how communication networks affect group performance requires taking into consideration the social learning strategies of individual team members. We show that efficient networks outperform inefficient networks when individuals rely on conformity by copying the most frequent solution among their contacts. However, inefficient networks are superior when individuals follow the best member by copying the group member with the highest payoff. In addition, groups relying on conformity based on a small sample of others excel at complex tasks, while groups following the best member achieve greatest performance for simple tasks. Our findings reconcile contradictory results in the literature and have broad implications for the study of social learning across disciplines.

Social learning strategies modify the effect of network structure on group performance

NASA Astrophysics Data System (ADS)

Barkoczi, Daniel; Galesic, Mirta

2016-10-01

The structure of communication networks is an important determinant of the capacity of teams, organizations and societies to solve policy, business and science problems. Yet, previous studies reached contradictory results about the relationship between network structure and performance, finding support for the superiority of both well-connected efficient and poorly connected inefficient network structures. Here we argue that understanding how communication networks affect group performance requires taking into consideration the social learning strategies of individual team members. We show that efficient networks outperform inefficient networks when individuals rely on conformity by copying the most frequent solution among their contacts. However, inefficient networks are superior when individuals follow the best member by copying the group member with the highest payoff. In addition, groups relying on conformity based on a small sample of others excel at complex tasks, while groups following the best member achieve greatest performance for simple tasks. Our findings reconcile contradictory results in the literature and have broad implications for the study of social learning across disciplines.
Bacteriophage P23-77 Capsid Protein Structures Reveal the Archetype of an Ancient Branch from a Major Virus Lineage

PubMed Central

Rissanen, Ilona; Grimes, Jonathan M.; Pawlowski, Alice; Mäntynen, Sari; Harlos, Karl; Bamford, Jaana K.H.; Stuart, David I.

2013-01-01

Summary It has proved difficult to classify viruses unless they are closely related since their rapid evolution hinders detection of remote evolutionary relationships in their genetic sequences. However, structure varies more slowly than sequence, allowing deeper evolutionary relationships to be detected. Bacteriophage P23-77 is an example of a newly identified viral lineage, with members inhabiting extreme environments. We have solved multiple crystal structures of the major capsid proteins VP16 and VP17 of bacteriophage P23-77. They fit the 14 Å resolution cryo-electron microscopy reconstruction of the entire virus exquisitely well, allowing us to propose a model for both the capsid architecture and viral assembly, quite different from previously published models. The structures of the capsid proteins and their mode of association to form the viral capsid suggest that the P23-77-like and adeno-PRD1 lineages of viruses share an extremely ancient common ancestor. PMID:23623731
A Cognitive Analysis of Students’ Mathematical Problem Solving Ability on Geometry

NASA Astrophysics Data System (ADS)

Rusyda, N. A.; Kusnandi, K.; Suhendra, S.

2017-09-01

The purpose of this research is to analyze of mathematical problem solving ability of students in one of secondary school on geometry. This research was conducted by using quantitative approach with descriptive method. Population in this research was all students of that school and the sample was twenty five students that was chosen by purposive sampling technique. Data of mathematical problem solving were collected through essay test. The results showed the percentage of achievement of mathematical problem solving indicators of students were: 1) solve closed mathematical problems with context in math was 50%; 2) solve the closed mathematical problems with the context beyond mathematics was 24%; 3) solving open mathematical problems with contexts in mathematics was 35%; And 4) solving open mathematical problems with contexts outside mathematics was 44%. Based on the percentage, it can be concluded that the level of achievement of mathematical problem solving ability in geometry still low. This is because students are not used to solving problems that measure mathematical problem solving ability, weaknesses remember previous knowledge, and lack of problem solving framework. So the students’ ability of mathematical problems solving need to be improved with implement appropriate learning strategy.
Knowledge acquisition from natural language for expert systems based on classification problem-solving methods

NASA Technical Reports Server (NTRS)

Gomez, Fernando

1989-01-01

It is shown how certain kinds of domain independent expert systems based on classification problem-solving methods can be constructed directly from natural language descriptions by a human expert. The expert knowledge is not translated into production rules. Rather, it is mapped into conceptual structures which are integrated into long-term memory (LTM). The resulting system is one in which problem-solving, retrieval and memory organization are integrated processes. In other words, the same algorithm and knowledge representation structures are shared by these processes. As a result of this, the system can answer questions, solve problems or reorganize LTM.
Task-specific modulation of adult humans' tool preferences: number of choices and size of the problem.

PubMed

Silva, Kathleen M; Gross, Thomas J; Silva, Francisco J

2015-03-01

In two experiments, we examined the effect of modifications to the features of a stick-and-tube problem on the stick lengths that adult humans used to solve the problem. In Experiment 1, we examined whether people's tool preferences for retrieving an out-of-reach object in a tube might more closely resemble those reported with laboratory crows if people could modify a single stick to an ideal length to solve the problem. Contrary to when adult humans have selected a tool from a set of ten sticks, asking people to modify a single stick to retrieve an object did not generally result in a stick whose length was related to the object's distance. Consistent with the prior research, though, the working length of the stick was related to the object's distance. In Experiment 2, we examined the effect of increasing the scale of the stick-and-tube problem on people's tool preferences. Increasing the scale of the task influenced people to select relatively shorter tools than had selected in previous studies. Although the causal structures of the tasks used in the two experiments were identical, their results were not. This underscores the necessity of studying physical cognition in relation to a particular causal structure by using a variety of tasks and methods.
The effect of metallicity on the atmospheres of exoplanets with fully coupled 3D hydrodynamics, equilibrium chemistry, and radiative transfer

NASA Astrophysics Data System (ADS)

Drummond, B.; Mayne, N. J.; Baraffe, I.; Tremblin, P.; Manners, J.; Amundsen, D. S.; Goyal, J.; Acreman, D.

2018-05-01

In this work, we have performed a series of simulations of the atmosphere of GJ 1214b assuming different metallicities using the Met Office Unified Model (UM). The UM is a general circulation model (GCM) that solves the deep, non-hydrostatic equations of motion and uses a flexible and accurate radiative transfer scheme, based on the two-stream and correlated-k approximations, to calculate the heating rates. In this work we consistently couple a well-tested Gibbs energy minimisation scheme to solve for the chemical equilibrium abundances locally in each grid cell for a general set of elemental abundances, further improving the flexibility and accuracy of the model. As the metallicity of the atmosphere is increased we find significant changes in the dynamical and thermal structure, with subsequent implications for the simulated phase curve. The trends that we find are qualitatively consistent with previous works, though with quantitative differences. We investigate in detail the effect of increasing the metallicity by splitting the mechanism into constituents, involving the mean molecular weight, the heat capacity and the opacities. We find the opacity effect to be the dominant mechanism in altering the circulation and thermal structure. This result highlights the importance of accurately computing the opacities and radiative transfer in 3D GCMs.
Balancing antagonistic time and resource utilization constraints in over-subscribed scheduling problems

NASA Technical Reports Server (NTRS)

Smith, Stephen F.; Pathak, Dhiraj K.

1991-01-01

In this paper, we report work aimed at applying concepts of constraint-based problem structuring and multi-perspective scheduling to an over-subscribed scheduling problem. Previous research has demonstrated the utility of these concepts as a means for effectively balancing conflicting objectives in constraint-relaxable scheduling problems, and our goal here is to provide evidence of their similar potential in the context of HST observation scheduling. To this end, we define and experimentally assess the performance of two time-bounded heuristic scheduling strategies in balancing the tradeoff between resource setup time minimization and satisfaction of absolute time constraints. The first strategy considered is motivated by dispatch-based manufacturing scheduling research, and employs a problem decomposition that concentrates local search on minimizing resource idle time due to setup activities. The second is motivated by research in opportunistic scheduling and advocates a problem decomposition that focuses attention on the goal activities that have the tightest temporal constraints. Analysis of experimental results gives evidence of differential superiority on the part of each strategy in different problem solving circumstances. A composite strategy based on recognition of characteristics of the current problem solving state is then defined and tested to illustrate the potential benefits of constraint-based problem structuring and multi-perspective scheduling in over-subscribe scheduling problems.
Structure of a premicellar complex of alkyl sulfates with the interfacial binding surfaces of four subunits of phospholipase A2.

PubMed

Pan, Ying H; Bahnson, Brian J

2010-07-01

The properties of three discrete premicellar complexes (E1#, E2#, E3#) of pig pancreatic group-IB secreted phospholipase A2 (sPLA2) with monodisperse alkyl sulfates have been characterized [Berg, O. G. et al., Biochemistry 43, 7999-8013, 2004]. Here we have solved the 2.7 A crystal structure of group-IB sPLA2 complexed with 12 molecules of octyl sulfate (C8S) in a form consistent with a tetrameric oligomeric that exists during the E1# phase of premicellar complexes. The alkyl tails of the C8S molecules are centered in the middle of the tetrameric cluster of sPLA2 subunits. Three of the four sPLA2 subunits also contain a C8S molecule in the active site pocket. The sulfate oxygen of a C8S ligand is complexed to the active site calcium in three of the four protein active sites. The interactions of the alkyl sulfate head group with Arg-6 and Lys-10, as well as the backbone amide of Met-20, are analogous to those observed in the previously solved sPLA2 crystal structures with bound phosphate and sulfate anions. The cluster of three anions found in the present structure is postulated to be the site for nucleating the binding of anionic amphiphiles to the interfacial surface of the protein, and therefore this binding interaction has implications for interfacial activation of the enzyme. Copyright (c) 2010 Elsevier B.V. All rights reserved.
W-algebra for solving problems with fuzzy parameters

NASA Astrophysics Data System (ADS)

Shevlyakov, A. O.; Matveev, M. G.

2018-03-01

A method of solving the problems with fuzzy parameters by means of a special algebraic structure is proposed. The structure defines its operations through operations on real numbers, which simplifies its use. It avoids deficiencies limiting applicability of the other known structures. Examples for solution of a quadratic equation, a system of linear equations and a network planning problem are given.
NCI Scientists Solve Structure of Protein that Enables MERS Virus to Spread | Poster

Cancer.gov

Scientists at the Frederick National Lab have produced three crystal structures that reveal a specific part of a protein that can be targeted to fight the Middle East respiratory syndrome coronavirus (MERS-CoV), which causes an emerging viral respiratory illness. Senior Investigator David Waugh, Ph.D., Macromolecular Crystallography Laboratory, has solved the structure of an
Anticipating students' reasoning and planning prompts in structured problem-solving lessons

NASA Astrophysics Data System (ADS)

Vale, Colleen; Widjaja, Wanty; Doig, Brian; Groves, Susie

2018-02-01

Structured problem-solving lessons are used to explore mathematical concepts such as pattern and relationships in early algebra, and regularly used in Japanese Lesson Study research lessons. However, enactment of structured problem-solving lessons which involves detailed planning, anticipation of student solutions and orchestration of whole-class discussion of solutions is an ongoing challenge for many teachers. Moreover, primary teachers have limited experience in teaching early algebra or mathematical reasoning actions such as generalising. In this study, the critical factors of enacting the structured problem-solving lessons used in Japanese Lesson Study to elicit and develop primary students' capacity to generalise are explored. Teachers from three primary schools participated in two Japanese Lesson Study teams for this study. The lesson plans and video recordings of teaching and post-lesson discussion of the two research lessons along with students' responses and learning are compared to identify critical factors. The anticipation of students' reasoning together with preparation of supporting and challenging prompts was critical for scaffolding students' capacity to grasp and communicate generality.
Mutations that stabilize the open state of the Erwinia chrisanthemi ligand-gated ion channel fail to change the conformation of the pore domain in crystals

PubMed Central

Gonzalez-Gutierrez, Giovanni; Lukk, Tiit; Agarwal, Vinayak; Papke, David; Nair, Satish K.; Grosman, Claudio

2012-01-01

The determination of structural models of the various stable states of an ion channel is a key step toward the characterization of its conformational dynamics. In the case of nicotinic-type receptors, different structures have been solved but, thus far, these different models have been obtained from different members of the superfamily. In the case of the bacterial member ELIC, a cysteamine-gated channel from Erwinia chrisanthemi, a structural model of the protein in the absence of activating ligand (and thus, conceivably corresponding to the closed state of this channel) has been previously generated. In this article, electrophysiological characterization of ELIC mutants allowed us to identify pore mutations that slow down the time course of desensitization to the extent that the channel seems not to desensitize at all for the duration of the agonist applications (>20 min). Thus, it seems reasonable to conclude that the probability of ELIC occupying the closed state is much lower for the ligand-bound mutants than for the unliganded wild-type channel. To gain insight into the conformation adopted by ELIC under these conditions, we solved the crystal structures of two of these mutants in the presence of a concentration of cysteamine that elicits an intracluster open probability of >0.9. Curiously, the obtained structural models turned out to be nearly indistinguishable from the model of the wild-type channel in the absence of bound agonist. Overall, our findings bring to light the limited power of functional studies in intact membranes when it comes to inferring the functional state of a channel in a crystal, at least in the case of the nicotinic-receptor superfamily. PMID:22474383
Macromolecular ab initio phasing enforcing secondary and tertiary structure.

PubMed

Millán, Claudia; Sammito, Massimo; Usón, Isabel

2015-01-01

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

ERIC Educational Resources Information Center

Overton, Tina L.; Potter, Nicholas M.

2011-01-01

Much research has been carried out on how students solve algorithmic and structured problems in chemistry. This study is concerned with how students solve open-ended, ill-defined problems in chemistry. Over 200 undergraduate chemistry students solved a number of open-ended problem in groups and individually. The three cognitive variables of…
Meshless method for solving fixed boundary problem of plasma equilibrium

NASA Astrophysics Data System (ADS)

Imazawa, Ryota; Kawano, Yasunori; Itami, Kiyoshi

2015-07-01

This study solves the Grad-Shafranov equation with a fixed plasma boundary by utilizing a meshless method for the first time. Previous studies have utilized a finite element method (FEM) to solve an equilibrium inside the fixed separatrix. In order to avoid difficulties of FEM (such as mesh problem, difficulty of coding, expensive calculation cost), this study focuses on the meshless methods, especially RBF-MFS and KANSA's method to solve the fixed boundary problem. The results showed that CPU time of the meshless methods was ten to one hundred times shorter than that of FEM to obtain the same accuracy.
Learning to Predict Combinatorial Structures

NASA Astrophysics Data System (ADS)

Vembu, Shankar

2009-12-01

The major challenge in designing a discriminative learning algorithm for predicting structured data is to address the computational issues arising from the exponential size of the output space. Existing algorithms make different assumptions to ensure efficient, polynomial time estimation of model parameters. For several combinatorial structures, including cycles, partially ordered sets, permutations and other graph classes, these assumptions do not hold. In this thesis, we address the problem of designing learning algorithms for predicting combinatorial structures by introducing two new assumptions: (i) The first assumption is that a particular counting problem can be solved efficiently. The consequence is a generalisation of the classical ridge regression for structured prediction. (ii) The second assumption is that a particular sampling problem can be solved efficiently. The consequence is a new technique for designing and analysing probabilistic structured prediction models. These results can be applied to solve several complex learning problems including but not limited to multi-label classification, multi-category hierarchical classification, and label ranking.
A Solution Adaptive Structured/Unstructured Overset Grid Flow Solver with Applications to Helicopter Rotor Flows

NASA Technical Reports Server (NTRS)

Duque, Earl P. N.; Biswas, Rupak; Strawn, Roger C.

1995-01-01

This paper summarizes a method that solves both the three dimensional thin-layer Navier-Stokes equations and the Euler equations using overset structured and solution adaptive unstructured grids with applications to helicopter rotor flowfields. The overset structured grids use an implicit finite-difference method to solve the thin-layer Navier-Stokes/Euler equations while the unstructured grid uses an explicit finite-volume method to solve the Euler equations. Solutions on a helicopter rotor in hover show the ability to accurately convect the rotor wake. However, isotropic subdivision of the tetrahedral mesh rapidly increases the overall problem size.
Can False Memories Prime Problem Solutions?

ERIC Educational Resources Information Center

Howe, Mark L.; Garner, Sarah R.; Dewhurst, Stephen A.; Ball, Linden J.

2010-01-01

Previous research has suggested that false memories can prime performance on related implicit and explicit memory tasks. The present research examined whether false memories can also be used to prime higher order cognitive processes, namely, insight-based problem solving. Participants were asked to solve a number of compound remote associate task…
Using Computer Simulations in Chemistry Problem Solving

ERIC Educational Resources Information Center

Avramiotis, Spyridon; Tsaparlis, Georgios

2013-01-01

This study is concerned with the effects of computer simulations of two novel chemistry problems on the problem solving ability of students. A control-experimental group, equalized by pair groups (n[subscript Exp] = n[subscript Ctrl] = 78), research design was used. The students had no previous experience of chemical practical work. Student…
A Cognitive Apprenticeship Approach to Facilitating Web-Based Collaborative Problem Solving

ERIC Educational Resources Information Center

Kuo, Fan-Ray; Hwang, Gwo-Jen; Chen, Szu-Chuang; Chen, Sherry Y.

2012-01-01

Enhancing students' problem-solving abilities has been recognized as an important and challenging issue for technology-enhanced learning. Thus, previous research has attempted to address this issue by developing various mechanisms, among which a cognitive apprenticeship model can particularly enhance students' abilities. However, it is not clear…

Solving Large Problems with a Small Working Memory

ERIC Educational Resources Information Center

Pizlo, Zygmunt; Stefanov, Emil

2013-01-01

We describe an important elaboration of our multiscale/multiresolution model for solving the Traveling Salesman Problem (TSP). Our previous model emulated the non-uniform distribution of receptors on the human retina and the shifts of visual attention. This model produced near-optimal solutions of TSP in linear time by performing hierarchical…
Transformational Leadership and Creative Problem-Solving: The Mediating Role of Psychological Safety and Reflexivity

ERIC Educational Resources Information Center

Carmeli, Abraham; Sheaffer, Zachary; Binyamin, Galy; Reiter-Palmon, Roni; Shimoni, Tali

2014-01-01

Previous research has pointed to the importance of transformational leadership in facilitating employees' creative outcomes. However, the mechanism by which transformational leadership cultivates employees' creative problem-solving capacity is not well understood. Drawing on theories of leadership, information processing and creativity,…
Measures of Potential Flexibility and Practical Flexibility in Equation Solving.

PubMed

Xu, Le; Liu, Ru-De; Star, Jon R; Wang, Jia; Liu, Ying; Zhen, Rui

2017-01-01

Researchers interested in mathematical proficiency have recently begun to explore the development of strategic flexibility, where flexibility is defined as knowledge of multiple strategies for solving a problem and the ability to implement an innovative strategy for a given problem solving circumstance. However, anecdotal findings from this literature indicate that students do not consistently use an innovative strategy for solving a given problem, even when these same students demonstrate knowledge of innovative strategies. This distinction, sometimes framed in the psychological literature as competence vs. performance-has not been previously studied for flexibility. In order to explore the competence/performance distinction in flexibility, this study developed and validated measures for potential flexibility (e.g., competence, or knowledge of multiple strategies) and practical flexibility (e.g., performance, use of innovative strategies) for solving equations. The measures were administrated to a sample of 158 Chinese middle school students through a Tri-Phase Flexibility Assessment, in which the students were asked to solve each equation, generate additional strategies, and evaluate own multiple strategies. Confirmatory factor analysis supported a two-factor model of potential and practical flexibility. Satisfactory internal consistency was found for the measures. Additional validity evidence included the significant association with flexibility measured with the previous method. Potential flexibility and practical flexibility were found to be distinct but related. The theoretical and practical implications of the concepts and their measures of potential flexibility and practical flexibility are discussed.
Measures of Potential Flexibility and Practical Flexibility in Equation Solving

PubMed Central

Xu, Le; Liu, Ru-De; Star, Jon R.; Wang, Jia; Liu, Ying; Zhen, Rui

2017-01-01

Researchers interested in mathematical proficiency have recently begun to explore the development of strategic flexibility, where flexibility is defined as knowledge of multiple strategies for solving a problem and the ability to implement an innovative strategy for a given problem solving circumstance. However, anecdotal findings from this literature indicate that students do not consistently use an innovative strategy for solving a given problem, even when these same students demonstrate knowledge of innovative strategies. This distinction, sometimes framed in the psychological literature as competence vs. performance—has not been previously studied for flexibility. In order to explore the competence/performance distinction in flexibility, this study developed and validated measures for potential flexibility (e.g., competence, or knowledge of multiple strategies) and practical flexibility (e.g., performance, use of innovative strategies) for solving equations. The measures were administrated to a sample of 158 Chinese middle school students through a Tri-Phase Flexibility Assessment, in which the students were asked to solve each equation, generate additional strategies, and evaluate own multiple strategies. Confirmatory factor analysis supported a two-factor model of potential and practical flexibility. Satisfactory internal consistency was found for the measures. Additional validity evidence included the significant association with flexibility measured with the previous method. Potential flexibility and practical flexibility were found to be distinct but related. The theoretical and practical implications of the concepts and their measures of potential flexibility and practical flexibility are discussed. PMID:28848481
Study of viscous flow about airfoils by the integro-differential method

NASA Technical Reports Server (NTRS)

Wu, J. C.; Sampath, S.

1975-01-01

An integro-differential method was used for numerically solving unsteady incompressible viscous flow problems. A computer program was prepared to solve the problem of an impulsively started 9% thick symmetric Joukowski airfoil at an angle of attack of 15 deg and a Reynolds number of 1000. Some of the results obtained for this problem were discussed and compared with related work completed previously. Two numerical procedures were used, an Alternating Direction Implicit (ADI) method and a Successive Line Relaxation (SLR) method. Generally, the ADI solution agrees well with the SLR solution and with previous results are stations away from the trailing edge. At the trailing edge station, the ADI solution differs substantially from previous results, while the vorticity profiles obtained from the SLR method there are in good qualitative agreement with previous results.
A homotopy algorithm for digital optimal projection control GASD-HADOC

NASA Technical Reports Server (NTRS)

Collins, Emmanuel G., Jr.; Richter, Stephen; Davis, Lawrence D.

1993-01-01

The linear-quadratic-gaussian (LQG) compensator was developed to facilitate the design of control laws for multi-input, multi-output (MIMO) systems. The compensator is computed by solving two algebraic equations for which standard closed-loop solutions exist. Unfortunately, the minimal dimension of an LQG compensator is almost always equal to the dimension of the plant and can thus often violate practical implementation constraints on controller order. This deficiency is especially highlighted when considering control-design for high-order systems such as flexible space structures. This deficiency motivated the development of techniques that enable the design of optimal controllers whose dimension is less than that of the design plant. A homotopy approach based on the optimal projection equations that characterize the necessary conditions for optimal reduced-order control. Homotopy algorithms have global convergence properties and hence do not require that the initializing reduced-order controller be close to the optimal reduced-order controller to guarantee convergence. However, the homotopy algorithm previously developed for solving the optimal projection equations has sublinear convergence properties and the convergence slows at higher authority levels and may fail. A new homotopy algorithm for synthesizing optimal reduced-order controllers for discrete-time systems is described. Unlike the previous homotopy approach, the new algorithm is a gradient-based, parameter optimization formulation and was implemented in MATLAB. The results reported may offer the foundation for a reliable approach to optimal, reduced-order controller design.
Micro-crystallography developments at GM/CA CAT at the APS.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Xu, S.; Makarov, O.; Benn, R.

2010-01-01

Recently, several important structures have been solved using micro-crystallographic techniques that previously could not have been solved with conventional crystallography. At GM/CA-CAT we continue to develop micro-crystallographic capabilities for difficult problems such as small crystals of large macromolecular complexes or membrane proteins grown in the lipidic cubic phase. This paper will describe three major upgrades to our arsenal of tools, 'mini-beam' collimators, active beamstop, and an improved goniostat. Our 'mini-beam' collimators have evolved to a new triple-collimator fabricated from molybdenum as a uni-body. This has significantly improved the robustness, ease of initial alignment, and reduction of background. More recently, twomore » prototypes of a quad-collimator have been developed and fabricated to provide a selection of mini-beams of 5, 10, 20 {mu}m and a 300 {mu}m scatter-guard on a single body. The smaller beams and samples have increased the demand on the tolerances of our goniostat. To meet these challenges we have designed and implemented a goniostat with a 1-micron peak-to-peak sphere of confusion. This is a significant improvement over the previous 6 micron sphere of confusion of the commercially available air-bearing and XY stages. Finally, an 'active beamstop' has been constructed. This will provide non-invasive, real time feedback at the sample during data collection.« less
Micro-Crystallography Developments at GM/CA-CAT at the APS

DOE Office of Scientific and Technical Information (OSTI.GOV)

Xu Shenglan; Makarov, Oleg; Benn, Rich

2010-06-23

Recently, several important structures have been solved using micro-crystallographic techniques that previously could not have been solved with conventional crystallography. At GM/CA-CAT we continue to develop micro-crystallographic capabilities for difficult problems such as small crystals of large macromolecular complexes or membrane proteins grown in the lipidic cubic phase. This paper will describe three major upgrades to our arsenal of tools, 'mini-beam' collimators, active beamstop, and an improved goniostat. Our 'mini-beam' collimators have evolved to a new triple-collimator fabricated from molybdenum as a uni-body. This has significantly improved the robustness, ease of initial alignment, and reduction of background. More recently, twomore » prototypes of a quad-collimator have been developed and fabricated to provide a selection of mini-beams of 5, 10, 20 {mu}m and a 300 {mu}m scatter-guard on a single body. The smaller beams and samples have increased the demand on the tolerances of our goniostat. To meet these challenges we have designed and implemented a goniostat with a 1-micron peak-to-peak sphere of confusion. This is a significant improvement over the previous 6 micron sphere of confusion of the commercially available air-bearing and XY stages. Finally, an 'active beamstop' has been constructed. This will provide non-invasive, real time feedback at the sample during data collection.« less
Self-Regulation in the Midst of Complexity: A Case Study of High School Physics Students Engaged in Ill-Structured Problem Solving

ERIC Educational Resources Information Center

Milbourne, Jeffrey David

2016-01-01

The purpose of this dissertation study was to explore the experiences of high school physics students who were solving complex, ill-structured problems, in an effort to better understand how self-regulatory behavior mediated the project experience. Consistent with Voss, Green, Post, and Penner's (1983) conception of an ill-structured problem in…
Using Jigsaw-Style Spectroscopy Problem-Solving to Elucidate Molecular Structure through Online Cooperative Learning

ERIC Educational Resources Information Center

Winschel, Grace A.; Everett, Renata K.; Coppola, Brian P.; Shultz, Ginger V.

2015-01-01

Cooperative learning was employed as an instructional approach to facilitate student development of spectroscopy problem solving skills. An interactive online environment was used as a framework to structure weekly discussions around spectroscopy problems outside of class. Weekly discussions consisted of modified jigsaw-style problem solving…
FNL Scientists and Collaborators Solve 3-D Structure of Key Protein in Alzheimer’s Disease | FNLCR Staging

Cancer.gov

Researchers at the Frederick National Lab (FNL) have collaborated in solving the three-dimensional structure of a key protein in Alzheimer’s disease, providing new insight into the basic mechanisms that give rise to the devastating illness. The pro
Finding the Optimal Scaffoldings for Learners' Epistemological Beliefs during Ill-Structured Problem Solving

ERIC Educational Resources Information Center

Shin, Suhkyung; Song, Hae-Deok

2016-01-01

This study investigates how scaffolding type and learners' epistemological beliefs influence ill-structured problem solving. The independent variables in this study include the type of scaffolding (task-supported, self-monitoring) and the student's epistemological belief level (more advanced, less advanced). The dependent variables include three…
Implementing the Japanese Problem-Solving Lesson Structure

ERIC Educational Resources Information Center

Groves, Susie

2013-01-01

While there has been worldwide interest in Japanese Lesson Study as a model for teacher professional learning, there has been less research into authentic implementation of the problem-solving lesson structure that underpins mathematics research lessons in Japan. Findings from a Lesson Study project involving teachers from three Victorian primary…
Auto-biometric for M-mode echocardiography

NASA Astrophysics Data System (ADS)

Zhang, Wei; Park, Jinhyong; Zhou, S. Kevin

2010-03-01

In this paper we present a system for fast and accurate detection of anatomical structures (calipers) in M-mode images. The task is challenging because of dramatic variations in their appearances. We propose to solve the problem in a progressive manner, which ensures both robustness and efficiency. It first obtains rough caliper localization using the intensity profile image. Then run a constrained search for accurate caliper positions. Markov Random Field (MRF) and warping image detectors are used for jointly considering appearance information and the geometric relationship between calipers. Extensive experiments show that our system achieves more accurate results and uses less time in comparison with previously reported work.
Development and Application of Agglomerated Multigrid Methods for Complex Geometries

NASA Technical Reports Server (NTRS)

Nishikawa, Hiroaki; Diskin, Boris; Thomas, James L.

2010-01-01

We report progress in the development of agglomerated multigrid techniques for fully un- structured grids in three dimensions, building upon two previous studies focused on efficiently solving a model diffusion equation. We demonstrate a robust fully-coarsened agglomerated multigrid technique for 3D complex geometries, incorporating the following key developments: consistent and stable coarse-grid discretizations, a hierarchical agglomeration scheme, and line-agglomeration/relaxation using prismatic-cell discretizations in the highly-stretched grid regions. A signi cant speed-up in computer time is demonstrated for a model diffusion problem, the Euler equations, and the Reynolds-averaged Navier-Stokes equations for 3D realistic complex geometries.
Investigating the role of future thinking in social problem solving.

PubMed

Noreen, Saima; Whyte, Katherine E; Dritschel, Barbara

2015-03-01

There is well-established evidence that both rumination and depressed mood negatively impact the ability to solve social problems. A preliminary stage of the social problem solving process may be the process of catapulting oneself forward in time to think about the consequences of a problem before attempting to solve it. The aim of the present study was to examine how thinking about the consequences of a social problem being resolved or unresolved prior to solving it influences the solution of the problem as a function of levels of rumination and dysphoric mood. Eighty six participants initially completed the Beck Depression Inventory- II (BDI-II) and the Ruminative Response Scale (RRS). They were then presented with six social problems and generated consequences for half of the problems being resolved and half of the problems remaining unresolved. Participants then solved some of the problems, and following a delay, were asked to recall all of the consequences previously generated. Participants reporting higher levels of depressed mood and rumination were less effective at generating problem solutions. Specifically, those reporting higher levels of rumination produced less effective solutions for social problems that they had previously generated unresolved than resolved consequences. We also found that individuals higher in rumination, irrespective of depressed mood recalled more of the unresolved consequences in a subsequent memory test. As participants did not solve problems for scenarios where no consequences were generated, no baseline measure of problem solving was obtained. Our results suggest thinking about the consequences of a problem remaining unresolved may impair the generation of effective solutions in individuals with higher levels of rumination. Copyright © 2014 Elsevier Ltd. All rights reserved.
Structure of Human Pancreatic Lipase-Related Protein 2 with the Lid in an Open Conformation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Eydoux, Cecilia; Spinelli, Silvia; Davis, Tara L.

2008-10-02

Access to the active site of pancreatic lipase (PL) is controlled by a surface loop, the lid, which normally undergoes conformational changes only upon addition of lipids or amphiphiles. Structures of PL with their lids in the open and functional conformation have required cocrystallization with amphiphiles. Here we report two crystal structures of wild-type and unglycosylated human pancreatic lipase-related protein 2 (HPLRP2) with the lid in an open conformation in the absence of amphiphiles. These structures solved independently are strikingly similar, with some residues of the lid being poorly defined in the electron-density map. The open conformation of the lidmore » is however different from that previously observed in classical liganded PL, suggesting different kinetic properties for HPLRP2. Here we show that the HPLRP2 is directly inhibited by E600, does not present interfacial activation, and acts preferentially on substrates forming monomers or small aggregates (micelles) dispersed in solution like monoglycerides, phospholipids and galactolipids, whereas classical PL displays reverse properties and a high specificity for unsoluble substrates like triglycerides and diglycerides forming oil-in-water interfaces. These biochemical properties imply that the lid of HPLRP2 is likely to spontaneously adopt in solution the open conformation observed in the crystal structure. This open conformation generates a large cavity capable of accommodating the digalactose polar head of galactolipids, similar to that previously observed in the active site of the guinea pig PLRP2, but absent from the classical PL. Most of the structural and kinetic properties of HPLRP2 were found to be different from those of rat PLRP2, the structure of which was previously obtained with the lid in a closed conformation. Our findings illustrate the essential role of the lid in determining the substrate specificity and the mechanism of action of lipases.« less
Structure of human pancreatic lipase-related protein 2 with the lid in an open conformation.

PubMed

Eydoux, Cécilia; Spinelli, Silvia; Davis, Tara L; Walker, John R; Seitova, Alma; Dhe-Paganon, Sirano; De Caro, Alain; Cambillau, Christian; Carrière, Frédéric

2008-09-09

Access to the active site of pancreatic lipase (PL) is controlled by a surface loop, the lid, which normally undergoes conformational changes only upon addition of lipids or amphiphiles. Structures of PL with their lids in the open and functional conformation have required cocrystallization with amphiphiles. Here we report two crystal structures of wild-type and unglycosylated human pancreatic lipase-related protein 2 (HPLRP2) with the lid in an open conformation in the absence of amphiphiles. These structures solved independently are strikingly similar, with some residues of the lid being poorly defined in the electron-density map. The open conformation of the lid is however different from that previously observed in classical liganded PL, suggesting different kinetic properties for HPLRP2. Here we show that the HPLRP2 is directly inhibited by E600, does not present interfacial activation, and acts preferentially on substrates forming monomers or small aggregates (micelles) dispersed in solution like monoglycerides, phospholipids and galactolipids, whereas classical PL displays reverse properties and a high specificity for unsoluble substrates like triglycerides and diglycerides forming oil-in-water interfaces. These biochemical properties imply that the lid of HPLRP2 is likely to spontaneously adopt in solution the open conformation observed in the crystal structure. This open conformation generates a large cavity capable of accommodating the digalactose polar head of galactolipids, similar to that previously observed in the active site of the guinea pig PLRP2, but absent from the classical PL. Most of the structural and kinetic properties of HPLRP2 were found to be different from those of rat PLRP2, the structure of which was previously obtained with the lid in a closed conformation. Our findings illustrate the essential role of the lid in determining the substrate specificity and the mechanism of action of lipases.
Identification of high school students' ability level of constructing free body diagrams to solve restricted and structured response items in force matter

NASA Astrophysics Data System (ADS)

Rahmaniar, Andinisa; Rusnayati, Heni; Sutiadi, Asep

2017-05-01

While solving physics problem particularly in force matter, it is needed to have the ability of constructing free body diagrams which can help students to analyse every force which acts on an object, the length of its vector and the naming of its force. Mix method was used to explain the result without any special treatment to participants. The participants were high school students in first grade totals 35 students. The purpose of this study is to identify students' ability level of constructing free body diagrams in solving restricted and structured response items. Considering of two types of test, every student would be classified into four levels ability of constructing free body diagrams which is every level has different characteristic and some students were interviewed while solving test in order to know how students solve the problem. The result showed students' ability of constructing free body diagrams on restricted response items about 34.86% included in no evidence of level, 24.11% inadequate level, 29.14% needs improvement level and 4.0% adequate level. On structured response items is about 16.59% included no evidence of level, 23.99% inadequate level, 36% needs improvement level, and 13.71% adequate level. Researcher found that students who constructed free body diagrams first and constructed free body diagrams correctly were more successful in solving restricted and structured response items.
Crystal Structure and Regulation of the Citrus Pol III Repressor MAF1 by Auxin and Phosphorylation.

PubMed

Soprano, Adriana Santos; Giuseppe, Priscila Oliveira de; Shimo, Hugo Massayoshi; Lima, Tatiani Brenelli; Batista, Fernanda Aparecida Heleno; Righetto, Germanna Lima; Pereira, José Geraldo de Carvalho; Granato, Daniela Campos; Nascimento, Andrey Fabricio Ziem; Gozzo, Fabio Cesar; de Oliveira, Paulo Sérgio Lopes; Figueira, Ana Carolina Migliorini; Smetana, Juliana Helena Costa; Paes Leme, Adriana Franco; Murakami, Mario Tyago; Benedetti, Celso Eduardo

2017-09-05

MAF1 is the main RNA polymerase (Pol) III repressor that controls cell growth in eukaryotes. The Citrus ortholog, CsMAF1, was shown to restrict cell growth in citrus canker disease but its role in plant development and disease is still unclear. We solved the crystal structure of the globular core of CsMAF1, which reveals additional structural elements compared with the previously available structure of hMAF1, and explored the dynamics of its flexible regions not present in the structure. CsMAF1 accumulated in the nucleolus upon leaf excision, and this translocation was inhibited by auxin and by mutation of the PKA phosphorylation site, S45, to aspartate. Additionally, mTOR phosphorylated recombinant CsMAF1 and the mTOR inhibitor AZD8055 blocked canker formation in normal but not CsMAF1-silenced plants. These results indicate that the role of TOR on cell growth induced by Xanthomonas citri depends on CsMAF1 and that auxin controls CsMAF1 interaction with Pol III in citrus. Copyright © 2017 Elsevier Ltd. All rights reserved.

GPCR-I-TASSER: A Hybrid Approach to G Protein-Coupled Receptor Structure Modeling and the Application to the Human Genome.

PubMed

Zhang, Jian; Yang, Jianyi; Jang, Richard; Zhang, Yang

2015-08-04

Experimental structure determination remains difficult for G protein-coupled receptors (GPCRs). We propose a new hybrid protocol to construct GPCR structure models that integrates experimental mutagenesis data with ab initio transmembrane (TM) helix assembly simulations. The method was tested on 24 known GPCRs where the ab initio TM-helix assembly procedure constructed the correct fold for 20 cases. When combined with weak homology and sparse mutagenesis restraints, the method generated correct folds for all the tested cases with an average Cα root-mean-square deviation 2.4 Å in the TM regions. The new hybrid protocol was applied to model all 1,026 GPCRs in the human genome, where 923 have a high confidence score and are expected to have correct folds; these contain many pharmaceutically important families with no previously solved structures, including Trace amine, Prostanoids, Releasing hormones, Melanocortins, Vasopressin, and Neuropeptide Y receptors. The results demonstrate new progress on genome-wide structure modeling of TM proteins. Copyright © 2015 Elsevier Ltd. All rights reserved.
Structure of the ThDP-dependent enzyme benzaldehyde lyase refined to 1.65 Å resolution

DOE Office of Scientific and Technical Information (OSTI.GOV)

Maraite, Andy; Schmidt, Thomas; Ansörge-Schumacher, Marion B.

2007-07-01

The X-ray crystal structure of the ThDP-dependent enzyme benzaldehyde lyase has been refined to 1.65 Å. Benzaldehyde lyase (BAL; EC 4.1.2.38) is a thiamine diphosphate (ThDP) dependent enzyme that catalyses the enantioselective carboligation of two molecules of benzaldehyde to form (R)-benzoin. BAL has hence aroused interest for its potential in the industrial synthesis of optically active benzoins and derivatives. The structure of BAL was previously solved to a resolution of 2.6 Å using MAD experiments on a selenomethionine derivative [Mosbacher et al. (2005 ▶), FEBS J.272, 6067–6076]. In this communication of parallel studies, BAL was crystallized in an alternative spacemore » group (P2{sub 1}2{sub 1}2{sub 1}) and its structure refined to a resolution of 1.65 Å, allowing detailed observation of the water structure, active-site interactions with ThDP and also the electron density for the co-solvent 2-methyl-2,4-pentanediol (MPD) at hydrophobic patches of the enzyme surface.« less
Protection of cooled blades of complex internal structure

NASA Technical Reports Server (NTRS)

Glamiche, P.

1977-01-01

The problem of general protection of cooled blades of complex internal structure was solved by a method called SF technique which makes possible the protection of both external and internal surfaces, as well as those of the orifices of cooling air, whatever their diameter. The SF method is most often applied in the case of pack process, at controlled or high activity; it can be of use on previously uncoated parts, but also on pieces already coated by a thermochemical, chemical or PVD method. The respective thickness of external and internal coatings may be precisely predetermined, no parasitic particle being liable to remain inside the parts after application of the protecting treatment. Results obtained to date by application of this method are illustrated by the presentation and examination of a various selection of advanced turbo engines.
Investigation of Conjugate Heat Transfer in Turbine Blades and Vanes

NASA Technical Reports Server (NTRS)

Kassab, A. J.; Kapat, J. S.

2001-01-01

We report on work carried out to develop a 3-D coupled Finite Volume/BEM-based temperature forward/flux back (TFFB) coupling algorithm to solve the conjugate heat transfer (CHT) which arises naturally in analysis of systems exposed to a convective environment. Here, heat conduction within a structure is coupled to heat transfer to the external fluid which is convecting heat into or out of the solid structure. There are two basic approaches to solving coupled fluid structural systems. The first is a direct coupling where the solution of the different fields is solved simultaneously in one large set of equations. The second approach is a loose coupling strategy where each set of field equations is solved to provide boundary conditions for the other. The equations are solved in turn until an iterated convergence criterion is met at the fluid-solid interface. The loose coupling strategy is particularly attractive when coupling auxiliary field equations to computational fluid dynamics codes. We adopt the latter method in which the BEM is used to solve heat conduction inside a structure which is exposed to a convective field which in turn is resolved by solving the NASA Glenn compressible Navier-Stokes finite volume code Glenn-HT. The BEM code features constant and bi-linear discontinuous elements and an ILU-preconditioned GMRES iterative solver for the resulting non-symmetric algebraic set arising in the conduction solution. Interface of flux and temperature is enforced at the solid/fluid interface, and a radial-basis function scheme is used to interpolated information between the CFD and BEM surface grids. Additionally, relaxation is implemented in passing the fluxes from the conduction solution to the fluid solution. Results from a simple test example are reported.
DOE Office of Scientific and Technical Information (OSTI.GOV)

AhYoung, Andrew P.; Lu, Brian; Cascio, Duilio

Membrane contact sites between organelles serve as molecular hubs for the exchange of metabolites and signals. In yeast, the Endoplasmic Reticulum – Mitochondrion Encounter Structure (ERMES) tethers these two organelles likely to facilitate the non-vesicular exchange of essential phospholipids. Present in Fungi and Amoebas but not in Metazoans, ERMES is composed of five distinct subunits; among those, Mdm12, Mmm1 and Mdm34 each contain an SMP domain functioning as a lipid transfer module. We previously showed that the SMP domains of Mdm12 and Mmm1 form a hetero-tetramer. Here we describe our strategy to diversify the number of Mdm12/Mmm1 complexes suited formore » structural studies. We use sequence analysis of orthologues combined to protein engineering of disordered regions to guide the design of protein constructs and expand the repertoire of Mdm12/Mmm1 complexes more likely to crystallize. Using this combinatorial approach we report crystals of Mdm12/Mmm1 ERMES complexes currently diffracting to 4.5 Å resolution and a new structure of Mdm12 solved at 4.1 Å resolution. Our structure reveals a monomeric form of Mdm12 with a conformationally dynamic N-terminal β-strand; it differs from a previously reported homodimeric structure where the N-terminal β strands where swapped to promote dimerization. Based on our electron microscopy data, we propose a refined pseudo-atomic model of the Mdm12/Mmm1 complex that agrees with our crystallographic and small-angle X-ray scattering (SAXS) solution data.« less
Problem solving and decisionmaking: An integration

NASA Technical Reports Server (NTRS)

Dieterly, D. L.

1980-01-01

An attempt was made to redress a critical fault of decisionmaking and problem solving research-a lack of a standard method to classify problem or decision states or conditions. A basic model was identified and expanded to indicate a possible taxonomy of conditions which may be used in reviewing previous research or for systematically pursuing new research designs. A generalization of the basic conditions was then made to indicate that the conditions are essentially the same for both concepts, problem solving and decisionmaking.
Structural design using equilibrium programming formulations

NASA Technical Reports Server (NTRS)

Scotti, Stephen J.

1995-01-01

Solutions to increasingly larger structural optimization problems are desired. However, computational resources are strained to meet this need. New methods will be required to solve increasingly larger problems. The present approaches to solving large-scale problems involve approximations for the constraints of structural optimization problems and/or decomposition of the problem into multiple subproblems that can be solved in parallel. An area of game theory, equilibrium programming (also known as noncooperative game theory), can be used to unify these existing approaches from a theoretical point of view (considering the existence and optimality of solutions), and be used as a framework for the development of new methods for solving large-scale optimization problems. Equilibrium programming theory is described, and existing design techniques such as fully stressed design and constraint approximations are shown to fit within its framework. Two new structural design formulations are also derived. The first new formulation is another approximation technique which is a general updating scheme for the sensitivity derivatives of design constraints. The second new formulation uses a substructure-based decomposition of the structure for analysis and sensitivity calculations. Significant computational benefits of the new formulations compared with a conventional method are demonstrated.
Enhancing memory and imagination improves problem solving among individuals with depression.

PubMed

McFarland, Craig P; Primosch, Mark; Maxson, Chelsey M; Stewart, Brandon T

2017-08-01

Recent work has revealed links between memory, imagination, and problem solving, and suggests that increasing access to detailed memories can lead to improved imagination and problem-solving performance. Depression is often associated with overgeneral memory and imagination, along with problem-solving deficits. In this study, we tested the hypothesis that an interview designed to elicit detailed recollections would enhance imagination and problem solving among both depressed and nondepressed participants. In a within-subjects design, participants completed a control interview or an episodic specificity induction prior to completing memory, imagination, and problem-solving tasks. Results revealed that compared to the control interview, the episodic specificity induction fostered increased detail generation in memory and imagination and more relevant steps on the problem-solving task among depressed and nondepressed participants. This study builds on previous work by demonstrating that a brief interview can enhance problem solving among individuals with depression and supports the notion that episodic memory plays a key role in problem solving. It should be noted, however, that the results of the interview are relatively short-lived.
The Efficacy of Using Diagrams When Solving Probability Word Problems in College

ERIC Educational Resources Information Center

Beitzel, Brian D.; Staley, Richard K.

2015-01-01

Previous experiments have shown a deleterious effect of visual representations on college students' ability to solve total- and joint-probability word problems. The present experiments used conditional-probability problems, known to be more difficult than total- and joint-probability problems. The diagram group was instructed in how to use tree…
Worry in Children: Changing Associations with Fear, Thinking, and Problem-Solving

ERIC Educational Resources Information Center

Carr, Imogen; Szabó, Marianna

2015-01-01

Worry in adults has been conceptualized as a thinking process involving problem-solving attempts about anticipated negative outcomes. This process is related to, though distinct from, fear. Previous research suggested that compared to adults, children's experience of worry is less strongly associated with thinking and more closely related to fear.…
Scaffold Seeking: A Reverse Design of Scaffolding in Computer-Supported Word Problem Solving

ERIC Educational Resources Information Center

Cheng, Hercy N. H.; Yang, Euphony F. Y.; Liao, Calvin C. Y.; Chang, Ben; Huang, Yana C. Y.; Chan, Tak-Wai

2015-01-01

Although well-designed scaffolding may assist students to accomplish learning tasks, its insufficient capability to dynamically assess students' abilities and to adaptively support them may result in the problem of overscaffolding. Our previous project has also shown that students using scaffolds to solve mathematical word problems for a long time…
The Moderation Role of Self-Perceived Maternal Empathy in Observed Mother-Child Collaborative Problem Solving

ERIC Educational Resources Information Center

de Oliveira, Ebenézer A.; Jackson, Emily A.

2017-01-01

Based on L. S. Vygotsky's sociocultural theory, previous scaffolding studies have examined some factors associated with adjustment of parental support during collaborative problem solving. However, a factor that remains unexplored in the literature is the potential relationship between parental empathy and parental support in collaborative problem…
Problem Order Implications for Learning

ERIC Educational Resources Information Center

Li, Nan; Cohen, William W.; Koedinger, Kenneth R.

2013-01-01

The order of problems presented to students is an important variable that affects learning effectiveness. Previous studies have shown that solving problems in a blocked order, in which all problems of one type are completed before the student is switched to the next problem type, results in less effective performance than does solving the problems…
The Cognitive Toolkit of Programming--Algorithmic Abstraction, Decomposition-Superposition

ERIC Educational Resources Information Center

Szlávi,Péter; Zsakó, László

2017-01-01

As a programmer when solving a problem, a number of conscious and unconscious cognitive operations are being performed. Problem-solving is a gradual and cyclic activity; as the mind is adjusting the problem to its schemas formed by its previous experiences, the programmer gets closer and closer to understanding and defining the problem. The…
Mental Capacity and Working Memory in Chemistry: Algorithmic "versus" Open-Ended Problem Solving

ERIC Educational Resources Information Center

St Clair-Thompson, Helen; Overton, Tina; Bugler, Myfanwy

2012-01-01

Previous research has revealed that problem solving and attainment in chemistry are constrained by mental capacity and working memory. However, the terms mental capacity and working memory come from different theories of cognitive resources, and are assessed using different tasks. The current study examined the relationships between mental…
Do New Caledonian crows solve physical problems through causal reasoning?

PubMed Central

Taylor, A.H.; Hunt, G.R.; Medina, F.S.; Gray, R.D.

2008-01-01

The extent to which animals other than humans can reason about physical problems is contentious. The benchmark test for this ability has been the trap-tube task. We presented New Caledonian crows with a series of two-trap versions of this problem. Three out of six crows solved the initial trap-tube. These crows continued to avoid the trap when the arbitrary features that had previously been associated with successful performances were removed. However, they did not avoid the trap when a hole and a functional trap were in the tube. In contrast to a recent primate study, the three crows then solved a causally equivalent but visually distinct problem—the trap-table task. The performance of the three crows across the four transfers made explanations based on chance, associative learning, visual and tactile generalization, and previous dispositions unlikely. Our findings suggest that New Caledonian crows can solve complex physical problems by reasoning both causally and analogically about causal relations. Causal and analogical reasoning may form the basis of the New Caledonian crow's exceptional tool skills. PMID:18796393
Arginine ADP-ribosylation mechanism based on structural snapshots of iota-toxin and actin complex

PubMed Central

Tsurumura, Toshiharu; Tsumori, Yayoi; Qiu, Hao; Oda, Masataka; Sakurai, Jun; Nagahama, Masahiro; Tsuge, Hideaki

2013-01-01

Clostridium perfringens iota-toxin (Ia) mono-ADP ribosylates Arg177 of actin, leading to cytoskeletal disorganization and cell death. To fully understand the reaction mechanism of arginine-specific mono-ADP ribosyl transferase, the structure of the toxin-substrate protein complex must be characterized. Recently, we solved the crystal structure of Ia in complex with actin and the nonhydrolyzable NAD+ analog βTAD (thiazole-4-carboxamide adenine dinucleotide); however, the structures of the NAD+-bound form (NAD+-Ia-actin) and the ADP ribosylated form [Ia-ADP ribosylated (ADPR)-actin] remain unclear. Accidentally, we found that ethylene glycol as cryo-protectant inhibits ADP ribosylation and crystallized the NAD+-Ia-actin complex. Here we report high-resolution structures of NAD+-Ia-actin and Ia-ADPR-actin obtained by soaking apo-Ia-actin crystal with NAD+ under different conditions. The structures of NAD+-Ia-actin and Ia-ADPR-actin represent the pre- and postreaction states, respectively. By assigning the βTAD-Ia-actin structure to the transition state, the strain-alleviation model of ADP ribosylation, which we proposed previously, is experimentally confirmed and improved. Moreover, this reaction mechanism appears to be applicable not only to Ia but also to other ADP ribosyltransferases. PMID:23382240
Structural genomics reveals EVE as a new ASCH/PUA-related domain

PubMed Central

Bertonati, Claudia; Punta, Marco; Fischer, Markus; Yachdav, Guy; Forouhar, Farhad; Zhou, Weihong; Kuzin, Alexander P.; Seetharaman, Jayaraman; Abashidze, Mariam; Ramelot, Theresa A.; Kennedy, Michael A.; Cort, John R.; Belachew, Adam; Hunt, John F.; Tong, Liang; Montelione, Gaetano T.; Rost, Burkhard

2014-01-01

Summary We report on several proteins recently solved by structural genomics consortia, in particular by the Northeast Structural Genomics consortium (NESG). The proteins considered in this study differ substantially in their sequences but they share a similar structural core, characterized by a pseudobarrel five-stranded beta sheet. This core corresponds to the PUA domain-like architecture in the SCOP database. By connecting sequence information with structural knowledge, we characterize a new subgroup of these proteins that we propose to be distinctly different from previously described PUA domain-like domains such as PUA proper or ASCH. We refer to these newly defined domains as EVE. Although EVE may have retained the ability of PUA domains to bind RNA, the available experimental and computational data suggests that both the details of its molecular function and its cellular function differ from those of other PUA domain-like domains. This study of EVE and its relatives illustrates how the combination of structure and genomics creates new insights by connecting a cornucopia of structures that map to the same evolutionary potential. Primary sequence information alone would have not been sufficient to reveal these evolutionary links. PMID:19191354
Structural Genomics Reveals EVE as a New ASCH/PUA-Related Domain

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bertonati, C.; Punta, M; Fischer, M

2008-01-01

We report on several proteins recently solved by structural genomics consortia, in particular by the Northeast Structural Genomics consortium (NESG). The proteins considered in this study differ substantially in their sequences but they share a similar structural core, characterized by a pseudobarrel five-stranded beta sheet. This core corresponds to the PUA domain-like architecture in the SCOP database. By connecting sequence information with structural knowledge, we characterize a new subgroup of these proteins that we propose to be distinctly different from previously described PUA domain-like domains such as PUA proper or ASCH. We refer to these newly defined domains as EVE.more » Although EVE may have retained the ability of PUA domains to bind RNA, the available experimental and computational data suggests that both the details of its molecular function and its cellular function differ from those of other PUA domain-like domains. This study of EVE and its relatives illustrates how the combination of structure and genomics creates new insights by connecting a cornucopia of structures that map to the same evolutionary potential. Primary sequence information alone would have not been sufficient to reveal these evolutionary links.« less
A Multivariate Model of Physics Problem Solving

ERIC Educational Resources Information Center

Taasoobshirazi, Gita; Farley, John

2013-01-01

A model of expertise in physics problem solving was tested on undergraduate science, physics, and engineering majors enrolled in an introductory-level physics course. Structural equation modeling was used to test hypothesized relationships among variables linked to expertise in physics problem solving including motivation, metacognitive planning,…

Factors That Effect Interagency Collaborations: Lessons During and Following the 2002 Winter Olympics

DTIC Science & Technology

2008-03-01

solving Formal control ( decision making ) Strategic planning (structure or process) Barriers PROBE / Ticklers Were there incentives... making ) Strategic planning (structure or process) 74 PROBE / Ticklers To what extend does interdependence needed for these...aspect Motivation Social capital Trust Leadership Interpersonal communication (people skills) Shared problem solving Formal control ( decision
Detangling the Interrelationships between Self- Regulation and Ill-Structured Problem Solving in Problem-Based Learning

ERIC Educational Resources Information Center

Ge, Xun; Law, Victor; Huang, Kun

2016-01-01

One of the goals for problem-based learning (PBL) is to promote self-regulation. Although self-regulation has been studied extensively, its interrelationships with ill-structured problem solving have been unclear. In order to clarify the interrelationships, this article proposes a conceptual framework illustrating the iterative processes among…
EXPECT: Explicit Representations for Flexible Acquisition

NASA Technical Reports Server (NTRS)

Swartout, BIll; Gil, Yolanda

1995-01-01

To create more powerful knowledge acquisition systems, we not only need better acquisition tools, but we need to change the architecture of the knowledge based systems we create so that their structure will provide better support for acquisition. Current acquisition tools permit users to modify factual knowledge but they provide limited support for modifying problem solving knowledge. In this paper, the authors argue that this limitation (and others) stem from the use of incomplete models of problem-solving knowledge and inflexible specification of the interdependencies between problem-solving and factual knowledge. We describe the EXPECT architecture which addresses these problems by providing an explicit representation for problem-solving knowledge and intent. Using this more explicit representation, EXPECT can automatically derive the interdependencies between problem-solving and factual knowledge. By deriving these interdependencies from the structure of the knowledge-based system itself EXPECT supports more flexible and powerful knowledge acquisition.
Functional classification of protein structures by local structure matching in graph representation.

PubMed

Mills, Caitlyn L; Garg, Rohan; Lee, Joslynn S; Tian, Liang; Suciu, Alexandru; Cooperman, Gene; Beuning, Penny J; Ondrechen, Mary Jo

2018-03-31

As a result of high-throughput protein structure initiatives, over 14,400 protein structures have been solved by structural genomics (SG) centers and participating research groups. While the totality of SG data represents a tremendous contribution to genomics and structural biology, reliable functional information for these proteins is generally lacking. Better functional predictions for SG proteins will add substantial value to the structural information already obtained. Our method described herein, Graph Representation of Active Sites for Prediction of Function (GRASP-Func), predicts quickly and accurately the biochemical function of proteins by representing residues at the predicted local active site as graphs rather than in Cartesian coordinates. We compare the GRASP-Func method to our previously reported method, structurally aligned local sites of activity (SALSA), using the ribulose phosphate binding barrel (RPBB), 6-hairpin glycosidase (6-HG), and Concanavalin A-like Lectins/Glucanase (CAL/G) superfamilies as test cases. In each of the superfamilies, SALSA and the much faster method GRASP-Func yield similar correct classification of previously characterized proteins, providing a validated benchmark for the new method. In addition, we analyzed SG proteins using our SALSA and GRASP-Func methods to predict function. Forty-one SG proteins in the RPBB superfamily, nine SG proteins in the 6-HG superfamily, and one SG protein in the CAL/G superfamily were successfully classified into one of the functional families in their respective superfamily by both methods. This improved, faster, validated computational method can yield more reliable predictions of function that can be used for a wide variety of applications by the community. © 2018 The Authors Protein Science published by Wiley Periodicals, Inc. on behalf of The Protein Society.
A General Architecture for Intelligent Tutoring of Diagnostic Classification Problem Solving

PubMed Central

Crowley, Rebecca S.; Medvedeva, Olga

2003-01-01

We report on a general architecture for creating knowledge-based medical training systems to teach diagnostic classification problem solving. The approach is informed by our previous work describing the development of expertise in classification problem solving in Pathology. The architecture envelops the traditional Intelligent Tutoring System design within the Unified Problem-solving Method description Language (UPML) architecture, supporting component modularity and reuse. Based on the domain ontology, domain task ontology and case data, the abstract problem-solving methods of the expert model create a dynamic solution graph. Student interaction with the solution graph is filtered through an instructional layer, which is created by a second set of abstract problem-solving methods and pedagogic ontologies, in response to the current state of the student model. We outline the advantages and limitations of this general approach, and describe it’s implementation in SlideTutor–a developing Intelligent Tutoring System in Dermatopathology. PMID:14728159
Evaluation of creative problem-solving abilities in undergraduate structural engineers through interdisciplinary problem-based learning

NASA Astrophysics Data System (ADS)

McCrum, Daniel Patrick

2017-11-01

For a structural engineer, effective communication and interaction with architects cannot be underestimated as a key skill to success throughout their professional career. Structural engineers and architects have to share a common language and understanding of each other in order to achieve the most desirable architectural and structural designs. This interaction and engagement develops during their professional career but needs to be nurtured during their undergraduate studies. The objective of this paper is to present the strategies employed to engage higher order thinking in structural engineering students in order to help them solve complex problem-based learning (PBL) design scenarios presented by architecture students. The strategies employed were applied in the experimental setting of an undergraduate module in structural engineering at Queen's University Belfast in the UK. The strategies employed were active learning to engage with content knowledge, the use of physical conceptual structural models to reinforce key concepts and finally, reinforcing the need for hand sketching of ideas to promote higher order problem-solving. The strategies employed were evaluated through student survey, student feedback and module facilitator (this author) reflection. The strategies were qualitatively perceived by the tutor and quantitatively evaluated by students in a cross-sectional study to help interaction with the architecture students, aid interdisciplinary learning and help students creatively solve problems (through higher order thinking). The students clearly enjoyed this module and in particular interacting with structural engineering tutors and students from another discipline.
A real-space approach to the X-ray phase problem

NASA Astrophysics Data System (ADS)

Liu, Xiangan

Over the past few decades, the phase problem of X-ray crystallography has been explored in reciprocal space in the so called direct methods . Here we investigate the problem using a real-space approach that bypasses the laborious procedure of frequent Fourier synthesis and peak picking. Starting from a completely random structure, we move the atoms around in real space to minimize a cost function. A Monte Carlo method named simulated annealing (SA) is employed to search the global minimum of the cost function which could be constructed in either real space or reciprocal space. In the hybrid minimal principle, we combine the dual space costs together. One part of the cost function monitors the probability distribution of the phase triplets, while the other is a real space cost function which represents the discrepancy between measured and calculated intensities. Compared to the single space cost functions, the dual space cost function has a greatly improved landscape and therefore could prevent the system from being trapped in metastable states. Thus, the structures of large molecules such as virginiamycin (C43H 49N7O10 · 3CH0OH), isoleucinomycin (C60H102N 6O18) and hexadecaisoleucinomycin (HEXIL) (C80H136 N8O24) can now be solved, whereas it would not be possible using the single cost function. When a molecule gets larger, the configurational space becomes larger, and the requirement of CPU time increases exponentially. The method of improved Monte Carlo sampling has demonstrated its capability to solve large molecular structures. The atoms are encouraged to sample the high density regions in space determined by an approximate density map which in turn is updated and modified by averaging and Fourier synthesis. This type of biased sampling has led to considerable reduction of the configurational space. It greatly improves the algorithm compared to the previous uniform sampling. Hence, for instance, 90% of computer run time could be cut in solving the complex structure of isoleucinomycin. Successful trial calculations include larger molecular structures such as HEXIL and a collagen-like peptide (PPG). Moving chemical fragment is proposed to reduce the degrees of freedom. Furthermore, stereochemical parameters are considered for geometric constraints and for a cost function related to chemical energy.
Structure of CC chemokine receptor 2 with orthosteric and allosteric antagonists

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zheng, Yi; Qin, Ling; Zacarías, Natalia V. Ortiz

CC chemokine receptor 2 (CCR2) is one of 19 members of the chemokine receptor subfamily of human class A G-protein-coupled receptors. CCR2 is expressed on monocytes, immature dendritic cells, and T-cell subpopulations, and mediates their migration towards endogenous CC chemokine ligands such as CCL2 (ref. 1). CCR2 and its ligands are implicated in numerous inflammatory and neurodegenerative diseases2 including atherosclerosis, multiple sclerosis, asthma, neuropathic pain, and diabetic nephropathy, as well as cancer3. These disease associations have motivated numerous preclinical studies and clinical trials4 (see http://www.clinicaltrials.gov) in search of therapies that target the CCR2–chemokine axis. To aid drug discovery efforts5, heremore » we solve a structure of CCR2 in a ternary complex with an orthosteric (BMS-681 (ref. 6)) and allosteric (CCR2-RA-[R]7) antagonist. BMS-681 inhibits chemokine binding by occupying the orthosteric pocket of the receptor in a previously unseen binding mode. CCR2-RA-[R] binds in a novel, highly druggable pocket that is the most intracellular allosteric site observed in class A G-protein-coupled receptors so far; this site spatially overlaps the G-protein-binding site in homologous receptors. CCR2-RA-[R] inhibits CCR2 non-competitively by blocking activation-associated conformational changes and formation of the G-protein-binding interface. The conformational signature of the conserved microswitch residues observed in double-antagonist-bound CCR2 resembles the most inactive G-protein-coupled receptor structures solved so far. Like other protein–protein interactions, receptor–chemokine complexes are considered challenging therapeutic targets for small molecules, and the present structure suggests diverse pocket epitopes that can be exploited to overcome obstacles in drug design.« less
Structure of CC Chemokine Receptor 2 with Orthosteric and Allosteric Antagonists

PubMed Central

Zheng, Yi; Qin, Ling; Ortiz Zacarías, Natalia V.; de Vries, Henk; Han, Gye Won; Gustavsson, Martin; Dabros, Marta; Zhao, Chunxia; Cherney, Robert J.; Carter, Percy; Stamos, Dean; Abagyan, Ruben; Cherezov, Vadim; Stevens, Raymond C.; IJzerman, Adriaan P.; Heitman, Laura H.; Tebben, Andrew; Kufareva, Irina; Handel, Tracy M.

2016-01-01

Summary CC chemokine receptor 2 (CCR2) is one of 19 members of the chemokine receptor subfamily of human Class A G protein-coupled receptors (GPCRs). CCR2 is expressed on monocytes, immature dendritic cells and T cell subpopulations, and mediates their migration towards endogenous CC chemokine ligands such as CCL21. CCR2 and its ligands are implicated in numerous inflammatory and neurodegenerative diseases2 including atherosclerosis, multiple sclerosis, asthma, neuropathic pain, and diabetic nephropathy, as well as cancer3. These disease associations have motivated numerous preclinical studies and clinical trials4 (see ClinicalTrials.gov) in search of therapies that target the CCR2:chemokine axis. To aid drug discovery efforts5, we solved a structure of CCR2 in a ternary complex with an orthosteric (BMS-6816) and allosteric (CCR2-RA-[R]7) antagonist. BMS-681 inhibits chemokine binding by occupying the orthosteric pocket of the receptor in a previously unseen binding mode. CCR2-RA-[R] binds in a novel, highly druggable pocket that is the most intracellular allosteric site observed in Class A GPCRs to date; this site spatially overlaps the G protein-binding site in homologous receptors. CCR2-RA-[R] inhibits CCR2 non-competitively by blocking activation-associated conformational changes and formation of the G protein-binding interface. The conformational signature of the conserved microswitch residues observed in double-antagonist-bound CCR2 resembles the most inactive GPCR structures solved to date. Like other protein:protein interactions, receptor:chemokine complexes are considered challenging therapeutic targets for small molecules, and the present structure suggests diverse pocket epitopes that can be exploited to overcome drug design obstacles. PMID:27926736
Structure of CPV17 polyhedrin determined by the improved analysis of serial femtosecond crystallographic data

DOE PAGES

Ginn, Helen M.; Messerschmidt, Marc; Ji, Xiaoyun; ...

2015-03-09

The X-ray free-electron laser (XFEL) allows the analysis of small weakly diffracting protein crystals, but has required very many crystals to obtain good data. Here we use an XFEL to determine the room temperature atomic structure for the smallest cytoplasmic polyhedrosis virus polyhedra yet characterized, which we failed to solve at a synchrotron. These protein microcrystals, roughly a micron across, accrue within infected cells. We use a new physical model for XFEL diffraction, which better estimates the experimental signal, delivering a high-resolution XFEL structure (1.75 Å), using fewer crystals than previously required for this resolution. The crystal lattice and proteinmore » core are conserved compared with a polyhedrin with less than 10% sequence identity. We explain how the conserved biological phenotype, the crystal lattice, is maintained in the face of extreme environmental challenge and massive evolutionary divergence. Our improved methods should open up more challenging biological samples to XFEL analysis.« less
Puzzle of magnetic moments of Ni clusters revisited using quantum Monte Carlo method.

PubMed

Lee, Hung-Wen; Chang, Chun-Ming; Hsing, Cheng-Rong

2017-02-28

The puzzle of the magnetic moments of small nickel clusters arises from the discrepancy between values predicted using density functional theory (DFT) and experimental measurements. Traditional DFT approaches underestimate the magnetic moments of nickel clusters. Two fundamental problems are associated with this puzzle, namely, calculating the exchange-correlation interaction accurately and determining the global minimum structures of the clusters. Theoretically, the two problems can be solved using quantum Monte Carlo (QMC) calculations and the ab initio random structure searching (AIRSS) method correspondingly. Therefore, we combined the fixed-moment AIRSS and QMC methods to investigate the magnetic properties of Ni n (n = 5-9) clusters. The spin moments of the diffusion Monte Carlo (DMC) ground states are higher than those of the Perdew-Burke-Ernzerhof ground states and, in the case of Ni 8-9 , two new ground-state structures have been discovered using the DMC calculations. The predicted results are closer to the experimental findings, unlike the results predicted in previous standard DFT studies.
4-N, 4-S & 4-O Chloroquine Analogues: Influence of Side Chain Length and Quinolyl Nitrogen pKa on Activity vs. Chloroquine Resistant Malaria+, #

PubMed Central

Natarajan, Jayakumar K.; Alumasa, John; Yearick, Kimberly; Ekoue-Kovi, Kekeli A.; Casabianca, Leah B.; de Dios, Angel C.; Wolf, Christian; Roepe, Paul D.

2009-01-01

Using predictions from heme – quinoline antimalarial complex structures, previous modifications of chloroquine (CQ), and hypotheses for chloroquine resistance (CQR), we synthesize and assay CQ analogues that test structure – function principles. We vary side chain length for both monoethyl and diethyl 4N CQ derivatives. We alter the pKa of the quinolyl N by introducing alkylthio or alkoxy substituents into the 4 position, and vary side chain length for these analogues. We introduce an additional titratable amino group to the side chain of 4O analogues with promising CQR strain selectivity and increase activity while retaining selectivity. We solve atomic resolution structures for complexes formed between representative 4N, 4S and 4O derivatives vs. μ-oxo dimeric heme, measure binding constants for monomeric vs. dimeric heme, and quantify hemozoin (Hz) formation inhibition in vitro. The data provide additional insight for the design of CQ analogues with improved activity vs. CQR malaria. PMID:18512900
4-N-, 4-S-, and 4-O-chloroquine analogues: influence of side chain length and quinolyl nitrogen pKa on activity vs chloroquine resistant malaria.

PubMed

Natarajan, Jayakumar K; Alumasa, John N; Yearick, Kimberly; Ekoue-Kovi, Kekeli A; Casabianca, Leah B; de Dios, Angel C; Wolf, Christian; Roepe, Paul D

2008-06-26

Using predictions from heme-quinoline antimalarial complex structures, previous modifications of chloroquine (CQ), and hypotheses for chloroquine resistance (CQR), we synthesize and assay CQ analogues that test structure-function principles. We vary side chain length for both monoethyl and diethyl 4-N CQ derivatives. We alter the pKa of the quinolyl N by introducing alkylthio or alkoxy substituents into the 4 position and vary side chain length for these analogues. We introduce an additional titratable amino group to the side chain of 4-O analogues with promising CQR strain selectivity and increase activity while retaining selectivity. We solve atomic resolution structures for complexes formed between representative 4-N, 4-S, and 4-O derivatives vs mu-oxo dimeric heme, measure binding constants for monomeric vs dimeric heme, and quantify hemozoin (Hz) formation inhibition in vitro. The data provide additional insight for the design of CQ analogues with improved activity vs CQR malaria.
The oxygenating constituent of 3,6-diketocamphane monooxygenase from the CAM plasmid of Pseudomonas putida: the first crystal structure of a type II Baeyer-Villiger monooxygenase.

PubMed

Isupov, Michail N; Schröder, Ewald; Gibson, Robert P; Beecher, Jean; Donadio, Giuliana; Saneei, Vahid; Dcunha, Stephlina A; McGhie, Emma J; Sayer, Christopher; Davenport, Colin F; Lau, Peter C; Hasegawa, Yoshie; Iwaki, Hiroaki; Kadow, Maria; Balke, Kathleen; Bornscheuer, Uwe T; Bourenkov, Gleb; Littlechild, Jennifer A

2015-11-01

The three-dimensional structures of the native enzyme and the FMN complex of the overexpressed form of the oxygenating component of the type II Baeyer-Villiger 3,6-diketocamphane monooxygenase have been determined to 1.9 Å resolution. The structure of this dimeric FMN-dependent enzyme, which is encoded on the large CAM plasmid of Pseudomonas putida, has been solved by a combination of multiple anomalous dispersion from a bromine crystal soak and molecular replacement using a bacterial luciferase model. The orientation of the isoalloxazine ring of the FMN cofactor in the active site of this TIM-barrel fold enzyme differs significantly from that previously observed in enzymes of the bacterial luciferase-like superfamily. The Ala77 residue is in a cis conformation and forms a β-bulge at the C-terminus of β-strand 3, which is a feature observed in many proteins of this superfamily.
Factor structure of essential social skills to be salespersons in retail market: implications for psychiatric rehabilitation.

PubMed

Cheung, Leo C C; Tsang, Hector W H

2005-12-01

This study continued the effort to apply social skills training to increase vocational outcomes of people with severe mental illness. We planned to identify factor structure of essential social skills necessary for mental health consumers who have a vocational preference to work as salesperson in retail market. Exploratory factor analysis of the results of a 26-item questionnaire survey suggested a five-factor solution: social skills when interacting with customers, problem-solving skills, knowledge and attitudes, flexibility, and skills for conflict prevention, which accounted for 65.1% of the total variance. With the factor solution, we developed a job-specific social skills training program (JSST) to help consumers who want to be salespersons. The structure and session design followed the basic format of a typical social skills training program. The way this JSST is to be used with the work-related social skills training model previously developed by the corresponding author to produce better vocational outcomes of consumers is suggested.
Automating the parallel processing of fluid and structural dynamics calculations

NASA Technical Reports Server (NTRS)

Arpasi, Dale J.; Cole, Gary L.

1987-01-01

The NASA Lewis Research Center is actively involved in the development of expert system technology to assist users in applying parallel processing to computational fluid and structural dynamic analysis. The goal of this effort is to eliminate the necessity for the physical scientist to become a computer scientist in order to effectively use the computer as a research tool. Programming and operating software utilities have previously been developed to solve systems of ordinary nonlinear differential equations on parallel scalar processors. Current efforts are aimed at extending these capabilities to systems of partial differential equations, that describe the complex behavior of fluids and structures within aerospace propulsion systems. This paper presents some important considerations in the redesign, in particular, the need for algorithms and software utilities that can automatically identify data flow patterns in the application program and partition and allocate calculations to the parallel processors. A library-oriented multiprocessing concept for integrating the hardware and software functions is described.
Dynamics of internal pore opening in KV channels probed by a fluorescent unnatural amino acid

PubMed Central

Kalstrup, Tanja; Blunck, Rikard

2013-01-01

Atomic-scale models on the gating mechanism of voltage-gated potassium channels (Kv) are based on linear interpolations between static structures of their initial and final state derived from crystallography and molecular dynamics simulations, and, thus, lack dynamic structural information. The lack of information on dynamics and intermediate states makes it difficult to associate the structural with the dynamic functional data obtained with electrophysiology. Although voltage-clamp fluorometry fills this gap, it is limited to sites extracellularly accessible, when the key region for gating is located at the cytosolic side of the channels. Here, we solved this problem by performing voltage-clamp fluorometry with a fluorescent unnatural amino acid. By using an orthogonal tRNA-synthetase pair, the fluorescent unnatural amino acid was incorporated in the Shaker voltage-gated potassium channel at key regions that were previously inaccessible. Thus, we defined which parts act independently and which parts act cooperatively and found pore opening to occur in two sequential transitions. PMID:23630265
University Students' Strategies for Constructing Hypothesis when Tackling Paper-and-Pencil Tasks in Physics

NASA Astrophysics Data System (ADS)

Guisasola, Jenaro; Ceberio, Mikel; Zubimendi, José Luis

2006-09-01

The study we present tries to explore how first year engineering students formulate hypotheses in order to construct their own problem solving structure when confronted with problems in physics. Under the constructivistic perspective of the teaching-learning process, the formulation of hypotheses plays a key role in contrasting the coherence of the students' ideas with the theoretical frame. The main research instrument used to identify students' reasoning is the written report by the student on how they have attempted four problem solving tasks in which they have been asked explicitly to formulate hypotheses. The protocols used in the assessment of the solutions consisted of a semi-quantitative study based on grids designed for the analysis of written answers. In this paper we have included two of the tasks used and the corresponding scheme for the categorisation of the answers. Details of the other two tasks are also outlined. According to our findings we would say that the majority of students judge a hypothesis to be plausible if it is congruent with their previous knowledge without rigorously checking it against the theoretical framework explained in class.
Conformal mapping for multiple terminals

PubMed Central

Wang, Weimin; Ma, Wenying; Wang, Qiang; Ren, Hao

2016-01-01

Conformal mapping is an important mathematical tool that can be used to solve various physical and engineering problems in many fields, including electrostatics, fluid mechanics, classical mechanics, and transformation optics. It is an accurate and convenient way to solve problems involving two terminals. However, when faced with problems involving three or more terminals, which are more common in practical applications, existing conformal mapping methods apply assumptions or approximations. A general exact method does not exist for a structure with an arbitrary number of terminals. This study presents a conformal mapping method for multiple terminals. Through an accurate analysis of boundary conditions, additional terminals or boundaries are folded into the inner part of a mapped region. The method is applied to several typical situations, and the calculation process is described for two examples of an electrostatic actuator with three electrodes and of a light beam splitter with three ports. Compared with previously reported results, the solutions for the two examples based on our method are more precise and general. The proposed method is helpful in promoting the application of conformal mapping in analysis of practical problems. PMID:27830746
A Chemical Approach to Understanding Oxide Surface Structure and Reactivity

NASA Astrophysics Data System (ADS)

Enterkin, James Andrew

Transmission electron microscopy and diffraction are powerful tools for solving complex structural problems. They complement other analytical techniques, such as x-ray diffraction, elucidating problems which cannot be solved by other techniques. One area where they are of particularly great value is in the determination of surface structures. The research presented herein uses electron microscopy and diffraction as the primary experimental techniques in the development of a chemistry of surface structures. High-resolution electron microscopy revealed that the La4Cu 3MoO12 structure has turbostratic disorder and a lower symmetry space group (Pm) than was previously found. The refinement of the x-ray data was significantly improved by using a disordered model and the Pm space group. A bond valence analysis confirmed that the disordered structure is the superior model. Strontium titanate, SrTiO3, single crystal surfaces were examined principally via transmission electron diffraction. A homologous series with intergrowths was discovered on the (110) surface of strontium titanate, marking the first time that these important concepts of solid state chemistry have been found at the surface. Atmospheric adsorbates, such as H2O and CO2, were found to help to stabilize undercoordinated surface structures on the (100) surface. It was shown that chemical bonding, bond valence, atomic coordination, and stoichiometry greatly influence the development of surface structures. Additionally, such chemistry based analysis was demonstrated to be able to predict surface structure stability and reactivity. Application of a modified Wulff construction to the observed shape of strontium titanate nanocuboids revealed that the surface structure and particle stoichiometry are interlinked, with control over one allowing equally precise control over the other. Platinum nanoparticles on the strontium titanate nanocuboids were shown via high resolution electron microscopy to have cube-on-cube epitaxy, with the shape of the platinum nanoparticles governed by the Winterbottom construction. Precise modification of the support surface will therefore allow engineering of supported metal particles with precise control over which facets are exposed. These results suggest that control over the support surface chemistry can be used to engineer thermodynamically stable, face selective catalysts.

Colorful Success: Preschoolers' Use of Perceptual Color Cues to Solve a Spatial Reasoning Problem

ERIC Educational Resources Information Center

Joh, Amy S.; Spivey, Leigh A.

2012-01-01

Spatial reasoning, a crucial skill for everyday actions, develops gradually during the first several years of childhood. Previous studies have shown that perceptual information and problem solving strategies are critical for successful spatial reasoning in young children. Here, we sought to link these two factors by examining children's use of…
Problem Solving as an Encoding Task: A Special Case of the Generation Effect

ERIC Educational Resources Information Center

Kizilirmak, Jasmin M.; Wiegmann, Berit; Richardson-Klavehn, Alan

2016-01-01

Recent evidence suggests that solving problems through insight can enhance long-term memory for the problem and its solution. Previous findings have shown that generation of the solution as well as experiencing a feeling of Aha! can have a beneficial relationship to later memory. These findings lead to the question of how learning in…
Varying Use of Conceptual Metaphors across Levels of Expertise in Thermodynamics

ERIC Educational Resources Information Center

Jeppsson, Fredrik; Haglund, Jesper; Amin, Tamer G.

2015-01-01

Many studies have previously focused on how people with different levels of expertise solve physics problems. In early work, focus was on characterising differences between experts and novices and a key finding was the central role that propositionally expressed principles and laws play in expert, but not novice, problem-solving. A more recent…
Social Problem Solving in High-Risk Mother-Child Dyads: An Intergenerational Study

ERIC Educational Resources Information Center

Martin, Julie P.; Stack, Dale M.; Serbin, Lisa A.; Schwartzman, Alex E.; Ledingham, Jane

2012-01-01

This study examined the contribution of maternal childhood histories of aggression and social withdrawal to the prediction of mother-child social problem solving in the next generation. Fifty-seven women (M = 37.32 years), previously rated (on a version of the pupil evaluation inventory) by their peers during childhood on measures of aggression…
Problem solving as a core strategy in the prevention of schizophrenia and other mental disorders.

PubMed

Falloon, I R

2000-11-01

To outline the rationale for implementing training in structured problem solving as a primary prevention strategy for major mental disorders. The evidence that training people in a structured method of solving their personal problems is an effective strategy in the treatment of established cases of schizophrenic and major mood disorders, is selectively reviewed. Most of the relevant research focused on the prevention of major recurrent episodes of psychosis. There is some evidence to support the hypothesis that this strategy may assist many people to achieve a full and sustained recovery from the clinical and social impairments of these disorders, especially when patients are taught to use structured problem solving with members of their personal resource groups, and they continue to take optimal doses of psychoactive medication. There is support for the hypothesis that the key therapeutic factor associated with these benefits is the improved efficiency of the management of life stress. The simplicity of problem solving, the educational methods used, and the widespread application to a person's lifestyle would appear to make this a possible candidate for a primary prevention program for major mental disorders. Guidebooks and teaching aids have been developed and show excellent consumer acceptance.
Solving the Problems of Iowa Food Deserts: Food Insecurity and Civic Structure

ERIC Educational Resources Information Center

Morton, Lois Wright; Bitto, Ella Annette; Oakland, Mary Jane; Sand, Mary

2005-01-01

Rural regions include places where food sources are not evenly distributed, leading to areas of concentration and food desert--places where few or no grocery stores exist. Individuals are hypothesized to depend on personal connections and the civic structure of where they live to help them solve the problem of food insecurity. We find that…
Fragmentation of Thinking Structure's Students to Solving the Problem of Application Definite Integral in Area

ERIC Educational Resources Information Center

Wibawa, Kadek Adi; Nusantara, Toto; Subanji; Parta, I. Nengah

2017-01-01

This study aims to reveal the fragmentation of thinking structure's students in solving the problems of application definite integral in area. Fragmentation is a term on the computer (storage) that is highly relevant correlated with theoretical constructions that occur in the human brain (memory). Almost every student has a different way to…
Developing Ill-Structured Problem-Solving Skills through Wilderness Education

ERIC Educational Resources Information Center

Collins, Rachel H.; Sibthorp, Jim; Gookin, John

2016-01-01

In a society that is becoming more dynamic, complex, and diverse, the ability to solve ill-structured problems (ISPs) has become an increasingly critical skill. Students who enter adult roles with the cognitive skills to address ISPs will be better able to assume roles in the emerging economies. Opportunities to develop and practice these skills…
Viewing or Visualising Which Concept Map Strategy Works Best on Problem-Solving Performance?

ERIC Educational Resources Information Center

Lee, Youngmin; Nelson, David W.

2005-01-01

The purpose of this study was to investigate the effects of two types of maps (generative vs. completed) and the amount of prior knowledge (high vs. low) on well-structured and ill-structured problem-solving performance. Forty-four undergraduates who were registered in an introductory instructional technology course participated in the study.…
Research Projects in Physics: A Mechanism for Teaching Ill-Structured Problem Solving

ERIC Educational Resources Information Center

Milbourne, Jeff; Bennett, Jonathan

2017-01-01

Physics education research has a tradition of studying problem solving, exploring themes such as physical intuition and differences between expert and novice problem solvers. However, most of this work has focused on traditional, or well-structured, problems, similar to what might appear in a textbook. Less work has been done with open-ended, or…
Perceptual Learning in Early Mathematics: Interacting with Problem Structure Improves Mapping, Solving and Fluency

ERIC Educational Resources Information Center

Thai, Khanh-Phuong; Son, Ji Y.; Hoffman, Jessica; Devers, Christopher; Kellman, Philip J.

2014-01-01

Mathematics is the study of structure but students think of math as solving problems according to rules. Students can learn procedures, but they often have trouble knowing when to apply learned procedures, especially to problems unlike those they trained with. In this study, the authors rely on the psychological mechanism of perceptual learning…
Insightful problem solving and emulation in brown capuchin monkeys.

PubMed

Renner, Elizabeth; Abramo, Allison M; Karen Hambright, M; Phillips, Kimberley A

2017-05-01

We investigated problem solving abilities of capuchin monkeys via the "floating object problem," a task in which the subject must use creative problem solving to retrieve a favored food item from the bottom of a clear tube. Some great apes have solved this problem by adding water to raise the object to a level at which it can be easily grabbed. We presented seven capuchins with the task over eight trials (four "dry" and four "wet"). None of the subjects solved the task, indicating that no capuchin demonstrated insightful problem solving under these experimental conditions. We then investigated whether capuchins would emulate a solution to the task. Seven subjects observed a human model solve the problem by pouring water from a cup into the tube, which brought the object to the top of the tube, allowing the subject to retrieve it. Subjects were then allowed to interact freely with an unfilled tube containing the object in the presence of water and objects that could be used to solve the task. While most subjects were unable to solve the task after viewing a demonstrator solve it, one subject did so, but in a unique way. Our results are consistent with some previous results in great ape species and indicate that capuchins do not spontaneously solve the floating object problem via insight.
Crystal structure of Escherichia coli L-arabinose isomerase (ECAI), the putative target of biological tagatose production.

PubMed

Manjasetty, Babu A; Chance, Mark R

2006-07-07

Escherichia coli L-arabinose isomerase (ECAI; EC 5.3.1.4) catalyzes the isomerization of L-arabinose to L-ribulose in vivo. This enzyme is also of commercial interest as it catalyzes the conversion of D-galactose to D-tagatose in vitro. The crystal structure of ECAI was solved and refined at 2.6 A resolution. The subunit structure of ECAI is organised into three domains: an N-terminal, a central and a C-terminal domain. It forms a crystallographic trimeric architecture in the asymmetric unit. Packing within the crystal suggests the idea that ECAI can form a hexameric assembly. Previous electron microscopic and biochemical studies supports that ECAI is hexameric in solution. A comparison with other known structures reveals that ECAI adopts a protein fold most similar to E. coli fucose isomerase (ECFI) despite very low sequence identity 9.7%. The structural similarity between ECAI and ECFI with regard to number of domains, overall fold, biological assembly, and active site architecture strongly suggests that the enzymes have functional similarities. Further, the crystal structure of ECAI forms a basis for identifying molecular determinants responsible for isomerization of arabinose to ribulose in vivo and galactose to tagatose in vitro.
Adaptive finite volume methods with well-balanced Riemann solvers for modeling floods in rugged terrain: Application to the Malpasset dam-break flood (France, 1959)

USGS Publications Warehouse

George, D.L.

2011-01-01

The simulation of advancing flood waves over rugged topography, by solving the shallow-water equations with well-balanced high-resolution finite volume methods and block-structured dynamic adaptive mesh refinement (AMR), is described and validated in this paper. The efficiency of block-structured AMR makes large-scale problems tractable, and allows the use of accurate and stable methods developed for solving general hyperbolic problems on quadrilateral grids. Features indicative of flooding in rugged terrain, such as advancing wet-dry fronts and non-stationary steady states due to balanced source terms from variable topography, present unique challenges and require modifications such as special Riemann solvers. A well-balanced Riemann solver for inundation and general (non-stationary) flow over topography is tested in this context. The difficulties of modeling floods in rugged terrain, and the rationale for and efficacy of using AMR and well-balanced methods, are presented. The algorithms are validated by simulating the Malpasset dam-break flood (France, 1959), which has served as a benchmark problem previously. Historical field data, laboratory model data and other numerical simulation results (computed on static fitted meshes) are shown for comparison. The methods are implemented in GEOCLAW, a subset of the open-source CLAWPACK software. All the software is freely available at. Published in 2010 by John Wiley & Sons, Ltd.
PowerPlay: Training an Increasingly General Problem Solver by Continually Searching for the Simplest Still Unsolvable Problem

PubMed Central

Schmidhuber, Jürgen

2013-01-01

Most of computer science focuses on automatically solving given computational problems. I focus on automatically inventing or discovering problems in a way inspired by the playful behavior of animals and humans, to train a more and more general problem solver from scratch in an unsupervised fashion. Consider the infinite set of all computable descriptions of tasks with possibly computable solutions. Given a general problem-solving architecture, at any given time, the novel algorithmic framework PowerPlay (Schmidhuber, 2011) searches the space of possible pairs of new tasks and modifications of the current problem solver, until it finds a more powerful problem solver that provably solves all previously learned tasks plus the new one, while the unmodified predecessor does not. Newly invented tasks may require to achieve a wow-effect by making previously learned skills more efficient such that they require less time and space. New skills may (partially) re-use previously learned skills. The greedy search of typical PowerPlay variants uses time-optimal program search to order candidate pairs of tasks and solver modifications by their conditional computational (time and space) complexity, given the stored experience so far. The new task and its corresponding task-solving skill are those first found and validated. This biases the search toward pairs that can be described compactly and validated quickly. The computational costs of validating new tasks need not grow with task repertoire size. Standard problem solver architectures of personal computers or neural networks tend to generalize by solving numerous tasks outside the self-invented training set; PowerPlay’s ongoing search for novelty keeps breaking the generalization abilities of its present solver. This is related to Gödel’s sequence of increasingly powerful formal theories based on adding formerly unprovable statements to the axioms without affecting previously provable theorems. The continually increasing repertoire of problem-solving procedures can be exploited by a parallel search for solutions to additional externally posed tasks. PowerPlay may be viewed as a greedy but practical implementation of basic principles of creativity (Schmidhuber, 2006a, 2010). A first experimental analysis can be found in separate papers (Srivastava et al., 2012a,b, 2013). PMID:23761771
Thinking in Italian: Problem-Solving Activities for the Italian Classroom.

ERIC Educational Resources Information Center

Danesi, Marcel

1985-01-01

Looks at devices that stimulate intralinguistic thinking patterns, that is, patterns that can only be induced by the structures and forms of the target language without any dependency upon native-language patterns. Focuses on problem-solving activities that help the learner develop modes of thought that can be solved "Italian." (SED)
A Structural Equation Model to Analyse the Antecedents to Students' Web-Based Problem-Solving Performance

ERIC Educational Resources Information Center

Hwang, Gwo-Jen; Kuo, Fan-Ray

2015-01-01

Web-based problem-solving, a compound ability of critical thinking, creative thinking, reasoning thinking and information-searching abilities, has been recognised as an important competence for elementary school students. Some researchers have reported the possible correlations between problem-solving competence and information searching ability;…
Problem Solving in Social Studies: Concepts and Critiques.

ERIC Educational Resources Information Center

Van Sickle, Ronald L.; Hoge, John D.

Recent developments in the field of cognitive psychology, particularly in the area of information processing, have shed light on the way people think in order to make decisions and solve problems. In addition, cooperative learning research has provided evidence of the effectiveness of cooperatively structured group work aimed at problem solving.…
Effects of a Research-Based Intervention to Improve Seventh-Grade Students' Proportional Problem Solving: A Cluster Randomized Trial

ERIC Educational Resources Information Center

Jitendra, Asha K.; Harwell, Michael R.; Dupuis, Danielle N.; Karl, Stacy R.; Lein, Amy E.; Simonson, Gregory; Slater, Susan C.

2015-01-01

This experimental study evaluated the effectiveness of a research-based intervention, schema-based instruction (SBI), on students' proportional problem solving. SBI emphasizes the underlying mathematical structure of problems, uses schematic diagrams to represent information in the problem text, provides explicit problem-solving and metacognitive…
Superitem Test: An Alternative Assessment Tool to Assess Students' Algebraic Solving Ability

ERIC Educational Resources Information Center

Lian, Lim Hooi; Yew, Wun Thiam; Idris, Noraini

2010-01-01

Superitem test based on the SOLO model (Structure of the Observing Learning Outcome) has become a powerful alternative assessment tool for monitoring the growth of students' cognitive ability in solving mathematics problems. This article focused on developing a superitem test to assess students' algebraic solving ability through interview method.…

A Contingency View of Problem Solving in Schools: A Case Analysis.

ERIC Educational Resources Information Center

Hanson, E. Mark; Brown, Michael E.

Patterns of problem-solving activity in one middle-class urban high school are examined and a problem solving model rooted in a conceptual framework of contingency theory is presented. Contingency theory stresses that as political, economic, and social conditions in an organization's environment become problematic, the internal structures of the…
Effects of a Research-Based Intervention to Improve Seventh-Grade Students' Proportional Problem Solving: A Cluster Randomized Trial

ERIC Educational Resources Information Center

Jitendra, Asha K.; Harwell, Michael R.; Dupuis, Danielle N.; Karl, Stacy R.; Lein, Amy E.; Simonson, Gregory; Slater, Susan C.

2015-01-01

This experimental study evaluated the effectiveness of a research-based intervention, schema-based instruction (SBI), on students' proportional problem solving. SBI emphasizes the underlying mathematical structure of problems, uses schematic diagrams to represent information in the problem text, provides explicit problem solving and metacognitive…
Problems of Complex Systems: A Model of System Problem Solving Applied to Schools.

ERIC Educational Resources Information Center

Cooke, Robert A.; Rousseau, Denise M.

Research of 25 Michigan elementary and secondary public schools is used to test a model relating organizations' problem-solving adequacy to their available inputs or resources and to the appropriateness of their structures. Problems that all organizations must solve, to avoid disorganization or entropy, include (1) getting inputs and producing…
Insights into the Structure of Dimeric RNA Helicase CsdA and Indispensable Role of Its C-Terminal Regions

DOE PAGES

Xu, Ling; Wang, Lijun; Peng, Junhui; ...

2017-12-05

CsdA has been proposed to be essential for the biogenesis of ribosome and gene regulation after cold shock. However, the structure of CsdA and the function of its long C-terminal regions are still unclear. For this study, we solved all of the domain structures of CsdA and found two previously uncharacterized auxiliary domains: a dimerization domain (DD) and an RNA-binding domain (RBD). Small-angle X-ray scattering experiments helped to track the conformational flexibilities of the helicase core domains and C-terminal regions. Biochemical assays revealed that DD is indispensable for stabilizing the CsdA dimeric structure. We also demonstrate for the first timemore » that CsdA functions as a stable dimer at low temperature. The C-terminal regions are critical for RNA binding and efficient enzymatic activities. CsdA_RBD could specifically bind to the regions with a preference for single-stranded G-rich RNA, which may help to bring the helicase core to unwind the adjacent duplex.« less
Alternative approximation concepts for space frame synthesis

NASA Technical Reports Server (NTRS)

Lust, R. V.; Schmit, L. A.

1985-01-01

A structural synthesis methodology for the minimum mass design of 3-dimensionall frame-truss structures under multiple static loading conditions and subject to limits on displacements, rotations, stresses, local buckling, and element cross-sectional dimensions is presented. A variety of approximation concept options are employed to yield near optimum designs after no more than 10 structural analyses. Available options include: (A) formulation of the nonlinear mathematcal programming problem in either reciprocal section property (RSP) or cross-sectional dimension (CSD) space; (B) two alternative approximate problem structures in each design space; and (C) three distinct assumptions about element end-force variations. Fixed element, design element linking, and temporary constraint deletion features are also included. The solution of each approximate problem, in either its primal or dual form, is obtained using CONMIN, a feasible directions program. The frame-truss synthesis methodology is implemented in the COMPASS computer program and is used to solve a variety of problems. These problems were chosen so that, in addition to exercising the various approximation concepts options, the results could be compared with previously published work.
An immersed-boundary method for flow–structure interaction in biological systems with application to phonation

PubMed Central

Luo, Haoxiang; Mittal, Rajat; Zheng, Xudong; Bielamowicz, Steven A.; Walsh, Raymond J.; Hahn, James K.

2008-01-01

A new numerical approach for modeling a class of flow–structure interaction problems typically encountered in biological systems is presented. In this approach, a previously developed, sharp-interface, immersed-boundary method for incompressible flows is used to model the fluid flow and a new, sharp-interface Cartesian grid, immersed boundary method is devised to solve the equations of linear viscoelasticity that governs the solid. The two solvers are coupled to model flow–structure interaction. This coupled solver has the advantage of simple grid generation and efficient computation on simple, single-block structured grids. The accuracy of the solid-mechanics solver is examined by applying it to a canonical problem. The solution methodology is then applied to the problem of laryngeal aerodynamics and vocal fold vibration during human phonation. This includes a three-dimensional eigen analysis for a multi-layered vocal fold prototype as well as two-dimensional, flow-induced vocal fold vibration in a modeled larynx. Several salient features of the aerodynamics as well as vocal-fold dynamics are presented. PMID:19936017
Insights into the Structure of Dimeric RNA Helicase CsdA and Indispensable Role of Its C-Terminal Regions

DOE Office of Scientific and Technical Information (OSTI.GOV)

Xu, Ling; Wang, Lijun; Peng, Junhui

CsdA has been proposed to be essential for the biogenesis of ribosome and gene regulation after cold shock. However, the structure of CsdA and the function of its long C-terminal regions are still unclear. For this study, we solved all of the domain structures of CsdA and found two previously uncharacterized auxiliary domains: a dimerization domain (DD) and an RNA-binding domain (RBD). Small-angle X-ray scattering experiments helped to track the conformational flexibilities of the helicase core domains and C-terminal regions. Biochemical assays revealed that DD is indispensable for stabilizing the CsdA dimeric structure. We also demonstrate for the first timemore » that CsdA functions as a stable dimer at low temperature. The C-terminal regions are critical for RNA binding and efficient enzymatic activities. CsdA_RBD could specifically bind to the regions with a preference for single-stranded G-rich RNA, which may help to bring the helicase core to unwind the adjacent duplex.« less
Insights into the Structure of Dimeric RNA Helicase CsdA and Indispensable Role of Its C-Terminal Regions.

PubMed

Xu, Ling; Wang, Lijun; Peng, Junhui; Li, Fudong; Wu, Lijie; Zhang, Beibei; Lv, Mengqi; Zhang, Jiahai; Gong, Qingguo; Zhang, Rongguang; Zuo, Xiaobing; Zhang, Zhiyong; Wu, Jihui; Tang, Yajun; Shi, Yunyu

2017-12-05

CsdA has been proposed to be essential for the biogenesis of ribosome and gene regulation after cold shock. However, the structure of CsdA and the function of its long C-terminal regions are still unclear. Here, we solved all of the domain structures of CsdA and found two previously uncharacterized auxiliary domains: a dimerization domain (DD) and an RNA-binding domain (RBD). Small-angle X-ray scattering experiments helped to track the conformational flexibilities of the helicase core domains and C-terminal regions. Biochemical assays revealed that DD is indispensable for stabilizing the CsdA dimeric structure. We also demonstrate for the first time that CsdA functions as a stable dimer at low temperature. The C-terminal regions are critical for RNA binding and efficient enzymatic activities. CsdA_RBD could specifically bind to the regions with a preference for single-stranded G-rich RNA, which may help to bring the helicase core to unwind the adjacent duplex. Copyright © 2017 Elsevier Ltd. All rights reserved.
Additive Mixing and Conformal Coating of Noniridescent Structural Colors with Robust Mechanical Properties Fabricated by Atomization Deposition.

PubMed

Li, Qingsong; Zhang, Yafeng; Shi, Lei; Qiu, Huihui; Zhang, Suming; Qi, Ning; Hu, Jianchen; Yuan, Wei; Zhang, Xiaohua; Zhang, Ke-Qin

2018-04-24

Artificial structural colors based on short-range-ordered amorphous photonic structures (APSs) have attracted great scientific and industrial interest in recent years. However, the previously reported methods of self-assembling colloidal nanoparticles lack fine control of the APS coating and fixation on substrates and poorly realize three-dimensional (3D) conformal coatings for objects with irregular or highly curved surfaces. In this paper, atomization deposition of silica colloidal nanoparticles with poly(vinyl alcohol) as the additive is proposed to solve the above problems. By finely controlling the thicknesses of APS coatings, additive mixing of noniridescent structural colors is easily realized. Based on the intrinsic omnidirectional feature of atomization, a one-step 3D homogeneous conformal coating is also readily realized on various irregular or highly curved surfaces, including papers, resins, metal plates, ceramics, and flexible silk fabrics. The vivid coatings on silk fabrics by atomization deposition possess robust mechanical properties, which are confirmed by rubbing and laundering tests, showing great potential in developing an environmentally friendly coloring technique in the textile industry.
Representation of molecular structure using quantum topology with inductive logic programming in structure-activity relationships.

PubMed

Buttingsrud, Bård; Ryeng, Einar; King, Ross D; Alsberg, Bjørn K

2006-06-01

The requirement of aligning each individual molecule in a data set severely limits the type of molecules which can be analysed with traditional structure activity relationship (SAR) methods. A method which solves this problem by using relations between objects is inductive logic programming (ILP). Another advantage of this methodology is its ability to include background knowledge as 1st-order logic. However, previous molecular ILP representations have not been effective in describing the electronic structure of molecules. We present a more unified and comprehensive representation based on Richard Bader's quantum topological atoms in molecules (AIM) theory where critical points in the electron density are connected through a network. AIM theory provides a wealth of chemical information about individual atoms and their bond connections enabling a more flexible and chemically relevant representation. To obtain even more relevant rules with higher coverage, we apply manual postprocessing and interpretation of ILP rules. We have tested the usefulness of the new representation in SAR modelling on classifying compounds of low/high mutagenicity and on a set of factor Xa inhibitors of high and low affinity.
The neuronal porosome complex in health and disease

PubMed Central

Naik, Akshata R; Lewis, Kenneth T

2015-01-01

Cup-shaped secretory portals at the cell plasma membrane called porosomes mediate the precision release of intravesicular material from cells. Membrane-bound secretory vesicles transiently dock and fuse at the base of porosomes facing the cytosol to expel pressurized intravesicular contents from the cell during secretion. The structure, isolation, composition, and functional reconstitution of the neuronal porosome complex have greatly progressed, providing a molecular understanding of its function in health and disease. Neuronal porosomes are 15 nm cup-shaped lipoprotein structures composed of nearly 40 proteins, compared to the 120 nm nuclear pore complex composed of >500 protein molecules. Membrane proteins compose the porosome complex, making it practically impossible to solve its atomic structure. However, atomic force microscopy and small-angle X-ray solution scattering studies have provided three-dimensional structural details of the native neuronal porosome at sub-nanometer resolution, providing insights into the molecular mechanism of its function. The participation of several porosome proteins previously implicated in neurotransmission and neurological disorders, further attest to the crosstalk between porosome proteins and their coordinated involvement in release of neurotransmitter at the synapse. PMID:26264442
The m1A(58) modification in eubacterial tRNA: An overview of tRNA recognition and mechanism of catalysis by TrmI.

PubMed

Dégut, Clément; Ponchon, Luc; Folly-Klan, Marcia; Barraud, Pierre; Tisné, Carine

2016-03-01

The enzymes of the TrmI family catalyze the formation of the m(1)A58 modification in tRNA. We previously solved the crystal structure of the Thermus thermophilus enzyme and conducted a biophysical study to characterize the interaction between TrmI and tRNA. TrmI enzymes are active as a tetramer and up to two tRNAs can bind to TrmI simultaneously. In this paper, we present the structures of two TrmI mutants (D170A and Y78A). These residues are conserved in the active site of TrmIs and their mutations result in a dramatic alteration of TrmI activity. Both structures of TrmI mutants revealed the flexibility of the N-terminal domain that is probably important to bind tRNA. The structure of TrmI Y78A catalytic domain is unmodified regarding the binding of the SAM co-factor and the conformation of residues potentially interacting with the substrate adenine. This structure reinforces the previously proposed role of Y78, i.e. stabilize the conformation of the A58 ribose needed to hold the adenosine in the active site. The structure of the D170A mutant shows a flexible active site with one loop occupying in part the place of the co-factor and the second loop moving at the entrance to the active site. This structure and recent data confirms the central role of D170 residue binding the amino moiety of SAM and the exocyclic amino group of adenine. Possible mechanisms for methyl transfer are then discussed. Copyright © 2015 Elsevier B.V. All rights reserved.
Pedagogy and/or technology: Making difference in improving students' problem solving skills

NASA Astrophysics Data System (ADS)

Hrepic, Zdeslav; Lodder, Katherine; Shaw, Kimberly A.

2013-01-01

Pen input computers combined with interactive software may have substantial potential for promoting active instructional methodologies and for facilitating students' problem solving ability. An excellent example is a study in which introductory physics students improved retention, conceptual understanding and problem solving abilities when one of three weekly lectures was replaced with group problem solving sessions facilitated with Tablet PCs and DyKnow software [1,2]. The research goal of the present study was to isolate the effect of the methodology itself (using additional time to teach problem solving) from that of the involved technology. In Fall 2011 we compared the performance of students taking the same introductory physics lecture course while enrolled in two separate problem-solving sections. One section used pen-based computing to facilitate group problem solving while the other section used low-tech methods for one third of the semester (covering Kinematics), and then traded technologies for the middle third of the term (covering Dynamics). Analysis of quiz, exam and standardized pre-post test results indicated no significant difference in scores of the two groups. Combining this result with those of previous studies implies primacy of pedagogy (collaborative problem solving itself) over technology for student learning in problem solving recitations.
Spontaneous gestures influence strategy choices in problem solving.

PubMed

Alibali, Martha W; Spencer, Robert C; Knox, Lucy; Kita, Sotaro

2011-09-01

Do gestures merely reflect problem-solving processes, or do they play a functional role in problem solving? We hypothesized that gestures highlight and structure perceptual-motor information, and thereby make such information more likely to be used in problem solving. Participants in two experiments solved problems requiring the prediction of gear movement, either with gesture allowed or with gesture prohibited. Such problems can be correctly solved using either a perceptual-motor strategy (simulation of gear movements) or an abstract strategy (the parity strategy). Participants in the gesture-allowed condition were more likely to use perceptual-motor strategies than were participants in the gesture-prohibited condition. Gesture promoted use of perceptual-motor strategies both for participants who talked aloud while solving the problems (Experiment 1) and for participants who solved the problems silently (Experiment 2). Thus, spontaneous gestures influence strategy choices in problem solving.
AI tools in computer based problem solving

NASA Technical Reports Server (NTRS)

Beane, Arthur J.

1988-01-01

The use of computers to solve value oriented, deterministic, algorithmic problems, has evolved a structured life cycle model of the software process. The symbolic processing techniques used, primarily in research, for solving nondeterministic problems, and those for which an algorithmic solution is unknown, have evolved a different model, much less structured. Traditionally, the two approaches have been used completely independently. With the advent of low cost, high performance 32 bit workstations executing identical software with large minicomputers and mainframes, it became possible to begin to merge both models into a single extended model of computer problem solving. The implementation of such an extended model on a VAX family of micro/mini/mainframe systems is described. Examples in both development and deployment of applications involving a blending of AI and traditional techniques are given.
Refining mortality estimates in shark demographic analyses: a Bayesian inverse matrix approach.

PubMed

Smart, Jonathan J; Punt, André E; White, William T; Simpfendorfer, Colin A

2018-01-18

Leslie matrix models are an important analysis tool in conservation biology that are applied to a diversity of taxa. The standard approach estimates the finite rate of population growth (λ) from a set of vital rates. In some instances, an estimate of λ is available, but the vital rates are poorly understood and can be solved for using an inverse matrix approach. However, these approaches are rarely attempted due to prerequisites of information on the structure of age or stage classes. This study addressed this issue by using a combination of Monte Carlo simulations and the sample-importance-resampling (SIR) algorithm to solve the inverse matrix problem without data on population structure. This approach was applied to the grey reef shark (Carcharhinus amblyrhynchos) from the Great Barrier Reef (GBR) in Australia to determine the demography of this population. Additionally, these outputs were applied to another heavily fished population from Papua New Guinea (PNG) that requires estimates of λ for fisheries management. The SIR analysis determined that natural mortality (M) and total mortality (Z) based on indirect methods have previously been overestimated for C. amblyrhynchos, leading to an underestimated λ. The updated Z distributions determined using SIR provided λ estimates that matched an empirical λ for the GBR population and corrected obvious error in the demographic parameters for the PNG population. This approach provides opportunity for the inverse matrix approach to be applied more broadly to situations where information on population structure is lacking. © 2018 by the Ecological Society of America.
A Rutile Chevron Modulation in Delafossite-Like Ga 3–x In 3 Ti x O 9+x/2

DOE Office of Scientific and Technical Information (OSTI.GOV)

Rickert, Karl; Boullay, Philippe; Malo, Sylvie

2016-05-02

The structure solution of the modulated, delafossite-related, orthorhombic Ga 3–xIn 3Ti xO 9+x/2 for x = 1.5 is reported here in conjunction with a model describing the modulation as a function of x for the entire system. Previously reported structures in the related A 3–xIn 3Ti xO 9+x/2 (A = Al, Cr, or Fe) systems use X-ray diffraction to determine that the anion lattice is the source of modulation. Neutron diffraction, with its enhanced sensitivity to light atoms, offers a route to solving the modulation and is used here, in combination with precession electron diffraction tomography (PEDT), to solve themore » structure of Ga 1.5In 3Ti 1.5O 9.75. We construct a model that describes the anion modulation through the formation of rutile chevrons as a function of x. This model accommodates the orthorhombic phase (1.5 ≤ x ≤ 2.1) in the Ga 3-xIn 3Ti xO 9+x/2 system, which transitions to a biphasic mixture (2.2 ≤ x ≤ 2.3) with a monoclinic, delafossite-related phase (2.4 ≤ x ≤ 2.5). The optical band gaps of this system are determined, and are stable at ~3.4 eV before a ~0.4 eV decrease between x = 1.9 and 2.0. After this decrease, stability resumes at ~3.0 eV. Resistance to oxidation and reduction is also presented.« less
DOE Office of Scientific and Technical Information (OSTI.GOV)

Jia, Xiaofei; Singh, Rajendra; Homann, Stefanie

The HIV-1 protein Nef inhibits antigen presentation by class I major histocompatibility complex (MHC-I). We determined the mechanism of this activity by solving the crystal structure of a protein complex comprising Nef, the MHC-I cytoplasmic domain (MHC-I CD) and the {mu}1 subunit of the clathrin adaptor protein complex 1. A ternary, cooperative interaction clamps the MHC-I CD into a narrow binding groove at the Nef-{mu}1 interface, which encompasses the cargo-recognition site of {mu}1 and the proline-rich strand of Nef. The Nef C terminus induces a previously unobserved conformational change in {mu}1, whereas the N terminus binds the Nef core tomore » position it optimally for complex formation. Positively charged patches on {mu}1 recognize acidic clusters in Nef and MHC-I. The structure shows how Nef functions as a clathrin-associated sorting protein to alter the specificity of host membrane trafficking and enable viral evasion of adaptive immunity.« less
Image size invariant visual cryptography for general access structures subject to display quality constraints.

PubMed

Lee, Kai-Hui; Chiu, Pei-Ling

2013-10-01

Conventional visual cryptography (VC) suffers from a pixel-expansion problem, or an uncontrollable display quality problem for recovered images, and lacks a general approach to construct visual secret sharing schemes for general access structures. We propose a general and systematic approach to address these issues without sophisticated codebook design. This approach can be used for binary secret images in non-computer-aided decryption environments. To avoid pixel expansion, we design a set of column vectors to encrypt secret pixels rather than using the conventional VC-based approach. We begin by formulating a mathematic model for the VC construction problem to find the column vectors for the optimal VC construction, after which we develop a simulated-annealing-based algorithm to solve the problem. The experimental results show that the display quality of the recovered image is superior to that of previous papers.
Finite element method analysis of band gap and transmission of two-dimensional metallic photonic crystals at terahertz frequencies.

PubMed

Degirmenci, Elif; Landais, Pascal

2013-10-20

Photonic band gap and transmission characteristics of 2D metallic photonic crystals at THz frequencies have been investigated using finite element method (FEM). Photonic crystals composed of metallic rods in air, in square and triangular lattice arrangements, are considered for transverse electric and transverse magnetic polarizations. The modes and band gap characteristics of metallic photonic crystal structure are investigated by solving the eigenvalue problem over a unit cell of the lattice using periodic boundary conditions. A photonic band gap diagram of dielectric photonic crystal in square lattice array is also considered and compared with well-known plane wave expansion results verifying our FEM approach. The photonic band gap designs for both dielectric and metallic photonic crystals are consistent with previous studies obtained by different methods. Perfect match is obtained between photonic band gap diagrams and transmission spectra of corresponding lattice structure.

Orientamento della prima fase della moschea al-Aqşā di Gerusalemme

NASA Astrophysics Data System (ADS)

Di Cesare, Michelina

2017-07-01

A new interpretation of the archaeological data regarding the first of the three pre-Crusader structural phases of al-Aqşā mosque in Jerusalem (Aqşā I) is proposed. It suggests that the building had an astronomical orientation like other 7th-century and early 8th-century mosques. Thus, Aqşā I would have been oriented towards the East rather than the South, as believed so far. This hypothesis would allow to solve the anomalies of the plan of Aqşā I. Indeed, by identifying the eastern wall rather than the southern as the qiblī wall, the aisles would not result perpendicular but parallel to it and running along the long side, as usual in Umayyad mosques. Consequently, the precocious appearance of the transept in Aqşā II would be due to the re-orientation of the previous structure.
The role of the global magnetic field and thermal conduction on the structure of the accretion disks of all models

NASA Astrophysics Data System (ADS)

Farahinezhad, M.; Khesali, A. R.

2018-05-01

In this paper, the effects of global magnetic field and thermal conduction on the vertical structure of the accretion disks has been investigated. In this study, four types disks were examined: Gas pressure dominated the standard disk, while radiation pressure dominated the standard disk, ADAF disk, slim disk. Moreover, the general shape of the magnetic field, including toroidal and poloidal components, is considered. The magnetohydrodynamic equations were solved in spherical coordinates using self-similar assumptions in the radial direction. Following previous authors, the polar velocity vθ is non-zero and Trφ was considered as a dominant component of the stress tensor. The results show that the disk becomes thicker compared to the non-magnetic fields. It has also been shown that the presence of the thermal conduction in the ADAF model makes the disk thicker; the disk is expanded in the standard model.
Problem-solving variability in older spouses: how is it linked to problem-, person-, and couple-characteristics?

PubMed

Hoppmann, Christiane A; Blanchard-Fields, Fredda

2011-09-01

Problem-solving does not take place in isolation and often involves social others such as spouses. Using repeated daily life assessments from 98 older spouses (M age = 72 years; M marriage length = 42 years), the present study examined theoretical notions from social-contextual models of coping regarding (a) the origins of problem-solving variability and (b) associations between problem-solving and specific problem-, person-, and couple- characteristics. Multilevel models indicate that the lion's share of variability in everyday problem-solving is located at the level of the problem situation. Importantly, participants reported more proactive emotion regulation and collaborative problem-solving for social than nonsocial problems. We also found person-specific consistencies in problem-solving. That is, older spouses high in Neuroticism reported more problems across the study period as well as less instrumental problem-solving and more passive emotion regulation than older spouses low in Neuroticism. Contrary to expectations, relationship satisfaction was unrelated to problem-solving in the present sample. Results are in line with the stress and coping literature in demonstrating that everyday problem-solving is a dynamic process that has to be viewed in the broader context in which it occurs. Our findings also complement previous laboratory-based work on everyday problem-solving by underscoring the benefits of examining everyday problem-solving as it unfolds in spouses' own environment.
Crystallographic Studies of Two Bacterial AntibioticResistance Enzymes: Aminoglycoside Phosphotransferase (2')-Ic and GES-1\\beta-lactamase

DOE Office of Scientific and Technical Information (OSTI.GOV)

Brynes, Laura; /Rensselaer Poly.

2007-10-31

Guiana Extended-Spectrum-1 (GES-1) and Aminoglycoside phosphotransferase (2')-Ic (APH(2')-Ic) are two bacteria-produced enzymes that essentially perform the same task: they provide resistance to an array of antibiotics. Both enzymes are part of a growing resistance problem in the medical world. In order to overcome the ever-growing arsenal of antibiotic-resistance enzymes, it is necessary to understand the molecular basis of their action. Accurate structures of these proteins have become an invaluable tool to do this. Using protein crystallography techniques and X-ray diffraction, the protein structure of GES-1 bound to imipenem (an inhibitor) has been solved. Also, APH(2')-Ic has been successfully crystallized, butmore » its structure was unable to be solved using molecular replacement using APH(2')-Ib as a search model. The structure of GES-1, with bound imipenem was solved to a resolution of 1.89A, and though the inhibitor is bound with only moderate occupancy, the structure shows crucial interactions inside the active site that render the enzyme unable to complete the hydrolysis of the {beta}-lactam ring. The APH(2')-Ic dataset could not be matched to the model, APH(2')-Ib, with which it shares 25% sequence identity. The structural information gained from GES-1, and future studies using isomorphous replacement to solve the APH(2')-Ic structure can aid directly to the creation of novel drugs to combat both of these classes of resistance enzymes.« less
Calculation of sheath and wake structure about a pillbox-shaped spacecraft in a flowing plasma

NASA Technical Reports Server (NTRS)

Parker, L. W.

1977-01-01

A computer program was used for studies of the disturbed zones around bodies in flowing plasmas, particularly spacecraft and their associated sheaths and wakes. The program solved a coupled Poisson-Vlasov system of nonlinear partial differential integral equations to obtain distributions of electric potential and ion and electron density about a finite length cylinder in a plasma flow at arbitrary ion Mach numbers. The approach was applicable to a larger range of parameters than other available approaches. In sample calculations, bodies up to 100 Debye lengths in radius were treated, that is, larger than any previously treated realistically. Applications were made to in-situ satellite experiments.
Uncovering a reconstructive solid-solid phase transition in a metal-organic framework.

PubMed

Longley, L; Li, N; Wei, F; Bennett, T D

2017-11-01

A nanoporous three-dimensional metal-organic framework (MOF), ZnPurBr undergoes a transition to a previously unreported high-temperature phase, ZnPurBr-ht. The transition, which proceeds without mass loss, is uncovered through the use of differential scanning calorimetry (DSC). The new crystal structure was solved using single-crystal X-ray diffraction, and the mechanical properties of both phases investigated by nanoindentation and density functional theory. The anisotropy of the calculated Young's moduli showed good agreement with the crystallographic alignment of the stiff purinate organic linker. The results provide a prototypical example of the importance of the use of DSC in the MOF field, where its use is not currently standard in characterization.
Market-based control strategy for long-span structures considering the multi-time delay issue

NASA Astrophysics Data System (ADS)

Li, Hongnan; Song, Jianzhu; Li, Gang

2017-01-01

To solve the different time delays that exist in the control device installed on spatial structures, in this study, discrete analysis using a 2 N precise algorithm was selected to solve the multi-time-delay issue for long-span structures based on the market-based control (MBC) method. The concept of interval mixed energy was introduced from computational structural mechanics and optimal control research areas, and it translates the design of the MBC multi-time-delay controller into a solution for the segment matrix. This approach transforms the serial algorithm in time to parallel computing in space, greatly improving the solving efficiency and numerical stability. The designed controller is able to consider the issue of time delay with a linear controlling force combination and is especially effective for large time-delay conditions. A numerical example of a long-span structure was selected to demonstrate the effectiveness of the presented controller, and the time delay was found to have a significant impact on the results.
The Role of Content Knowledge in Ill-Structured Problem Solving for High School Physics Students

ERIC Educational Resources Information Center

Milbourne, Jeff; Wiebe, Eric

2018-01-01

While Physics Education Research has a rich tradition of problem-solving scholarship, most of the work has focused on more traditional, well-defined problems. Less work has been done with ill-structured problems, problems that are better aligned with the engineering and design-based scenarios promoted by the Next Generation Science Standards. This…
Comparing Multiple Solutions in the Structured Problem Solving: Deconstructing Japanese Lessons from Learner's Perspective

ERIC Educational Resources Information Center

Hino, Keiko

2015-01-01

The purpose of this study is to enhance our understanding of how students listen and attend to multiple solutions proposed by their classmates during the activity of comparison. This study examines ten consecutive lessons in each of the two eighth-grade classrooms in Tokyo that are organized in the style of "structured problem solving".…
Insightful problem solving in an Asian elephant.

PubMed

Foerder, Preston; Galloway, Marie; Barthel, Tony; Moore, Donald E; Reiss, Diana

2011-01-01

The "aha" moment or the sudden arrival of the solution to a problem is a common human experience. Spontaneous problem solving without evident trial and error behavior in humans and other animals has been referred to as insight. Surprisingly, elephants, thought to be highly intelligent, have failed to exhibit insightful problem solving in previous cognitive studies. We tested whether three Asian elephants (Elephas maximus) would use sticks or other objects to obtain food items placed out-of-reach and overhead. Without prior trial and error behavior, a 7-year-old male Asian elephant showed spontaneous problem solving by moving a large plastic cube, on which he then stood, to acquire the food. In further testing he showed behavioral flexibility, using this technique to reach other items and retrieving the cube from various locations to use as a tool to acquire food. In the cube's absence, he generalized this tool utilization technique to other objects and, when given smaller objects, stacked them in an attempt to reach the food. The elephant's overall behavior was consistent with the definition of insightful problem solving. Previous failures to demonstrate this ability in elephants may have resulted not from a lack of cognitive ability but from the presentation of tasks requiring trunk-held sticks as potential tools, thereby interfering with the trunk's use as a sensory organ to locate the targeted food.
Singular perturbation solutions of steady-state Poisson-Nernst-Planck systems.

PubMed

Wang, Xiang-Sheng; He, Dongdong; Wylie, Jonathan J; Huang, Huaxiong

2014-02-01

We study the Poisson-Nernst-Planck (PNP) system with an arbitrary number of ion species with arbitrary valences in the absence of fixed charges. Assuming point charges and that the Debye length is small relative to the domain size, we derive an asymptotic formula for the steady-state solution by matching outer and boundary layer solutions. The case of two ionic species has been extensively studied, the uniqueness of the solution has been proved, and an explicit expression for the solution has been obtained. However, the case of three or more ions has received significantly less attention. Previous work has indicated that the solution may be nonunique and that even obtaining numerical solutions is a difficult task since one must solve complicated systems of nonlinear equations. By adopting a methodology that preserves the symmetries of the PNP system, we show that determining the outer solution effectively reduces to solving a single scalar transcendental equation. Due to the simple form of the transcendental equation, it can be solved numerically in a straightforward manner. Our methodology thus provides a standard procedure for solving the PNP system and we illustrate this by solving some practical examples. Despite the fact that for three ions, previous studies have indicated that multiple solutions may exist, we show that all except for one of these solutions are unphysical and thereby prove the existence and uniqueness for the three-ion case.
Nonlinear tuning techniques of plasmonic nano-filters

NASA Astrophysics Data System (ADS)

Kotb, Rehab; Ismail, Yehea; Swillam, Mohamed A.

2015-02-01

In this paper, a fitting model to the propagation constant and the losses of Metal-Insulator-Metal (MIM) plasmonic waveguide is proposed. Using this model, the modal characteristics of MIM plasmonic waveguide can be solved directly without solving Maxwell's equations from scratch. As a consequence, the simulation time and the computational cost that are needed to predict the response of different plasmonic structures can be reduced significantly. This fitting model is used to develop a closed form model that describes the behavior of a plasmonic nano-filter. Easy and accurate mechanisms to tune the filter are investigated and analyzed. The filter tunability is based on using a nonlinear dielectric material with Pockels or Kerr effect. The tunability is achieved by applying an external voltage or through controlling the input light intensity. The proposed nano-filter supports both red and blue shift in the resonance response depending on the type of the used non-linear material. A new approach to control the input light intensity by applying an external voltage to a previous stage is investigated. Therefore, the filter tunability to a stage that has Kerr material can be achieved by applying voltage to a previous stage that has Pockels material. Using this method, the Kerr effect can be achieved electrically instead of varying the intensity of the input source. This technique enhances the ability of the device integration for on-chip applications. Tuning the resonance wavelength with high accuracy, minimum insertion loss and high quality factor is obtained using these approaches.
Primary School Children's Strategies in Solving Contingency Table Problems: The Role of Intuition and Inhibition

ERIC Educational Resources Information Center

Obersteiner, Andreas; Bernhard, Matthias; Reiss, Kristina

2015-01-01

Understanding contingency table analysis is a facet of mathematical competence in the domain of data and probability. Previous studies have shown that even young children are able to solve specific contingency table problems, but apply a variety of strategies that are actually invalid. The purpose of this paper is to describe primary school…
To Draw or Not to Draw? Examining the Necessity of Problem Diagrams Using Massive Open Online Course Experiments

ERIC Educational Resources Information Center

Chen, Zhongzhou; Demirci, Neset; Choi, Youn-Jeng; Pritchard, David E.

2017-01-01

Previous research on problem diagrams suggested that including a supportive diagram, one that does not provide necessary problem solving information, may bring little, or even negative, benefit to students' problem solving success. We tested the usefulness of problem diagrams on 12 different physics problems (6A/B experiments) in our massive open…
Students' Problem Solving as Mediated by Their Cognitive Tool Use: A Study of Tool Use Patterns

ERIC Educational Resources Information Center

Liu, M.; Horton, L. R.; Corliss, S. B.; Svinicki, M. D.; Bogard, T.; Kim, J.; Chang, M.

2009-01-01

The purpose of this study was to use multiple data sources, both objective and subjective, to capture students' thinking processes as they were engaged in problem solving, examine the cognitive tool use patterns, and understand what tools were used and why they were used. The findings of this study confirmed previous research and provided clear…
Approach to Mathematical Problem Solving and Students' Belief Systems: Two Case Studies

ERIC Educational Resources Information Center

Callejo, Maria Luz; Vila, Antoni

2009-01-01

The goal of the study reported here is to gain a better understanding of the role of belief systems in the approach phase to mathematical problem solving. Two students of high academic performance were selected based on a previous exploratory study of 61 students 12-13 years old. In this study we identified different types of approaches to…
Methodological and Epistemological Issues on Linear Regression Applied to Psychometric Variables in Problem Solving: Rethinking Variance

ERIC Educational Resources Information Center

Stamovlasis, Dimitrios

2010-01-01

The aim of the present paper is two-fold. First, it attempts to support previous findings on the role of some psychometric variables, such as, M-capacity, the degree of field dependence-independence, logical thinking and the mobility-fixity dimension, on students' achievement in chemistry problem solving. Second, the paper aims to raise some…
The Effects of Using Diagramming as a Representational Technique on High School Students' Achievement in Solving Math Word Problems

ERIC Educational Resources Information Center

Banerjee, Banmali

2010-01-01

Methods and procedures for successfully solving math word problems have been, and continue to be a mystery to many U.S. high school students. Previous studies suggest that the contextual and mathematical understanding of a word problem, along with the development of schemas and their related external representations, positively contribute to…
An accurate, fast, and scalable solver for high-frequency wave propagation

NASA Astrophysics Data System (ADS)

Zepeda-Núñez, L.; Taus, M.; Hewett, R.; Demanet, L.

2017-12-01

In many science and engineering applications, solving time-harmonic high-frequency wave propagation problems quickly and accurately is of paramount importance. For example, in geophysics, particularly in oil exploration, such problems can be the forward problem in an iterative process for solving the inverse problem of subsurface inversion. It is important to solve these wave propagation problems accurately in order to efficiently obtain meaningful solutions of the inverse problems: low order forward modeling can hinder convergence. Additionally, due to the volume of data and the iterative nature of most optimization algorithms, the forward problem must be solved many times. Therefore, a fast solver is necessary to make solving the inverse problem feasible. For time-harmonic high-frequency wave propagation, obtaining both speed and accuracy is historically challenging. Recently, there have been many advances in the development of fast solvers for such problems, including methods which have linear complexity with respect to the number of degrees of freedom. While most methods scale optimally only in the context of low-order discretizations and smooth wave speed distributions, the method of polarized traces has been shown to retain optimal scaling for high-order discretizations, such as hybridizable discontinuous Galerkin methods and for highly heterogeneous (and even discontinuous) wave speeds. The resulting fast and accurate solver is consequently highly attractive for geophysical applications. To date, this method relies on a layered domain decomposition together with a preconditioner applied in a sweeping fashion, which has limited straight-forward parallelization. In this work, we introduce a new version of the method of polarized traces which reveals more parallel structure than previous versions while preserving all of its other advantages. We achieve this by further decomposing each layer and applying the preconditioner to these new components separately and in parallel. We demonstrate that this produces an even more effective and parallelizable preconditioner for a single right-hand side. As before, additional speed can be gained by pipelining several right-hand-sides.
NCI Scientists Solve Structure of Protein that Enables MERS Virus to Spread | Poster

Cancer.gov

Scientists at the Frederick National Lab have produced three crystal structures that reveal a specific part of a protein that can be targeted to fight the Middle East respiratory syndrome coronavirus (MERS-CoV), which causes an emerging viral respiratory illness. Senior Investigator David Waugh, Ph.D., Macromolecular Crystallography Laboratory, has solved the structure of an enzyme known as the 3C-like protease (3CLpro), which, if blocked, can prevent the virus from replicating...

Insight into cofactor recognition in arylamine N-acetyltransferase enzymes: structure of Mesorhizobium loti arylamine N-acetyltransferase in complex with coenzyme A.

PubMed

Xu, Ximing; Li de la Sierra-Gallay, Inés; Kubiak, Xavier; Duval, Romain; Chaffotte, Alain F; Dupret, Jean Marie; Haouz, Ahmed; Rodrigues-Lima, Fernando

2015-02-01

Arylamine N-acetyltransferases (NATs) are xenobiotic metabolizing enzymes that catalyze the acetyl-CoA-dependent acetylation of arylamines. To better understand the mode of binding of the cofactor by this family of enzymes, the structure of Mesorhizobium loti NAT1 [(RHILO)NAT1] was determined in complex with CoA. The F42W mutant of (RHILO)NAT1 was used as it is well expressed in Escherichia coli and displays enzymatic properties similar to those of the wild type. The apo and holo structures of (RHILO)NAT1 F42W were solved at 1.8 and 2 Å resolution, respectively. As observed in the Mycobacterium marinum NAT1-CoA complex, in (RHILO)NAT1 CoA binding induces slight structural rearrangements that are mostly confined to certain residues of its `P-loop'. Importantly, it was found that the mode of binding of CoA is highly similar to that of M. marinum NAT1 but different from the modes reported for Bacillus anthracis NAT1 and Homo sapiens NAT2. Therefore, in contrast to previous data, this study shows that different orthologous NATs can bind their cofactors in a similar way, suggesting that the mode of binding CoA in this family of enzymes is less diverse than previously thought. Moreover, it supports the notion that the presence of the `mammalian/eukaryotic insertion loop' in certain NAT enzymes impacts the mode of binding CoA by imposing structural constraints.
The Effects of Polya's Heuristic and Diary Writing on Children's Problem Solving

ERIC Educational Resources Information Center

Hensberry, Karina K. R.; Jacobbe, Tim

2012-01-01

This paper presents the results of a study that aimed at increasing students' problem-solving skills. Polya's (1985) heuristic for problem solving was used and students were required to articulate their thought processes through the use of a structured diary. The diary prompted students to answer questions designed to engage them in the phases of…
Analysing the Relationship between the Problem-Solving-Related Beliefs, Competence and Teaching of Three Cypriot Primary Teachers

ERIC Educational Resources Information Center

Andrews, Paul; Xenofontos, Constantinos

2015-01-01

In this article, we analyse the problem-solving-related beliefs, competence and classroom practice of three Cypriot upper-primary teachers. Data derived from semi-structured interviews focused on teachers' beliefs about the nature of mathematical problems, problem-solving, and their competence as both problem-solvers and teachers of…
Do Cases Teach Themselves? A Comparison of Case Library Prompts in Supporting Problem-Solving during Argumentation

ERIC Educational Resources Information Center

Tawfik, Andrew A.

2017-01-01

Theorists have argued instructional strategies that emphasize ill-structured problem solving are an effective means to support higher order learning skills such as argumentation. However, argumentation is often difficult because novices lack the expertise or experience needed to solve contextualized problems. One way to supplement this lack of…
Syntactic Awareness and Arithmetic Word Problem Solving in Children with and without Learning Disabilities

ERIC Educational Resources Information Center

Peake, Christian; Jiménez, Juan E.; Rodríguez, Cristina; Bisschop, Elaine; Villarroel, Rebeca

2015-01-01

Arithmetic word problem (AWP) solving is a highly demanding task for children with learning disabilities (LD) since verbal and mathematical information have to be integrated. This study examines specifically how syntactic awareness (SA), the ability to manage the grammatical structures of language, affects AWP solving. Three groups of children in…
Modeling visual problem solving as analogical reasoning.

PubMed

Lovett, Andrew; Forbus, Kenneth

2017-01-01

We present a computational model of visual problem solving, designed to solve problems from the Raven's Progressive Matrices intelligence test. The model builds on the claim that analogical reasoning lies at the heart of visual problem solving, and intelligence more broadly. Images are compared via structure mapping, aligning the common relational structure in 2 images to identify commonalities and differences. These commonalities or differences can themselves be reified and used as the input for future comparisons. When images fail to align, the model dynamically rerepresents them to facilitate the comparison. In our analysis, we find that the model matches adult human performance on the Standard Progressive Matrices test, and that problems which are difficult for the model are also difficult for people. Furthermore, we show that model operations involving abstraction and rerepresentation are particularly difficult for people, suggesting that these operations may be critical for performing visual problem solving, and reasoning more generally, at the highest level. (PsycINFO Database Record (c) 2016 APA, all rights reserved).
Metaphor and analogy in everyday problem solving.

PubMed

Keefer, Lucas A; Landau, Mark J

2016-11-01

Early accounts of problem solving focused on the ways people represent information directly related to target problems and possible solutions. Subsequent theory and research point to the role of peripheral influences such as heuristics and bodily states. We discuss how metaphor and analogy similarly influence stages of everyday problem solving: Both processes mentally map features of a target problem onto the structure of a relatively more familiar concept. When individuals apply this structure, they use a well-known concept as a framework for reasoning about real world problems and candidate solutions. Early studies found that analogy use helped people gain insight into novel problems. More recent research on metaphor goes further to show that activating mappings has subtle, sometimes surprising effects on judgment and reasoning in everyday problem solving. These findings highlight situations in which mappings can help or hinder efforts to solve problems. WIREs Cogn Sci 2016, 7:394-405. doi: 10.1002/wcs.1407 For further resources related to this article, please visit the WIREs website. © 2016 Wiley Periodicals, Inc.
Syntactic Awareness and Arithmetic Word Problem Solving in Children With and Without Learning Disabilities.

PubMed

Peake, Christian; Jiménez, Juan E; Rodríguez, Cristina; Bisschop, Elaine; Villarroel, Rebeca

2015-01-01

Arithmetic word problem (AWP) solving is a highly demanding task for children with learning disabilities (LD) since verbal and mathematical information have to be integrated. This study examines specifically how syntactic awareness (SA), the ability to manage the grammatical structures of language, affects AWP solving. Three groups of children in elementary education were formed: children with arithmetic learning disabilities (ALD), children with reading learning disabilities (RLD), and children with comorbid arithmetic and reading learning disabilities (ARLD). Mediation analysis confirmed that SA was a mediator variable for both groups of children with reading disabilities when solving AWPs, but not for children in the ALD group. All groups performed below the control group in the problem solving task. When SA was controlled for, semantic structure and position of the unknown set were variables that affected both groups with ALD. Specifically, children with ALD only were more affected by the place of the unknown set. © Hammill Institute on Disabilities 2014.
Scalable direct Vlasov solver with discontinuous Galerkin method on unstructured mesh.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Xu, J.; Ostroumov, P. N.; Mustapha, B.

2010-12-01

This paper presents the development of parallel direct Vlasov solvers with discontinuous Galerkin (DG) method for beam and plasma simulations in four dimensions. Both physical and velocity spaces are in two dimesions (2P2V) with unstructured mesh. Contrary to the standard particle-in-cell (PIC) approach for kinetic space plasma simulations, i.e., solving Vlasov-Maxwell equations, direct method has been used in this paper. There are several benefits to solving a Vlasov equation directly, such as avoiding noise associated with a finite number of particles and the capability to capture fine structure in the plasma. The most challanging part of a direct Vlasov solvermore » comes from higher dimensions, as the computational cost increases as N{sup 2d}, where d is the dimension of the physical space. Recently, due to the fast development of supercomputers, the possibility has become more realistic. Many efforts have been made to solve Vlasov equations in low dimensions before; now more interest has focused on higher dimensions. Different numerical methods have been tried so far, such as the finite difference method, Fourier Spectral method, finite volume method, and spectral element method. This paper is based on our previous efforts to use the DG method. The DG method has been proven to be very successful in solving Maxwell equations, and this paper is our first effort in applying the DG method to Vlasov equations. DG has shown several advantages, such as local mass matrix, strong stability, and easy parallelization. These are particularly suitable for Vlasov equations. Domain decomposition in high dimensions has been used for parallelization; these include a highly scalable parallel two-dimensional Poisson solver. Benchmark results have been shown and simulation results will be reported.« less
Representational task formats and problem solving strategies in kinematics and work

NASA Astrophysics Data System (ADS)

Ibrahim, Bashirah; Rebello, N. Sanjay

2012-06-01

Previous studies have reported that students employed different problem solving approaches when presented with the same task structured with different representations. In this study, we explored and compared students’ strategies as they attempted tasks from two topical areas, kinematics and work. Our participants were 19 engineering students taking a calculus-based physics course. The tasks were presented in linguistic, graphical, and symbolic forms and requested either a qualitative solution or a value. The analysis was both qualitative and quantitative in nature focusing principally on the characteristics of the strategies employed as well as the underlying reasoning for their applications. A comparison was also made for the same student’s approach with the same kind of representation across the two topics. Additionally, the participants’ overall strategies across the different tasks, in each topic, were considered. On the whole, we found that the students prefer manipulating equations irrespective of the representational format of the task. They rarely recognized the applicability of a “qualitative” approach to solve the problem although they were aware of the concepts involved. Even when the students included visual representations in their solutions, they seldom used these representations in conjunction with the mathematical part of the problem. Additionally, the students were not consistent in their approach for interpreting and solving problems with the same kind of representation across the two topical areas. The representational format, level of prior knowledge, and familiarity with a topic appeared to influence their strategies, their written responses, and their ability to recognize qualitative ways to attempt a problem. The nature of the solution does not seem to impact the strategies employed to handle the problem.
Evolutions of fluctuation modes and inner structures of global stock markets

NASA Astrophysics Data System (ADS)

Yan, Yan; Wang, Lei; Liu, Maoxin; Chen, Xiaosong

2016-09-01

The paper uses empirical data, including 42 globally main stock indices in the period 1996-2014, to systematically study the evolution of fluctuation modes and inner structures of global stock markets. The data are large in scale considering both time and space. A covariance matrix-based principle fluctuation mode analysis (PFMA) is used to explore the properties of the global stock markets. It has been ignored by previous studies that covariance matrix is more suitable than the correlation matrix to be the basis of PFMA. It is found that the principle fluctuation modes of global stock markets are in the same directions, and global stock markets are divided into three clusters, which are found to be closely related to the countries’ locations with exceptions of China, Russia and Czech Republic. A time-stable correlation network constructing method is proposed to solve the problem of high-level statistical uncertainty when the estimated periods are very short, and the complex dynamic network (CDN) is constructed to investigate the evolution of inner structures. The results show when the clusters emerge and how long the clusters exist. When the 2008 financial crisis broke out, the indices form one cluster. After these crises, only the European cluster still exists. These findings complement the previous studies, and can help investors and regulators to understand the global stock markets.
Extraction of a group-pair relation: problem-solving relation from web-board documents.

PubMed

Pechsiri, Chaveevan; Piriyakul, Rapepun

2016-01-01

This paper aims to extract a group-pair relation as a Problem-Solving relation, for example a DiseaseSymptom-Treatment relation and a CarProblem-Repair relation, between two event-explanation groups, a problem-concept group as a symptom/CarProblem-concept group and a solving-concept group as a treatment-concept/repair concept group from hospital-web-board and car-repair-guru-web-board documents. The Problem-Solving relation (particularly Symptom-Treatment relation) including the graphical representation benefits non-professional persons by supporting knowledge of primarily solving problems. The research contains three problems: how to identify an EDU (an Elementary Discourse Unit, which is a simple sentence) with the event concept of either a problem or a solution; how to determine a problem-concept EDU boundary and a solving-concept EDU boundary as two event-explanation groups, and how to determine the Problem-Solving relation between these two event-explanation groups. Therefore, we apply word co-occurrence to identify a problem-concept EDU and a solving-concept EDU, and machine-learning techniques to solve a problem-concept EDU boundary and a solving-concept EDU boundary. We propose using k-mean and Naïve Bayes to determine the Problem-Solving relation between the two event-explanation groups involved with clustering features. In contrast to previous works, the proposed approach enables group-pair relation extraction with high accuracy.
Design of Composite Structures Using Knowledge-Based and Case Based Reasoning

NASA Technical Reports Server (NTRS)

Lambright, Jonathan Paul

1996-01-01

A method of using knowledge based and case based reasoning to assist designers during conceptual design tasks of composite structures was proposed. The cooperative use of heuristics, procedural knowledge, and previous similar design cases suggests a potential reduction in design cycle time and ultimately product lead time. The hypothesis of this work is that the design process of composite structures can be improved by using Case-Based Reasoning (CBR) and Knowledge-Based (KB) reasoning in the early design stages. The technique of using knowledge-based and case-based reasoning facilitates the gathering of disparate information into one location that is easily and readily available. The method suggests that the inclusion of downstream life-cycle issues into the conceptual design phase reduces potential of defective, and sub-optimal composite structures. Three industry experts were interviewed extensively. The experts provided design rules, previous design cases, and test problems. A Knowledge Based Reasoning system was developed using the CLIPS (C Language Interpretive Procedural System) environment and a Case Based Reasoning System was developed using the Design Memory Utility For Sharing Experiences (MUSE) xviii environment. A Design Characteristic State (DCS) was used to document the design specifications, constraints, and problem areas using attribute-value pair relationships. The DCS provided consistent design information between the knowledge base and case base. Results indicated that the use of knowledge based and case based reasoning provided a robust design environment for composite structures. The knowledge base provided design guidance from well defined rules and procedural knowledge. The case base provided suggestions on design and manufacturing techniques based on previous similar designs and warnings of potential problems and pitfalls. The case base complemented the knowledge base and extended the problem solving capability beyond the existence of limited well defined rules. The findings indicated that the technique is most effective when used as a design aid and not as a tool to totally automate the composites design process. Other areas of application and implications for future research are discussed.
Estimation of splitting functions from Earth's normal mode spectra using the neighbourhood algorithm

NASA Astrophysics Data System (ADS)

Pachhai, Surya; Tkalčić, Hrvoje; Masters, Guy

2016-01-01

The inverse problem for Earth structure from normal mode data is strongly non-linear and can be inherently non-unique. Traditionally, the inversion is linearized by taking partial derivatives of the complex spectra with respect to the model parameters (i.e. structure coefficients), and solved in an iterative fashion. This method requires that the earthquake source model is known. However, the release of energy in large earthquakes used for the analysis of Earth's normal modes is not simple. A point source approximation is often inadequate, and a more complete account of energy release at the source is required. In addition, many earthquakes are required for the solution to be insensitive to the initial constraints and regularization. In contrast to an iterative approach, the autoregressive linear inversion technique conveniently avoids the need for earthquake source parameters, but it also requires a number of events to achieve full convergence when a single event does not excite all singlets well. To build on previous improvements, we develop a technique to estimate structure coefficients (and consequently, the splitting functions) using a derivative-free parameter search, known as neighbourhood algorithm (NA). We implement an efficient forward method derived using the autoregresssion of receiver strips, and this allows us to search over a multiplicity of structure coefficients in a relatively short time. After demonstrating feasibility of the use of NA in synthetic cases, we apply it to observations of the inner core sensitive mode 13S2. The splitting function of this mode is dominated by spherical harmonic degree 2 axisymmetric structure and is consistent with the results obtained from the autoregressive linear inversion. The sensitivity analysis of multiple events confirms the importance of the Bolivia, 1994 earthquake. When this event is used in the analysis, as little as two events are sufficient to constrain the splitting functions of 13S2 mode. Apart from not requiring the knowledge of earthquake source, the newly developed technique provides an approximate uncertainty measure of the structure coefficients and allows us to control the type of structure solved for, for example to establish if elastic structure is sufficient.
Efficient reanalysis of structures by a direct modification method. [local stiffness modifications of large structures

NASA Technical Reports Server (NTRS)

Raibstein, A. I.; Kalev, I.; Pipano, A.

1976-01-01

A procedure for the local stiffness modifications of large structures is described. It enables structural modifications without an a priori definition of the changes in the original structure and without loss of efficiency due to multiple loading conditions. The solution procedure, implemented in NASTRAN, involved the decomposed stiffness matrix and the displacement vectors of the original structure. It solves the modified structure exactly, irrespective of the magnitude of the stiffness changes. In order to investigate the efficiency of the present procedure and to test its applicability within a design environment, several real and large structures were solved. The results of the efficiency studies indicate that the break-even point of the procedure varies between 8% and 60% stiffness modifications, depending upon the structure's characteristics and the options employed.
Who Is Your Champion? A Close Look at How Plant and Animal Structures Can Help Solve a Problem

ERIC Educational Resources Information Center

Walker, Caryn; Ethington, Roberta L.; Stark, Alyssa Y.

2016-01-01

Everyone has problems, from the smallest ant competing for a food source to the largest elephant needing to cool down. Fortunately, organisms have structures that function to help them solve these problems. So when a group of fourth-grade students look for solutions to their problems, who do they turn to? A biological champion, of course! Plants…
Uniformity and nonuniformity of neural activities correlated to different insight problem solving.

PubMed

Zhao, Q; Li, Y; Shang, X; Zhou, Z; Han, L

2014-06-13

Previous studies on the neural basis of insight reflected weak consistency except for the anterior cingulate cortex. The present work adopted the semantic and homophonic punny riddle to explore the uniformity and nonuniformity of neural activities correlated to different insight problem solving. Results showed that in the early period of insight solving, the semantic and homophonic punny riddles induced a common N350-500 over the central scalp. However, during -400 to 0 ms before the riddles were solved, the semantic punny riddles induced a positive event-related potential (ERP) deflection over the temporal cortex for retrieving the extensive semantic information, while the homophonic punny riddles induced a positive ERP deflection over the temporal cortex and a negative one in the left frontal cortex which might reflect the semantic and phonological information processing respectively. Our study indicated that different insight problem solving should have the same cognitive process of detecting cognitive conflicts, but have different ways to solve the conflicts. Copyright © 2014 IBRO. Published by Elsevier Ltd. All rights reserved.
Insights into Strand Exchange in BTB Domain Dimers from the Crystal Structures of FAZF and Miz1

DOE Office of Scientific and Technical Information (OSTI.GOV)

Stogios, Peter J.; Cuesta-Seijo, Jose Antonio; Chen, Lu

2010-09-22

The BTB domain is a widely distributed protein-protein interaction motif that is often found at the N-terminus of zinc finger transcription factors. Previous crystal structures of BTB domains have revealed tightly interwound homodimers, with the N-terminus from one chain forming a two-stranded anti-parallel {beta}-sheet with a strand from the other chain. We have solved the crystal structures of the BTB domains from Fanconi anemia zinc finger (FAZF) and Miz1 (Myc-interacting zinc finger 1) to resolutions of 2.0 {angstrom} and 2.6 {angstrom}, respectively. Unlike previous examples of BTB domain structures, the FAZF BTB domain is a nonswapped dimer, with each N-terminalmore » {beta}-strand associated with its own chain. As a result, the dimerization interface in the FAZF BTB domain is about half as large as in the domain-swapped dimers. The Miz1 BTB domain resembles a typical swapped BTB dimer, although it has a shorter N-terminus that is not able to form the interchain sheet. Using cysteine cross-linking, we confirmed that the promyelocytic leukemia zinc finger (PLZF) BTB dimer is strand exchanged in solution, while the FAZF BTB dimer is not. A phylogenic tree of the BTB fold based on both sequence and structural features shows that the common ancestor of the BTB domain in BTB-ZF (bric a brac, tramtrack, broad-complex zinc finger) proteins was a domain-swapped dimer. The differences in the N-termini seen in the FAZF and Miz1 BTB domains appear to be more recent developments in the structural evolution of the domain.« less
Moving your eyes to solution: effects of movements on the perception of a problem-solving task.

PubMed

Werner, K; Raab, M

2014-01-01

There is ample evidence suggesting a bidirectional connection between bodily movements and cognitive processes, such as problem solving. Current research suggests that previous movements can influence the problem-solving process, but it is unclear what phase of this process is affected. Therefore, we investigated participants' gaze behaviour in the first phase of arithmetic problem solving with two groups (plus group, minus group) to explore a spatial bias toward the left or the right while perceiving a problem-solving task (the water-jar problem) after two different movements-that is, for the plus group, sorting marbles from two outer bowls into one in the middle, and for the minus group, sorting marbles from the middle bowl to the outer ones. We showed a right shift of spatial bias for the plus and to the left for the minus group in the perception and problem tasks. Although movements affected gaze, the groups did not differ in their overall problem-solving strategies; however, the first correct solutions did differ. This study provides further evidence of sensorimotor effects on problem solving and spatial bias and offers insight into how a two-phase problem-solving process is guided by sensorimotor information.
Single-layer TiO x reconstructions on SrTiO 3 (111): (√7 × √7)R19.1°, (√13 × √13)R13.9°, and related structures

DOE Office of Scientific and Technical Information (OSTI.GOV)

Andersen, Tassie K.; Wang, Shuqiu; Castell, Martin R.

The atomic structures of two reconstructions, (√7 × √7)R19.1° and (√13 × √13)R13.9°, on the SrTiO 3 (111) surface were determined using a combination of density functional theory and scanning tunneling microscopy data and simulations. The combination of these methods allows for potential surface structures to be generated and verified in the absence of diffraction data, providing another tool for solving surface reconstructions. These reconstructions belong to the same stoichiometric, nSrTiO 3 • mTiO 2, structural family made up of an interconnected, single layer of edge-sharing TiO 6 and TiO 5[] octahedra. This family is found to include the previously-solvedmore » (2 × 2)a reconstruction as its smallest unit-cell sized member and serves as a tool for better understanding and predicting the structure of other reconstructions of arbitrary surface unit-cell size on SrTiO 3 (111). This reconstruction family and the calculations of surface energies for different hypothesis structures also shed light on the structure of Schottky defects observed on these reconstructed SrTO 3 (111) surfaces.« less

Structure of N-acetyl-[beta]-D-glucosaminidase (GcnA) from the Endocarditis Pathogen Streptococcus gordonii and its Complex with the Mechanism-based Inhibitor NAG-thiazoline

DOE Office of Scientific and Technical Information (OSTI.GOV)

Langley, David B.; Harty, Derek W.S.; Jacques, Nicholas A.

2008-09-17

The crystal structure of GcnA, an N-acetyl-{beta}-D-glucosaminidase from Streptococcus gordonii, was solved by multiple wavelength anomalous dispersion phasing using crystals of selenomethionine-substituted protein. GcnA is a homodimer with subunits each comprised of three domains. The structure of the C-terminal {alpha}-helical domain has not been observed previously and forms a large dimerization interface. The fold of the N-terminal domain is observed in all structurally related glycosidases although its function is unknown. The central domain has a canonical ({beta}/{alpha}){sub 8} TIM-barrel fold which harbours the active site. The primary sequence and structure of this central domain identifies the enzyme as a familymore » 20 glycosidase. Key residues implicated in catalysis have different conformations in two different crystal forms, which probably represent active and inactive conformations of the enzyme. The catalytic mechanism for this class of glycoside hydrolase, where the substrate rather than the enzyme provides the cleavage-inducing nucleophile, has been confirmed by the structure of GcnA complexed with a putative reaction intermediate analogue, N-acetyl-{beta}-D-glucosamine-thiazoline. The catalytic mechanism is discussed in light of these and other family 20 structures.« less
Structural analysis of β-glucosidase mutants derived from a hyperthermophilic tetrameric structure

PubMed Central

Nakabayashi, Makoto; Kataoka, Misumi; Mishima, Yumiko; Maeno, Yuka; Ishikawa, Kazuhiko

2014-01-01

β-Glucosidase from Pyrococcus furiosus (BGLPf) is a hyperthermophilic tetrameric enzyme which can degrade cellooligosaccharides to glucose under hyperthermophilic conditions and thus holds promise for the saccharification of lignocellulosic biomass at high temperature. Prior to the production of large amounts of this enzyme, detailed information regarding the oligomeric structure of the enzyme is required. Several crystals of BGLPf have been prepared over the past ten years, but its crystal structure had not been solved until recently. In 2011, the first crystal structure of BGLPf was solved and a model was constructed at somewhat low resolution (2.35 Å). In order to obtain more detailed structural data on BGLPf, the relationship between its tetrameric structure and the quality of the crystal was re-examined. A dimeric form of BGLPf was constructed and its crystal structure was solved at a resolution of 1.70 Å using protein-engineering methods. Furthermore, using the high-resolution crystal structural data for the dimeric form, a monomeric form of BGLPf was constructed which retained the intrinsic activity of the tetrameric form. The thermostability of BGLPf is affected by its oligomeric structure. Here, the biophysical and biochemical properties of engineered dimeric and monomeric BGLPfs are reported, which are promising prototype models to apply to the saccharification reaction. Furthermore, details regarding the oligomeric structures of BGLPf and the reasons why the mutations yielded improved crystal structures are discussed. PMID:24598756
Variation in Brain Regions Associated with Fear and Learning in Contrasting Climates

PubMed Central

Roth, Timothy C.; Gallagher, Caitlin M.; LaDage, Lara D.; Pravosudov, Vladimir V.

2012-01-01

In environments where resources are difficult to obtain and enhanced cognitive capabilities might be adaptive, brain structures associated with cognitive traits may also be enhanced. In our previous studies, we documented a clear and significant relationship among environmental conditions, memory and hippocampal structure using ten populations of black-capped chickadees (Poecile atricapillus) over a large geographic range. In addition, focusing on just the two populations from the geographical extremes of our large-scale comparison, Alaska and Kansas, we found enhanced problem-solving capabilities and reduced neophobia in a captive-raised population of black-capped chickadees originating from the energetically demanding environment (Alaska) relative to conspecifics from the milder environment (Kansas). Here, we focused on three brain regions, the arcopallium (AP), the nucleus taeniae of the amygdala and the lateral striatum (LSt), that have been implicated to some extent in aspects of these behaviors in order to investigate whether potential differences in these brain areas may be associated with our previously detected differences in cognition. We compared the variation in neuron number and volumes of these regions between these populations, in both wild-caught birds and captive-raised individuals. Consistent with our behavioral observations, wild-caught birds from Kansas had a larger AP volume than their wild-caught conspecifics from Alaska, which possessed a higher density of neurons in the LSt. However, there were no other significant differences between populations in the wild-caught and captive-raised groups. Interestingly, individuals from the wild had larger LSt and AP volumes with more neurons than those raised in captivity. Overall, we provide some evidence that population-related differences in problem solving and neophobia may be associated with differences in volume and neuron numbers of our target brain regions. However, the relationship is not completely clear, and our study raises numerous questions about the relationship between the brain and behavior, especially in captive animals. PMID:22286546
A Simple Label Switching Algorithm for Semisupervised Structural SVMs.

PubMed

Balamurugan, P; Shevade, Shirish; Sundararajan, S

2015-10-01

In structured output learning, obtaining labeled data for real-world applications is usually costly, while unlabeled examples are available in abundance. Semisupervised structured classification deals with a small number of labeled examples and a large number of unlabeled structured data. In this work, we consider semisupervised structural support vector machines with domain constraints. The optimization problem, which in general is not convex, contains the loss terms associated with the labeled and unlabeled examples, along with the domain constraints. We propose a simple optimization approach that alternates between solving a supervised learning problem and a constraint matching problem. Solving the constraint matching problem is difficult for structured prediction, and we propose an efficient and effective label switching method to solve it. The alternating optimization is carried out within a deterministic annealing framework, which helps in effective constraint matching and avoiding poor local minima, which are not very useful. The algorithm is simple and easy to implement. Further, it is suitable for any structured output learning problem where exact inference is available. Experiments on benchmark sequence labeling data sets and a natural language parsing data set show that the proposed approach, though simple, achieves comparable generalization performance.
The Acquisition of Problem-Solving Skills in Mathematics: How Animations Can Aid Understanding of Structural Problem Features and Solution Procedures

ERIC Educational Resources Information Center

Scheiter, Katharina; Gerjets, Peter; Schuh, Julia

2010-01-01

In this paper the augmentation of worked examples with animations for teaching problem-solving skills in mathematics is advocated as an effective instructional method. First, in a cognitive task analysis different knowledge prerequisites are identified for solving mathematical word problems. Second, it is argued that so called hybrid animations…
Structuring an Adult Learning Environment. Part IV: Establishing an Environment for Problem Solving.

ERIC Educational Resources Information Center

Frankel, Alan; Brennan, James

Through the years, many researchers have advanced theories of problem solving. Probably the best definition of problem solving to apply to adult learning programs is Wallas' (1926) four-stage theory. The stages are (1) a preparation, (2) an incubation period, (3) a moment of illumination, and (4) final application or verification of the solution.…
Interfaces Leading Groups of Learners to Make Their Shared Problem-Solving Organization Explicit

ERIC Educational Resources Information Center

Moguel, P.; Tchounikine, P.; Tricot, A.

2012-01-01

In this paper, we consider collective problem-solving challenges and a particular structuring objective: lead groups of learners to make their shared problem-solving organization explicit. Such an objective may be considered as a way to lead learners to consider building and maintaining a shared organization, and/or as a way to provide a basis for…
A Computer Program for Solving a Set of Conditional Maximum Likelihood Equations Arising in the Rasch Model for Questionnaires.

ERIC Educational Resources Information Center

Andersen, Erling B.

A computer program for solving the conditional likelihood equations arising in the Rasch model for questionnaires is described. The estimation method and the computational problems involved are described in a previous research report by Andersen, but a summary of those results are given in two sections of this paper. A working example is also…
Development of the Nuclear-Electronic Orbital Approach and Applications to Ionic Liquids and Tunneling Processes

DTIC Science & Technology

2010-02-24

electronic Schrodinger equation . In previous grant cycles, we implemented the NEO approach at the Hartree-Fock (NEO-HF),13 configuration interaction...electronic and nuclear molecular orbitals. The resulting electronic and nuclear Hartree-Fock-Roothaan equations are solved iteratively until self...directly into the standard Hartree- Fock-Roothaan equations , which are solved iteratively to self-consistency. The density matrix representation
Bio-Inspired Human-Level Machine Learning

DTIC Science & Technology

2015-10-25

extensions to high-level cognitive functions such as anagram solving problem. 15. SUBJECT TERMS 16. SECURITY CLASSIFICATION OF: 17. LIMITATION OF...extensions to high-level cognitive functions such as anagram solving problem. We expect that the bio-inspired human-level machine learning combined with...numbers of 1011 neurons and 1014 synaptic connections in the human brain. In previous work, we experimentally demonstrated the feasibility of cognitive
Children's Understanding of the Arithmetic Concepts of Inversion and Associativity

ERIC Educational Resources Information Center

Robinson, Katherine M.; Ninowski, Jerilyn E.; Gray, Melissa L.

2006-01-01

Previous studies have shown that even preschoolers can solve inversion problems of the form a + b - b by using the knowledge that addition and subtraction are inverse operations. In this study, a new type of inversion problem of the form d x e [divided by] e was also examined. Grade 6 and 8 students solved inversion problems of both types as well…
A Biologically Plausible Architecture of the Striatum to Solve Context-Dependent Reinforcement Learning Tasks.

PubMed

Shivkumar, Sabyasachi; Muralidharan, Vignesh; Chakravarthy, V Srinivasa

2017-01-01

Basal ganglia circuit is an important subcortical system of the brain thought to be responsible for reward-based learning. Striatum, the largest nucleus of the basal ganglia, serves as an input port that maps cortical information. Microanatomical studies show that the striatum is a mosaic of specialized input-output structures called striosomes and regions of the surrounding matrix called the matrisomes. We have developed a computational model of the striatum using layered self-organizing maps to capture the center-surround structure seen experimentally and explain its functional significance. We believe that these structural components could build representations of state and action spaces in different environments. The striatum model is then integrated with other components of basal ganglia, making it capable of solving reinforcement learning tasks. We have proposed a biologically plausible mechanism of action-based learning where the striosome biases the matrisome activity toward a preferred action. Several studies indicate that the striatum is critical in solving context dependent problems. We build on this hypothesis and the proposed model exploits the modularity of the striatum to efficiently solve such tasks.
Augmented neural networks and problem structure-based heuristics for the bin-packing problem

NASA Astrophysics Data System (ADS)

Kasap, Nihat; Agarwal, Anurag

2012-08-01

In this article, we report on a research project where we applied augmented-neural-networks (AugNNs) approach for solving the classical bin-packing problem (BPP). AugNN is a metaheuristic that combines a priority rule heuristic with the iterative search approach of neural networks to generate good solutions fast. This is the first time this approach has been applied to the BPP. We also propose a decomposition approach for solving harder BPP, in which subproblems are solved using a combination of AugNN approach and heuristics that exploit the problem structure. We discuss the characteristics of problems on which such problem structure-based heuristics could be applied. We empirically show the effectiveness of the AugNN and the decomposition approach on many benchmark problems in the literature. For the 1210 benchmark problems tested, 917 problems were solved to optimality and the average gap between the obtained solution and the upper bound for all the problems was reduced to under 0.66% and computation time averaged below 33 s per problem. We also discuss the computational complexity of our approach.
A Biologically Plausible Architecture of the Striatum to Solve Context-Dependent Reinforcement Learning Tasks

PubMed Central

Shivkumar, Sabyasachi; Muralidharan, Vignesh; Chakravarthy, V. Srinivasa

2017-01-01

Basal ganglia circuit is an important subcortical system of the brain thought to be responsible for reward-based learning. Striatum, the largest nucleus of the basal ganglia, serves as an input port that maps cortical information. Microanatomical studies show that the striatum is a mosaic of specialized input-output structures called striosomes and regions of the surrounding matrix called the matrisomes. We have developed a computational model of the striatum using layered self-organizing maps to capture the center-surround structure seen experimentally and explain its functional significance. We believe that these structural components could build representations of state and action spaces in different environments. The striatum model is then integrated with other components of basal ganglia, making it capable of solving reinforcement learning tasks. We have proposed a biologically plausible mechanism of action-based learning where the striosome biases the matrisome activity toward a preferred action. Several studies indicate that the striatum is critical in solving context dependent problems. We build on this hypothesis and the proposed model exploits the modularity of the striatum to efficiently solve such tasks. PMID:28680395
Improving the Accuracy of the Chebyshev Rational Approximation Method Using Substeps

DOE PAGES

Isotalo, Aarno; Pusa, Maria

2016-05-01

The Chebyshev Rational Approximation Method (CRAM) for solving the decay and depletion of nuclides is shown to have a remarkable decrease in error when advancing the system with the same time step and microscopic reaction rates as the previous step. This property is exploited here to achieve high accuracy in any end-of-step solution by dividing a step into equidistant sub-steps. The computational cost of identical substeps can be reduced significantly below that of an equal number of regular steps, as the LU decompositions for the linear solves required in CRAM only need to be formed on the first substep. Themore » improved accuracy provided by substeps is most relevant in decay calculations, where there have previously been concerns about the accuracy and generality of CRAM. Lastly, with substeps, CRAM can solve any decay or depletion problem with constant microscopic reaction rates to an extremely high accuracy for all nuclides with concentrations above an arbitrary limit.« less
Vertical distribution of vibrational energy of molecular nitrogen in a stable auroral red arc and its effect on ionospheric electron densities. Ph.D. Thesis - Catholic Univ. of Am.

NASA Technical Reports Server (NTRS)

Newton, G. P.

1973-01-01

Previous solutions of the problem of the distribution of vibrationally excited molecular nitrogen in the thermosphere have either assumed a Boltzmann distribution and considered diffusion as one of the loss processes or solved for the energy level populations and neglected diffusion. Both of the previous approaches are combined by solving the time dependent continuity equations, including the diffusion process, for the first six energy levels of molecular nitrogen for conditions in the thermosphere corresponding to a stable auroral red arc. The primary source of molecular nitrogen excitation was subexcitation, and inelastic collisions between thermal electrons and molecular nitrogen. The reaction rates for this process were calculated from published cross section calculations. The loss processes for vibrational energy were electron and atomic oxygen quenching and vibrational energy exchange. The coupled sets of nonlinear, partial differential equations were solved numerically by employing finite difference equations.
Vaccinia Virus Immunomodulator A46: A Lipid and Protein-Binding Scaffold for Sequestering Host TIR-Domain Proteins

PubMed Central

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

2016-01-01

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

NASA Technical Reports Server (NTRS)

Devasia, S.

1996-01-01

Given a desired output trajectory, inversion-based techniques find input-state trajectories required to exactly track the output. These inversion-based techniques have been successfully applied to the endpoint tracking control of multijoint flexible manipulators and to aircraft control. The specified output trajectory uniquely determines the required input and state trajectories that are found through inversion. These input-state trajectories exactly track the desired output; however, they might not meet acceptable performance requirements. For example, during slewing maneuvers of flexible structures, the structural deformations, which depend on the required state trajectories, may be unacceptably large. Further, the required inputs might cause actuator saturation during an exact tracking maneuver, for example, in the flight control of conventional takeoff and landing aircraft. In such situations, a compromise is desired between the tracking requirement and other goals such as reduction of internal vibrations and prevention of actuator saturation; the desired output trajectory needs to redesigned. Here, we pose the trajectory redesign problem as an optimization of a general quadratic cost function and solve it in the context of linear systems. The solution is obtained as an off-line prefilter of the desired output trajectory. An advantage of our technique is that the prefilter is independent of the particular trajectory. The prefilter can therefore be precomputed, which is a major advantage over other optimization approaches. Previous works have addressed the issue of preshaping inputs to minimize residual and in-maneuver vibrations for flexible structures; Since the command preshaping is computed off-line. Further minimization of optimal quadratic cost functions has also been previously use to preshape command inputs for disturbance rejection. All of these approaches are applicable when the inputs to the system are known a priori. Typically, outputs (not inputs) are specified in tracking problems, and hence the input trajectories have to be computed. The inputs to the system are however, difficult to determine for non-minimum phase systems like flexible structures. One approach to solve this problem is to (1) choose a tracking controller (the desired output trajectory is now an input to the closed-loop system and (2) redesign this input to the closed-loop system. Thus we effectively perform output redesign. These redesigns are however, dependent on the choice of the tracking controllers. Thus the controller optimization and trajectory redesign problems become coupled; this coupled optimization is still an open problem. In contrast, we decouple the trajectory redesign problem from the choice of feedback-based tracking controller. It is noted that our approach remains valid when a particular tracking controller is chosen. In addition, the formulation of our problem not only allows for the minimization of residual vibration as in available techniques but also allows for the optimal reduction fo vibrations during the maneuver, e.g., the altitude control of flexible spacecraft. We begin by formulating the optimal output trajectory redesign problem and then solve it in the context of general linear systems. This theory is then applied to an example flexible structure, and simulation results are provided.
Optical signal processing using photonic reservoir computing

NASA Astrophysics Data System (ADS)

Salehi, Mohammad Reza; Dehyadegari, Louiza

2014-10-01

As a new approach to recognition and classification problems, photonic reservoir computing has such advantages as parallel information processing, power efficient and high speed. In this paper, a photonic structure has been proposed for reservoir computing which is investigated using a simple, yet, non-partial noisy time series prediction task. This study includes the application of a suitable topology with self-feedbacks in a network of SOA's - which lends the system a strong memory - and leads to adjusting adequate parameters resulting in perfect recognition accuracy (100%) for noise-free time series, which shows a 3% improvement over previous results. For the classification of noisy time series, the rate of accuracy showed a 4% increase and amounted to 96%. Furthermore, an analytical approach was suggested to solve rate equations which led to a substantial decrease in the simulation time, which is an important parameter in classification of large signals such as speech recognition, and better results came up compared with previous works.
A voxel-based finite element model for the prediction of bladder deformation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Chai Xiangfei; Herk, Marcel van; Hulshof, Maarten C. C. M.

2012-01-15

Purpose: A finite element (FE) bladder model was previously developed to predict bladder deformation caused by bladder filling change. However, two factors prevent a wide application of FE models: (1) the labor required to construct a FE model with high quality mesh and (2) long computation time needed to construct the FE model and solve the FE equations. In this work, we address these issues by constructing a low-resolution voxel-based FE bladder model directly from the binary segmentation images and compare the accuracy and computational efficiency of the voxel-based model used to simulate bladder deformation with those of a classicalmore » FE model with a tetrahedral mesh. Methods: For ten healthy volunteers, a series of MRI scans of the pelvic region was recorded at regular intervals of 10 min over 1 h. For this series of scans, the bladder volume gradually increased while rectal volume remained constant. All pelvic structures were defined from a reference image for each volunteer, including bladder wall, small bowel, prostate (male), uterus (female), rectum, pelvic bone, spine, and the rest of the body. Four separate FE models were constructed from these structures: one with a tetrahedral mesh (used in previous study), one with a uniform hexahedral mesh, one with a nonuniform hexahedral mesh, and one with a low-resolution nonuniform hexahedral mesh. Appropriate material properties were assigned to all structures and uniform pressure was applied to the inner bladder wall to simulate bladder deformation from urine inflow. Performance of the hexahedral meshes was evaluated against the performance of the standard tetrahedral mesh by comparing the accuracy of bladder shape prediction and computational efficiency. Results: FE model with a hexahedral mesh can be quickly and automatically constructed. No substantial differences were observed between the simulation results of the tetrahedral mesh and hexahedral meshes (<1% difference in mean dice similarity coefficient to manual contours and <0.02 cm difference in mean standard deviation of residual errors). The average equation solving time (without manual intervention) for the first two types of hexahedral meshes increased to 2.3 h and 2.6 h compared to the 1.1 h needed for the tetrahedral mesh, however, the low-resolution nonuniform hexahedral mesh dramatically decreased the equation solving time to 3 min without reducing accuracy. Conclusions: Voxel-based mesh generation allows fast, automatic, and robust creation of finite element bladder models directly from binary segmentation images without user intervention. Even the low-resolution voxel-based hexahedral mesh yields comparable accuracy in bladder shape prediction and more than 20 times faster in computational speed compared to the tetrahedral mesh. This approach makes it more feasible and accessible to apply FE method to model bladder deformation in adaptive radiotherapy.« less

Solution and reasoning reuse in space planning and scheduling applications

NASA Technical Reports Server (NTRS)

Verfaillie, Gerard; Schiex, Thomas

1994-01-01

In the space domain, as in other domains, the CSP (Constraint Satisfaction Problems) techniques are increasingly used to represent and solve planning and scheduling problems. But these techniques have been developed to solve CSP's which are composed of fixed sets of variables and constraints, whereas many planning and scheduling problems are dynamic. It is therefore important to develop methods which allow a new solution to be rapidly found, as close as possible to the previous one, when some variables or constraints are added or removed. After presenting some existing approaches, this paper proposes a simple and efficient method, which has been developed on the basis of the dynamic backtracking algorithm. This method allows previous solution and reasoning to be reused in the framework of a CSP which is close to the previous one. Some experimental results on general random CSPs and on operation scheduling problems for remote sensing satellites are given.
Development of Pantothenate Analogs That Can Treat Combat-Related Infections

DTIC Science & Technology

2014-04-01

determined by the molecular replacement method using the structure of S. aureus PanK excluding bound AMPPNP as a search model ( PDB code 2EWS). The...were solved by molecular replacement using the program PHASER11 and the EcPanK structure as a search model ( PDB : 1SQ5). The models went through...aureus PanK (SaPanK) complexed with N5- Pan (months 1-3) We solved the structure of the SaPanK�N5-Pan complex by the molecular replacement method
Human Problem Solving in Fault Diagnosis Tasks

DTIC Science & Technology

1986-04-01

Troubleshooting by Application of Structural Knowledge (TASK) . . . . . . . . . . . . . . . * 3 Framwork for Aiding the Understanding of Logical...focused subsequent investigations. Further, the models contributed to building an overall conceptual view of human problem solving. The aj JL BmnA in
A Structured Approach to Teaching Applied Problem Solving through Technology Assessment.

ERIC Educational Resources Information Center

Fischbach, Fritz A.; Sell, Nancy J.

1986-01-01

Describes an approach to problem solving based on real-world problems. Discusses problem analysis and definitions, preparation of briefing documents, solution finding techniques (brainstorming and synectics), solution evaluation and judgment, and implementation. (JM)
Monomer structure of a hyperthermophilic β-glucosidase mutant forming a dodecameric structure in the crystal form

PubMed Central

Nakabayashi, Makoto; Kataoka, Misumi; Watanabe, Masahiro; Ishikawa, Kazuhiko

2014-01-01

One of the β-glucosidases from Pyrococcus furiosus (BGLPf) is found to be a hyperthermophilic tetrameric enzyme that can degrade cellooligosaccharides. Recently, the crystal structures of the tetrameric and dimeric forms were solved. Here, a new monomeric form of BGLPf was constructed by removing the C-terminal region of the enzyme and its crystal structure was solved at a resolution of 2.8 Å in space group P1. It was discovered that the mutant enzyme forms a unique dodecameric structure consisting of two hexameric rings in the asymmetric unit of the crystal. Under biological conditions, the mutant enzyme forms a monomer. This result helps explain how BGLPf has attained its oligomeric structure and thermostability. PMID:25005077
Computational structural mechanics engine structures computational simulator

NASA Technical Reports Server (NTRS)

Chamis, C. C.

1989-01-01

The Computational Structural Mechanics (CSM) program at Lewis encompasses: (1) fundamental aspects for formulating and solving structural mechanics problems, and (2) development of integrated software systems to computationally simulate the performance/durability/life of engine structures.
Reponse dynamique des structures sous charges de vent

NASA Astrophysics Data System (ADS)

Gani, Ferawati

The main purpose of this research is to assemble numerical tools that allows realistic dynamic study of structures under wind loading. The availability of such numerical tools is becoming more important for the industry, following previous experiences in structural damages after extreme wind events. The methodology of the present study involves two main steps: (i) preparing the wind loading according to its spatial and temporal correlations by using digitally generated wind or real measured wind; (ii) preparing the numerical model that captures the characteristics of the real structures and respects all the necessary numerical requirements to pursue transient dynamic analyses. The thesis is presented as an ensemble of four articles written for refereed journals and conferences that showcase the contributions of the present study to the advancement of transient dynamic study of structures under wind loading, on the wind model itself (the first article) and on the application of the wind study on complex structures (the next three articles). The articles presented are as follows: (a) the evaluation of three-dimensional correlations of wind, an important issue for more precise prediction of wind loading for flexible and line-like structures, the results presented in this first article helps design engineers to choose a more suitable models to define three-dimensional wind loading; (b) the refinement of design for solar photovoltaic concentrator-tracker structure developed for utility scale, this study addressed concerns related strict operational criteria and fatigue under wind load for a large parabolic truss structure; (c) the study of guyed towers for TLs, the applicability of the static-equivalent method from the current industry documents for the design of this type of flexible TL support was questioned, a simplified method to improve the wind design was proposed; (d) the fundamental issue of nonlinear behaviour under extreme wind loading for single-degree-of-freedom systems is evaluated here, the use of real measured hurricane and winter storm have highlighted the possible interest of taking into account the ductility in the extreme wind loading design. The present research project has shown the versatility of the use of the developed wind study methodology to solve concerns related to different type of complex structures. In addition, this study proposes simplified methods that are useful for practical engineers when there is the need to solve similar problems. Key words: nonlinear, dynamic, wind, guyed tower, parabolic structure, ductility.
Structure of the N-terminal fragment of Escherichia coli Lon protease

DOE Office of Scientific and Technical Information (OSTI.GOV)

Li, Mi; Gustchina, Alla; Rasulova, Fatima S.

2010-10-22

The structure of a recombinant construct consisting of residues 1-245 of Escherichia coli Lon protease, the prototypical member of the A-type Lon family, is reported. This construct encompasses all or most of the N-terminal domain of the enzyme. The structure was solved by SeMet SAD to 2.6 {angstrom} resolution utilizing trigonal crystals that contained one molecule in the asymmetric unit. The molecule consists of two compact subdomains and a very long C-terminal {alpha}-helix. The structure of the first subdomain (residues 1-117), which consists mostly of {beta}-strands, is similar to that of the shorter fragment previously expressed and crystallized, whereas themore » second subdomain is almost entirely helical. The fold and spatial relationship of the two subdomains, with the exception of the C-terminal helix, closely resemble the structure of BPP1347, a 203-amino-acid protein of unknown function from Bordetella parapertussis, and more distantly several other proteins. It was not possible to refine the structure to satisfactory convergence; however, since almost all of the Se atoms could be located on the basis of their anomalous scattering the correctness of the overall structure is not in question. The structure reported here was also compared with the structures of the putative substrate-binding domains of several proteins, showing topological similarities that should help in defining the binding sites used by Lon substrates.« less
SITEX 2.0: Projections of protein functional sites on eukaryotic genes. Extension with orthologous genes.

PubMed

Medvedeva, Irina V; Demenkov, Pavel S; Ivanisenko, Vladimir A

2017-04-01

Functional sites define the diversity of protein functions and are the central object of research of the structural and functional organization of proteins. The mechanisms underlying protein functional sites emergence and their variability during evolution are distinguished by duplication, shuffling, insertion and deletion of the exons in genes. The study of the correlation between a site structure and exon structure serves as the basis for the in-depth understanding of sites organization. In this regard, the development of programming resources that allow the realization of the mutual projection of exon structure of genes and primary and tertiary structures of encoded proteins is still the actual problem. Previously, we developed the SitEx system that provides information about protein and gene sequences with mapped exon borders and protein functional sites amino acid positions. The database included information on proteins with known 3D structure. However, data with respect to orthologs was not available. Therefore, we added the projection of sites positions to the exon structures of orthologs in SitEx 2.0. We implemented a search through database using site conservation variability and site discontinuity through exon structure. Inclusion of the information on orthologs allowed to expand the possibilities of SitEx usage for solving problems regarding the analysis of the structural and functional organization of proteins. Database URL: http://www-bionet.sscc.ru/sitex/ .
The crystal structure of P450-TT heme-domain provides the first structural insights into the versatile class VII P450s.

PubMed

Tavanti, Michele; Porter, Joanne L; Levy, Colin W; Gómez Castellanos, J Rubén; Flitsch, Sabine L; Turner, Nicholas J

2018-07-02

The first crystal structure of a class VII P450, CYP116B46 from Tepidiphilus thermophilus, has been solved at 1.9 Å resolution. The structure reveals overall conservation of the P450-fold and a water conduit around the I-helix. Active site residues have been identified and sequence comparisons have been made with other class VII enzymes. A structure similarity search demonstrated that the P450-TT structure is similar to enzymes capable of oxy-functionalization of fatty acids, terpenes, macrolides, steroids and statins. The insight gained from solving this structure will provide a guideline for future engineering and modelling studies on this catalytically promiscuous class of enzymes. Copyright © 2018 Elsevier Inc. All rights reserved.
Solving the Hamilton-Jacobi equation for general relativity

NASA Astrophysics Data System (ADS)

Parry, J.; Salopek, D. S.; Stewart, J. M.

1994-03-01

We demonstrate a systematic method for solving the Hamilton-Jacobi equation for general relativity with the inclusion of matter fields. The generating functional is expanded in a series of spatial gradients. Each term is manifestly invariant under reparametrizations of the spatial coordinates (``gauge invariant''). At each order we solve the Hamiltonian constraint using a conformal transformation of the three-metric as well as a line integral in superspace. This gives a recursion relation for the generating functional which then may be solved to arbitrary order simply by functionally differentiating previous orders. At fourth order in spatial gradients we demonstrate solutions for irrotational dust as well as for a scalar field. We explicitly evolve the three-metric to the same order. This method can be used to derive the Zel'dovich approximation for general relativity.
How preschool executive functioning predicts several aspects of math achievement in Grades 1 and 3: A longitudinal study.

PubMed

Viterbori, Paola; Usai, M Carmen; Traverso, Laura; De Franchis, Valentina

2015-12-01

This longitudinal study analyzes whether selected components of executive function (EF) measured during the preschool period predict several indices of math achievement in primary school. Six EF measures were assessed in a sample of 5-year-old children (N = 175). The math achievement of the same children was then tested in Grades 1 and 3 using both a composite math score and three single indices of written calculation, arithmetical facts, and problem solving. Using previous results obtained from the same sample of children, a confirmatory factor analysis examining the latent EF structure in kindergarten indicated that a two-factor model provided the best fit for the data. In this model, inhibition and working memory (WM)-flexibility were separate dimensions. A full structural equation model was then used to test the hypothesis that math achievement (the composite math score and single math scores) in Grades 1 and 3 could be explained by the two EF components comprising the kindergarten model. The results indicate that the WM-flexibility component measured during the preschool period substantially predicts mathematical achievement, especially in Grade 3. The math composite scores were predicted by the WM-flexibility factor at both grade levels. In Grade 3, both problem solving and arithmetical facts were predicted by the WM-flexibility component. The results empirically support interventions that target EF as an important component of early childhood mathematics education. Copyright © 2015 Elsevier Inc. All rights reserved.
Revising explanatory models to accommodate anomalous genetic phenomena: Problem solving in the context of discovery

NASA Astrophysics Data System (ADS)

Hafner, Robert; Stewart, Jim

Past problem-solving research has provided a basis for helping students structure their knowledge and apply appropriate problem-solving strategies to solve problems for which their knowledge (or mental models) of scientific phenomena is adequate (model-using problem solving). This research examines how problem solving in the domain of Mendelian genetics proceeds in situations where solvers' mental models are insufficient to solve problems at hand (model-revising problem solving). Such situations require solvers to use existing models to recognize anomalous data and to revise those models to accommodate the data. The study was conducted in the context of 9-week high school genetics course and addressed: the heuristics charactenstic of successful model-revising problem solving: the nature of the model revisions, made by students as well as the nature of model development across problem types; and the basis upon which solvers decide that a revised model is sufficient (that t has both predictive and explanatory power).
Small-x asymptotics of the quark helicity distribution: Analytic results

DOE PAGES

Kovchegov, Yuri V.; Pitonyak, Daniel; Sievert, Matthew D.

2017-06-15

In this Letter, we analytically solve the evolution equations for the small-x asymptotic behavior of the (flavor singlet) quark helicity distribution in the large- N c limit. Here, these evolution equations form a set of coupled integro-differential equations, which previously could only be solved numerically. This approximate numerical solution, however, revealed simplifying properties of the small-x asymptotics, which we exploit here to obtain an analytic solution.
Solving complex band structure problems with the FEAST eigenvalue algorithm

NASA Astrophysics Data System (ADS)

Laux, S. E.

2012-08-01

With straightforward extension, the FEAST eigenvalue algorithm [Polizzi, Phys. Rev. B 79, 115112 (2009)] is capable of solving the generalized eigenvalue problems representing traveling-wave problems—as exemplified by the complex band-structure problem—even though the matrices involved are complex, non-Hermitian, and singular, and hence outside the originally stated range of applicability of the algorithm. The obtained eigenvalues/eigenvectors, however, contain spurious solutions which must be detected and removed. The efficiency and parallel structure of the original algorithm are unaltered. The complex band structures of Si layers of varying thicknesses and InAs nanowires of varying radii are computed as test problems.
Structure of the human transcobalamin beta domain in four distinct states

PubMed Central

Bloch, Joël S.; Ruetz, Markus; Kräutler, Bernhard

2017-01-01

Vitamin B12 (cyanocobalamin, CNCbl) is an essential cofactor-precursor for two biochemical reactions in humans. When ingested, cobalamins (Cbl) are transported via a multistep transport system into the bloodstream, where the soluble protein transcobalamin (TC) binds Cbl and the complex is taken up into the cells via receptor mediated endocytosis. Crystal structures of TC in complex with CNCbl have been solved previously. However, the initial steps of holo-TC assembly have remained elusive. Here, we present four crystal structures of the beta domain of human TC (TC-beta) in different substrate-bound states. These include the apo and CNCbl-bound states, providing insight into the early steps of holo-TC assembly. We found that in vitro assembly of TC-alpha and TC-beta to a complex was Cbl-dependent. We also determined the structure of TC-beta in complex with cobinamide (Cbi), an alternative substrate, shedding light on the specificity of TC. We finally determined the structure of TC-beta in complex with an inhibitory antivitamin B12 (anti-B12). We used this structure to model the binding of anti-B12 into full-length holo-TC and could rule out that the inhibitory function of anti-B12 was based on an inability to form a functional complex with TC. PMID:28910388
Further reduction of minimal first-met bad markings for the computationally efficient synthesis of a maximally permissive controller

NASA Astrophysics Data System (ADS)

Liu, GaiYun; Chao, Daniel Yuh

2015-08-01

To date, research on the supervisor design for flexible manufacturing systems focuses on speeding up the computation of optimal (maximally permissive) liveness-enforcing controllers. Recent deadlock prevention policies for systems of simple sequential processes with resources (S3PR) reduce the computation burden by considering only the minimal portion of all first-met bad markings (FBMs). Maximal permissiveness is ensured by not forbidding any live state. This paper proposes a method to further reduce the size of minimal set of FBMs to efficiently solve integer linear programming problems while maintaining maximal permissiveness using a vector-covering approach. This paper improves the previous work and achieves the simplest structure with the minimal number of monitors.
The origin and evolution of human glutaminases and their atypical C-terminal ankyrin repeats

DOE PAGES

Pasquali, Camila Cristina; Islam, Zeyaul; Adamoski, Douglas; ...

2017-05-19

On the basis of tissue-specific enzyme activity and inhibition by catalytic products, Hans Krebs first demonstrated the existence of multiple glutaminases in mammals. Currently, two human genes are known to encode at least four glutaminase isoforms. But, the phylogeny of these medically relevant enzymes remains unclear, prompting us to investigate their origin and evolution. Using prokaryotic and eukaryotic glutaminase sequences, we built a phylogenetic tree whose topology suggested that the multidomain architecture was inherited from bacterial ancestors, probably simultaneously with the hosting of the proto-mitochondrion endosymbiont. We propose an evolutionary model wherein the appearance of the most active enzyme isoform,more » glutaminase C (GAC), which is expressed in many cancers, was a late retrotransposition event that occurred in fishes from the Chondrichthyes class. The ankyrin (ANK) repeats in the glutaminases were acquired early in their evolution. In order to obtain information on ANK folding, we solved two high-resolution structures of the ANK repeat-containing C termini of both kidney-type glutaminase (KGA) and GLS2 isoforms (glutaminase B and liver-type glutaminase). We also found that the glutaminase ANK repeats form unique intramolecular contacts through two highly conserved motifs; curiously, this arrangement occludes a region usually involved in ANK-mediated protein-protein interactions. We also solved the crystal structure of full-length KGA and present a small-angle X-ray scattering model for full-length GLS2. These structures explain these proteins' compromised ability to assemble into catalytically active supra-tetrameric filaments, as previously shown for GAC. Collectively, these results provide information about glutaminases that may aid in the design of isoform-specific glutaminase inhibitors.« less
The ACTIVE conceptual framework as a structural equation model.

PubMed

Gross, Alden L; Payne, Brennan R; Casanova, Ramon; Davoudzadeh, Pega; Dzierzewski, Joseph M; Farias, Sarah; Giovannetti, Tania; Ip, Edward H; Marsiske, Michael; Rebok, George W; Schaie, K Warner; Thomas, Kelsey; Willis, Sherry; Jones, Richard N

2018-01-01

Background/Study Context: Conceptual frameworks are analytic models at a high level of abstraction. Their operationalization can inform randomized trial design and sample size considerations. The Advanced Cognitive Training for Independent and Vital Elderly (ACTIVE) conceptual framework was empirically tested using structural equation modeling (N=2,802). ACTIVE was guided by a conceptual framework for cognitive training in which proximal cognitive abilities (memory, inductive reasoning, speed of processing) mediate treatment-related improvement in primary outcomes (everyday problem-solving, difficulty with activities of daily living, everyday speed, driving difficulty), which in turn lead to improved secondary outcomes (health-related quality of life, health service utilization, mobility). Measurement models for each proximal, primary, and secondary outcome were developed and tested using baseline data. Each construct was then combined in one model to evaluate fit (RMSEA, CFI, normalized residuals of each indicator). To expand the conceptual model and potentially inform future trials, evidence of modification of structural model parameters was evaluated by age, years of education, sex, race, and self-rated health status. Preconceived measurement models for memory, reasoning, speed of processing, everyday problem-solving, instrumental activities of daily living (IADL) difficulty, everyday speed, driving difficulty, and health-related quality of life each fit well to the data (all RMSEA < .05; all CFI > .95). Fit of the full model was excellent (RMSEA = .038; CFI = .924). In contrast with previous findings from ACTIVE regarding who benefits from training, interaction testing revealed associations between proximal abilities and primary outcomes are stronger on average by nonwhite race, worse health, older age, and less education (p < .005). Empirical data confirm the hypothesized ACTIVE conceptual model. Findings suggest that the types of people who show intervention effects on cognitive performance potentially may be different from those with the greatest chance of transfer to real-world activities.
General stability of composite panels reinforced with flexible rods taking account of the side boundary conditions

NASA Astrophysics Data System (ADS)

Dudchenko, A. A.; Elpat'evskii, A. N.

1995-07-01

Reinforced panels are the basic load-bearing elements of various structures. Optimization of massive structures requires consideration of deformation of the panel cross-sections. This is particularly important in determining the bearing strength at buckling. The load scheme, conditions for fixation of the panel cross-section, and bend-torsional stiffness taking account of the deformation of the rod cross-section affect the buckling load in real structures. The stress distribution prior to buckling must be known to solve the buckling problem properly. The stress in the panel is proportional to the active load. The stress distribution is assumed to be known according to our previous method [1]. The load scheme and panel dimensions are shown in Fig. 1. The stress distribution in the panel prior to buckling can be found using Eqs. (1)-(3). A view of the cross-section is given in Fig. 1. The displacements in the panel at buckling for the boundary area are found using Eqs. (4)-(6), while the stresses in the skin and stiffness are found using Eq. (7). Roots k1 and k2 are those of the characteristic equation and β is a dimensionless coordinate. The problem was solved using variational theory. The potential energy is given by Eqs. (8) and (9) by orihogonalization of Eqs. (5). The basic equations are converted to Eqs. (10) by evaluation of the components in Eqs. (8) and (9). Its calculation (11) gives the compression load. Optimization of parameter α gives the critical strength P1 = 6.93 kN (without taking account of the boundary area) and P2 = 5.31 kN (taking account of the boundary area).

The origin and evolution of human glutaminases and their atypical C-terminal ankyrin repeats

DOE Office of Scientific and Technical Information (OSTI.GOV)

Pasquali, Camila Cristina; Islam, Zeyaul; Adamoski, Douglas

On the basis of tissue-specific enzyme activity and inhibition by catalytic products, Hans Krebs first demonstrated the existence of multiple glutaminases in mammals. Currently, two human genes are known to encode at least four glutaminase isoforms. But, the phylogeny of these medically relevant enzymes remains unclear, prompting us to investigate their origin and evolution. Using prokaryotic and eukaryotic glutaminase sequences, we built a phylogenetic tree whose topology suggested that the multidomain architecture was inherited from bacterial ancestors, probably simultaneously with the hosting of the proto-mitochondrion endosymbiont. We propose an evolutionary model wherein the appearance of the most active enzyme isoform,more » glutaminase C (GAC), which is expressed in many cancers, was a late retrotransposition event that occurred in fishes from the Chondrichthyes class. The ankyrin (ANK) repeats in the glutaminases were acquired early in their evolution. In order to obtain information on ANK folding, we solved two high-resolution structures of the ANK repeat-containing C termini of both kidney-type glutaminase (KGA) and GLS2 isoforms (glutaminase B and liver-type glutaminase). We also found that the glutaminase ANK repeats form unique intramolecular contacts through two highly conserved motifs; curiously, this arrangement occludes a region usually involved in ANK-mediated protein-protein interactions. We also solved the crystal structure of full-length KGA and present a small-angle X-ray scattering model for full-length GLS2. These structures explain these proteins' compromised ability to assemble into catalytically active supra-tetrameric filaments, as previously shown for GAC. Collectively, these results provide information about glutaminases that may aid in the design of isoform-specific glutaminase inhibitors.« less
Rediscovery in a Course for Nonscientists: Use of Molecular Models to Solve Classical Structural Problems

ERIC Educational Resources Information Center

Wood, Gordon W.

1975-01-01

Describes exercises using simple ball and stick models which students with no chemistry background can solve in the context of the original discovery. Examples include the tartaric acid and benzene problems. (GS)
CoCoNUT: an efficient system for the comparison and analysis of genomes

PubMed Central

2008-01-01

Background Comparative genomics is the analysis and comparison of genomes from different species. This area of research is driven by the large number of sequenced genomes and heavily relies on efficient algorithms and software to perform pairwise and multiple genome comparisons. Results Most of the software tools available are tailored for one specific task. In contrast, we have developed a novel system CoCoNUT (Computational Comparative geNomics Utility Toolkit) that allows solving several different tasks in a unified framework: (1) finding regions of high similarity among multiple genomic sequences and aligning them, (2) comparing two draft or multi-chromosomal genomes, (3) locating large segmental duplications in large genomic sequences, and (4) mapping cDNA/EST to genomic sequences. Conclusion CoCoNUT is competitive with other software tools w.r.t. the quality of the results. The use of state of the art algorithms and data structures allows CoCoNUT to solve comparative genomics tasks more efficiently than previous tools. With the improved user interface (including an interactive visualization component), CoCoNUT provides a unified, versatile, and easy-to-use software tool for large scale studies in comparative genomics. PMID:19014477
Inverse design of an isotropic suspended Kirchhoff rod: theoretical and numerical results on the uniqueness of the natural shape.

PubMed

Bertails-Descoubes, Florence; Derouet-Jourdan, Alexandre; Romero, Victor; Lazarus, Arnaud

2018-04-01

Solving the equations for Kirchhoff elastic rods has been widely explored for decades in mathematics, physics and computer science, with significant applications in the modelling of thin flexible structures such as DNA, hair or climbing plants. As demonstrated in previous experimental and theoretical studies, the natural curvature plays an important role in the equilibrium shape of a Kirchhoff rod, even in the simple case where the rod is isotropic and suspended under gravity. In this paper, we investigate the reverse problem: can we characterize the natural curvature of a suspended isotropic rod, given an equilibrium curve? We prove that although there exists an infinite number of natural curvatures that are compatible with the prescribed equilibrium, they are all equivalent in the sense that they correspond to a unique natural shape for the rod. This natural shape can be computed efficiently by solving in sequence three linear initial value problems, starting from any framing of the input curve. We provide several numerical experiments to illustrate this uniqueness result, and finally discuss its potential impact on non-invasive parameter estimation and inverse design of thin elastic rods.
Self Organizing Maps for use in Deep Inelastic Scattering

NASA Astrophysics Data System (ADS)

Askanazi, Evan

2015-04-01

Self Organizing Maps are a type of artificial neural network that has been proven to be particularly useful in solving complex problems in neural biology, engineering, robotics and physics. We are attempting to use the Self Organizing Map to solve problems and probe phenomenological patterns in subatomic physics, specifically in Deep Inelastic Scattering (DIS). In DIS there is a cross section in electron hadron scattering that is dependent on the momentum fraction x of the partons in the hadron and the momentum transfer of the virtual photon exchanged. There is a soft cross part of this cross section that currently can only be found through experimentation; this soft part is comprised of Structure Functions which in turn are comprised of the Parton Distribution Functions (PDFs). We aim to use the Self Organizing Process, or SOP, to take theoretical models of these PDFs and fit it to the previous, known data. The SOP will also be used to probe the behavior of the PDFs in particular at large x values, in order to observe how they congregate. The ability of the SOPto take multidimensional data and convert it into two dimensional output is anticipated to be particularly useful in achieving this aim.
Inverse design of an isotropic suspended Kirchhoff rod: theoretical and numerical results on the uniqueness of the natural shape

NASA Astrophysics Data System (ADS)

Bertails-Descoubes, Florence; Derouet-Jourdan, Alexandre; Romero, Victor; Lazarus, Arnaud

2018-04-01

Solving the equations for Kirchhoff elastic rods has been widely explored for decades in mathematics, physics and computer science, with significant applications in the modelling of thin flexible structures such as DNA, hair or climbing plants. As demonstrated in previous experimental and theoretical studies, the natural curvature plays an important role in the equilibrium shape of a Kirchhoff rod, even in the simple case where the rod is isotropic and suspended under gravity. In this paper, we investigate the reverse problem: can we characterize the natural curvature of a suspended isotropic rod, given an equilibrium curve? We prove that although there exists an infinite number of natural curvatures that are compatible with the prescribed equilibrium, they are all equivalent in the sense that they correspond to a unique natural shape for the rod. This natural shape can be computed efficiently by solving in sequence three linear initial value problems, starting from any framing of the input curve. We provide several numerical experiments to illustrate this uniqueness result, and finally discuss its potential impact on non-invasive parameter estimation and inverse design of thin elastic rods.
Modeling social learning of language and skills.

PubMed

Vogt, Paul; Haasdijk, Evert

2010-01-01

We present a model of social learning of both language and skills, while assuming—insofar as possible—strict autonomy, virtual embodiment, and situatedness. This model is built by integrating various previous models of language development and social learning, and it is this integration that, under the mentioned assumptions, provides novel challenges. The aim of the article is to investigate what sociocognitive mechanisms agents should have in order to be able to transmit language from one generation to the next so that it can be used as a medium to transmit internalized rules that represent skill knowledge. We have performed experiments where this knowledge solves the familiar poisonous-food problem. Simulations reveal under what conditions, regarding population structure, agents can successfully solve this problem. In addition to issues relating to perspective taking and mutual exclusivity, we show that agents need to coordinate interactions so that they can establish joint attention in order to form a scaffold for language learning, which in turn forms a scaffold for the learning of rule-based skills. Based on these findings, we conclude by hypothesizing that social learning at one level forms a scaffold for the social learning at another, higher level, thus contributing to the accumulation of cultural knowledge.
Photonic band structures solved by a plane-wave-based transfer-matrix method.

PubMed

Li, Zhi-Yuan; Lin, Lan-Lan

2003-04-01

Transfer-matrix methods adopting a plane-wave basis have been routinely used to calculate the scattering of electromagnetic waves by general multilayer gratings and photonic crystal slabs. In this paper we show that this technique, when combined with Bloch's theorem, can be extended to solve the photonic band structure for 2D and 3D photonic crystal structures. Three different eigensolution schemes to solve the traditional band diagrams along high-symmetry lines in the first Brillouin zone of the crystal are discussed. Optimal rules for the Fourier expansion over the dielectric function and electromagnetic fields with discontinuities occurring at the boundary of different material domains have been employed to accelerate the convergence of numerical computation. Application of this method to an important class of 3D layer-by-layer photonic crystals reveals the superior convergency of this different approach over the conventional plane-wave expansion method.
Combined fast multipole-QR compression technique for solving electrically small to large structures for broadband applications

NASA Technical Reports Server (NTRS)

Jandhyala, Vikram (Inventor); Chowdhury, Indranil (Inventor)

2011-01-01

An approach that efficiently solves for a desired parameter of a system or device that can include both electrically large fast multipole method (FMM) elements, and electrically small QR elements. The system or device is setup as an oct-tree structure that can include regions of both the FMM type and the QR type. An iterative solver is then used to determine a first matrix vector product for any electrically large elements, and a second matrix vector product for any electrically small elements that are included in the structure. These matrix vector products for the electrically large elements and the electrically small elements are combined, and a net delta for a combination of the matrix vector products is determined. The iteration continues until a net delta is obtained that is within predefined limits. The matrix vector products that were last obtained are used to solve for the desired parameter.
A Graph Based Backtracking Algorithm for Solving General CSPs

NASA Technical Reports Server (NTRS)

Pang, Wanlin; Goodwin, Scott D.

2003-01-01

Many AI tasks can be formalized as constraint satisfaction problems (CSPs), which involve finding values for variables subject to constraints. While solving a CSP is an NP-complete task in general, tractable classes of CSPs have been identified based on the structure of the underlying constraint graphs. Much effort has been spent on exploiting structural properties of the constraint graph to improve the efficiency of finding a solution. These efforts contributed to development of a class of CSP solving algorithms called decomposition algorithms. The strength of CSP decomposition is that its worst-case complexity depends on the structural properties of the constraint graph and is usually better than the worst-case complexity of search methods. Its practical application is limited, however, since it cannot be applied if the CSP is not decomposable. In this paper, we propose a graph based backtracking algorithm called omega-CDBT, which shares merits and overcomes the weaknesses of both decomposition and search approaches.
Distinct peptide binding specificities of Src homology 3 (SH3) protein domains can be determined by modulation of local energetics across the binding interface.

PubMed

Gorelik, Maryna; Davidson, Alan R

2012-03-16

The yeast Nbp2p SH3 and Bem1p SH3b domains bind certain target peptides with similar high affinities, yet display vastly different affinities for other targets. To investigate this unusual behavior, we have solved the structure of the Nbp2p SH3-Ste20 peptide complex and compared it with the previously determined structure of the Bem1p SH3b bound to the same peptide. Although the Ste20 peptide interacts with both domains in a structurally similar manner, extensive in vitro studies with domain and peptide mutants revealed large variations in interaction strength across the binding interface of the two complexes. Whereas the Nbp2p SH3 made stronger contacts with the peptide core RXXPXXP motif, the Bem1p SH3b domain made stronger contacts with residues flanking the core motif. Remarkably, this modulation of local binding energetics can explain the distinct and highly nuanced binding specificities of these two domains.
Effects of Ohmic Resistance on Dynamic Characteristics and Impedance of Micro/Nano Cantilever Beam resonators

NASA Astrophysics Data System (ADS)

Rezazadeh, Ghader; Keyvani, Aliasghar; Sadeghi, Morteza H.; Bahrami, Manouchehr

2013-06-01

Effects of Ohmic resistance on MEMS/NEMS vibrating structures that have always been dismissed in some situations may cause important changes in resonance properties and impedance parameters of the MEMS/NEMS based circuits. In this paper it is aimed to present a theoretical model to precisely investigate the problem on a simple cantilever-substrate resonator. In this favor the Ohm's current law and charge conservation law have been merged to find a differential Equation for voltage propagation on the beam and because mostly nano structures are expected as the scope of the problem, modified couple stress theory is used to formulate the dynamic motion of the beam. The two governing equations were coupled and both nonlinear that have been solved simultaneously using a Galerkin based state space formulation. The obtained results that are in exact agreement with previous works show that dynamic pull-in voltage, switching time, and impedance of structure as a MEMS capacitor especially in frequencies higher than natural resonance frequency strongly relay on electrical resistance of the beam and substrate material.
Zebavidin - An Avidin-Like Protein from Zebrafish

PubMed Central

Taskinen, Barbara; Zmurko, Joanna; Ojanen, Markus; Kukkurainen, Sampo; Parthiban, Marimuthu; Määttä, Juha A. E.; Leppiniemi, Jenni; Jänis, Janne; Parikka, Mataleena; Turpeinen, Hannu; Rämet, Mika; Pesu, Marko; Johnson, Mark S.; Kulomaa, Markku S.; Airenne, Tomi T.; Hytönen, Vesa P.

2013-01-01

The avidin protein family members are well known for their high affinity towards D-biotin and high structural stability. These properties make avidins valuable tools for a wide range of biotechnology applications. We have identified a new member of the avidin family in the zebrafish (Danio rerio) genome, hereafter called zebavidin. The protein is highly expressed in the gonads of both male and female zebrafish and in the gills of male fish, but our data suggest that zebavidin is not crucial for the developing embryo. Biophysical and structural characterisation of zebavidin revealed distinct properties not found in any previously characterised avidins. Gel filtration chromatography and native mass spectrometry suggest that the protein forms dimers in the absence of biotin at low ionic strength, but assembles into tetramers upon binding biotin. Ligand binding was analysed using radioactive and fluorescently labelled biotin and isothermal titration calorimetry. Moreover, the crystal structure of zebavidin in complex with biotin was solved at 2.4 Å resolution and unveiled unique ligand binding and subunit interface architectures; the atomic-level details support our physicochemical observations. PMID:24204770
STRUCTURAL PROPERTIES OF NON-SPHERICAL DARK HALOS IN MILKY WAY AND ANDROMEDA DWARF SPHEROIDAL GALAXIES

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hayashi, Kohei; Chiba, Masashi, E-mail: kohei.hayashi@ipmu.jp, E-mail: chiba@astr.tohoku.ac.jp

We investigate the non-spherical density structure of dark halos of the dwarf spheroidal (dSph) galaxies in the Milky Way and Andromeda galaxies based on revised axisymmetric mass models from our previous work. The models we adopt here fully take into account velocity anisotropy of tracer stars confined within a flattened dark halo. Applying our models to the available kinematic data of the 12 bright dSphs, we find that these galaxies associate with, in general, elongated dark halos, even considering the effect of this velocity anisotropy of stars. We also find that the best-fit parameters, especially for the shapes of darkmore » halos and velocity anisotropy, are susceptible to both the availability of velocity data in the outer regions and the effect of the lack of sample stars in each spatial bin. Thus, to obtain more realistic limits on dark halo structures, we require photometric and kinematic data over much larger areas in the dSphs than previously explored. The results obtained from the currently available data suggest that the shapes of dark halos in the dSphs are more elongated than those of ΛCDM subhalos. This mismatch needs to be solved by theory including baryon components and the associated feedback to dark halos as well as by further observational limits in larger areas of dSphs. It is also found that more diffuse dark halos may have undergone consecutive star formation history, thereby implying that dark-halo structure plays an important role in star formation activity.« less
Crystal Structures of the Histo-Aspartic Protease (HAP) from Plasmodium falciparum

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bhaumik, Prasenjit; Xiao, Huogen; Parr, Charity L.

The structures of recombinant histo-aspartic protease (HAP) from malaria-causing parasite Plasmodium falciparum as apoenzyme and in complex with two inhibitors, pepstatin A and KNI-10006, were solved at 2.5-, 3.3-, and 3.05-{angstrom} resolutions, respectively. In the apoenzyme crystals, HAP forms a tight dimer not seen previously in any aspartic protease. The interactions between the monomers affect the conformation of two flexible loops, the functionally important 'flap' (residues 70-83) and its structural equivalent in the C-terminal domain (residues 238-245), as well as the orientation of helix 225-235. The flap is found in an open conformation in the apoenzyme. Unexpectedly, the active sitemore » of the apoenzyme contains a zinc ion tightly bound to His32 and Asp215 from one monomer and to Glu278A from the other monomer, with the coordination of Zn resembling that seen in metalloproteases. The flap is closed in the structure of the pepstatin A complex, whereas it is open in the complex with KNI-10006. Although the binding mode of pepstatin A is significantly different from that in other pepsin-like aspartic proteases, its location in the active site makes unlikely the previously proposed hypothesis that HAP is a serine protease. The binding mode of KNI-10006 is unusual compared with the binding of other inhibitors from the KNI series to aspartic proteases. The novel features of the HAP active site could facilitate design of specific inhibitors used in the development of antimalarial drugs.« less
Allosteric modulation of Ras positions Q61 for a direct role in catalysis

DOE Office of Scientific and Technical Information (OSTI.GOV)

Buhrman, Greg; Holzapfel, Genevieve; Fetics, Susan

2010-11-03

Ras and its effector Raf are key mediators of the Ras/Raf/MEK/ERK signal transduction pathway. Mutants of residue Q61 impair the GTPase activity of Ras and are found prominently in human cancers. Yet the mechanism through which Q61 contributes to catalysis has been elusive. It is thought to position the catalytic water molecule for nucleophilic attack on the {gamma}-phosphate of GTP. However, we previously solved the structure of Ras from crystals with symmetry of the space group R32 in which switch II is disordered and found that the catalytic water molecule is present. Here we present a structure of wild-type Rasmore » with calcium acetate from the crystallization mother liquor bound at a site remote from the active site and likely near the membrane. This results in a shift in helix 3/loop 7 and a network of H-bonding interactions that propagates across the molecule, culminating in the ordering of switch II and placement of Q61 in the active site in a previously unobserved conformation. This structure suggests a direct catalytic role for Q61 where it interacts with a water molecule that bridges one of the {gamma}-phosphate oxygen atoms to the hydroxyl group of Y32 to stabilize the transition state of the hydrolysis reaction. We propose that Raf together with the binding of Ca{sup 2+} and a negatively charged group mimicked in our structure by the acetate molecule induces the ordering of switch I and switch II to complete the active site of Ras.« less
Topometry optimization of sheet metal structures for crashworthiness design using hybrid cellular automata

NASA Astrophysics Data System (ADS)

Mozumder, Chandan K.

The objective in crashworthiness design is to generate plastically deformable energy absorbing structures which can satisfy the prescribed force-displacement (FD) response. The FD behavior determines the reaction force, displacement and the internal energy that the structure should withstand. However, attempts to include this requirement in structural optimization problems remain scarce. The existing commercial optimization tools utilize models under static loading conditions because of the complexities associated with dynamic/impact loading. Due to the complexity of a crash event and the consequent time required to numerically analyze the dynamic response of the structure, classical methods (i.e., gradient-based and direct) are not well developed to solve this undertaking. This work presents an approach under the framework of the hybrid cellular automaton (HCA) method to solve the above challenge. The HCA method has been successfully applied to nonlinear transient topology optimization for crashworthiness design. In this work, the HCA algorithm has been utilized to develop an efficient methodology for synthesizing shell-based sheet metal structures with optimal material thickness distribution under a dynamic loading event using topometry optimization. This method utilizes the cellular automata (CA) computing paradigm and nonlinear transient finite element analysis (FEA) via ls-dyna. In this method, a set field variables is driven to their target states by changing a convenient set of design variables (e.g., thickness). These rules operate locally in cells within a lattice that only know local conditions. The field variables associated with the cells are driven to a setpoint to obtain the desired structure. This methodology is used to design for structures with controlled energy absorption with specified buckling zones. The peak reaction force and the maximum displacement are also constrained to meet the desired safety level according to passenger safety regulations. Design for prescribed FD response by minimizing the error between the actual response and desired FD curve is implemented. With the use of HCA rules, manufacturability constraints (e.g., rolling) and structures which can be manufactured by special techniques, such as, tailor-welded blanks (TWB), have also been implemented. This methodology is applied to shock-absorbing structural components for passengers in a crashing vehicle. These results are compared to previous designs showing the benefits of the method introduced in this work.
Algorithm for solving the linear Cauchy problem for large systems of ordinary differential equations with the use of parallel computations

DOE Office of Scientific and Technical Information (OSTI.GOV)

Moryakov, A. V., E-mail: sailor@orc.ru

2016-12-15

An algorithm for solving the linear Cauchy problem for large systems of ordinary differential equations is presented. The algorithm for systems of first-order differential equations is implemented in the EDELWEISS code with the possibility of parallel computations on supercomputers employing the MPI (Message Passing Interface) standard for the data exchange between parallel processes. The solution is represented by a series of orthogonal polynomials on the interval [0, 1]. The algorithm is characterized by simplicity and the possibility to solve nonlinear problems with a correction of the operator in accordance with the solution obtained in the previous iterative process.
The method of space-time and conservation element and solution element: A new approach for solving the Navier-Stokes and Euler equations

NASA Technical Reports Server (NTRS)

Chang, Sin-Chung

1995-01-01

A new numerical framework for solving conservation laws is being developed. This new framework differs substantially in both concept and methodology from the well-established methods, i.e., finite difference, finite volume, finite element, and spectral methods. It is conceptually simple and designed to overcome several key limitations of the above traditional methods. A two-level scheme for solving the convection-diffusion equation is constructed and used to illuminate the major differences between the present method and those previously mentioned. This explicit scheme, referred to as the a-mu scheme, has two independent marching variables.
Reasoning by analogy as an aid to heuristic theorem proving.

NASA Technical Reports Server (NTRS)

Kling, R. E.

1972-01-01

When heuristic problem-solving programs are faced with large data bases that contain numbers of facts far in excess of those needed to solve any particular problem, their performance rapidly deteriorates. In this paper, the correspondence between a new unsolved problem and a previously solved analogous problem is computed and invoked to tailor large data bases to manageable sizes. This paper outlines the design of an algorithm for generating and exploiting analogies between theorems posed to a resolution-logic system. These algorithms are believed to be the first computationally feasible development of reasoning by analogy to be applied to heuristic theorem proving.

Learning from external environments using Soar

NASA Technical Reports Server (NTRS)

Laird, John E.

1989-01-01

Soar, like the previous PRODIGY and Theo, is a problem-solving architecture that attempts to learn from experience; unlike them, it takes a more uniform approach, using a single forward-chaining architecture for planning and execution. Its single learning mechanism, designated 'chunking', is domain-independent. Two developmental approaches have been employed with Soar: the first of these allows the architecture to attempt a problem on its own, while the second involves a degree of external guidance. This learning through guidance is integrated with general problem-solving and autonomous learning, leading to an avoidance of human interaction for simple problems that Soar can solve on its own.
PROSPECTIVE ASSOCIATIONS OF DEPRESSIVE RUMINATION AND SOCIAL PROBLEM SOLVING WITH DEPRESSION: A 6-MONTH LONGITUDINAL STUDY(.).

PubMed

Hasegawa, Akira; Hattori, Yosuke; Nishimura, Haruki; Tanno, Yoshihiko

2015-06-01

The main purpose of this study was to examine whether depressive rumination and social problem solving are prospectively associated with depressive symptoms. Nonclinical university students (N = 161, 64 men, 97 women; M age = 19.7 yr., SD = 3.6, range = 18-61) recruited from three universities in Japan completed the Beck Depression Inventory-Second Edition (BDI-II), the Ruminative Responses Scale, Social Problem-Solving Inventory-Revised Short Version (SPSI-R:S), and the Means-Ends Problem-Solving Procedure at baseline, and the BDI-II again at 6 mo. later. A stepwise multiple regression analysis with the BDI-II and all subscales of the rumination and social problem solving measures as independent variables indicated that only the BDI-II scores and the Impulsivity/carelessness style subscale of the SPSI-R:S at Time 1 were significantly associated with BDI-II scores at Time 2 (β = 0.73, 0.12, respectively; independent variables accounted for 58.8% of the variance). These findings suggest that in Japan an impulsive and careless problem-solving style was prospectively associated with depressive symptomatology 6 mo. later, as contrasted with previous findings of a cycle of rumination and avoidance problem-solving style.
Diagrams benefit symbolic problem-solving.

PubMed

Chu, Junyi; Rittle-Johnson, Bethany; Fyfe, Emily R

2017-06-01

The format of a mathematics problem often influences students' problem-solving performance. For example, providing diagrams in conjunction with story problems can benefit students' understanding, choice of strategy, and accuracy on story problems. However, it remains unclear whether providing diagrams in conjunction with symbolic equations can benefit problem-solving performance as well. We tested the impact of diagram presence on students' performance on algebra equation problems to determine whether diagrams increase problem-solving success. We also examined the influence of item- and student-level factors to test the robustness of the diagram effect. We worked with 61 seventh-grade students who had received 2 months of pre-algebra instruction. Students participated in an experimenter-led classroom session. Using a within-subjects design, students solved algebra problems in two matched formats (equation and equation-with-diagram). The presence of diagrams increased equation-solving accuracy and the use of informal strategies. This diagram benefit was independent of student ability and item complexity. The benefits of diagrams found previously for story problems generalized to symbolic problems. The findings are consistent with cognitive models of problem-solving and suggest that diagrams may be a useful additional representation of symbolic problems. © 2017 The British Psychological Society.
Intuitive Feelings of Warmth and Confidence in Insight and Noninsight Problem Solving of Magic Tricks.

PubMed

Hedne, Mikael R; Norman, Elisabeth; Metcalfe, Janet

2016-01-01

The focus of the current study is on intuitive feelings of insight during problem solving and the extent to which such feelings are predictive of successful problem solving. We report the results from an experiment (N = 51) that applied a procedure where the to-be-solved problems were 32 short (15 s) video recordings of magic tricks. The procedure included metacognitive ratings similar to the "warmth ratings" previously used by Metcalfe and colleagues, as well as confidence ratings. At regular intervals during problem solving, participants indicated the perceived closeness to the correct solution. Participants also indicated directly whether each problem was solved by insight or not. Problems that people claimed were solved by insight were characterized by higher accuracy and higher confidence than noninsight solutions. There was no difference between the two types of solution in warmth ratings, however. Confidence ratings were more strongly associated with solution accuracy for noninsight than insight trials. Moreover, for insight trials the participants were more likely to repeat their incorrect solutions on a subsequent recognition test. The results have implications for understanding people's metacognitive awareness of the cognitive processes involved in problem solving. They also have general implications for our understanding of how intuition and insight are related.
Intuitive Feelings of Warmth and Confidence in Insight and Noninsight Problem Solving of Magic Tricks

PubMed Central

Hedne, Mikael R.; Norman, Elisabeth; Metcalfe, Janet

2016-01-01

The focus of the current study is on intuitive feelings of insight during problem solving and the extent to which such feelings are predictive of successful problem solving. We report the results from an experiment (N = 51) that applied a procedure where the to-be-solved problems were 32 short (15 s) video recordings of magic tricks. The procedure included metacognitive ratings similar to the “warmth ratings” previously used by Metcalfe and colleagues, as well as confidence ratings. At regular intervals during problem solving, participants indicated the perceived closeness to the correct solution. Participants also indicated directly whether each problem was solved by insight or not. Problems that people claimed were solved by insight were characterized by higher accuracy and higher confidence than noninsight solutions. There was no difference between the two types of solution in warmth ratings, however. Confidence ratings were more strongly associated with solution accuracy for noninsight than insight trials. Moreover, for insight trials the participants were more likely to repeat their incorrect solutions on a subsequent recognition test. The results have implications for understanding people's metacognitive awareness of the cognitive processes involved in problem solving. They also have general implications for our understanding of how intuition and insight are related. PMID:27630598
Unconscious processing modulates creative problem solving: evidence from an electrophysiological study.

PubMed

Gao, Ying; Zhang, Hao

2014-05-01

Previous behavioral studies have identified the significant role of subliminal cues in creative problem solving. However, neural mechanisms of such unconscious processing remain poorly understood. Here we utilized an event-related potential (ERP) approach and sandwich mask technique to investigate cerebral activities underlying the unconscious processing of cues in creative problem solving. College students were instructed to solve divergent problems under three different conditions (conscious cue, unconscious cue and no-cue conditions). Our data showed that creative problem solving can benefit from unconscious cues, although not as much as from conscious cues. More importantly, we found that there are crucial ERP components associated with unconscious processing of cues in solving divergent problems. Similar to the processing of conscious cues, processing unconscious cues in problem solving involves the semantic activation of unconscious cues (N280-340) in the right inferior parietal lobule (BA 40), new association formation (P350-450) in the right parahippocampal gyrus (BA 36), and mental representation transformation (P500-760) in the right superior temporal gyrus (BA 22). The present results suggest that creative problem solving can be modulated by unconscious processing of enlightening information that is weakly diffused in the semantic network beyond our conscious awareness. Copyright © 2014 Elsevier Inc. All rights reserved.
Optimal estimation retrievals of the atmospheric structure and composition of HD 189733b from secondary eclipse spectroscopy

NASA Astrophysics Data System (ADS)

Lee, J.-M.; Fletcher, L. N.; Irwin, P. G. J.

2012-02-01

Recent spectroscopic observations of transiting hot Jupiters have permitted the derivation of the thermal structure and molecular abundances of H2O, CO2, CO and CH4 in these extreme atmospheres. Here, for the first time, we apply the technique of optimal estimation to determine the thermal structure and composition of an exoplanet by solving the inverse problem. The development of a suite of radiative transfer and retrieval tools for exoplanet atmospheres is described, building upon a retrieval algorithm which is extensively used in the study of our own Solar system. First, we discuss the plausibility of detection of different molecules in the dayside atmosphere of HD 189733b and the best-fitting spectrum retrieved from all publicly available sets of secondary eclipse observations between 1.45 and 24 μm. Additionally, we use contribution functions to assess the vertical sensitivity of the emission spectrum to temperatures and molecular composition. Over the altitudes probed by the contribution functions, the retrieved thermal structure shows an isothermal upper atmosphere overlying a deeper adiabatic layer (temperature decreasing with altitude), which is consistent with previously reported dynamical and observational results. The formal uncertainties on retrieved parameters are estimated conservatively using an analysis of the cross-correlation functions and the degeneracy between different atmospheric properties. The formal solution of the inverse problem suggests that the uncertainties on retrieved parameters are larger than suggested in previous studies, and that the presence of CO and CH4 is only marginally supported by the available data. Nevertheless, by including as broad a wavelength range as possible in the retrieval, we demonstrate that available spectra of HD 189733b can constrain a family of potential solutions for the atmospheric structure.
Effects of the Problem-Posing Approach on Students' Problem Solving Skills and Metacognitive Awareness in Science Education

NASA Astrophysics Data System (ADS)

Akben, Nimet

2018-05-01

The interrelationship between mathematics and science education has frequently been emphasized, and common goals and approaches have often been adopted between disciplines. Improving students' problem-solving skills in mathematics and science education has always been given special attention; however, the problem-posing approach which plays a key role in mathematics education has not been commonly utilized in science education. As a result, the purpose of this study was to better determine the effects of the problem-posing approach on students' problem-solving skills and metacognitive awareness in science education. This was a quasi-experimental based study conducted with 61 chemistry and 40 physics students; a problem-solving inventory and a metacognitive awareness inventory were administered to participants both as a pre-test and a post-test. During the 2017-2018 academic year, problem-solving activities based on the problem-posing approach were performed with the participating students during their senior year in various university chemistry and physics departments throughout the Republic of Turkey. The study results suggested that structured, semi-structured, and free problem-posing activities improve students' problem-solving skills and metacognitive awareness. These findings indicated not only the usefulness of integrating problem-posing activities into science education programs but also the need for further research into this question.
ROY Revisited, Again: The Eighth Solved Structure

DOE PAGES

Tan, Melissa; Shtukenberg, Alexander G.; Zhu, Shengcai; ...

2018-01-01

X-ray powder diffraction and crystal structure prediction (CSP) algorithms were used in synergy to establish the crystal structure of the eighth polymorph of 5-methyl-2-[(2-nitrophenyl)amino]-3-thiophenecarbonitrile (ROY), form R05. R05 crystallizes in the monoclinic space group P2_1 with lattice parameters a = 11.479(4) Å, b = 11.030(1) Å, c = 10.840(6) Å, β = 118.23(1)°. This is both the first acentric ROY polymorph, and the first with Z' > 1. The torsion angles defined by the S-C-N-C atom sequence of each molecule in the asymmetric unit are -34.0° and 44.9°. These angles fall between those previously determined for the red and orangemore » forms of ROY. Hirshfeld surface analysis was employed to understand the crystal packing and intermolecular interactions in R05 and an updated energy stability ranking was determined using computational methods. Finally, although the application of CSP was critical to the structure solution of R05, energy stability rankings determined using a series of DFT vdW-inclusive models substantially deviate from experiment, indicating that ROY polymorphism continues to be a challenge for CSP.« less
The solution structure of the pentatricopeptide repeat protein PPR10 upon binding atpH RNA

PubMed Central

Gully, Benjamin S.; Cowieson, Nathan; Stanley, Will A.; Shearston, Kate; Small, Ian D.; Barkan, Alice; Bond, Charles S.

2015-01-01

The pentatricopeptide repeat (PPR) protein family is a large family of RNA-binding proteins that is characterized by tandem arrays of a degenerate 35-amino-acid motif which form an α-solenoid structure. PPR proteins influence the editing, splicing, translation and stability of specific RNAs in mitochondria and chloroplasts. Zea mays PPR10 is amongst the best studied PPR proteins, where sequence-specific binding to two RNA transcripts, atpH and psaJ, has been demonstrated to follow a recognition code where the identity of two amino acids per repeat determines the base-specificity. A recently solved ZmPPR10:psaJ complex crystal structure suggested a homodimeric complex with considerably fewer sequence-specific protein–RNA contacts than inferred previously. Here we describe the solution structure of the ZmPPR10:atpH complex using size-exclusion chromatography-coupled synchrotron small-angle X-ray scattering (SEC-SY-SAXS). Our results support prior evidence that PPR10 binds RNA as a monomer, and that it does so in a manner that is commensurate with a canonical and predictable RNA-binding mode across much of the RNA–protein interface. PMID:25609698
CorA Is a Copper Repressible Surface-Associated Copper(I)-Binding Protein Produced in Methylomicrobium album BG8

PubMed Central

Johnson, Kenneth A.; Ve, Thomas; Larsen, Øivind; Pedersen, Rolf B.; Lillehaug, Johan R.; Jensen, Harald B.; Helland, Ronny; Karlsen, Odd A.

2014-01-01

CorA is a copper repressible protein previously identified in the methanotrophic bacterium Methylomicrobium album BG8. In this work, we demonstrate that CorA is located on the cell surface and binds one copper ion per protein molecule, which, based on X-ray Absorption Near Edge Structure analysis, is in the reduced state (Cu(I)). The structure of endogenously expressed CorA was solved using X-ray crystallography. The 1.6 Å three-dimensional structure confirmed the binding of copper and revealed that the copper atom was coordinated in a mononuclear binding site defined by two histidines, one water molecule, and the tryptophan metabolite, kynurenine. This arrangement of the copper-binding site is similar to that of its homologous protein MopE* from Metylococcus capsulatus Bath, confirming the importance of kynurenine for copper binding in these proteins. Our findings show that CorA has an overall fold similar to MopE, including the unique copper(I)-binding site and most of the secondary structure elements. We suggest that CorA plays a role in the M. album BG8 copper acquisition. PMID:24498370
FlaF is a β-sandwich protein that anchors the archaellum in the archaeal cell envelope by binding the S-layer protein

DOE PAGES

Banerjee, Ankan; Tsai, Chi -Lin; Chaudhury, Paushali; ...

2015-05-01

Archaea employ the archaellum, a type IV pilus-like nanomachine, for swimming motility. In the crenarchaeon Sulfolobus acidocaldarius, the archaellum consists of seven proteins: FlaB/X/G/F/H/I/J. FlaF is conserved and essential for archaellum assembly but no FlaF structures exist. Here, we truncated the FlaF N terminus and solved 1.5-Å and 1.65-Å resolution crystal structures of this monotopic membrane protein. Structures revealed an N-terminal α-helix and an eight-strand β-sandwich, immunoglobulin-like fold with striking similarity to S-layer proteins. Crystal structures, X-ray scattering, and mutational analyses suggest dimer assembly is needed for in vivo function. The sole cell envelope component of S. acidocaldarius is amore » paracrystalline S-layer, and FlaF specifically bound to S-layer protein, suggesting that its interaction domain is located in the pseudoperiplasm with its N-terminal helix in the membrane. From these data, FlaF may act as the previously unknown archaellum stator protein that anchors the rotating archaellum to the archaeal cell envelope.« less
Integrated Force Method for Indeterminate Structures

NASA Technical Reports Server (NTRS)

Hopkins, Dale A.; Halford, Gary R.; Patnaik, Surya N.

2008-01-01

Two methods of solving indeterminate structural-mechanics problems have been developed as products of research on the theory of strain compatibility. In these methods, stresses are considered to be the primary unknowns (in contrast to strains and displacements being considered as the primary unknowns in some prior methods). One of these methods, denoted the integrated force method (IFM), makes it possible to compute stresses, strains, and displacements with high fidelity by use of modest finite-element models that entail relatively small amounts of computation. The other method, denoted the completed Beltrami Mitchell formulation (CBMF), enables direct determination of stresses in an elastic continuum with general boundary conditions, without the need to first calculate displacements as in traditional methods. The equilibrium equation, the compatibility condition, and the material law are the three fundamental concepts of the theory of structures. For almost 150 years, it has been commonly supposed that the theory is complete. However, until now, the understanding of the compatibility condition remained incomplete, and the compatibility condition was confused with the continuity condition. Furthermore, the compatibility condition as applied to structures in its previous incomplete form was inconsistent with the strain formulation in elasticity.
Edge grouping combining boundary and region information.

PubMed

Stahl, Joachim S; Wang, Song

2007-10-01

This paper introduces a new edge-grouping method to detect perceptually salient structures in noisy images. Specifically, we define a new grouping cost function in a ratio form, where the numerator measures the boundary proximity of the resulting structure and the denominator measures the area of the resulting structure. This area term introduces a preference towards detecting larger-size structures and, therefore, makes the resulting edge grouping more robust to image noise. To find the optimal edge grouping with the minimum grouping cost, we develop a special graph model with two different kinds of edges and then reduce the grouping problem to finding a special kind of cycle in this graph with a minimum cost in ratio form. This optimal cycle-finding problem can be solved in polynomial time by a previously developed graph algorithm. We implement this edge-grouping method, test it on both synthetic data and real images, and compare its performance against several available edge-grouping and edge-linking methods. Furthermore, we discuss several extensions of the proposed method, including the incorporation of the well-known grouping cues of continuity and intensity homogeneity, introducing a factor to balance the contributions from the boundary and region information, and the prevention of detecting self-intersecting boundaries.
ROY Revisited, Again: The Eighth Solved Structure

DOE Office of Scientific and Technical Information (OSTI.GOV)

Tan, Melissa; Shtukenberg, Alexander G.; Zhu, Shengcai

X-ray powder diffraction and crystal structure prediction (CSP) algorithms were used in synergy to establish the crystal structure of the eighth polymorph of 5-methyl-2-[(2-nitrophenyl)amino]-3-thiophenecarbonitrile (ROY), form R05. R05 crystallizes in the monoclinic space group P2_1 with lattice parameters a = 11.479(4) Å, b = 11.030(1) Å, c = 10.840(6) Å, β = 118.23(1)°. This is both the first acentric ROY polymorph, and the first with Z' > 1. The torsion angles defined by the S-C-N-C atom sequence of each molecule in the asymmetric unit are -34.0° and 44.9°. These angles fall between those previously determined for the red and orangemore » forms of ROY. Hirshfeld surface analysis was employed to understand the crystal packing and intermolecular interactions in R05 and an updated energy stability ranking was determined using computational methods. Finally, although the application of CSP was critical to the structure solution of R05, energy stability rankings determined using a series of DFT vdW-inclusive models substantially deviate from experiment, indicating that ROY polymorphism continues to be a challenge for CSP.« less
Analytical method for analysis of electromagnetic scattering from inhomogeneous spherical structures using duality principles

NASA Astrophysics Data System (ADS)

Kiani, M.; Abdolali, A.; Safari, M.

2018-03-01

In this article, an analytical approach is presented for the analysis of electromagnetic (EM) scattering from radially inhomogeneous spherical structures (RISSs) based on the duality principle. According to the spherical symmetry, similar angular dependencies in all the regions are considered using spherical harmonics. To extract the radial dependency, the system of differential equations of wave propagation toward the inhomogeneity direction is equated with the dual planar ones. A general duality between electromagnetic fields and parameters and scattering parameters of the two structures is introduced. The validity of the proposed approach is verified through a comprehensive example. The presented approach substitutes a complicated problem in spherical coordinate to an easy, well posed, and previously solved problem in planar geometry. This approach is valid for all continuously varying inhomogeneity profiles. One of the major advantages of the proposed method is the capability of studying two general and applicable types of RISSs. As an interesting application, a class of lens antenna based on the physical concept of the gradient refractive index material is introduced. The approach is used to analyze the EM scattering from the structure and validate strong performance of the lens.
The oxygenating constituent of 3,6-diketocamphane monooxygenase from the CAM plasmid of Pseudomonas putida: the first crystal structure of a type II Baeyer–Villiger monooxygenase

DOE Office of Scientific and Technical Information (OSTI.GOV)

Isupov, Michail N.; Schröder, Ewald; Gibson, Robert P.

The first crystal structure of a type II Baeyer–Villiger monooxygenase reveals a different ring orientation of its FMN cofactor compared with other related bacterial luciferase-family enzymes. The three-dimensional structures of the native enzyme and the FMN complex of the overexpressed form of the oxygenating component of the type II Baeyer–Villiger 3,6-diketocamphane monooxygenase have been determined to 1.9 Å resolution. The structure of this dimeric FMN-dependent enzyme, which is encoded on the large CAM plasmid of Pseudomonas putida, has been solved by a combination of multiple anomalous dispersion from a bromine crystal soak and molecular replacement using a bacterial luciferase model.more » The orientation of the isoalloxazine ring of the FMN cofactor in the active site of this TIM-barrel fold enzyme differs significantly from that previously observed in enzymes of the bacterial luciferase-like superfamily. The Ala77 residue is in a cis conformation and forms a β-bulge at the C-terminus of β-strand 3, which is a feature observed in many proteins of this superfamily.« less
Hematin−Hematin Self-Association States Involved in the Formation and Reactivity of the Malaria Parasite Pigment, Hemozoin

DOE Office of Scientific and Technical Information (OSTI.GOV)

Klonis, Nectarios; Dilanian, Ruben; Hanssen, Eric

The malaria parasite pigment, hemozoin, is a crystal of ferriprotoporphyrin IX (FP-Fe(III)), a product of hemoglobin digestion. Hemozoin formation is essential for FP-Fe(III) detoxification in the parasite; it is the main target of quinoline antimalarials and can modulate immune and inflammation responses. To gain further insight into the likely mechanisms of crystal formation and hemozoin reactivity, we have reanalyzed the crystal structure data for {beta}-hematin and solved the crystal structure of Plasmodium falciparum hemozoin. The analysis reveals that the structures are very similar and highlights two previously unexplored modes of FP-Fe(III) self-association involving {pi}-{pi} interactions that may initiate crystal formationmore » and help to stabilize the extended structure. Hemozoin can be considered to be a crystal composed of {pi}-{pi} dimers stabilized by iron-carboxylate linkages. As a result, it is predicted that two surfaces of the crystal would consist of {pi}-{pi} dimers with Fe(III) partly exposed to solvent and capable of undergoing redox reactions. Accordingly, we demonstrate that the crystal possesses both general peroxidase activity and the ability to cause lipid oxidation.« less
DOE Office of Scientific and Technical Information (OSTI.GOV)

Brandao, T.; Robinson, H; Johnson, S

Catalysis by the Yersinia protein-tyrosine phosphatase YopH is significantly impaired by the mutation of the conserved Trp354 residue to Phe. Though not a catalytic residue, this Trp is a hinge residue in a conserved flexible loop (the WPD-loop) that must close during catalysis. To learn why this seemingly conservative mutation reduces catalysis by 2 orders of magnitude, we have solved high-resolution crystal structures for the W354F YopH in the absence and in the presence of tungstate and vanadate. Oxyanion binding to the P-loop in W354F is analogous to that observed in the native enzyme. However, the WPD-loop in the presencemore » of oxyanions assumes a half-closed conformation, in contrast to the fully closed state observed in structures of the native enzyme. This observation provides an explanation for the impaired general acid catalysis observed in kinetic experiments with Trp mutants. A 1.4 Angstroms structure of the W354F mutant obtained in the presence of vanadate reveals an unusual divanadate species with a cyclic [VO]2 core, which has precedent in small molecules but has not been previously reported in a protein crystal structure.« less
An estimated 5% of new protein structures solved today represent a new Pfam family

DOE Office of Scientific and Technical Information (OSTI.GOV)

Mistry, Jaina; Kloppmann, Edda; Rost, Burkhard

2013-11-01

This study uses the Pfam database to show that the sequence redundancy of protein structures deposited in the PDB is increasing. The possible reasons behind this trend are discussed. High-resolution structural knowledge is key to understanding how proteins function at the molecular level. The number of entries in the Protein Data Bank (PDB), the repository of all publicly available protein structures, continues to increase, with more than 8000 structures released in 2012 alone. The authors of this article have studied how structural coverage of the protein-sequence space has changed over time by monitoring the number of Pfam families that acquiredmore » their first representative structure each year from 1976 to 2012. Twenty years ago, for every 100 new PDB entries released, an estimated 20 Pfam families acquired their first structure. By 2012, this decreased to only about five families per 100 structures. The reasons behind the slower pace at which previously uncharacterized families are being structurally covered were investigated. It was found that although more than 50% of current Pfam families are still without a structural representative, this set is enriched in families that are small, functionally uncharacterized or rich in problem features such as intrinsically disordered and transmembrane regions. While these are important constraints, the reasons why it may not yet be time to give up the pursuit of a targeted but more comprehensive structural coverage of the protein-sequence space are discussed.« less

The effects of cumulative practice on mathematics problem solving.

PubMed

Mayfield, Kristin H; Chase, Philip N

2002-01-01

This study compared three different methods of teaching five basic algebra rules to college students. All methods used the same procedures to teach the rules and included four 50-question review sessions interspersed among the training of the individual rules. The differences among methods involved the kinds of practice provided during the four review sessions. Participants who received cumulative practice answered 50 questions covering a mix of the rules learned prior to each review session. Participants who received a simple review answered 50 questions on one previously trained rule. Participants who received extra practice answered 50 extra questions on the rule they had just learned. Tests administered after each review included new questions for applying each rule (application items) and problems that required novel combinations of the rules (problem-solving items). On the final test, the cumulative group outscored the other groups on application and problem-solving items. In addition, the cumulative group solved the problem-solving items significantly faster than the other groups. These results suggest that cumulative practice of component skills is an effective method of training problem solving.
The effects of cumulative practice on mathematics problem solving.

PubMed Central

Mayfield, Kristin H; Chase, Philip N

2002-01-01

This study compared three different methods of teaching five basic algebra rules to college students. All methods used the same procedures to teach the rules and included four 50-question review sessions interspersed among the training of the individual rules. The differences among methods involved the kinds of practice provided during the four review sessions. Participants who received cumulative practice answered 50 questions covering a mix of the rules learned prior to each review session. Participants who received a simple review answered 50 questions on one previously trained rule. Participants who received extra practice answered 50 extra questions on the rule they had just learned. Tests administered after each review included new questions for applying each rule (application items) and problems that required novel combinations of the rules (problem-solving items). On the final test, the cumulative group outscored the other groups on application and problem-solving items. In addition, the cumulative group solved the problem-solving items significantly faster than the other groups. These results suggest that cumulative practice of component skills is an effective method of training problem solving. PMID:12102132
Crystal Structures of MEK1 Binary and Ternary Complexes with Nucleotides and Inhibitors

DOE Office of Scientific and Technical Information (OSTI.GOV)

Fischmann, Thierry O.; Smith, Catherine K.; Mayhood, Todd W.

MEK1 is a member of the MAPK signal transduction pathway that responds to growth factors and cytokines. We have determined that the kinase domain spans residues 35-382 by proteolytic cleavage. The complete kinase domain has been crystallized and its X-ray crystal structure as a complex with magnesium and ATP-{gamma}S determined at 2.1 {angstrom}. Unlike crystals of a truncated kinase domain previously published, the crystals of the intact domain can be grown either as a binary complex with a nucleotide or as a ternary complex with a nucleotide and one of a multitude of allosteric inhibitors. Further, the crystals allow formore » the determination of costructures with ATP competitive inhibitors. We describe the structures of nonphosphorylated MEK1 (npMEK1) binary complexes with ADP and K252a, an ATP-competitive inhibitor (see Table 1), at 1.9 and 2.7 {angstrom} resolution, respectively. Ternary complexes have also been solved between npMEK1, a nucleotide, and an allosteric non-ATP competitive inhibitor: ATP-{gamma}S with compound 1 and ADP with either U0126 or the MEK1 clinical candidate PD325089 at 1.8, 2.0, and 2.5 {angstrom}, respectively. Compound 1 is structurally similar to PD325901. These structures illustrate fundamental differences among various mechanisms of inhibition at the molecular level. Residues 44-51 have previously been shown to play a negative regulatory role in MEK1 activity. The crystal structure of the integral kinase domain provides a structural rationale for the role of these residues. They form helix A and repress enzymatic activity by stabilizing an inactive conformation in which helix C is displaced from its active state position. Finally, the structure provides for the first time a molecular rationale that explains how mutations in MEK may lead to the cardio-facio-cutaneous syndrome.« less
X-ray laser diffraction for structure determination of the rhodopsin-arrestin complex

NASA Astrophysics Data System (ADS)

Zhou, X. Edward; Gao, Xiang; Barty, Anton; Kang, Yanyong; He, Yuanzheng; Liu, Wei; Ishchenko, Andrii; White, Thomas A.; Yefanov, Oleksandr; Han, Gye Won; Xu, Qingping; de Waal, Parker W.; Suino-Powell, Kelly M.; Boutet, Sébastien; Williams, Garth J.; Wang, Meitian; Li, Dianfan; Caffrey, Martin; Chapman, Henry N.; Spence, John C. H.; Fromme, Petra; Weierstall, Uwe; Stevens, Raymond C.; Cherezov, Vadim; Melcher, Karsten; Xu, H. Eric

2016-04-01

Serial femtosecond X-ray crystallography (SFX) using an X-ray free electron laser (XFEL) is a recent advancement in structural biology for solving crystal structures of challenging membrane proteins, including G-protein coupled receptors (GPCRs), which often only produce microcrystals. An XFEL delivers highly intense X-ray pulses of femtosecond duration short enough to enable the collection of single diffraction images before significant radiation damage to crystals sets in. Here we report the deposition of the XFEL data and provide further details on crystallization, XFEL data collection and analysis, structure determination, and the validation of the structural model. The rhodopsin-arrestin crystal structure solved with SFX represents the first near-atomic resolution structure of a GPCR-arrestin complex, provides structural insights into understanding of arrestin-mediated GPCR signaling, and demonstrates the great potential of this SFX-XFEL technology for accelerating crystal structure determination of challenging proteins and protein complexes.
X-ray laser diffraction for structure determination of the rhodopsin-arrestin complex.

PubMed

Zhou, X Edward; Gao, Xiang; Barty, Anton; Kang, Yanyong; He, Yuanzheng; Liu, Wei; Ishchenko, Andrii; White, Thomas A; Yefanov, Oleksandr; Han, Gye Won; Xu, Qingping; de Waal, Parker W; Suino-Powell, Kelly M; Boutet, Sébastien; Williams, Garth J; Wang, Meitian; Li, Dianfan; Caffrey, Martin; Chapman, Henry N; Spence, John C H; Fromme, Petra; Weierstall, Uwe; Stevens, Raymond C; Cherezov, Vadim; Melcher, Karsten; Xu, H Eric

2016-04-12

Serial femtosecond X-ray crystallography (SFX) using an X-ray free electron laser (XFEL) is a recent advancement in structural biology for solving crystal structures of challenging membrane proteins, including G-protein coupled receptors (GPCRs), which often only produce microcrystals. An XFEL delivers highly intense X-ray pulses of femtosecond duration short enough to enable the collection of single diffraction images before significant radiation damage to crystals sets in. Here we report the deposition of the XFEL data and provide further details on crystallization, XFEL data collection and analysis, structure determination, and the validation of the structural model. The rhodopsin-arrestin crystal structure solved with SFX represents the first near-atomic resolution structure of a GPCR-arrestin complex, provides structural insights into understanding of arrestin-mediated GPCR signaling, and demonstrates the great potential of this SFX-XFEL technology for accelerating crystal structure determination of challenging proteins and protein complexes.
X-ray laser diffraction for structure determination of the rhodopsin-arrestin complex

PubMed Central

Zhou, X. Edward; Gao, Xiang; Barty, Anton; Kang, Yanyong; He, Yuanzheng; Liu, Wei; Ishchenko, Andrii; White, Thomas A.; Yefanov, Oleksandr; Han, Gye Won; Xu, Qingping; de Waal, Parker W.; Suino-Powell, Kelly M.; Boutet, Sébastien; Williams, Garth J.; Wang, Meitian; Li, Dianfan; Caffrey, Martin; Chapman, Henry N.; Spence, John C.H.; Fromme, Petra; Weierstall, Uwe; Stevens, Raymond C.; Cherezov, Vadim; Melcher, Karsten; Xu, H. Eric

2016-01-01

Serial femtosecond X-ray crystallography (SFX) using an X-ray free electron laser (XFEL) is a recent advancement in structural biology for solving crystal structures of challenging membrane proteins, including G-protein coupled receptors (GPCRs), which often only produce microcrystals. An XFEL delivers highly intense X-ray pulses of femtosecond duration short enough to enable the collection of single diffraction images before significant radiation damage to crystals sets in. Here we report the deposition of the XFEL data and provide further details on crystallization, XFEL data collection and analysis, structure determination, and the validation of the structural model. The rhodopsin-arrestin crystal structure solved with SFX represents the first near-atomic resolution structure of a GPCR-arrestin complex, provides structural insights into understanding of arrestin-mediated GPCR signaling, and demonstrates the great potential of this SFX-XFEL technology for accelerating crystal structure determination of challenging proteins and protein complexes. PMID:27070998
Students using visual thinking to learn science in a Web-based environment

NASA Astrophysics Data System (ADS)

Plough, Jean Margaret

United States students' science test scores are low, especially in problem solving, and traditional science instruction could be improved. Consequently, visual thinking, constructing science structures, and problem solving in a web-based environment may be valuable strategies for improving science learning. This ethnographic study examined the science learning of fifteen fourth grade students in an after school computer club involving diverse students at an inner city school. The investigation was done from the perspective of the students, and it described the processes of visual thinking, web page construction, and problem solving in a web-based environment. The study utilized informal group interviews, field notes, Visual Learning Logs, and student web pages, and incorporated a Standards-Based Rubric which evaluated students' performance on eight science and technology standards. The Visual Learning Logs were drawings done on the computer to represent science concepts related to the Food Chain. Students used the internet to search for information on a plant or animal of their choice. Next, students used this internet information, with the information from their Visual Learning Logs, to make web pages on their plant or animal. Later, students linked their web pages to form Science Structures. Finally, students linked their Science Structures with the structures of other students, and used these linked structures as models for solving problems. Further, during informal group interviews, students answered questions about visual thinking, problem solving, and science concepts. The results of this study showed clearly that (1) making visual representations helped students understand science knowledge, (2) making links between web pages helped students construct Science Knowledge Structures, and (3) students themselves said that visual thinking helped them learn science. In addition, this study found that when using Visual Learning Logs, the main overall ideas of the science concepts were usually represented accurately. Further, looking for information on the internet may cause new problems in learning. Likewise, being absent, starting late, and/or dropping out all may negatively influence students' proficiency on the standards. Finally, the way Science Structures are constructed and linked may provide insights into the way individual students think and process information.
A systematic linear space approach to solving partially described inverse eigenvalue problems

NASA Astrophysics Data System (ADS)

Hu, Sau-Lon James; Li, Haujun

2008-06-01

Most applications of the inverse eigenvalue problem (IEP), which concerns the reconstruction of a matrix from prescribed spectral data, are associated with special classes of structured matrices. Solving the IEP requires one to satisfy both the spectral constraint and the structural constraint. If the spectral constraint consists of only one or few prescribed eigenpairs, this kind of inverse problem has been referred to as the partially described inverse eigenvalue problem (PDIEP). This paper develops an efficient, general and systematic approach to solve the PDIEP. Basically, the approach, applicable to various structured matrices, converts the PDIEP into an ordinary inverse problem that is formulated as a set of simultaneous linear equations. While solving simultaneous linear equations for model parameters, the singular value decomposition method is applied. Because of the conversion to an ordinary inverse problem, other constraints associated with the model parameters can be easily incorporated into the solution procedure. The detailed derivation and numerical examples to implement the newly developed approach to symmetric Toeplitz and quadratic pencil (including mass, damping and stiffness matrices of a linear dynamic system) PDIEPs are presented. Excellent numerical results for both kinds of problem are achieved under the situations that have either unique or infinitely many solutions.
AZTEC: A parallel iterative package for the solving linear systems

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hutchinson, S.A.; Shadid, J.N.; Tuminaro, R.S.

1996-12-31

We describe a parallel linear system package, AZTEC. The package incorporates a number of parallel iterative methods (e.g. GMRES, biCGSTAB, CGS, TFQMR) and preconditioners (e.g. Jacobi, Gauss-Seidel, polynomial, domain decomposition with LU or ILU within subdomains). Additionally, AZTEC allows for the reuse of previous preconditioning factorizations within Newton schemes for nonlinear methods. Currently, a number of different users are using this package to solve a variety of PDE applications.
Human deoxyhaemoglobin-2,3-diphosphoglycerate complex low-salt structure at 2.5 A resolution.

PubMed

Richard, V; Dodson, G G; Mauguen, Y

1993-09-20

The haemoglobin-2,3-diphosphoglycerate complex structure has been solved at 2.5 A resolution using crystals grown from low-salt solutions. The results show some important differences with the precedent haemoglobin-2,3-diphosphoglycerate high-salt structure solved by Arnone. First, we observe a loss of symmetry in the binding site, secondly both of the lysine residues 82 beta interact with 2,3-diphosphoglycerate at the same time, each making two contacts. This level of interaction is in agreement with the functional behaviour of natural haemoglobin mutants with mutations at the 2,3-diphosphoglycerate binding site.
Implementing a Loosely Coupled Fluid Structure Interaction Finite Element Model in PHASTA

NASA Astrophysics Data System (ADS)

Pope, David

Fluid Structure Interaction problems are an important multi-physics phenomenon in the design of aerospace vehicles and other engineering applications. A variety of computational fluid dynamics solvers capable of resolving the fluid dynamics exist. PHASTA is one such computational fluid dynamics solver. Enhancing the capability of PHASTA to resolve Fluid-Structure Interaction first requires implementing a structural dynamics solver. The implementation also requires a correction of the mesh used to solve the fluid equations to account for the deformation of the structure. This results in mesh motion and causes the need for an Arbitrary Lagrangian-Eulerian modification to the fluid dynamics equations currently implemented in PHASTA. With the implementation of both structural dynamics physics, mesh correction, and the Arbitrary Lagrangian-Eulerian modification of the fluid dynamics equations, PHASTA is made capable of solving Fluid-Structure Interaction problems.
How cryo‐electron microscopy and X‐ray crystallography complement each other

PubMed Central

Wang, Jia‐Wei

2016-01-01

Abstract With the ability to resolve structures of macromolecules at atomic resolution, X‐ray crystallography has been the most powerful tool in modern structural biology. At the same time, recent technical improvements have triggered a resolution revolution in the single particle cryo‐EM method. While the two methods are different in many respects, from sample preparation to structure determination, they both have the power to solve macromolecular structures at atomic resolution. It is important to understand the unique advantages and caveats of the two methods in solving structures and to appreciate the complementary nature of the two methods in structural biology. In this review we provide some examples, and discuss how X‐ray crystallography and cryo‐EM can be combined in deciphering structures of macromolecules for our full understanding of their biological mechanisms. PMID:27543495
How cryo-electron microscopy and X-ray crystallography complement each other.

PubMed

Wang, Hong-Wei; Wang, Jia-Wei

2017-01-01

With the ability to resolve structures of macromolecules at atomic resolution, X-ray crystallography has been the most powerful tool in modern structural biology. At the same time, recent technical improvements have triggered a resolution revolution in the single particle cryo-EM method. While the two methods are different in many respects, from sample preparation to structure determination, they both have the power to solve macromolecular structures at atomic resolution. It is important to understand the unique advantages and caveats of the two methods in solving structures and to appreciate the complementary nature of the two methods in structural biology. In this review we provide some examples, and discuss how X-ray crystallography and cryo-EM can be combined in deciphering structures of macromolecules for our full understanding of their biological mechanisms. © 2016 The Protein Society.
Automated MAD and MIR structure solution

PubMed Central

Terwilliger, Thomas C.; Berendzen, Joel

1999-01-01

Obtaining an electron-density map from X-ray diffraction data can be difficult and time-consuming even after the data have been collected, largely because MIR and MAD structure determinations currently require many subjective evaluations of the qualities of trial heavy-atom partial structures before a correct heavy-atom solution is obtained. A set of criteria for evaluating the quality of heavy-atom partial solutions in macromolecular crystallography have been developed. These have allowed the conversion of the crystal structure-solution process into an optimization problem and have allowed its automation. The SOLVE software has been used to solve MAD data sets with as many as 52 selenium sites in the asymmetric unit. The automated structure-solution process developed is a major step towards the fully automated structure-determination, model-building and refinement procedure which is needed for genomic scale structure determinations. PMID:10089316
The influence of achievement goals on the constructive activity of low achievers during collaborative problem solving.

PubMed

Gabriele, Anthony J

2007-03-01

Previous research on small-group learning has found that level of constructive activity (solving or explaining how to solve problems using ideas stated or implied in the explanation provided by a partner) was a better predictor of post-test achievement than either a student's prior achievement or the quality of help received (Webb, Troper, & Fall, 1995). The purpose of this study was to extend this research by examining the influence of additional factors, in particular, achievement goals and comprehension monitoring, on low achieving students' constructive activity after receiving help from a high achieving peer. Thirty-two low achieving upper elementary students from an urban school district in the mid-west of the United States were paired with high achieving partners. Videotape data from a previously reported study on peer collaboration were transcribed and reanalyzed. In that study, dyads were randomly assigned instructions designed to induce either a learning or performance goal and were videotaped as they worked together to solve a set of mathematical word problems. The following day, students were individually post-tested on problems similar to the ones worked on in pairs. Consistent with previous research, low achieving students' level of constructive activity predicted post-test performance. In addition, constructive activity was found to mediate the relationship between achievement goals and learning. However, achievement goals were not related to low achievers constructive use of help. Instead, achievement goals were related to low achievers' relative accuracy in comprehension monitoring, which in turn was related to level of constructive activity. The meaning of these results for understanding the processes by which low achievers learn from peer help and implications for classroom practice are discussed.
Problem Solving in Physics: Undergraduates' Framing, Procedures, and Decision Making

NASA Astrophysics Data System (ADS)

Modir, Bahar

In this dissertation I will start with the broad research question of what does problem solving in upper division physics look like? My focus in this study is on students' problem solving in physics theory courses. Some mathematical formalisms are common across all physics core courses such as using the process of separation of variables, doing Taylor series, or using the orthogonality properties of mathematical functions to set terms equal to zero. However, there are slight differences in their use of these mathematical formalisms across different courses, possibly because of how students map different physical systems to these processes. Thus, my first main research question aims to answer how students perform these recurring processes across upper division physics courses. I break this broad question into three particular research questions: What knowledge pieces do students use to make connections between physics and procedural math? How do students use their knowledge pieces coherently to provide reasoning strategies in estimation problems? How do students look ahead into the problem to read the information out of the physical scenario to align their use of math in physics? Building on the previous body of the literature, I will use the theory family of Knowledge in Pieces and provide evidence to expand this theoretical foundation. I will compare my study with previous studies and provide suggestions on how to generalize these theory expansions for future use. My experimental data mostly come from video-based classroom data. Students in groups of 2-4 students solve in-class problems in quantum mechanics and electromagnetic fields 1 courses collaboratively. In addition, I will analyze clinical interviews to demonstrate how a single case study student plays an epistemic game to estimate the total energy in a hurricane. My second research question is more focused on a particular instructional context. How do students frame problem solving in quantum mechanics? I will lay out a new theoretical framework based in epistemic framing that separates the problem solving space into four frames divided along two axes. The first axis models students' framing in math and physics, expanded through the second axis of conceptual problem solving and algorithmic problem solving. I use this framework to show how students navigate problem solving. Lastly, I will use this developed framework to interpret existing difficulties in quantum mechanics.
Complex Problem Solving--More than Reasoning?

ERIC Educational Resources Information Center

Wustenberg, Sascha; Greiff, Samuel; Funke, Joachim

2012-01-01

This study investigates the internal structure and construct validity of Complex Problem Solving (CPS), which is measured by a "Multiple-Item-Approach." It is tested, if (a) three facets of CPS--"rule identification" (adequateness of strategies), "rule knowledge" (generated knowledge) and "rule application"…
Age-related changes in strategic variations during arithmetic problem solving: The role of executive control.

PubMed

Hinault, T; Lemaire, P

2016-01-01

In this review, we provide an overview of how age-related changes in executive control influence aging effects in arithmetic processing. More specifically, we consider the role of executive control in strategic variations with age during arithmetic problem solving. Previous studies found that age-related differences in arithmetic performance are associated with strategic variations. That is, when they accomplish arithmetic problem-solving tasks, older adults use fewer strategies than young adults, use strategies in different proportions, and select and execute strategies less efficiently. Here, we review recent evidence, suggesting that age-related changes in inhibition, cognitive flexibility, and working memory processes underlie age-related changes in strategic variations during arithmetic problem solving. We discuss both behavioral and neural mechanisms underlying age-related changes in these executive control processes. © 2016 Elsevier B.V. All rights reserved.
Method for the Direct Solve of the Many-Body Schrödinger Wave Equation

NASA Astrophysics Data System (ADS)

Jerke, Jonathan; Tymczak, C. J.; Poirier, Bill

We report on theoretical and computational developments towards a computationally efficient direct solve of the many-body Schrödinger wave equation for electronic systems. This methodology relies on two recent developments pioneered by the authors: 1) the development of a Cardinal Sine basis for electronic structure calculations; and 2) the development of a highly efficient and compact representation of multidimensional functions using the Canonical tensor rank representation developed by Belykin et. al. which we have adapted to electronic structure problems. We then show several relevant examples of the utility and accuracy of this methodology, scaling with system size, and relevant convergence issues of the methodology. Method for the Direct Solve of the Many-Body Schrödinger Wave Equation.
The pseudo-Boolean optimization approach to form the N-version software structure

NASA Astrophysics Data System (ADS)

Kovalev, I. V.; Kovalev, D. I.; Zelenkov, P. V.; Voroshilova, A. A.

2015-10-01

The problem of developing an optimal structure of N-version software system presents a kind of very complex optimization problem. This causes the use of deterministic optimization methods inappropriate for solving the stated problem. In this view, exploiting heuristic strategies looks more rational. In the field of pseudo-Boolean optimization theory, the so called method of varied probabilities (MVP) has been developed to solve problems with a large dimensionality. Some additional modifications of MVP have been made to solve the problem of N-version systems design. Those algorithms take into account the discovered specific features of the objective function. The practical experiments have shown the advantage of using these algorithm modifications because of reducing a search space.

Damage tolerant design using collapse techniques

NASA Technical Reports Server (NTRS)

Haftka, R. T.

1982-01-01

A new approach to the design of structures for improved global damage tolerance is presented. In its undamaged condition the structure is designed subject to strength, displacement and buckling constraints. In the damaged condition the only constraint is that the structure will not collapse. The collapse load calculation is formulated as a maximization problem and solved by an interior extended penalty function. The design for minimum weight subject to constraints on the undamaged structure and a specified level of the collapse load is a minimization problem which is also solved by a penalty function formulation. Thus the overall problem is of a nested or multilevel optimization. Examples are presented to demonstrate the difference between the present and more traditional approaches.
A Crystallographic Study of the Role of Sequence Context in Thymine Glycol Bypass by a Replicative DNA Polymerase Serendipitously Sheds Light on the Exonuclease Complex

DOE Office of Scientific and Technical Information (OSTI.GOV)

Aller, Pierre; Duclos, Stéphanie; Wallace, Susan S.

2012-06-27

Thymine glycol (Tg) is the most common oxidation product of thymine and is known to be a strong block to replicative DNA polymerases. A previously solved structure of the bacteriophage RB69 DNA polymerase (RB69 gp43) in complex with Tg in the sequence context 5'-G-Tg-G shed light on how Tg blocks primer elongation: The protruding methyl group of the oxidized thymine displaces the adjacent 5'-G, which can no longer serve as a template for primer elongation [Aller, P., Rould, M. A., Hogg, M, Wallace, S. S. and Doublie S. (2007). A structural rationale for stalling of a replicative DNA polymerase atmore » the most common oxidative thymine lesion, thymine glycol. Proc. Natl. Acad. Sci. USA, 104, 814-818.]. Several studies showed that in the sequence context 5'-C-Tg-purine, Tg is more likely to be bypassed by Klenow fragment, an A-family DNA polymerase. We set out to investigate the role of sequence context in Tg bypass in a B-family polymerase and to solve the crystal structures of the bacteriophage RB69 DNA polymerase in complex with Tg-containing DNA in the three remaining sequence contexts: 5'-A-Tg-G, 5'-T-Tg-G, and 5'-C-Tg-G. A combination of several factors - including the associated exonuclease activity, the nature of the 3' and 5' bases surrounding Tg, and the cis-trans interconversion of Tg - influences Tg bypass. We also visualized for the first time the structure of a well-ordered exonuclease complex, allowing us to identify and confirm the role of key residues (Phe123, Met256, and Tyr257) in strand separation and in the stabilization of the primer strand in the exonuclease site.« less
Structured scaffolding for reflection and problem solving in diabetes self-management: qualitative study of mobile diabetes detective.

PubMed

Mamykina, Lena; Heitkemper, Elizabeth M; Smaldone, Arlene M; Kukafka, Rita; Cole-Lewis, Heather; Davidson, Patricia G; Mynatt, Elizabeth D; Tobin, Jonathan N; Cassells, Andrea; Goodman, Carrie; Hripcsak, George

2016-01-01

To investigate subjective experiences and patterns of engagement with a novel electronic tool for facilitating reflection and problem solving for individuals with type 2 diabetes, Mobile Diabetes Detective (MoDD). In this qualitative study, researchers conducted semi-structured interviews with individuals from economically disadvantaged communities and ethnic minorities who are participating in a randomized controlled trial of MoDD. The transcripts of the interviews were analyzed using inductive thematic analysis; usage logs were analyzed to determine how actively the study participants used MoDD. Fifteen participants in the MoDD randomized controlled trial were recruited for the qualitative interviews. Usage log analysis showed that, on average, during the 4 weeks of the study, the study participants logged into MoDD twice per week, reported 120 blood glucose readings, and set two behavioral goals. The qualitative interviews suggested that individuals used MoDD to follow the steps of the problem-solving process, from identifying problematic blood glucose patterns, to exploring behavioral triggers contributing to these patterns, to selecting alternative behaviors, to implementing these behaviors while monitoring for improvements in glycemic control. This qualitative study suggested that informatics interventions for reflection and problem solving can provide structured scaffolding for facilitating these processes by guiding users through the different steps of the problem-solving process and by providing them with context-sensitive evidence and practice-based knowledge related to diabetes self-management on each of those steps. This qualitative study suggested that MoDD was perceived as a useful tool in engaging individuals in self-monitoring, reflection, and problem solving. © The Author 2016. Published by Oxford University Press on behalf of the American Medical Informatics Association. All rights reserved. For Permissions, please email: journals.permissions@oup.com.
SIMBAD : a sequence-independent molecular-replacement pipeline

DOE PAGES

Simpkin, Adam J.; Simkovic, Felix; Thomas, Jens M. H.; ...

2018-06-08

The conventional approach to finding structurally similar search models for use in molecular replacement (MR) is to use the sequence of the target to search against those of a set of known structures. Sequence similarity often correlates with structure similarity. Given sufficient similarity, a known structure correctly positioned in the target cell by the MR process can provide an approximation to the unknown phases of the target. An alternative approach to identifying homologous structures suitable for MR is to exploit the measured data directly, comparing the lattice parameters or the experimentally derived structure-factor amplitudes with those of known structures. Here,more » SIMBAD , a new sequence-independent MR pipeline which implements these approaches, is presented. SIMBAD can identify cases of contaminant crystallization and other mishaps such as mistaken identity (swapped crystallization trays), as well as solving unsequenced targets and providing a brute-force approach where sequence-dependent search-model identification may be nontrivial, for example because of conformational diversity among identifiable homologues. The program implements a three-step pipeline to efficiently identify a suitable search model in a database of known structures. The first step performs a lattice-parameter search against the entire Protein Data Bank (PDB), rapidly determining whether or not a homologue exists in the same crystal form. The second step is designed to screen the target data for the presence of a crystallized contaminant, a not uncommon occurrence in macromolecular crystallography. Solving structures with MR in such cases can remain problematic for many years, since the search models, which are assumed to be similar to the structure of interest, are not necessarily related to the structures that have actually crystallized. To cater for this eventuality, SIMBAD rapidly screens the data against a database of known contaminant structures. Where the first two steps fail to yield a solution, a final step in SIMBAD can be invoked to perform a brute-force search of a nonredundant PDB database provided by the MoRDa MR software. Through early-access usage of SIMBAD , this approach has solved novel cases that have otherwise proved difficult to solve.« less
SIMBAD : a sequence-independent molecular-replacement pipeline

DOE Office of Scientific and Technical Information (OSTI.GOV)

Simpkin, Adam J.; Simkovic, Felix; Thomas, Jens M. H.

The conventional approach to finding structurally similar search models for use in molecular replacement (MR) is to use the sequence of the target to search against those of a set of known structures. Sequence similarity often correlates with structure similarity. Given sufficient similarity, a known structure correctly positioned in the target cell by the MR process can provide an approximation to the unknown phases of the target. An alternative approach to identifying homologous structures suitable for MR is to exploit the measured data directly, comparing the lattice parameters or the experimentally derived structure-factor amplitudes with those of known structures. Here,more » SIMBAD , a new sequence-independent MR pipeline which implements these approaches, is presented. SIMBAD can identify cases of contaminant crystallization and other mishaps such as mistaken identity (swapped crystallization trays), as well as solving unsequenced targets and providing a brute-force approach where sequence-dependent search-model identification may be nontrivial, for example because of conformational diversity among identifiable homologues. The program implements a three-step pipeline to efficiently identify a suitable search model in a database of known structures. The first step performs a lattice-parameter search against the entire Protein Data Bank (PDB), rapidly determining whether or not a homologue exists in the same crystal form. The second step is designed to screen the target data for the presence of a crystallized contaminant, a not uncommon occurrence in macromolecular crystallography. Solving structures with MR in such cases can remain problematic for many years, since the search models, which are assumed to be similar to the structure of interest, are not necessarily related to the structures that have actually crystallized. To cater for this eventuality, SIMBAD rapidly screens the data against a database of known contaminant structures. Where the first two steps fail to yield a solution, a final step in SIMBAD can be invoked to perform a brute-force search of a nonredundant PDB database provided by the MoRDa MR software. Through early-access usage of SIMBAD , this approach has solved novel cases that have otherwise proved difficult to solve.« less
Insights into the Membrane Interactions of the Saposin-Like Proteins Na-SLP-1 and Ac-SLP-1 from Human and Dog Hookworm

PubMed Central

Willis, Charlene; Wang, Conan K.; Osman, Asiah; Simon, Anne; Pickering, Darren; Mulvenna, Jason; Riboldi-Tunicliffe, Alan; Jones, Malcolm K.; Loukas, Alex; Hofmann, Andreas

2011-01-01

Saposin-like proteins (SAPLIPs) from soil-transmitted helminths play pivotal roles in host-pathogen interactions and have a high potential as targets for vaccination against parasitic diseases. We have identified two non-orthologous SAPLIPs from human and dog hookworm, Na-SLP-1 and Ac-SLP-1, and solved their three-dimensional crystal structures. Both proteins share the property of membrane binding as monitored by liposome co-pelleting assays and monolayer adsorption. Neither SAPLIP displayed any significant haemolytic or bactericidal activity. Based on the structural information, as well as the results from monolayer adsorption, we propose models of membrane interactions for both SAPLIPs. Initial membrane contact of the monomeric Na-SLP-1 is most likely by electrostatic interactions between the membrane surface and a prominent basic surface patch. In case of the dimeric Ac-SLP-1, membrane interactions are most likely initiated by a unique tryptophan residue that has previously been implicated in membrane interactions in other SAPLIPs. PMID:21991310
Insights into the membrane interactions of the saposin-like proteins Na-SLP-1 and Ac-SLP-1 from human and dog hookworm.

PubMed

Willis, Charlene; Wang, Conan K; Osman, Asiah; Simon, Anne; Pickering, Darren; Mulvenna, Jason; Riboldi-Tunicliffe, Alan; Jones, Malcolm K; Loukas, Alex; Hofmann, Andreas

2011-01-01

Saposin-like proteins (SAPLIPs) from soil-transmitted helminths play pivotal roles in host-pathogen interactions and have a high potential as targets for vaccination against parasitic diseases. We have identified two non-orthologous SAPLIPs from human and dog hookworm, Na-SLP-1 and Ac-SLP-1, and solved their three-dimensional crystal structures. Both proteins share the property of membrane binding as monitored by liposome co-pelleting assays and monolayer adsorption. Neither SAPLIP displayed any significant haemolytic or bactericidal activity. Based on the structural information, as well as the results from monolayer adsorption, we propose models of membrane interactions for both SAPLIPs. Initial membrane contact of the monomeric Na-SLP-1 is most likely by electrostatic interactions between the membrane surface and a prominent basic surface patch. In case of the dimeric Ac-SLP-1, membrane interactions are most likely initiated by a unique tryptophan residue that has previously been implicated in membrane interactions in other SAPLIPs.
Assessing the utility of phase-space-localized basis functions: Exploiting direct product structure and a new basis function selection procedure

DOE Office of Scientific and Technical Information (OSTI.GOV)

Brown, James, E-mail: 9jhb3@queensu.ca; Carrington, Tucker, E-mail: Tucker.Carrington@queensu.ca

In this paper we show that it is possible to use an iterative eigensolver in conjunction with Halverson and Poirier’s symmetrized Gaussian (SG) basis [T. Halverson and B. Poirier, J. Chem. Phys. 137, 224101 (2012)] to compute accurate vibrational energy levels of molecules with as many as five atoms. This is done, without storing and manipulating large matrices, by solving a regular eigenvalue problem that makes it possible to exploit direct-product structure. These ideas are combined with a new procedure for selecting which basis functions to use. The SG basis we work with is orders of magnitude smaller than themore » basis made by using a classical energy criterion. We find significant convergence errors in previous calculations with SG bases. For sum-of-product Hamiltonians, SG bases large enough to compute accurate levels are orders of magnitude larger than even simple pruned bases composed of products of harmonic oscillator functions.« less
Incorporation of copper ions into crystals of T2 copper-depleted laccase from Botrytis aclada

DOE Office of Scientific and Technical Information (OSTI.GOV)

Osipov, E. M., E-mail: e.m.osipov@gmail.com; Polyakov, K. M.; Engelhardt Institute of Molecular Biology, Vavilova str. 32, Moscow 119991

2015-11-18

The restoration of the native form of laccase from B. aclada from the type 2 copper-depleted form of the enzyme was investigated. Copper ions were found to be incorporated into the active site after soaking the depleted enzyme in a Cu{sup +}-containing solution. Laccases belong to the class of multicopper oxidases catalyzing the oxidation of phenols accompanied by the reduction of molecular oxygen to water without the formation of hydrogen peroxide. The activity of laccases depends on the number of Cu atoms per enzyme molecule. The structure of type 2 copper-depleted laccase from Botrytis aclada has been solved previously. Withmore » the aim of obtaining the structure of the native form of the enzyme, crystals of the depleted laccase were soaked in Cu{sup +}- and Cu{sup 2+}-containing solutions. Copper ions were found to be incorporated into the active site only when Cu{sup +} was used. A comparative analysis of the native and depleted forms of the enzymes was performed.« less
A synergistic approach to protein crystallization: Combination of a fixed-arm carrier with surface entropy reduction

PubMed Central

Moon, Andrea F; Mueller, Geoffrey A; Zhong, Xuejun; Pedersen, Lars C

2010-01-01

Protein crystallographers are often confronted with recalcitrant proteins not readily crystallizable, or which crystallize in problematic forms. A variety of techniques have been used to surmount such obstacles: crystallization using carrier proteins or antibody complexes, chemical modification, surface entropy reduction, proteolytic digestion, and additive screening. Here we present a synergistic approach for successful crystallization of proteins that do not form diffraction quality crystals using conventional methods. This approach combines favorable aspects of carrier-driven crystallization with surface entropy reduction. We have generated a series of maltose binding protein (MBP) fusion constructs containing different surface mutations designed to reduce surface entropy and encourage crystal lattice formation. The MBP advantageously increases protein expression and solubility, and provides a streamlined purification protocol. Using this technique, we have successfully solved the structures of three unrelated proteins that were previously unattainable. This crystallization technique represents a valuable rescue strategy for protein structure solution when conventional methods fail. PMID:20196072
The Force-Free Magnetosphere of a Rotating Black Hole

NASA Technical Reports Server (NTRS)

Contopoulos, Ioannis; Kazanas, Demosthenes; Papadopoulos, Demetrios B.

2013-01-01

We revisit the Blandford-Znajek process and solve the fundamental equation that governs the structure of the steady-state force-free magnetosphere around a Kerr black hole. The solution depends on the distributions of the magnetic field angular velocity and the poloidal electric current. These are not arbitrary. They are determined self-consistently by requiring that magnetic field lines cross smoothly the two singular surfaces of the problem: the inner "light surface" located inside the ergosphere and the outer "light surface" which is the generalization of the pulsar light cylinder.We find the solution for the simplest possible magnetic field configuration, the split monopole, through a numerical iterative relaxation method analogous to the one that yields the structure of the steady-state axisymmetric force-free pulsar magnetosphere. We obtain the rate of electromagnetic extraction of energy and confirm the results of Blandford and Znajek and of previous time-dependent simulations. Furthermore, we discuss the physical applicability of magnetic field configurations that do not cross both "light surfaces."
Do clients' problem-solving appraisals predict career counseling outcomes or vice versa? A reanalysis of Heppner, et al.

PubMed

Lee, Dong-Gwi; Park, Hyun-Joo; Heppner, Mary J

2009-12-01

Using Heppner, et al.'s data from 2004, this study tested career counseling clients in the United States on problem-solving appraisal scores and career-related variables. A cross-lagged panel design with structural equation modeling was used. Results supported the link between clients' precounseling problem-solving appraisal scores and career outcome. This finding held for career decision-making, but not for vocational identity. The study provided further support for Heppner, et al.'s findings, highlighting the influential role of clients' problem-solving appraisals in advancing their career decision-making processes.
Simplified method to solve sound transmission through structures lined with elastic porous material.

PubMed

Lee, J H; Kim, J

2001-11-01

An approximate analysis method is developed to calculate sound transmission through structures lined with porous material. Because the porous material has both the solid phase and fluid phase, three wave components exist in the material, which makes the related analysis very complicated. The main idea in developing the approximate method is very simple: modeling the porous material using only the strongest of the three waves, which in effect idealizes the material as an equivalent fluid. The analysis procedure has to be conducted in two steps. In the first step, sound transmission through a flat double panel with a porous liner of infinite extents, which has the same cross sectional construction as the actual structure, is solved based on the full theory and the strongest wave component is identified. In the second step sound transmission through the actual structure is solved modeling the porous material as an equivalent fluid while using the actual geometry of the structure. The development and validation of the method are discussed in detail. As an application example, the transmission loss through double walled cylindrical shells with a porous core is calculated utilizing the simplified method.
Crystal structure of norcoclaurine-6-O-methyltransferase, a key rate-limiting step in the synthesis of benzylisoquinoline alkaloids.

PubMed

Robin, Adeline Y; Giustini, Cécile; Graindorge, Matthieu; Matringe, Michel; Dumas, Renaud

2016-09-01

Growing pharmaceutical interest in benzylisoquinoline alkaloids (BIA) coupled with their chemical complexity make metabolic engineering of microbes to create alternative platforms of production an increasingly attractive proposition. However, precise knowledge of rate-limiting enzymes and negative feedback inhibition by end-products of BIA metabolism is of paramount importance for this emerging field of synthetic biology. In this work we report the structural characterization of (S)-norcoclaurine-6-O-methyltransferase (6OMT), a key rate-limiting step enzyme involved in the synthesis of reticuline, the final intermediate to be shared between the different end-products of BIA metabolism, such as morphine, papaverine, berberine and sanguinarine. Four different crystal structures of the enzyme from Thalictrum flavum (Tf 6OMT) were solved: the apoenzyme, the complex with S-adenosyl-l-homocysteine (SAH), the complexe with SAH and the substrate and the complex with SAH and a feedback inhibitor, sanguinarine. The Tf 6OMT structural study provides a molecular understanding of its substrate specificity, active site structure and reaction mechanism. This study also clarifies the inhibition of Tf 6OMT by previously suggested feedback inhibitors. It reveals its high and time-dependent sensitivity toward sanguinarine. © 2016 The Authors The Plant Journal © 2016 John Wiley & Sons Ltd.
Structural insights into the catalytic mechanism of a family 18 exo-chitinase

PubMed Central

van Aalten, D. M. F.; Komander, D.; Synstad, B.; Gåseidnes, S.; Peter, M. G.; Eijsink, V. G. H.

2001-01-01

Chitinase B (ChiB) from Serratia marcescens is a family 18 exo-chitinase whose catalytic domain has a TIM-barrel fold with a tunnel-shaped active site. We have solved structures of three ChiB complexes that reveal details of substrate binding, substrate-assisted catalysis, and product displacement. The structure of an inactive ChiB mutant (E144Q) complexed with a pentameric substrate (binding in subsites −2 to +3) shows closure of the “roof” of the active site tunnel. It also shows that the sugar in the −1 position is distorted to a boat conformation, thus providing structural evidence in support of a previously proposed catalytic mechanism. The structures of the active enzyme complexed to allosamidin (an analogue of a proposed reaction intermediate) and of the active enzyme soaked with pentameric substrate show events after cleavage of the glycosidic bond. The latter structure shows reopening of the roof of the active site tunnel and enzyme-assisted product displacement in the +1 and +2 sites, allowing a water molecule to approach the reaction center. Catalysis is accompanied by correlated structural changes in the core of the TIM barrel that involve conserved polar residues whose functions were hitherto unknown. These changes simultaneously contribute to stabilization of the reaction intermediate and alternation of the pKa of the catalytic acid during the catalytic cycle. PMID:11481469
Modeling ligand recognition at the P2Y12 receptor in light of X-ray structural information

NASA Astrophysics Data System (ADS)

Paoletta, Silvia; Sabbadin, Davide; von Kügelgen, Ivar; Hinz, Sonja; Katritch, Vsevolod; Hoffmann, Kristina; Abdelrahman, Aliaa; Straßburger, Jens; Baqi, Younis; Zhao, Qiang; Stevens, Raymond C.; Moro, Stefano; Müller, Christa E.; Jacobson, Kenneth A.

2015-08-01

The G protein-coupled P2Y12 receptor (P2Y12R) is an important antithrombotic target and of great interest for pharmaceutical discovery. Its recently solved, highly divergent crystallographic structures in complex either with nucleotides (full or partial agonist) or with a nonnucleotide antagonist raise the question of which structure is more useful to understand ligand recognition. Therefore, we performed extensive molecular modeling studies based on these structures and mutagenesis, to predict the binding modes of major classes of P2Y12R ligands previously reported. Various nucleotide derivatives docked readily to the agonist-bound P2Y12R, but uncharged nucleotide-like antagonist ticagrelor required a hybrid receptor resembling the agonist-bound P2Y12R except for the top portion of TM6. Supervised molecular dynamics (SuMD) of ticagrelor binding indicated interactions with the extracellular regions of P2Y12R, defining possible meta-binding sites. Ureas, sulfonylureas, sulfonamides, anthraquinones and glutamic acid piperazines docked readily to the antagonist-bound P2Y12R. Docking dinucleotides at both agonist- and antagonist-bound structures suggested interactions with two P2Y12R pockets. Thus, our structure-based approach consistently rationalized the main structure-activity relationships within each ligand class, giving useful information for designing improved ligands.
The Role of Content Knowledge in Ill-Structured Problem Solving for High School Physics Students

NASA Astrophysics Data System (ADS)

Milbourne, Jeff; Wiebe, Eric

2018-02-01

While Physics Education Research has a rich tradition of problem-solving scholarship, most of the work has focused on more traditional, well-defined problems. Less work has been done with ill-structured problems, problems that are better aligned with the engineering and design-based scenarios promoted by the Next Generation Science Standards. This study explored the relationship between physics content knowledge and ill-structured problem solving for two groups of high school students with different levels of content knowledge. Both groups of students completed an ill-structured problem set, using a talk-aloud procedure to narrate their thought process as they worked. Analysis of the data focused on identifying students' solution pathways, as well as the obstacles that prevented them from reaching "reasonable" solutions. Students with more content knowledge were more successful reaching reasonable solutions for each of the problems, experiencing fewer obstacles. These students also employed a greater variety of solution pathways than those with less content knowledge. Results suggest that a student's solution pathway choice may depend on how she perceives the problem.
Structure of a Burkholderia pseudomallei Trimeric Autotransporter Adhesin Head

PubMed Central

Edwards, Thomas E.; Phan, Isabelle; Abendroth, Jan; Dieterich, Shellie H.; Masoudi, Amir; Guo, Wenjin; Hewitt, Stephen N.; Kelley, Angela; Leibly, David; Brittnacher, Mitch J.; Staker, Bart L.; Miller, Samuel I.; Van Voorhis, Wesley C.; Myler, Peter J.; Stewart, Lance J.

2010-01-01

Background Pathogenic bacteria adhere to the host cell surface using a family of outer membrane proteins called Trimeric Autotransporter Adhesins (TAAs). Although TAAs are highly divergent in sequence and domain structure, they are all conceptually comprised of a C-terminal membrane anchoring domain and an N-terminal passenger domain. Passenger domains consist of a secretion sequence, a head region that facilitates binding to the host cell surface, and a stalk region. Methodology/Principal Findings Pathogenic species of Burkholderia contain an overabundance of TAAs, some of which have been shown to elicit an immune response in the host. To understand the structural basis for host cell adhesion, we solved a 1.35 Å resolution crystal structure of a BpaA TAA head domain from Burkholderia pseudomallei, the pathogen that causes melioidosis. The structure reveals a novel fold of an intricately intertwined trimer. The BpaA head is composed of structural elements that have been observed in other TAA head structures as well as several elements of previously unknown structure predicted from low sequence homology between TAAs. These elements are typically up to 40 amino acids long and are not domains, but rather modular structural elements that may be duplicated or omitted through evolution, creating molecular diversity among TAAs. Conclusions/Significance The modular nature of BpaA, as demonstrated by its head domain crystal structure, and of TAAs in general provides insights into evolution of pathogen-host adhesion and may provide an avenue for diagnostics. PMID:20862217
In Search of Structures: How Does the Mind Explore Infinity?

ERIC Educational Resources Information Center

Singer, Florence Mihaela; Voica, Cristian

2010-01-01

When reasoning about infinite sets, children seem to activate four categories of conceptual structures: geometric (g-structures), arithmetic (a-structures), fractal-type (f-structures), and density-type (d-structures). Students select different problem-solving strategies depending on the structure they recognize within the problem domain. They…
How are things adding up? Neural differences between arithmetic operations are due to general problem solving strategies.

PubMed

Tschentscher, Nadja; Hauk, Olaf

2014-05-15

A number of previous studies have interpreted differences in brain activation between arithmetic operation types (e.g. addition and multiplication) as evidence in favor of distinct cortical representations, processes or neural systems. It is still not clear how differences in general task complexity contribute to these neural differences. Here, we used a mental arithmetic paradigm to disentangle brain areas related to general problem solving from those involved in operation type specific processes (addition versus multiplication). We orthogonally varied operation type and complexity. Importantly, complexity was defined not only based on surface criteria (for example number size), but also on the basis of individual participants' strategy ratings, which were validated in a detailed behavioral analysis. We replicated previously reported operation type effects in our analyses based on surface criteria. However, these effects vanished when controlling for individual strategies. Instead, procedural strategies contrasted with memory retrieval reliably activated fronto-parietal and motor regions, while retrieval strategies activated parietal cortices. This challenges views that operation types rely on partially different neural systems, and suggests that previously reported differences between operation types may have emerged due to invalid measures of complexity. We conclude that mental arithmetic is a powerful paradigm to study brain networks of abstract problem solving, as long as individual participants' strategies are taken into account. Copyright © 2014 Elsevier Inc. All rights reserved.

Structural Basis for Assembly of the MnIV/FeIII Cofactor in the Class Ic Ribonucleotide Reductase from Chlamydia trachomatis‡

PubMed Central

Dassama, Laura M.K.; Krebs, Carsten; Bollinger, J. Martin; Rosenzweig, Amy C.; Boal, Amie K.

2013-01-01

The class Ic ribonucleotide reductase (RNR) from Chlamydia trachomatis (Ct) employs a MnIV/FeIII cofactor in each monomer of its β2 subunit to initiate nucleotide reduction. The cofactor forms by reaction of MnII/FeII-β2 with O2. Previously, in vitro cofactor assembly from apo β2 and divalent metal ions produced a mixture of two forms, with Mn in site 1 (MnIV/FeIII) or site 2 (FeIII/MnIV), of which the more active MnIV/FeIII product predominates. Here we have addressed the basis for metal site-selectivity by solving X-ray crystal structures of apo, MnII, and MnII/FeII complexes of Ct β2. A structure obtained anaerobically with equimolar MnII, FeII, and apo protein reveals exclusive incorporation of MnII in site 1 and FeII in site 2, in contrast to the more modest site-selectivity achieved previously. Site-specificity is controlled thermodynamically by the apo protein structure, as only minor adjustments of ligands occur upon metal binding. Additional structures imply that, by itself, MnII binds in either site. Together the structures are consistent with a model for in vitro cofactor assembly in which FeII specificity for site 2 drives assembly of the appropriately configured heterobimetallic center, provided that FeII is substoichiometric. This model suggests that use of an MnIV/FeIII cofactor in vivo could be an adaptation to FeII limitation. A 1.8 Å resolution model of the MnII/FeII-β2 complex reveals additional structural determinants for activation of the cofactor, including a proposed site for side-on (η2) addition of O2 to FeII and a short (3.2 Å) MnII-FeII interionic distance, promoting formation of the MnIV/FeIV activation intermediate. PMID:23924396
An embodied perspective on expertise in solving the problem of making a geologic map

NASA Astrophysics Data System (ADS)

Callahan, Caitlin Norah

The task of constructing a geologic map is a cognitively and physically demanding field-based problem. The map produced is understood to be an individual's two-dimensional interpretation or mental model of the three-dimensional underlying geology. A popular view within the geoscience community is that teaching students how to make a geologic map is valuable for preparing them to deal with disparate and incomplete data sets, for helping them develop problem-solving skills, and for acquiring expertise in geology. Few previous studies have focused specifically on expertise in geologic mapping. Drawing from literature related to expertise, to problem solving, and to mental models, two overarching research questions were identified: How do geologists of different levels of expertise constrain and solve an ill-structured problem such as making a geologic map? How do geologists address the uncertainties inherent to the processes and interpretations involved in solving a geologic mapping problem? These questions were answered using a methodology that captured the physical actions, expressed thoughts, and navigation paths of geologists as they made a geologic map. Eight geologists, from novice to expert, wore a head-mounted video camera with an attached microphone to record those actions and thoughts, creating "video logs" while in the field. The video logs were also time-stamped, which allowed the visual and audio data to be synchronized with the GPS data that tracked participants' movements in the field. Analysis of the video logs yielded evidence that all eight participants expressed thoughts that reflected the process of becoming mentally situated in the mapping task (e.g. relating between distance on a map and distance in three-dimensional space); the prominence of several of these early thoughts waned in the expressed thoughts later in the day. All participants collected several types of data while in the field; novices, however, did so more continuously throughout the day whereas the experts collected more of their data earlier in the day. Experts and novices also differed in that experts focused more on evaluating certainty in their interpretations; the novices focused more on evaluating the certainty of their observations and sense of location.
Genetic-evolution-based optimization methods for engineering design

NASA Technical Reports Server (NTRS)

Rao, S. S.; Pan, T. S.; Dhingra, A. K.; Venkayya, V. B.; Kumar, V.

1990-01-01

This paper presents the applicability of a biological model, based on genetic evolution, for engineering design optimization. Algorithms embodying the ideas of reproduction, crossover, and mutation are developed and applied to solve different types of structural optimization problems. Both continuous and discrete variable optimization problems are solved. A two-bay truss for maximum fundamental frequency is considered to demonstrate the continuous variable case. The selection of locations of actuators in an actively controlled structure, for minimum energy dissipation, is considered to illustrate the discrete variable case.
On the method of least squares. II. [for calculation of covariance matrices and optimization algorithms

NASA Technical Reports Server (NTRS)

Jefferys, W. H.

1981-01-01

A least squares method proposed previously for solving a general class of problems is expanded in two ways. First, covariance matrices related to the solution are calculated and their interpretation is given. Second, improved methods of solving the normal equations related to those of Marquardt (1963) and Fletcher and Powell (1963) are developed for this approach. These methods may converge in cases where Newton's method diverges or converges slowly.
[Evolution of methodical approaches to solve problem of evaluating and predicting the thermal status of cosmonauts in the real flight].

PubMed

Kuznets, E I; Bobrov, A F; Bekreneva, L N; Mikhailova, L I; Utekhin, B A; Pruzhinina, T I; Iakovleva, E V; Chadov, V I

1996-01-01

The problem of evaluating and predicting the thermal status of a cosmonaut in the long-term space mission is a pressing one and remains to be solved. The previous studies indicated that the best plan to be followed is to evaluate the thermal status of a cosmonaut during his egress into outer space with the use of the procedure of parotid thermometry of the mean body temperature.
Functional Techniques for Data Analysis

NASA Technical Reports Server (NTRS)

Tomlinson, John R.

1997-01-01

This dissertation develops a new general method of solving Prony's problem. Two special cases of this new method have been developed previously. They are the Matrix Pencil and the Osculatory Interpolation. The dissertation shows that they are instances of a more general solution type which allows a wide ranging class of linear functional to be used in the solution of the problem. This class provides a continuum of functionals which provide new methods that can be used to solve Prony's problem.
Difficult macromolecular structures determined using X-ray diffraction techniques.

PubMed

Hernández-Santoyo, Alejandra

2012-07-01

Macromolecular crystallography has been, for the last few decades, the main source of structural information of biological macromolecular systems and it is one of the most powerful techniques for the analysis of enzyme mechanisms and macromolecular interactions at the atomic level. In addition, it is also an extremely powerful tool for drug design. Recent technological and methodological developments in macromolecular X-ray crystallography have allowed solving structures that until recently were considered difficult or even impossible, such as structures at atomic or subatomic resolution or large macromolecular complexes and assemblies at low resolution. These developments have also helped to solve the 3D-structure of macromolecules from twin crystals. Recently, this technique complemented with cryo-electron microscopy and neutron crystallography has provided the structure of large macromolecular machines with great precision allowing understanding of the mechanisms of their function.
Non-recursive augmented Lagrangian algorithms for the forward and inverse dynamics of constrained flexible multibodies

NASA Technical Reports Server (NTRS)

Bayo, Eduardo; Ledesma, Ragnar

1993-01-01

A technique is presented for solving the inverse dynamics of flexible planar multibody systems. This technique yields the non-causal joint efforts (inverse dynamics) as well as the internal states (inverse kinematics) that produce a prescribed nominal trajectory of the end effector. A non-recursive global Lagrangian approach is used in formulating the equations for motion as well as in solving the inverse dynamics equations. Contrary to the recursive method previously presented, the proposed method solves the inverse problem in a systematic and direct manner for both open-chain as well as closed-chain configurations. Numerical simulation shows that the proposed procedure provides an excellent tracking of the desired end effector trajectory.
Numerical techniques in radiative heat transfer for general, scattering, plane-parallel media

NASA Technical Reports Server (NTRS)

Sharma, A.; Cogley, A. C.

1982-01-01

The study of radiative heat transfer with scattering usually leads to the solution of singular Fredholm integral equations. The present paper presents an accurate and efficient numerical method to solve certain integral equations that govern radiative equilibrium problems in plane-parallel geometry for both grey and nongrey, anisotropically scattering media. In particular, the nongrey problem is represented by a spectral integral of a system of nonlinear integral equations in space, which has not been solved previously. The numerical technique is constructed to handle this unique nongrey governing equation as well as the difficulties caused by singular kernels. Example problems are solved and the method's accuracy and computational speed are analyzed.
The development of structural x-ray crystallography

NASA Astrophysics Data System (ADS)

Woolfson, M. M.

2018-03-01

From its birth in 1912, when only the simplest structures could be solved, x-ray structural crystallography is now able to solve macromolecular structures containing many thousands of independent non-hydrogen atoms. This progress has depended on, and been driven by, great technical advances in the development of powerful synchrotron x-ray sources, advanced automated equipment for the collection and storage of large data sets and powerful computers to deal with everything from data processing to running programmes employing complex algorithms for the automatic solution of structures. The sheer number of developments in the subject over the past century makes it impossible for this review to be exhaustive, but it will describe some major developments that will enable the reader to understand how the subject has grown from its humble beginnings to what it is today.
Choosing order of operations to accelerate strip structure analysis in parameter range

NASA Astrophysics Data System (ADS)

Kuksenko, S. P.; Akhunov, R. R.; Gazizov, T. R.

2018-05-01

The paper considers the issue of using iteration methods in solving the sequence of linear algebraic systems obtained in quasistatic analysis of strip structures with the method of moments. Using the analysis of 4 strip structures, the authors have proved that additional acceleration (up to 2.21 times) of the iterative process can be obtained during the process of solving linear systems repeatedly by means of choosing a proper order of operations and a preconditioner. The obtained results can be used to accelerate the process of computer-aided design of various strip structures. The choice of the order of operations to accelerate the process is quite simple, universal and could be used not only for strip structure analysis but also for a wide range of computational problems.
Sound transmission through triple-panel structures lined with poroelastic materials

NASA Astrophysics Data System (ADS)

Liu, Yu

2015-03-01

In this paper, previous theories on the prediction of sound transmission loss for a double-panel structure lined with poroelastic materials are extended to address the problem of a triple-panel structure. Six typical configurations are considered for a triple-panel structure based on the method of coupling the porous layers to the facing panels which determines critically the sound insulation performance of the system. The transfer matrix method is employed to solve the system by applying appropriate types of boundary conditions for these configurations. The transmission loss of the triple-panel structures in a diffuse sound field is calculated as a function of frequency and compared with that of corresponding double-panel structures. Generally, the triple-panel structure with poroelastic linings has superior acoustic performance to the double-panel counterpart, remarkably in the mid-high frequency range and possibly at low frequencies, by selecting appropriate configurations in which those with two air gaps in the structure exhibit the best overall performance over the entire frequency range. The poroelastic lining significantly lowers the cut-on frequency above which the triple-panel structure exhibits noticeably higher transmission loss. Compared with a double-panel structure, the wider range of system parameters for a triple-panel structure due to the additional partition provides more design space for tuning the sound insulation performance. Despite the increased structural complexity, the triple-panel structure lined with poroelastic materials has the obvious advantages in sound transmission loss while without the penalties in weight and volume, and is hence a promising replacement for the widely used double-panel sandwich structure.
A computer program to find the kernel of a polynomial operator

NASA Technical Reports Server (NTRS)

Gejji, R. R.

1976-01-01

This paper presents a FORTRAN program written to solve for the kernel of a matrix of polynomials with real coefficients. It is an implementation of Sain's free modular algorithm for solving the minimal design problem of linear multivariable systems. The structure of the program is discussed, together with some features as they relate to questions of implementing the above method. An example of the use of the program to solve a design problem is included.
Designing for Decision Making

ERIC Educational Resources Information Center

Jonassen, David H.

2012-01-01

Decision making is the most common kind of problem solving. It is also an important component skill in other more ill-structured and complex kinds of problem solving, including policy problems and design problems. There are different kinds of decisions, including choices, acceptances, evaluations, and constructions. After describing the centrality…
Alternative Constraint Handling Technique for Four-Bar Linkage Path Generation

NASA Astrophysics Data System (ADS)

Sleesongsom, S.; Bureerat, S.

2018-03-01

This paper proposes an extension of a new concept for path generation from our previous work by adding a new constraint handling technique. The propose technique was initially designed for problems without prescribed timing by avoiding the timing constraint, while remain constraints are solving with a new constraint handling technique. The technique is one kind of penalty technique. The comparative study is optimisation of path generation problems are solved using self-adaptive population size teaching-learning based optimization (SAP-TLBO) and original TLBO. In this study, two traditional path generation test problem are used to test the proposed technique. The results show that the new technique can be applied with the path generation problem without prescribed timing and gives better results than the previous technique. Furthermore, SAP-TLBO outperforms the original one.
Functionalized graphene-based cathode for highly reversible lithium-sulfur batteries.

PubMed

Kim, Jin Won; Ocon, Joey D; Park, Dong-Won; Lee, Jaeyoung

2014-05-01

In this article, we highlight the salient issues in the development of lithium-sulfur battery (LSB) cathodes, present different points of view in solving them, and argue, why in the future, functionalized graphene or graphene oxide might be the ultimate solution towards LSB commercialization. As shown by previous studies and also in our recent work, functionalized graphene and graphene oxide enhance the reversibility of the charge-discharge process by trapping polysulfides in the oxygen functional groups on the graphene surface, thus minimizing polysulfide dissolution. This will be helpful for the rational design of new cathode structures based on graphene for LSBs with minimal capacity fading, low extra cost, and without the unnecessary weight increase caused by metal/metal oxide additives. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.
Epistemic game for answer making in learning about hydrostatics

NASA Astrophysics Data System (ADS)

Chen, Ying; Irving, Paul W.; Sayre, Eleanor C.

2013-06-01

Previous research into problem solving in physics resulted in researchers introducing six epistemic games to describe the organizational structures of locally coherent resources. We present a new epistemic game—the “answer-making epistemic game”—which was identified in this paper through the analysis of interviews carried out to validate a survey focusing on students’ understanding of Archimedes’ principle and Pascal’s law. In the game, the ultimate goal is a solution to a problem posed by the survey. Students may remember or intuit an answer, then use conceptual and/or mathematical reasoning to justify it. Alternately, they may use conceptual and/or mathematical reasoning to generate an answer. We demonstrate how students generate their solutions using these two different paths and discuss some implications for instruction.
ISPAN (Interactive Stiffened Panel Analysis): A tool for quick concept evaluation and design trade studies

NASA Technical Reports Server (NTRS)

Hairr, John W.; Dorris, William J.; Ingram, J. Edward; Shah, Bharat M.

1993-01-01

Interactive Stiffened Panel Analysis (ISPAN) modules, written in FORTRAN, were developed to provide an easy to use tool for creating finite element models of composite material stiffened panels. The modules allow the user to interactively construct, solve and post-process finite element models of four general types of structural panel configurations using only the panel dimensions and properties as input data. Linear, buckling and post-buckling solution capability is provided. This interactive input allows rapid model generation and solution by non finite element users. The results of a parametric study of a blade stiffened panel are presented to demonstrate the usefulness of the ISPAN modules. Also, a non-linear analysis of a test panel was conducted and the results compared to measured data and previous correlation analysis.
Structural factoring approach for analyzing stochastic networks

NASA Technical Reports Server (NTRS)

Hayhurst, Kelly J.; Shier, Douglas R.

1991-01-01

The problem of finding the distribution of the shortest path length through a stochastic network is investigated. A general algorithm for determining the exact distribution of the shortest path length is developed based on the concept of conditional factoring, in which a directed, stochastic network is decomposed into an equivalent set of smaller, generally less complex subnetworks. Several network constructs are identified and exploited to reduce significantly the computational effort required to solve a network problem relative to complete enumeration. This algorithm can be applied to two important classes of stochastic path problems: determining the critical path distribution for acyclic networks and the exact two-terminal reliability for probabilistic networks. Computational experience with the algorithm was encouraging and allowed the exact solution of networks that have been previously analyzed only by approximation techniques.
Computational aeroelastic analysis of aircraft wings including geometry nonlinearity

NASA Astrophysics Data System (ADS)

Tian, Binyu

The objective of the present study is to show the ability of solving fluid structural interaction problems more realistically by including the geometric nonlinearity of the structure so that the aeroelastic analysis can be extended into the onset of flutter, or in the post flutter regime. A nonlinear Finite Element Analysis software is developed based on second Piola-Kirchhoff stress and Green-Lagrange strain. The second Piola-Kirchhoff stress and Green-Lagrange strain is a pair of energetically conjugated tensors that can accommodate arbitrary large structural deformations and deflection, to study the flutter phenomenon. Since both of these tensors are objective tensors, i.e., the rigid-body motion has no contribution to their components, the movement of the body, including maneuvers and deformation, can be included. The nonlinear Finite Element Analysis software developed in this study is verified with ANSYS, NASTRAN, ABAQUS, and IDEAS for the linear static, nonlinear static, linear dynamic and nonlinear dynamic structural solutions. To solve the flow problems by Euler/Navier equations, the current nonlinear structural software is then embedded into ENSAERO, which is an aeroelastic analysis software package developed at NASA Ames Research Center. The coupling of the two software, both nonlinear in their own field, is achieved by domain decomposition method first proposed by Guruswamy. A procedure has been set for the aeroelastic analysis process. The aeroelastic analysis results have been obtained for fight wing in the transonic regime for various cases. The influence dynamic pressure on flutter has been checked for a range of Mach number. Even though the current analysis matches the general aeroelastic characteristic, the numerical value not match very well with previous studies and needs farther investigations. The flutter aeroelastic analysis results have also been plotted at several time points. The influences of the deforming wing geometry can be well seen in those plots. The movement of shock changes the aerodynamic load distribution on the wing. The effect of viscous on aeroelastic analysis is also discussed. Also compared are the flutter solutions with, or without the structural nonlinearity. As can be seen, linear structural solution goes to infinite, which can not be true in reality. The nonlinear solution is more realistic and can be used to understand the fluid and structure interaction behavior, to control, or prevent disastrous events. (Abstract shortened by UMI.)

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