Structural assessment of a Space Station solar dynamic heat receiver thermal energy storage canister

NASA Technical Reports Server (NTRS)

Tong, M. T.; Kerslake, T. W.; Thompson, R. L.

1988-01-01

This paper assesses the structural performance of a Space Station thermal energy storage (TES) canister subject to orbital solar flux variation and engine cold start-up operating conditions. The impact of working fluid temperature and salt-void distribution on the canister structure are assessed. Both analytical and experimental studies were conducted to determine the temperature distribution of the canister. Subsequent finite-element structural analyses of the canister were performed using both analytically and experimentally obtained temperatures. The Arrhenius creep law was incorporated into the procedure, using secondary creep data for the canister material, Haynes-188 alloy. The predicted cyclic creep strain accumulations at the hot spot were used to assess the structural performance of the canister. In addition, the structural performance of the canister based on the analytically-determined temperature was compared with that based on the experimentally-measured temperature data.

Structural assessment of a space station solar dynamic heat receiver thermal energy storage canister

NASA Technical Reports Server (NTRS)

Thompson, R. L.; Kerslake, T. W.; Tong, M. T.

1988-01-01

The structural performance of a space station thermal energy storage (TES) canister subject to orbital solar flux variation and engine cold start up operating conditions was assessed. The impact of working fluid temperature and salt-void distribution on the canister structure are assessed. Both analytical and experimental studies were conducted to determine the temperature distribution of the canister. Subsequent finite element structural analyses of the canister were performed using both analytically and experimentally obtained temperatures. The Arrhenius creep law was incorporated into the procedure, using secondary creep data for the canister material, Haynes 188 alloy. The predicted cyclic creep strain accumulations at the hot spot were used to assess the structural performance of the canister. In addition, the structural performance of the canister based on the analytically determined temperature was compared with that based on the experimentally measured temperature data.

Crystal structure prediction supported by incomplete experimental data

NASA Astrophysics Data System (ADS)

Tsujimoto, Naoto; Adachi, Daiki; Akashi, Ryosuke; Todo, Synge; Tsuneyuki, Shinji

2018-05-01

We propose an efficient theoretical scheme for structure prediction on the basis of the idea of combining methods, which optimize theoretical calculation and experimental data simultaneously. In this scheme, we formulate a cost function based on a weighted sum of interatomic potential energies and a penalty function which is defined with partial experimental data totally insufficient for conventional structure analysis. In particular, we define the cost function using "crystallinity" formulated with only peak positions within the small range of the x-ray-diffraction pattern. We apply this method to well-known polymorphs of SiO2 and C with up to 108 atoms in the simulation cell and show that it reproduces the correct structures efficiently with very limited information of diffraction peaks. This scheme opens a new avenue for determining and predicting structures that are difficult to determine by conventional methods.

Refinement of NMR structures using implicit solvent and advanced sampling techniques.

PubMed

Chen, Jianhan; Im, Wonpil; Brooks, Charles L

2004-12-15

NMR biomolecular structure calculations exploit simulated annealing methods for conformational sampling and require a relatively high level of redundancy in the experimental restraints to determine quality three-dimensional structures. Recent advances in generalized Born (GB) implicit solvent models should make it possible to combine information from both experimental measurements and accurate empirical force fields to improve the quality of NMR-derived structures. In this paper, we study the influence of implicit solvent on the refinement of protein NMR structures and identify an optimal protocol of utilizing these improved force fields. To do so, we carry out structure refinement experiments for model proteins with published NMR structures using full NMR restraints and subsets of them. We also investigate the application of advanced sampling techniques to NMR structure refinement. Similar to the observations of Xia et al. (J.Biomol. NMR 2002, 22, 317-331), we find that the impact of implicit solvent is rather small when there is a sufficient number of experimental restraints (such as in the final stage of NMR structure determination), whether implicit solvent is used throughout the calculation or only in the final refinement step. The application of advanced sampling techniques also seems to have minimal impact in this case. However, when the experimental data are limited, we demonstrate that refinement with implicit solvent can substantially improve the quality of the structures. In particular, when combined with an advanced sampling technique, the replica exchange (REX) method, near-native structures can be rapidly moved toward the native basin. The REX method provides both enhanced sampling and automatic selection of the most native-like (lowest energy) structures. An optimal protocol based on our studies first generates an ensemble of initial structures that maximally satisfy the available experimental data with conventional NMR software using a simplified force field and then refines these structures with implicit solvent using the REX method. We systematically examine the reliability and efficacy of this protocol using four proteins of various sizes ranging from the 56-residue B1 domain of Streptococcal protein G to the 370-residue Maltose-binding protein. Significant improvement in the structures was observed in all cases when refinement was based on low-redundancy restraint data. The proposed protocol is anticipated to be particularly useful in early stages of NMR structure determination where a reliable estimate of the native fold from limited data can significantly expedite the overall process. This refinement procedure is also expected to be useful when redundant experimental data are not readily available, such as for large multidomain biomolecules and in solid-state NMR structure determination.

Predictive and Experimental Approaches for Elucidating Protein–Protein Interactions and Quaternary Structures

PubMed Central

Nealon, John Oliver; Philomina, Limcy Seby

2017-01-01

The elucidation of protein–protein interactions is vital for determining the function and action of quaternary protein structures. Here, we discuss the difficulty and importance of establishing protein quaternary structure and review in vitro and in silico methods for doing so. Determining the interacting partner proteins of predicted protein structures is very time-consuming when using in vitro methods, this can be somewhat alleviated by use of predictive methods. However, developing reliably accurate predictive tools has proved to be difficult. We review the current state of the art in predictive protein interaction software and discuss the problem of scoring and therefore ranking predictions. Current community-based predictive exercises are discussed in relation to the growth of protein interaction prediction as an area within these exercises. We suggest a fusion of experimental and predictive methods that make use of sparse experimental data to determine higher resolution predicted protein interactions as being necessary to drive forward development. PMID:29206185

Relation between native ensembles and experimental structures of proteins

PubMed Central

Best, Robert B.; Lindorff-Larsen, Kresten; DePristo, Mark A.; Vendruscolo, Michele

2006-01-01

Different experimental structures of the same protein or of proteins with high sequence similarity contain many small variations. Here we construct ensembles of “high-sequence similarity Protein Data Bank” (HSP) structures and consider the extent to which such ensembles represent the structural heterogeneity of the native state in solution. We find that different NMR measurements probing structure and dynamics of given proteins in solution, including order parameters, scalar couplings, and residual dipolar couplings, are remarkably well reproduced by their respective high-sequence similarity Protein Data Bank ensembles; moreover, we show that the effects of uncertainties in structure determination are insufficient to explain the results. These results highlight the importance of accounting for native-state protein dynamics in making comparisons with ensemble-averaged experimental data and suggest that even a modest number of structures of a protein determined under different conditions, or with small variations in sequence, capture a representative subset of the true native-state ensemble. PMID:16829580

Theoretical and experimental studies of the current–voltage and capacitance–voltage of HEMT structures and field-effect transistors

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

Tarasova, E. A.; Obolenskaya, E. S., E-mail: obolensk@rf.unn.ru; Hananova, A. V.

The sensitivity of classical n{sup +}/n{sup –} GaAs and AlGaN/GaN structures with a 2D electron gas (HEMT) and field-effect transistors based on these structures to γ-neutron exposure is studied. The levels of their radiation hardness were determined. A method for experimental study of the structures on the basis of a differential analysis of their current–voltage characteristics is developed. This method makes it possible to determine the structure of the layers in which radiation-induced defects accumulate. A procedure taking into account changes in the plate area of the experimentally measured barrier-contact capacitance associated with the emergence of clusters of radiation-induced defectsmore » that form dielectric inclusions in the 2D-electron-gas layer is presented for the first time.« less

Rapid experimental measurements of physicochemical properties to inform models and testing.

PubMed

Nicolas, Chantel I; Mansouri, Kamel; Phillips, Katherine A; Grulke, Christopher M; Richard, Ann M; Williams, Antony J; Rabinowitz, James; Isaacs, Kristin K; Yau, Alice; Wambaugh, John F

2018-05-02

The structures and physicochemical properties of chemicals are important for determining their potential toxicological effects, toxicokinetics, and route(s) of exposure. These data are needed to prioritize the risk for thousands of environmental chemicals, but experimental values are often lacking. In an attempt to efficiently fill data gaps in physicochemical property information, we generated new data for 200 structurally diverse compounds, which were rigorously selected from the USEPA ToxCast chemical library, and whose structures are available within the Distributed Structure-Searchable Toxicity Database (DSSTox). This pilot study evaluated rapid experimental methods to determine five physicochemical properties, including the log of the octanol:water partition coefficient (known as log(K ow ) or logP), vapor pressure, water solubility, Henry's law constant, and the acid dissociation constant (pKa). For most compounds, experiments were successful for at least one property; log(K ow ) yielded the largest return (176 values). It was determined that 77 ToxPrint structural features were enriched in chemicals with at least one measurement failure, indicating which features may have played a role in rapid method failures. To gauge consistency with traditional measurement methods, the new measurements were compared with previous measurements (where available). Since quantitative structure-activity/property relationship (QSAR/QSPR) models are used to fill gaps in physicochemical property information, 5 suites of QSPRs were evaluated for their predictive ability and chemical coverage or applicability domain of new experimental measurements. The ability to have accurate measurements of these properties will facilitate better exposure predictions in two ways: 1) direct input of these experimental measurements into exposure models; and 2) construction of QSPRs with a wider applicability domain, as their predicted physicochemical values can be used to parameterize exposure models in the absence of experimental data. Published by Elsevier B.V.

Structural-acoustic coupling in aircraft fuselage structures

NASA Technical Reports Server (NTRS)

Mathur, Gopal P.; Simpson, Myles A.

1992-01-01

Results of analytical and experimental investigations of structural-acoustic coupling phenomenon in an aircraft fuselage are described. The structural and acoustic cavity modes of DC-9 fuselage were determined using a finite element approach to vibration analysis. Predicted structural and acoustic dispersion curves were used to determine possible occurrences of structural-acoustic coupling for the fuselage. An aft section of DC-9 aircraft fuselage, housed in an anechoic chamber, was used for experimental investigations. The test fuselage was excited by a shaker and vibration response and interior sound field were measured using accelerometer and microphone arrays. The wavenumber-frequency structural and cavity response maps were generated from the measured data. Analysis and interpretation of the spatial plots and wavenumber maps provided the required information on modal characteristics, fuselage response and structural-acoustic coupling.

Membrane proteins structures: A review on computational modeling tools.

PubMed

Almeida, Jose G; Preto, Antonio J; Koukos, Panagiotis I; Bonvin, Alexandre M J J; Moreira, Irina S

2017-10-01

Membrane proteins (MPs) play diverse and important functions in living organisms. They constitute 20% to 30% of the known bacterial, archaean and eukaryotic organisms' genomes. In humans, their importance is emphasized as they represent 50% of all known drug targets. Nevertheless, experimental determination of their three-dimensional (3D) structure has proven to be both time consuming and rather expensive, which has led to the development of computational algorithms to complement the available experimental methods and provide valuable insights. This review highlights the importance of membrane proteins and how computational methods are capable of overcoming challenges associated with their experimental characterization. It covers various MP structural aspects, such as lipid interactions, allostery, and structure prediction, based on methods such as Molecular Dynamics (MD) and Machine-Learning (ML). Recent developments in algorithms, tools and hybrid approaches, together with the increase in both computational resources and the amount of available data have resulted in increasingly powerful and trustworthy approaches to model MPs. Even though MPs are elementary and important in nature, the determination of their 3D structure has proven to be a challenging endeavor. Computational methods provide a reliable alternative to experimental methods. In this review, we focus on computational techniques to determine the 3D structure of MP and characterize their binding interfaces. We also summarize the most relevant databases and software programs available for the study of MPs. Copyright © 2017 Elsevier B.V. All rights reserved.

Structure of fluorescent metal clusters on a DNA template.

NASA Astrophysics Data System (ADS)

Vdovichev, A. A.; Sych, T. S.; Reveguk, Z. V.; Smirnova, A. A.; Maksimov, D. A.; Ramazanov, R. R.; Kononov, A. I.

2016-08-01

Luminescent metal clusters are a subject of growing interest in recent years due to their bright emission from visible to near infrared range. Detailed structure of the fluorescent complexes of Ag and other metal clusters with ligands still remains a challenging task. In this joint experimental and theoretical study we synthesized Ag-DNA complexes on a DNA oligonucleotide emitting in violet- green spectral range. The structure of DNA template was determined by means of various spectral measurements (CD, MS, XPS). Comparison of the experimental fluorescent excitation spectra and calculated absorption spectra for different QM/MM optimized structures allowed us to determine the detailed structure of the green cluster containing three silver atoms in the stem of the DNA hairpin structure stabilized by cytosine-Ag+-cytosine bonds.

Determination of pKa and the corresponding structures of quinclorac using combined experimental and theoretical approaches

NASA Astrophysics Data System (ADS)

Song, Dean; Sun, Huiqing; Jiang, Xiaohua; Kong, Fanyu; Qiang, Zhimin; Zhang, Aiqian; Liu, Huijuan; Qu, Jiuhui

2018-01-01

As an emerging environmental contaminant, the herbicide quinclorac has attracted much attention in recent years. However, a very fundamental issue, the acid dissociation of quinclorac has not yet to be studied in detail. Herein, the pKa value and the corresponding structures of quinclorac were systematically investigated using combined experimental and theoretical approaches. The experimental pKa of quinclorac was determined by the spectrophotometric method to be 2.65 at 25 °C with ionic strength of 0.05 M, and was corrected to be 2.56 at ionic strength of zero. The molecular structures of quinclorac were then located by employing the DFT calculation. The anionic quinclorac was directly located with the carboxylic group perpendicular to the aromatic ring, while neutral quinclorac was found to be the equivalent twin structures. The result was further confirmed by analyzing the UV/Vis and MS-MS2 spectra from both experimental and theoretical viewpoints. By employing the QSPR approach, the theoretical pKa of QCR was determined to be 2.50, which is excellent agreement with the experimental result obtained herein. The protonation of QCR at the carboxylic group instead of the quinoline structure was attributed to the weak electronegative property of nitrogen atom induced by the electron-withdrawing groups. It is anticipated that this work could not only help in gaining a deep insight into the acid dissociation of quinclorac but also offering the key information on its reaction and interaction with others.

Attitude Control of Flexible Structures.

DTIC Science & Technology

1990-09-01

arm has been determined experimentally and compared with analytical * predictions obtained by using the GIFTS finite element analysis program. The...frequencies of the flexible arm have been determined experimentally and compared with analytical predictiens obtained by using the GIFTS finite element...exception of the first mode. Table V shows the difference between the frequencies obtained from the GIFTS program and the experimental values. TABLE

Comprehensive 3D-modeling of allergenic proteins and amino acid composition of potential conformational IgE epitopes

PubMed Central

Oezguen, Numan; Zhou, Bin; Negi, Surendra S.; Ivanciuc, Ovidiu; Schein, Catherine H.; Labesse, Gilles; Braun, Werner

2008-01-01

Similarities in sequences and 3D structures of allergenic proteins provide vital clues to identify clinically relevant IgE cross-reactivities. However, experimental 3D structures are available in the Protein Data Bank for only 5% (45/829) of all allergens catalogued in the Structural Database of Allergenic Proteins (SDAP, http://fermi.utmb.edu/SDAP). Here, an automated procedure was used to prepare 3D-models of all allergens where there was no experimentally determined 3D structure or high identity (95%) to another protein of known 3D structure. After a final selection by quality criteria, 433 reliable 3D models were retained and are available from our SDAP Website. The new 3D models extensively enhance our knowledge of allergen structures. As an example of their use, experimentally derived “continuous IgE epitopes” were mapped on 3 experimentally determined structures and 13 of our 3D-models of allergenic proteins. Large portions of these continuous sequences are not entirely on the surface and therefore cannot interact with IgE or other proteins. Only the surface exposed residues are constituents of “conformational IgE epitopes” which are not in all cases continuous in sequence. The surface exposed parts of the experimental determined continuous IgE epitopes showed a distinct statistical distribution as compared to their presence in typical protein-protein interfaces. The amino acids Ala, Ser, Asn, Gly and particularly Lys have a high propensity to occur in IgE binding sites. The 3D-models will facilitate further analysis of the common properties of IgE binding sites of allergenic proteins. PMID:18621419

Diffraction-Based Density Restraints for Membrane and Membrane-Peptide Molecular Dynamics Simulations

PubMed Central

Benz, Ryan W.; Nanda, Hirsh; Castro-Román, Francisco; White, Stephen H.; Tobias, Douglas J.

2006-01-01

We have recently shown that current molecular dynamics (MD) atomic force fields are not yet able to produce lipid bilayer structures that agree with experimentally-determined structures within experimental errors. Because of the many advantages offered by experimentally validated simulations, we have developed a novel restraint method for membrane MD simulations that uses experimental diffraction data. The restraints, introduced into the MD force field, act upon specified groups of atoms to restrain their mean positions and widths to values determined experimentally. The method was first tested using a simple liquid argon system, and then applied to a neat dioleoylphosphatidylcholine (DOPC) bilayer at 66% relative humidity and to the same bilayer containing the peptide melittin. Application of experiment-based restraints to the transbilayer double-bond and water distributions of neat DOPC bilayers led to distributions that agreed with the experimental values. Based upon the experimental structure, the restraints improved the simulated structure in some regions while introducing larger differences in others, as might be expected from imperfect force fields. For the DOPC-melittin system, the experimental transbilayer distribution of melittin was used as a restraint. The addition of the peptide caused perturbations of the simulated bilayer structure, but which were larger than observed experimentally. The melittin distribution of the simulation could be fit accurately to a Gaussian with parameters close to the observed ones, indicating that the restraints can be used to produce an ensemble of membrane-bound peptide conformations that are consistent with experiments. Such ensembles pave the way for understanding peptide-bilayer interactions at the atomic level. PMID:16950837

Experimental and calculated structural parameters of 5-trihalomethyl-4,5-dihydro-1 H-pyrazole derivatives, novel analgesic agents

NASA Astrophysics Data System (ADS)

Machado, Pablo; Campos, Patrick T.; Lima, Glauber R.; Rosa, Fernanda A.; Flores, Alex F. C.; Bonacorso, Helio G.; Zanatta, Nilo; Martins, Marcos A. P.

2009-01-01

The crystal structures of four novel analgesic agents, methyl 5-hydroxy-3- or 4-methyl-5-trichloro[trifluoro]methyl-4,5-dihydro-1 H-pyrazole-1-carboxylate, have been determined by X-ray diffractometry. The data demonstrated that the molecular packing was stabilized mainly by O sbnd H⋯O hydrogen bonds of the 5-hydroxy and 1-carboxymethyl groups. The 4,5-dihydro-1 H-pyrazole rings were obtained as almost planar structures showing RMS deviation at a range of 0.0052-0.0805 Å. Additionally, computational investigation using semi-empirical AM1 and PM3 methods were performed to find a correlation between experimental and calculated geometrical parameters. The data obtained suggest that the structural data furnished by the AM1 method is in better agreement with those experimentally determined for the above compounds.

An Evaluation of Material Properties Using EMA and FEM

NASA Astrophysics Data System (ADS)

Ďuriš, Rastislav; Labašová, Eva

2016-12-01

The main goal of the paper is the determination of material properties from experimentally measured natural frequencies. A combination of two approaches to structural dynamics testing was applied: the experimental measurements of natural frequencies were performed by Experimental Modal Analysis (EMA) and the numerical simulations, were carried out by Finite Element Analysis (FEA). The optimization methods were used to determine the values of density and elasticity modulus of a specimen based on the experimental results.

NIAS-Server: Neighbors Influence of Amino acids and Secondary Structures in Proteins.

PubMed

Borguesan, Bruno; Inostroza-Ponta, Mario; Dorn, Márcio

2017-03-01

The exponential growth in the number of experimentally determined three-dimensional protein structures provide a new and relevant knowledge about the conformation of amino acids in proteins. Only a few of probability densities of amino acids are publicly available for use in structure validation and prediction methods. NIAS (Neighbors Influence of Amino acids and Secondary structures) is a web-based tool used to extract information about conformational preferences of amino acid residues and secondary structures in experimental-determined protein templates. This information is useful, for example, to characterize folds and local motifs in proteins, molecular folding, and can help the solution of complex problems such as protein structure prediction, protein design, among others. The NIAS-Server and supplementary data are available at http://sbcb.inf.ufrgs.br/nias .

’Coxiella Burnetii’ Vaccine Development: Lipopolysaccharide Structural Analysis

DTIC Science & Technology

1991-02-20

Analytical instrumentation and methodology is presented for the determination of endotoxin -related structures at much improved sensitivity and... ENDOTOXIN CHARACTERIZATION BY SFC .......................... 10 III. COXIELLA BURNETII LPS CHARACTERIZATION A. EXPERIMENTAL...period for the determination of endotoxin -related structures at much improved sensitivity and specificity. Reports, and their applications, are listed in

g-Factor of heavy ions: a new access to the fine structure constant.

PubMed

Shabaev, V M; Glazov, D A; Oreshkina, N S; Volotka, A V; Plunien, G; Kluge, H-J; Quint, W

2006-06-30

A possibility for a determination of the fine structure constant in experiments on the bound-electron g-factor is examined. It is found that studying a specific difference of the g-factors of B- and H-like ions of the same spinless isotope in the Pb region to the currently accessible experimental accuracy of 7 x 10(-10) would lead to a determination of the fine structure constant to an accuracy which is better than that of the currently accepted value. Further improvements of the experimental and theoretical accuracy could provide a value of the fine structure constant which is several times more precise than the currently accepted one.

Calculated and scale model experimentally measured scattering from metallic structures in Instrument Landing System

DOT National Transportation Integrated Search

1974-03-01

Comparison is made of theoretically calculated and experimentally determined scattering from metallic tilted rectangles and vertical cylindrical scatterers. The scattering was experimentally measured in a scale model range at the Watertown Arsenal, W...

Sample size determinations for group-based randomized clinical trials with different levels of data hierarchy between experimental and control arms.

PubMed

Heo, Moonseong; Litwin, Alain H; Blackstock, Oni; Kim, Namhee; Arnsten, Julia H

2017-02-01

We derived sample size formulae for detecting main effects in group-based randomized clinical trials with different levels of data hierarchy between experimental and control arms. Such designs are necessary when experimental interventions need to be administered to groups of subjects whereas control conditions need to be administered to individual subjects. This type of trial, often referred to as a partially nested or partially clustered design, has been implemented for management of chronic diseases such as diabetes and is beginning to emerge more commonly in wider clinical settings. Depending on the research setting, the level of hierarchy of data structure for the experimental arm can be three or two, whereas that for the control arm is two or one. Such different levels of data hierarchy assume correlation structures of outcomes that are different between arms, regardless of whether research settings require two or three level data structure for the experimental arm. Therefore, the different correlations should be taken into account for statistical modeling and for sample size determinations. To this end, we considered mixed-effects linear models with different correlation structures between experimental and control arms to theoretically derive and empirically validate the sample size formulae with simulation studies.

Epitope mapping of the domains of human angiotensin converting enzyme.

PubMed

Kugaevskaya, Elena V; Kolesanova, Ekaterina F; Kozin, Sergey A; Veselovsky, Alexander V; Dedinsky, Ilya R; Elisseeva, Yulia E

2006-06-01

Somatic angiotensin converting enzyme (sACE), contains in its single chain two homologous domains (called N- and C-domains), each bearing a functional zinc-dependent active site. The present study aims to define the differences between two sACE domains and to localize experimentally revealed antigenic determinants (B-epitopes) in the recently determined three-dimensional structure of testicular tACE. The predicted linear antigenic determinants of human sACE were determined by peptide scanning ("PEPSCAN") approach. Essential difference was demonstrated between locations of the epitopes in the N- and C-domains. Comparison of arrangement of epitopes in the human domains with the corresponding sequences of some mammalian sACEs enabled to classify the revealed antigenic determinants as variable or conserved areas. The location of antigenic determinants with respect to various structural elements and to functionally important sites of the human sACE C-domain was estimated. The majority of antigenic sites of the C-domain were located at the irregular elements and at the boundaries of secondary structure elements. The data show structural differences between the sACE domains. The experimentally revealed antigenic determinants were in agreement with the recently determined crystal tACE structure. New potential applications are open to successfully produce mono-specific and group-specific antipeptide antibodies.

A Laboratory Exercise in the Determination of Carbohydrate Structures.

ERIC Educational Resources Information Center

White, Bernard J.; Robyt, John F.

1988-01-01

Describes an experiment in which students are given a naturally occurring oligosaccharide as an unknown and are asked to determine both its monosaccharide composition and its structure. Discusses methods and experimental techniques including thin layer chromatography and the use of enzymes. (CW)

D2N: Distance to the native.

PubMed

Mishra, Avinash; Rana, Prashant Singh; Mittal, Aditya; Jayaram, B

2014-10-01

Root-mean-square-deviation (RMSD), of computationally-derived protein structures from experimentally determined structures, is a critical index to assessing protein-structure-prediction-algorithms (PSPAs). The development of PSPAs to obtain 0Å RMSD from native structures is considered central to computational biology. However, till date it has been quite challenging to measure how far a predicted protein structure is from its native - in the absence of a known experimental/native structure. In this work, we report the development of a metric "D2N" (distance to the native) - that predicts the "RMSD" of any structure without actually knowing the native structure. By combining physico-chemical properties and known universalities in spatial organization of soluble proteins to develop D2N, we demonstrate the ability to predict the distance of a proposed structure to within ±1.5Ǻ error with a remarkable average accuracy of 93.6% for structures below 5Ǻ from the native. We believe that this work opens up a completely new avenue towards assigning reliable structures to whole proteomes even in the absence of experimentally determined native structures. The D2N tool is freely available at http://www.scfbio-iitd.res.in/software/d2n.jsp. Copyright © 2014 Elsevier B.V. All rights reserved.

Update of the equations of the limit state of the structural material with the realization of their deformation

NASA Astrophysics Data System (ADS)

Zenkov, E. V.

2018-01-01

Two methods are given in the article by considering the type of stressed-Deformed state (SDS) based on equations limit condition and analyzing the results of laboratory tests of special specimens for mechanical testing, focus having destruction thereof in the same view of SDS as in focus possible destruction of the structural member. The considered limited use of these methods in terms of considering physically consistent strength criterion type Pisarenko-Lebedev. A revised design-experimental procedure for determining the strength of the material of the structure, combining therein the elements of these two methods, consisting in determining the strength parameters of construction material, entering criterion equation Pisarenko-Lebedev, considering the actual appearance of the region-of-interest SDS structure. The implementation of the procedure is performed on the basis of the selection of the respective experimental laboratory specimens for mechanical testing, plan SDS in working zone coinciding with a SDS: structure whose strength is evaluated. The refinement process limit state equations demonstrated in determining 50CrV4 steel strength parameters, being in a state of biaxial stretching. Design-experimentally determined by, that steel for a given voltage limit value is almost a quarter of its value is reduced compared to the conventional tensile strength. value is reduced compared to the conventional tensile strength.

The heavy atom microwave structure of 2-methyltetrahydrofuran

NASA Astrophysics Data System (ADS)

Van, Vinh; Stahl, Wolfgang; Nguyen, Ha Vinh Lam

2016-11-01

The rotational spectra of 2-methyltetrahydrofuran have been observed using a pulsed molecular beam Fourier transform microwave spectrometer operating in the frequency range 2-26.5 GHz. Conformational analysis using quantum chemical calculations yields two stable conformers; both of them possess an envelope structure. The conformational transformation can occur via two different transition states. The Cremer-Pople notation for five-membered rings is chosen for describing the conformations. Only one conformer with equatorial position of the methyl group is assigned in the experimental spectrum. The fits of its parent species, 13C- and 18O-isotopologues result in highly accurate molecular parameters, and enable the determination of a heavy atom rs structure using Kraitchman's equations. This experimentally determined structure is in excellent agreement with the structure calculated by anharmonic frequency calculations.

Determination of the structural damping coefficients of six full-scale helicopter rotor blades of different materials and methods of construction

NASA Technical Reports Server (NTRS)

Gibson, Frederick W

1956-01-01

Results of an experimental investigation of the structural damping of six full-scale helicopter rotor blades, made to determine the variation of structural damping with materials and methods of construction, are presented. The damping of the blades was determined for the first three flapwise bending modes, first chordwise bending mode, and first torsion mode. The contribution of structural damping to the total damping of the blades is discussed for several aerodynamic conditions in order to point out situations where structural damping is significant.

Biophysics of cadherin adhesion.

PubMed

Leckband, Deborah; Sivasankar, Sanjeevi

2012-01-01

Since the identification of cadherins and the publication of the first crystal structures, the mechanism of cadherin adhesion, and the underlying structural basis have been studied with a number of different experimental techniques, different classical cadherin subtypes, and cadherin fragments. Earlier studies based on biophysical measurements and structure determinations resulted in seemingly contradictory findings regarding cadherin adhesion. However, recent experimental data increasingly reveal parallels between structures, solution binding data, and adhesion-based biophysical measurements that are beginning to both reconcile apparent differences and generate a more comprehensive model of cadherin-mediated cell adhesion. This chapter summarizes the functional, structural, and biophysical findings relevant to cadherin junction assembly and adhesion. We emphasize emerging parallels between findings obtained with different experimental approaches. Although none of the current models accounts for all of the available experimental and structural data, this chapter discusses possible origins of apparent discrepancies, highlights remaining gaps in current knowledge, and proposes challenges for further study.

Exploration of RNA structure spaces

NASA Technical Reports Server (NTRS)

Fox, G. E.

1991-01-01

In order to understand the structure of real structure spaces, we are studying the 5S rRNA structure space experimentally. A plasmid containing a synthetic 5S rRNA gene, two rRNA promoters, and transcription terminators has been assembled. Assays are conducted to determine if the foreign 5S rRNA is expressed, and to see whether or not it is incorporated into ribosomes. Evolutionary competition is used to determine the relative fitness of strains containing the foreign 5S rRNA and a control 5S rRNA. By using site directed mutagenesis, a number of mutants can be made in order to study the boundaries of the structure space and how sharply defined they are. By making similar studies in the vicinity of structure space, it will be possible to determine how homogeneous the 5S rRNA structure space is. Useable experimental protocols have been developed, and a number of mutants have already been studied. Initial results suggest an explanation of why single stranded regions of the RNA are less subject to mutation than double stranded regions.

Determination of the three-dimensional structure of oligosaccharides in the solid state from experimental 13C NMR data and ab initio chemical shift surfaces.

PubMed

Sergeyev, Ivan; Moyna, Guillermo

2005-05-02

A novel method for the determination of the three-dimensional (3D) structure of oligosaccharides in the solid state using experimental 13C NMR data is presented. The approach employs this information, combined with 13C chemical shift surfaces (CSSs) for the glycosidic bond carbons in the generation of NMR pseudopotential energy functions suitable for use as constraints in molecular modeling simulations. Application of the method to trehalose, cellobiose, and cellotetraose produces 3D models that agree remarkably well with the reported X-ray structures, with phi and psi dihedral angles that are within 10 degrees from the ones observed in the crystals. The usefulness of the approach is further demonstrated in the determination of the 3D structure of the cellohexaose, an hexasaccharide for which no X-ray data has been reported, as well as in the generation of accurate structural models for cellulose II and amylose V6.

The Researches on Damage Detection Method for Truss Structures

NASA Astrophysics Data System (ADS)

Wang, Meng Hong; Cao, Xiao Nan

2018-06-01

This paper presents an effective method to detect damage in truss structures. Numerical simulation and experimental analysis were carried out on a damaged truss structure under instantaneous excitation. The ideal excitation point and appropriate hammering method were determined to extract time domain signals under two working conditions. The frequency response function and principal component analysis were used for data processing, and the angle between the frequency response function vectors was selected as a damage index to ascertain the location of a damaged bar in the truss structure. In the numerical simulation, the time domain signal of all nodes was extracted to determine the location of the damaged bar. In the experimental analysis, the time domain signal of a portion of the nodes was extracted on the basis of an optimal sensor placement method based on the node strain energy coefficient. The results of the numerical simulation and experimental analysis showed that the damage detection method based on the frequency response function and principal component analysis could locate the damaged bar accurately.

Recent developments in structural proteomics for protein structure determination.

PubMed

Liu, Hsuan-Liang; Hsu, Jyh-Ping

2005-05-01

The major challenges in structural proteomics include identifying all the proteins on the genome-wide scale, determining their structure-function relationships, and outlining the precise three-dimensional structures of the proteins. Protein structures are typically determined by experimental approaches such as X-ray crystallography or nuclear magnetic resonance (NMR) spectroscopy. However, the knowledge of three-dimensional space by these techniques is still limited. Thus, computational methods such as comparative and de novo approaches and molecular dynamic simulations are intensively used as alternative tools to predict the three-dimensional structures and dynamic behavior of proteins. This review summarizes recent developments in structural proteomics for protein structure determination; including instrumental methods such as X-ray crystallography and NMR spectroscopy, and computational methods such as comparative and de novo structure prediction and molecular dynamics simulations.

Revisiting the blind tests in crystal structure prediction: accurate energy ranking of molecular crystals.

PubMed

Asmadi, Aldi; Neumann, Marcus A; Kendrick, John; Girard, Pascale; Perrin, Marc-Antoine; Leusen, Frank J J

2009-12-24

In the 2007 blind test of crystal structure prediction hosted by the Cambridge Crystallographic Data Centre (CCDC), a hybrid DFT/MM method correctly ranked each of the four experimental structures as having the lowest lattice energy of all the crystal structures predicted for each molecule. The work presented here further validates this hybrid method by optimizing the crystal structures (experimental and submitted) of the first three CCDC blind tests held in 1999, 2001, and 2004. Except for the crystal structures of compound IX, all structures were reminimized and ranked according to their lattice energies. The hybrid method computes the lattice energy of a crystal structure as the sum of the DFT total energy and a van der Waals (dispersion) energy correction. Considering all four blind tests, the crystal structure with the lowest lattice energy corresponds to the experimentally observed structure for 12 out of 14 molecules. Moreover, good geometrical agreement is observed between the structures determined by the hybrid method and those measured experimentally. In comparison with the correct submissions made by the blind test participants, all hybrid optimized crystal structures (apart from compound II) have the smallest calculated root mean squared deviations from the experimentally observed structures. It is predicted that a new polymorph of compound V exists under pressure.

Determining modulus of elasticity of ancient structural timber

Treesearch

Houjiang Zhang; Lei Zhu; Yanliang Sun; Xiping Wang; Haicheng Yan

2011-01-01

During maintenance of ancient timber architectures, it is important to determine mechanical properties of the wood component materials non-destructively and effectively, so that degraded members may be replaced or repaired to avoid structural failure. Experimental materials are four larch (Larix principis-rupprechtii Mayr.) components, which were taken down from the...

Acoustic-Structure Interaction in Rocket Engines: Validation Testing

NASA Technical Reports Server (NTRS)

Davis, R. Benjamin; Joji, Scott S.; Parks, Russel A.; Brown, Andrew M.

2009-01-01

While analyzing a rocket engine component, it is often necessary to account for any effects that adjacent fluids (e.g., liquid fuels or oxidizers) might have on the structural dynamics of the component. To better characterize the fully coupled fluid-structure system responses, an analytical approach that models the system as a coupled expansion of rigid wall acoustic modes and in vacuo structural modes has been proposed. The present work seeks to experimentally validate this approach. To experimentally observe well-coupled system modes, the test article and fluid cavities are designed such that the uncoupled structural frequencies are comparable to the uncoupled acoustic frequencies. The test measures the natural frequencies, mode shapes, and forced response of cylindrical test articles in contact with fluid-filled cylindrical and/or annular cavities. The test article is excited with a stinger and the fluid-loaded response is acquired using a laser-doppler vibrometer. The experimentally determined fluid-loaded natural frequencies are compared directly to the results of the analytical model. Due to the geometric configuration of the test article, the analytical model is found to be valid for natural modes with circumferential wave numbers greater than four. In the case of these modes, the natural frequencies predicted by the analytical model demonstrate excellent agreement with the experimentally determined natural frequencies.

Hydrodynamic Radii of Intrinsically Disordered Proteins Determined from Experimental Polyproline II Propensities

PubMed Central

Tomasso, Maria E.; Tarver, Micheal J.; Devarajan, Deepa; Whitten, Steven T.

2016-01-01

The properties of disordered proteins are thought to depend on intrinsic conformational propensities for polyproline II (PP II) structure. While intrinsic PP II propensities have been measured for the common biological amino acids in short peptides, the ability of these experimentally determined propensities to quantitatively reproduce structural behavior in intrinsically disordered proteins (IDPs) has not been established. Presented here are results from molecular simulations of disordered proteins showing that the hydrodynamic radius (R h) can be predicted from experimental PP II propensities with good agreement, even when charge-based considerations are omitted. The simulations demonstrate that R h and chain propensity for PP II structure are linked via a simple power-law scaling relationship, which was tested using the experimental R h of 22 IDPs covering a wide range of peptide lengths, net charge, and sequence composition. Charge effects on R h were found to be generally weak when compared to PP II effects on R h. Results from this study indicate that the hydrodynamic dimensions of IDPs are evidence of considerable sequence-dependent backbone propensities for PP II structure that qualitatively, if not quantitatively, match conformational propensities measured in peptides. PMID:26727467

The young person's guide to the PDB.

PubMed

Minor, Wladek; Dauter, Zbigniew; Jaskolski, Mariusz

The Protein Data Bank (PDB), created in 1971 when merely seven protein crystal structures were known, today holds over 120, 000 experimentally-determined three-dimensional models of macromolecules, including gigantic structures comprised of hundreds of thousands of atoms, such as ribosomes and viruses. Most of the deposits come from X-ray crystallography experiments, with important contributions also made by NMR spectroscopy and, recently, by the fast growing Cryo-Electron Microscopy. Although the determination of a macromolecular crystal structure is now facilitated by advanced experimental tools and by sophisticated software, it is still a highly complicated research process requiring specialized training, skill, experience and a bit of luck. Understanding the plethora of structural information provided by the PDB requires that its users (consumers) have at least a rudimentary initiation. This is the purpose of this educational overview.

A structural model of polyglutamine determined from a host-guest method combining experiments and landscape theory.

PubMed

Finke, John M; Cheung, Margaret S; Onuchic, José N

2004-09-01

Modeling the structure of natively disordered peptides has proved difficult due to the lack of structural information on these peptides. In this work, we use a novel application of the host-guest method, combining folding theory with experiments, to model the structure of natively disordered polyglutamine peptides. Initially, a minimalist molecular model (C(alpha)C(beta)) of CI2 is developed with a structurally based potential and captures many of the folding properties of CI2 determined from experiments. Next, polyglutamine "guest" inserts of increasing length are introduced into the CI2 "host" model and the polyglutamine is modeled to match the resultant change in CI2 thermodynamic stability between simulations and experiments. The polyglutamine model that best mimics the experimental changes in CI2 thermodynamic stability has 1), a beta-strand dihedral preference and 2), an attractive energy between polyglutamine atoms 0.75-times the attractive energy between the CI2 host Go-contacts. When free-energy differences in the CI2 host-guest system are correctly modeled at varying lengths of polyglutamine guest inserts, the kinetic folding rates and structural perturbation of these CI2 insert mutants are also correctly captured in simulations without any additional parameter adjustment. In agreement with experiments, the residues showing structural perturbation are located in the immediate vicinity of the loop insert. The simulated polyglutamine loop insert predominantly adopts extended random coil conformations, a structural model consistent with low resolution experimental methods. The agreement between simulation and experimental CI2 folding rates, CI2 structural perturbation, and polyglutamine insert structure show that this host-guest method can select a physically realistic model for inserted polyglutamine. If other amyloid peptides can be inserted into stable protein hosts and the stabilities of these host-guest mutants determined, this novel host-guest method may prove useful to determine structural preferences of these intractable but biologically relevant protein fragments.

Kernel structures for Clouds

NASA Technical Reports Server (NTRS)

Spafford, Eugene H.; Mckendry, Martin S.

1986-01-01

An overview of the internal structure of the Clouds kernel was presented. An indication of how these structures will interact in the prototype Clouds implementation is given. Many specific details have yet to be determined and await experimentation with an actual working system.

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

PubMed Central

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

2011-01-01

Chlamydia trachomatis is a medically important pathogen that encodes a relatively high percentage of proteins with unknown function. The three-dimensional structure of a protein can be very informative regarding the protein's functional characteristics; however, determining protein structures experimentally can be very challenging. Computational methods that model protein structures with sufficient accuracy to facilitate functional studies have had notable successes. To evaluate the accuracy and potential impact of computational protein structure modeling of hypothetical proteins encoded by Chlamydia, a successful computational method termed I-TASSER was utilized to model the three-dimensional structure of a hypothetical protein encoded by open reading frame (ORF) CT296. CT296 has been reported to exhibit functional properties of a divalent cation transcription repressor (DcrA), with similarity to the Escherichia coli iron-responsive transcriptional repressor, Fur. Unexpectedly, the I-TASSER model of CT296 exhibited no structural similarity to any DNA-interacting proteins or motifs. To validate the I-TASSER-generated model, the structure of CT296 was solved experimentally using X-ray crystallography. Impressively, the ab initio I-TASSER-generated model closely matched (2.72-Å Cα root mean square deviation [RMSD]) the high-resolution (1.8-Å) crystal structure of CT296. Modeled and experimentally determined structures of CT296 share structural characteristics of non-heme Fe(II) 2-oxoglutarate-dependent enzymes, although key enzymatic residues are not conserved, suggesting a unique biochemical process is likely associated with CT296 function. Additionally, functional analyses did not support prior reports that CT296 has properties shared with divalent cation repressors such as Fur. PMID:21965559

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

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

Kemege, Kyle E.; Hickey, John M.; Lovell, Scott

2012-02-13

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

Damage of composite structures: Detection technique, dynamic response and residual strength

NASA Astrophysics Data System (ADS)

Lestari, Wahyu

2001-10-01

Reliable and accurate health monitoring techniques can prevent catastrophic failures of structures. Conventional damage detection methods are based on visual or localized experimental methods and very often require prior information concerning the vicinity of the damage or defect. The structure must also be readily accessible for inspections. The techniques are also labor intensive. In comparison to these methods, health-monitoring techniques that are based on the structural dynamic response offers unique information on failure of structures. However, systematic relations between the experimental data and the defect are not available and frequently, the number of vibration modes needed for an accurate identification of defects is much higher than the number of modes that can be readily identified in the experiment. These motivated us to develop an experimental data based detection method with systematic relationships between the experimentally identified information and the analytical or mathematical model representing the defective structures. The developed technique use changes in vibrational curvature modes and natural frequencies. To avoid misinterpretation of the identified information, we also need to understand the effects of defects on the structural dynamic response prior to developing health-monitoring techniques. In this thesis work we focus on two type of defects in composite structures, namely delamination and edge notch like defect. Effects of nonlinearity due to the presence of defect and due to the axial stretching are studied for beams with delamination. Once defects are detected in a structure, next concern is determining the effects of the defects on the strength of the structure and its residual stiffness under dynamic loading. In this thesis, energy release rate due to dynamic loading in a delaminated structure is studied, which will be a foundation toward determining the residual strength of the structure.

Automated determination of fibrillar structures by simultaneous model building and fiber diffraction refinement.

PubMed

Potrzebowski, Wojciech; André, Ingemar

2015-07-01

For highly oriented fibrillar molecules, three-dimensional structures can often be determined from X-ray fiber diffraction data. However, because of limited information content, structure determination and validation can be challenging. We demonstrate that automated structure determination of protein fibers can be achieved by guiding the building of macromolecular models with fiber diffraction data. We illustrate the power of our approach by determining the structures of six bacteriophage viruses de novo using fiber diffraction data alone and together with solid-state NMR data. Furthermore, we demonstrate the feasibility of molecular replacement from monomeric and fibrillar templates by solving the structure of a plant virus using homology modeling and protein-protein docking. The generated models explain the experimental data to the same degree as deposited reference structures but with improved structural quality. We also developed a cross-validation method for model selection. The results highlight the power of fiber diffraction data as structural constraints.

Document boundary determination using structural and lexical analysis

NASA Astrophysics Data System (ADS)

Taghva, Kazem; Cartright, Marc-Allen

2009-01-01

The document boundary determination problem is the process of identifying individual documents in a stack of papers. In this paper, we report on a classification system for automation of this process. The system employs features based on document structure and lexical content. We also report on experimental results to support the effectiveness of this system.

The Scientific Program of the U.S. Naval Research Laboratory

DTIC Science & Technology

1958-07-01

systems, using mock-ups and simulated inputs. (2) Experimental determination of the quantitative parameters of systems, such as data-handling ability, time...naval service of equipment on ships, planes, and mis- siles are recorded, analyzed, and simulated . Methods are developed for the improve- ment of...H01 - NUCLEAR CONSTITUENTS AND STRUCTURE Theoretical and experimental studies concerned with elementary particles , field theory, nuclear structure

HalX: an open-source LIMS (Laboratory Information Management System) for small- to large-scale laboratories.

PubMed

Prilusky, Jaime; Oueillet, Eric; Ulryck, Nathalie; Pajon, Anne; Bernauer, Julie; Krimm, Isabelle; Quevillon-Cheruel, Sophie; Leulliot, Nicolas; Graille, Marc; Liger, Dominique; Trésaugues, Lionel; Sussman, Joel L; Janin, Joël; van Tilbeurgh, Herman; Poupon, Anne

2005-06-01

Structural genomics aims at the establishment of a universal protein-fold dictionary through systematic structure determination either by NMR or X-ray crystallography. In order to catch up with the explosive amount of protein sequence data, the structural biology laboratories are spurred to increase the speed of the structure-determination process. To achieve this goal, high-throughput robotic approaches are increasingly used in all the steps leading from cloning to data collection and even structure interpretation is becoming more and more automatic. The progress made in these areas has begun to have a significant impact on the more 'classical' structural biology laboratories, dramatically increasing the number of individual experiments. This automation creates the need for efficient data management. Here, a new piece of software, HalX, designed as an 'electronic lab book' that aims at (i) storage and (ii) easy access and use of all experimental data is presented. This should lead to much improved management and tracking of structural genomics experimental data.

Problems in obtaining perfect images by single-particle electron cryomicroscopy of biological structures in amorphous ice.

PubMed

Henderson, Richard; McMullan, Greg

2013-02-01

Theoretical considerations together with simulations of single-particle electron cryomicroscopy images of biological assemblies in ice demonstrate that atomic structures should be obtainable from images of a few thousand asymmetric units, provided the molecular weight of the whole assembly being studied is greater than the minimum needed for accurate position and orientation determination. However, with present methods of specimen preparation and current microscope and detector technologies, many more particles are needed, and the alignment of smaller assemblies is difficult or impossible. Only larger structures, with enough signal to allow good orientation determination and with enough images to allow averaging of many hundreds of thousands or even millions of asymmetric units, have successfully produced high-resolution maps. In this review, we compare the contrast of experimental electron cryomicroscopy images of two smaller molecular assemblies, namely apoferritin and beta-galactosidase, with that expected from perfect simulated images calculated from their known X-ray structures. We show that the contrast and signal-to-noise ratio of experimental images still require significant improvement before it will be possible to realize the full potential of single-particle electron cryomicroscopy. In particular, although reasonably good orientations can be obtained for beta-galactosidase, we have been unable to obtain reliable orientation determination from experimental images of apoferritin. Simulations suggest that at least 2-fold improvement of the contrast in experimental images at ~10 Å resolution is needed and should be possible.

Data Mining of Macromolecular Structures.

PubMed

van Beusekom, Bart; Perrakis, Anastassis; Joosten, Robbie P

2016-01-01

The use of macromolecular structures is widespread for a variety of applications, from teaching protein structure principles all the way to ligand optimization in drug development. Applying data mining techniques on these experimentally determined structures requires a highly uniform, standardized structural data source. The Protein Data Bank (PDB) has evolved over the years toward becoming the standard resource for macromolecular structures. However, the process selecting the data most suitable for specific applications is still very much based on personal preferences and understanding of the experimental techniques used to obtain these models. In this chapter, we will first explain the challenges with data standardization, annotation, and uniformity in the PDB entries determined by X-ray crystallography. We then discuss the specific effect that crystallographic data quality and model optimization methods have on structural models and how validation tools can be used to make informed choices. We also discuss specific advantages of using the PDB_REDO databank as a resource for structural data. Finally, we will provide guidelines on how to select the most suitable protein structure models for detailed analysis and how to select a set of structure models suitable for data mining.

Designing synthetic RNAs to determine the relevance of structural motifs in picornavirus IRES elements

NASA Astrophysics Data System (ADS)

Fernandez-Chamorro, Javier; Lozano, Gloria; Garcia-Martin, Juan Antonio; Ramajo, Jorge; Dotu, Ivan; Clote, Peter; Martinez-Salas, Encarnacion

2016-04-01

The function of Internal Ribosome Entry Site (IRES) elements is intimately linked to their RNA structure. Viral IRES elements are organized in modular domains consisting of one or more stem-loops that harbor conserved RNA motifs critical for internal initiation of translation. A conserved motif is the pyrimidine-tract located upstream of the functional initiation codon in type I and II picornavirus IRES. By computationally designing synthetic RNAs to fold into a structure that sequesters the polypyrimidine tract in a hairpin, we establish a correlation between predicted inaccessibility of the pyrimidine tract and IRES activity, as determined in both in vitro and in vivo systems. Our data supports the hypothesis that structural sequestration of the pyrimidine-tract within a stable hairpin inactivates IRES activity, since the stronger the stability of the hairpin the higher the inhibition of protein synthesis. Destabilization of the stem-loop immediately upstream of the pyrimidine-tract also decreases IRES activity. Our work introduces a hybrid computational/experimental method to determine the importance of structural motifs for biological function. Specifically, we show the feasibility of using the software RNAiFold to design synthetic RNAs with particular sequence and structural motifs that permit subsequent experimental determination of the importance of such motifs for biological function.

Identification of Extracellular Segments by Mass Spectrometry Improves Topology Prediction of Transmembrane Proteins.

PubMed

Langó, Tamás; Róna, Gergely; Hunyadi-Gulyás, Éva; Turiák, Lilla; Varga, Julia; Dobson, László; Várady, György; Drahos, László; Vértessy, Beáta G; Medzihradszky, Katalin F; Szakács, Gergely; Tusnády, Gábor E

2017-02-13

Transmembrane proteins play crucial role in signaling, ion transport, nutrient uptake, as well as in maintaining the dynamic equilibrium between the internal and external environment of cells. Despite their important biological functions and abundance, less than 2% of all determined structures are transmembrane proteins. Given the persisting technical difficulties associated with high resolution structure determination of transmembrane proteins, additional methods, including computational and experimental techniques remain vital in promoting our understanding of their topologies, 3D structures, functions and interactions. Here we report a method for the high-throughput determination of extracellular segments of transmembrane proteins based on the identification of surface labeled and biotin captured peptide fragments by LC/MS/MS. We show that reliable identification of extracellular protein segments increases the accuracy and reliability of existing topology prediction algorithms. Using the experimental topology data as constraints, our improved prediction tool provides accurate and reliable topology models for hundreds of human transmembrane proteins.

HIV Structural Database

National Institute of Standards and Technology Data Gateway

SRD 102 HIV Structural Database (Web, free access)   The HIV Protease Structural Database is an archive of experimentally determined 3-D structures of Human Immunodeficiency Virus 1 (HIV-1), Human Immunodeficiency Virus 2 (HIV-2) and Simian Immunodeficiency Virus (SIV) Proteases and their complexes with inhibitors or products of substrate cleavage.

The structure of carbodiimide, HNCNH

NASA Astrophysics Data System (ADS)

Jabs, Wolfgang; Winnewisser, Manfred; Belov, Sergei P.; Lewen, Frank; Maiwald, Frank; Winnewisser, Gisbert

An experimentally determined rs -type structure of HNCNH is reported: rNH = 1.0074 A, rCN = 1.2242 A, /HNC = 118.63, /NCN = 170.63, /HN NH = 88.99 . The number of digits quoted allow for errors with two significant figures. In order to obtain these values we recorded rotational-torsional spectra of HN13CNH, H15NC15NH and DNCND, by using isotopically enriched cyanamide. A chemical equilibrium exists between carbodiimide, HNCNH, and the more stable isomer cyanamide, H2NCN, which strongly favours cyanamide (approximately 1:115 at 110 oC). The expensive C- and N-substituted isotopomers could only be investigated in the millimetre wave region, while for DNCND the far infrared spectrum between 10-350 cm-1 was also recorded. Rotational constants of the three isotopomers, as well as of the parent species, were determined by fitting the assigned spectral transitions to the Watson Hamiltonian in S reduction. Using fitting programs written by Schwendeman and Rudolph, r0, rs and rrho m structures of HNCNH were derived. The experimentally determined structural parameters are compared with an ab initio re structure.

The young person’s guide to the PDB*

PubMed Central

Minor, Wladek; Dauter, Zbigniew; Jaskolski, Mariusz

2017-01-01

The Protein Data Bank (PDB), created in 1971 when merely seven protein crystal structures were known, today holds over 120,000 experimentally-determined three-dimensional models of macromolecules, including gigantic structures comprised of hundreds of thousands of atoms, such as ribosomes and viruses. Most of the deposits come from X-ray crystallography experiments, with important contributions also made by NMR spectroscopy and, recently, by the fast growing Cryo-Electron Microscopy. Although the determination of a macromolecular crystal structure is now facilitated by advanced experimental tools and by sophisticated software, it is still a highly complicated research process requiring specialized training, skill, experience and a bit of luck. Understanding the plethora of structural information provided by the PDB requires that its users (consumers) have at least a rudimentary initiation. This is the purpose of this educational overview. PMID:28132477

Structural modeling of aircraft tires

NASA Technical Reports Server (NTRS)

Clark, S. K.; Dodge, R. N.; Lackey, J. I.; Nybakken, G. H.

1973-01-01

A theoretical and experimental investigation of the feasibility of determining the mechanical properties of aircraft tires from small-scale model tires was accomplished. The theoretical results indicate that the macroscopic static and dynamic mechanical properties of aircraft tires can be accurately determined from the scale model tires although the microscopic and thermal properties of aircraft tires can not. The experimental investigation was conducted on a scale model of a 40 x 12, 14 ply rated, type 7 aircraft tire with a scaling factor of 8.65. The experimental results indicate that the scale model tire exhibited the same static mechanical properties as the prototype tire when compared on a dimensionless basis. The structural modeling concept discussed in this report is believed to be exact for mechanical properties of aircraft tires under static, rolling, and transient conditions.

Structure and Dynamics of Type III Secretion Effector Protein ExoU As determined by SDSL-EPR Spectroscopy in Conjunction with De Novo Protein Folding

PubMed Central

2017-01-01

ExoU is a 74 kDa cytotoxin that undergoes substantial conformational changes as part of its function, that is, it has multiple thermodynamically stable conformations that interchange depending on its environment. Such flexible proteins pose unique challenges to structural biology: (1) not only is it often difficult to determine structures by X-ray crystallography for all biologically relevant conformations because of the flat energy landscape (2) but also experimental conditions can easily perturb the biologically relevant conformation. The first challenge can be overcome by applying orthogonal structural biology techniques that are capable of observing alternative, biologically relevant conformations. The second challenge can be addressed by determining the structure in the same biological state with two independent techniques under different experimental conditions. If both techniques converge to the same structural model, the confidence that an unperturbed biologically relevant conformation is observed increases. To this end, we determine the structure of the C-terminal domain of the effector protein, ExoU, from data obtained by electron paramagnetic resonance spectroscopy in conjunction with site-directed spin labeling and in silico de novo structure determination. Our protocol encompasses a multimodule approach, consisting of low-resolution topology sampling, clustering, and high-resolution refinement. The resulting model was compared with an ExoU model in complex with its chaperone SpcU obtained previously by X-ray crystallography. The two models converged to a minimal RMSD100 of 3.2 Å, providing evidence that the unbound structure of ExoU matches the fold observed in complex with SpcU. PMID:28691114

A semi-supervised learning approach for RNA secondary structure prediction.

PubMed

Yonemoto, Haruka; Asai, Kiyoshi; Hamada, Michiaki

2015-08-01

RNA secondary structure prediction is a key technology in RNA bioinformatics. Most algorithms for RNA secondary structure prediction use probabilistic models, in which the model parameters are trained with reliable RNA secondary structures. Because of the difficulty of determining RNA secondary structures by experimental procedures, such as NMR or X-ray crystal structural analyses, there are still many RNA sequences that could be useful for training whose secondary structures have not been experimentally determined. In this paper, we introduce a novel semi-supervised learning approach for training parameters in a probabilistic model of RNA secondary structures in which we employ not only RNA sequences with annotated secondary structures but also ones with unknown secondary structures. Our model is based on a hybrid of generative (stochastic context-free grammars) and discriminative models (conditional random fields) that has been successfully applied to natural language processing. Computational experiments indicate that the accuracy of secondary structure prediction is improved by incorporating RNA sequences with unknown secondary structures into training. To our knowledge, this is the first study of a semi-supervised learning approach for RNA secondary structure prediction. This technique will be useful when the number of reliable structures is limited. Copyright © 2015 Elsevier Ltd. All rights reserved.

Quantifying Nucleic Acid Ensembles with X-ray Scattering Interferometry.

PubMed

Shi, Xuesong; Bonilla, Steve; Herschlag, Daniel; Harbury, Pehr

2015-01-01

The conformational ensemble of a macromolecule is the complete description of the macromolecule's solution structures and can reveal important aspects of macromolecular folding, recognition, and function. However, most experimental approaches determine an average or predominant structure, or follow transitions between states that each can only be described by an average structure. Ensembles have been extremely difficult to experimentally characterize. We present the unique advantages and capabilities of a new biophysical technique, X-ray scattering interferometry (XSI), for probing and quantifying structural ensembles. XSI measures the interference of scattered waves from two heavy metal probes attached site specifically to a macromolecule. A Fourier transform of the interference pattern gives the fractional abundance of different probe separations directly representing the multiple conformation states populated by the macromolecule. These probe-probe distance distributions can then be used to define the structural ensemble of the macromolecule. XSI provides accurate, calibrated distance in a model-independent fashion with angstrom scale sensitivity in distances. XSI data can be compared in a straightforward manner to atomic coordinates determined experimentally or predicted by molecular dynamics simulations. We describe the conceptual framework for XSI and provide a detailed protocol for carrying out an XSI experiment. © 2015 Elsevier Inc. All rights reserved.

Predicting gaseous reaction rates of short chain chlorinated paraffins with ·OH: overcoming the difficulty in experimental determination.

PubMed

Li, Chao; Xie, Hong-Bin; Chen, Jingwen; Yang, Xianhai; Zhang, Yifei; Qiao, Xianliang

2014-12-02

Short chain chlorinated paraffins (SCCPs) are under evaluation for inclusion in the Stockholm Convention on persistent organic pollutants. However, information on their reaction rate constants with gaseous ·OH (kOH) is unavailable, limiting the evaluation of their persistence in the atmosphere. Experimental determination of kOH is confined by the unavailability of authentic chemical standards for some SCCP congeners. In this study, we evaluated and selected density functional theory (DFT) methods to predict kOH of SCCPs, by comparing the experimental kOH values of six polychlorinated alkanes (PCAs) with those calculated by the different theoretical methods. We found that the M06-2X/6-311+G(3df,2pd)//B3LYP/6-311 +G(d,p) method is time-effective and can be used to predict kOH of PCAs. Moreover, based on the calculated kOH of nine SCCPs and available experimental kOH values of 22 PCAs with low carbon chain, a quantitative structure-activity relationship (QSAR) model was developed. The molecular structural characteristics determining the ·OH reaction rate were discussed. logkOH was found to negatively correlate with the percentage of chlorine substitutions (Cl%). The DFT calculation method and the QSAR model are important alternatives to the conventional experimental determination of kOH for SCCPs, and are prospective in predicting their persistence in the atmosphere.

Fine structure of heliumlike ions and determination of the fine structure constant.

PubMed

Pachucki, Krzysztof; Yerokhin, Vladimir A

2010-02-19

We report a calculation of the fine-structure splitting in light heliumlike atoms, which accounts for all quantum electrodynamical effects up to order alpha{5} Ry. For the helium atom, we resolve the previously reported disagreement between theory and experiment and determine the fine-structure constant with an accuracy of 31 ppb. The calculational results are extensively checked by comparison with the experimental data for different nuclear charges and by evaluation of the hydrogenic limit of individual corrections.

Determination of an ensemble of structures representing the intermediate state of the bacterial immunity protein Im7.

PubMed

Gsponer, Joerg; Hopearuoho, Harri; Whittaker, Sara B-M; Spence, Graham R; Moore, Geoffrey R; Paci, Emanuele; Radford, Sheena E; Vendruscolo, Michele

2006-01-03

We present a detailed structural characterization of the intermediate state populated during the folding and unfolding of the bacterial immunity protein Im7. We achieve this result by incorporating a variety of experimental data available for this species in molecular dynamics simulations. First, we define the structure of the exchange-competent intermediate state of Im7 by using equilibrium hydrogen-exchange protection factors. Second, we use this ensemble to predict Phi-values and compare the results with the experimentally determined Phi-values of the kinetic refolding intermediate. Third, we predict chemical-shift measurements and compare them with the measured chemical shifts of a mutational variant of Im7 for which the kinetic folding intermediate is the most stable state populated at equilibrium. Remarkably, we found that the properties of the latter two species are predicted with high accuracy from the exchange-competent intermediate that we determined, suggesting that these three states are characterized by a similar architecture in which helices I, II, and IV are aligned in a native-like, but reorganized, manner. Furthermore, the structural ensemble that we obtained enabled us to rationalize the results of tryptophan fluorescence experiments in the WT protein and a series of mutational variants. The results show that the integration of diverse sets of experimental data at relatively low structural resolution is a powerful approach that can provide insights into the structural organization of this conformationally heterogeneous three-helix intermediate with unprecedented detail and highlight the importance of both native and non-native interactions in stabilizing its structure.

Fingerprint-Based Structure Retrieval Using Electron Density

PubMed Central

Yin, Shuangye; Dokholyan, Nikolay V.

2010-01-01

We present a computational approach that can quickly search a large protein structural database to identify structures that fit a given electron density, such as determined by cryo-electron microscopy. We use geometric invariants (fingerprints) constructed using 3D Zernike moments to describe the electron density, and reduce the problem of fitting of the structure to the electron density to simple fingerprint comparison. Using this approach, we are able to screen the entire Protein Data Bank and identify structures that fit two experimental electron densities determined by cryo-electron microscopy. PMID:21287628

Fingerprint-based structure retrieval using electron density.

PubMed

Yin, Shuangye; Dokholyan, Nikolay V

2011-03-01

We present a computational approach that can quickly search a large protein structural database to identify structures that fit a given electron density, such as determined by cryo-electron microscopy. We use geometric invariants (fingerprints) constructed using 3D Zernike moments to describe the electron density, and reduce the problem of fitting of the structure to the electron density to simple fingerprint comparison. Using this approach, we are able to screen the entire Protein Data Bank and identify structures that fit two experimental electron densities determined by cryo-electron microscopy. Copyright © 2010 Wiley-Liss, Inc.

Experimental Determination of Aerodynamic Damping in a Three-Stage Transonic Axial-Flow Compressor. Degree awarded by Case Western Reserve Univ.

NASA Technical Reports Server (NTRS)

Newman, Frederick A.

1988-01-01

Rotor blade aerodynamic damping is experimentally determined in a three-stage transonic axial flow compressor having design aerodynamic performance goals of 4.5:1 pressure ratio and 65.5 lbm/sec weight flow. The combined damping associated with each mode is determined by a least squares fit of a single degree of freedom system transfer function to the nonsynchronous portion of the rotor blade strain gauge output power spectra. The combined damping consists of aerodynamic and structural and mechanical damping. The aerodynamic damping varies linearly with the inlet total pressure for a given equivalent speed, equivalent mass flow, and pressure ratio while structural and mechanical damping are assumed to be constant. The combined damping is determined at three inlet total pressure levels to obtain the aerodynamic damping. The third stage rotor blade aerodynamic damping is presented and discussed for 70, 80, 90, and 100 percent design equivalent speed. The compressor overall performance and experimental Campbell diagrams for the third stage rotor blade row are also presented.

Seven-year responses of trees to experimental hurricane effects in a tropical rainforest, Puerto Rico

Treesearch

Jess K. Zimmerman; James Aaron Hogan; Aaron B. Shiels; John E. Bithorn; Samuel Matta Carmona; Nicholas Brokaw

2014-01-01

We experimentally manipulated key components of severe hurricane disturbance, canopy openness and detritus deposition, to determine the independent and interactive effects of these components on tree recruitment, forest structure, and diversity in a wet tropical forest in the Luquillo Experimental Forest, Puerto Rico. Canopy openness was increased by trimming branches...

Experimental determination of thermodynamic equilibrium in biocatalytic transamination.

PubMed

Tufvesson, Pär; Jensen, Jacob S; Kroutil, Wolfgang; Woodley, John M

2012-08-01

The equilibrium constant is a critical parameter for making rational design choices in biocatalytic transamination for the synthesis of chiral amines. However, very few reports are available in the scientific literature determining the equilibrium constant (K) for the transamination of ketones. Various methods for determining (or estimating) equilibrium have previously been suggested, both experimental as well as computational (based on group contribution methods). However, none of these were found suitable for determining the equilibrium constant for the transamination of ketones. Therefore, in this communication we suggest a simple experimental methodology which we hope will stimulate more accurate determination of thermodynamic equilibria when reporting the results of transaminase-catalyzed reactions in order to increase understanding of the relationship between substrate and product molecular structure on reaction thermodynamics. Copyright © 2012 Wiley Periodicals, Inc.

Modeling the assembly order of multimeric heteroprotein complexes

PubMed Central

Esquivel-Rodriguez, Juan; Terashi, Genki; Christoffer, Charles; Shin, Woong-Hee

2018-01-01

Protein-protein interactions are the cornerstone of numerous biological processes. Although an increasing number of protein complex structures have been determined using experimental methods, relatively fewer studies have been performed to determine the assembly order of complexes. In addition to the insights into the molecular mechanisms of biological function provided by the structure of a complex, knowing the assembly order is important for understanding the process of complex formation. Assembly order is also practically useful for constructing subcomplexes as a step toward solving the entire complex experimentally, designing artificial protein complexes, and developing drugs that interrupt a critical step in the complex assembly. There are several experimental methods for determining the assembly order of complexes; however, these techniques are resource-intensive. Here, we present a computational method that predicts the assembly order of protein complexes by building the complex structure. The method, named Path-LzerD, uses a multimeric protein docking algorithm that assembles a protein complex structure from individual subunit structures and predicts assembly order by observing the simulated assembly process of the complex. Benchmarked on a dataset of complexes with experimental evidence of assembly order, Path-LZerD was successful in predicting the assembly pathway for the majority of the cases. Moreover, when compared with a simple approach that infers the assembly path from the buried surface area of subunits in the native complex, Path-LZerD has the strong advantage that it can be used for cases where the complex structure is not known. The path prediction accuracy decreased when starting from unbound monomers, particularly for larger complexes of five or more subunits, for which only a part of the assembly path was correctly identified. As the first method of its kind, Path-LZerD opens a new area of computational protein structure modeling and will be an indispensable approach for studying protein complexes. PMID:29329283

Modeling the assembly order of multimeric heteroprotein complexes.

PubMed

Peterson, Lenna X; Togawa, Yoichiro; Esquivel-Rodriguez, Juan; Terashi, Genki; Christoffer, Charles; Roy, Amitava; Shin, Woong-Hee; Kihara, Daisuke

2018-01-01

Protein-protein interactions are the cornerstone of numerous biological processes. Although an increasing number of protein complex structures have been determined using experimental methods, relatively fewer studies have been performed to determine the assembly order of complexes. In addition to the insights into the molecular mechanisms of biological function provided by the structure of a complex, knowing the assembly order is important for understanding the process of complex formation. Assembly order is also practically useful for constructing subcomplexes as a step toward solving the entire complex experimentally, designing artificial protein complexes, and developing drugs that interrupt a critical step in the complex assembly. There are several experimental methods for determining the assembly order of complexes; however, these techniques are resource-intensive. Here, we present a computational method that predicts the assembly order of protein complexes by building the complex structure. The method, named Path-LzerD, uses a multimeric protein docking algorithm that assembles a protein complex structure from individual subunit structures and predicts assembly order by observing the simulated assembly process of the complex. Benchmarked on a dataset of complexes with experimental evidence of assembly order, Path-LZerD was successful in predicting the assembly pathway for the majority of the cases. Moreover, when compared with a simple approach that infers the assembly path from the buried surface area of subunits in the native complex, Path-LZerD has the strong advantage that it can be used for cases where the complex structure is not known. The path prediction accuracy decreased when starting from unbound monomers, particularly for larger complexes of five or more subunits, for which only a part of the assembly path was correctly identified. As the first method of its kind, Path-LZerD opens a new area of computational protein structure modeling and will be an indispensable approach for studying protein complexes.

Local and average structure of Mn- and La-substituted BiFeO3

NASA Astrophysics Data System (ADS)

Jiang, Bo; Selbach, Sverre M.

2017-06-01

The local and average structure of solid solutions of the multiferroic perovskite BiFeO3 is investigated by synchrotron X-ray diffraction (XRD) and electron density functional theory (DFT) calculations. The average experimental structure is determined by Rietveld refinement and the local structure by total scattering data analyzed in real space with the pair distribution function (PDF) method. With equal concentrations of La on the Bi site or Mn on the Fe site, La causes larger structural distortions than Mn. Structural models based on DFT relaxed geometry give an improved fit to experimental PDFs compared to models constrained by the space group symmetry. Berry phase calculations predict a higher ferroelectric polarization than the experimental literature values, reflecting that structural disorder is not captured in either average structure space group models or DFT calculations with artificial long range order imposed by periodic boundary conditions. Only by including point defects in a supercell, here Bi vacancies, can DFT calculations reproduce the literature results on the structure and ferroelectric polarization of Mn-substituted BiFeO3. The combination of local and average structure sensitive experimental methods with DFT calculations is useful for illuminating the structure-property-composition relationships in complex functional oxides with local structural distortions.

Local and average structure of Mn- and La-substituted BiFeO 3

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

Jiang, Bo; Selbach, Sverre M.

2017-06-01

The local and average structure of solid solutions of the multiferroic perovskite BiFeO 3 is investigated by synchrotron X-ray diffraction (XRD) and electron density functional theory (DFT) calculations. The average experimental structure is determined by Rietveld refinement and the local structure by total scattering data analyzed in real space with the pair distribution function (PDF) method. With equal concentrations of La on the Bi site or Mn on the Fe site, La causes larger structural distortions than Mn. Structural models based on DFT relaxed geometry give an improved fit to experimental PDFs compared to models constrained by the space groupmore » symmetry. Berry phase calculations predict a higher ferroelectric polarization than the experimental literature values, reflecting that structural disorder is not captured in either average structure space group models or DFT calculations with artificial long range order imposed by periodic boundary conditions. Only by including point defects in a supercell, here Bi vacancies, can DFT calculations reproduce the literature results on the structure and ferroelectric polarization of Mn-substituted BiFeO 3. The combination of local and average structure sensitive experimental methods with DFT calculations is useful for illuminating the structure-property-composition relationships in complex functional oxides with local structural distortions.« less

Taking structure searches to the next dimension.

PubMed

Schafferhans, Andrea; Rost, Burkhard

2014-07-08

Structure comparisons are now the first step when a new experimental high-resolution protein structure has been determined. In this issue of Structure, Wiederstein and colleagues describe their latest tool for comparing structures, which gives us the unprecedented power to discover crucial structural connections between whole complexes of proteins in the full structural database in real time. Copyright © 2014 Elsevier Ltd. All rights reserved.

Data archiving and availability in an era of open science.

PubMed

Baker, Edward N

2017-01-01

The importance of preserving and making available the original experimental data underlying biological structural models is discussed, both for crystallography, where the raw data images pose particular challenges, and for other structure determination techniques.

Structural and electronic properties of L-amino acids

NASA Astrophysics Data System (ADS)

Tulip, P. R.; Clark, S. J.

2005-05-01

The structural and electronic properties of four L-amino acids alanine, leucine, isoleucine, and valine have been investigated using density functional theory (DFT) and the generalized gradient approximation. Within the crystals, it is found that the constituent molecules adopt zwitterionic configurations, in agreement with experimental work. Lattice constants are found to be in good agreement with experimentally determined values, although certain discrepancies do exist due to the description of van der Waals interactions. We find that these materials possess wide DFT band gaps in the region of 5 eV, with electrons highly localized to the constituent molecules. It is found that the main mechanisms behind crystal formation are dipolar interactions and hydrogen bonding of a primarily electrostatic character, in agreement with current biochemical understanding of these systems. The electronic structure suggests that the amine and carboxy functional groups are dominant in determining band structure.

Structural studies of homoisoflavonoids: NMR spectroscopy, X-ray diffraction, and theoretical calculations

NASA Astrophysics Data System (ADS)

Sievänen, Elina; Toušek, Jaromír; Lunerová, Kamila; Marek, Jaromír; Jankovská, Dagmar; Dvorská, Margita; Marek, Radek

2010-08-01

In this article we present a detailed structural investigation for five homoisoflavonoids, molecules important from the pharmacological point of view. For studying the electron distribution as well as its influence on the physicochemical properties, NMR spectroscopy, X-ray diffraction, and theoretical calculations have been used. Nuclear magnetic shieldings obtained by using DFT calculations for optimized molecular geometries are correlated with the experimentally determined chemical shifts. The theoretical data are well in agreement with the experimental values. The single crystal X-ray structures of homoisoflavonoid derivatives 1, 3, and 4 have been solved. The molecular geometries and crystal packing determined by X-ray diffraction are used for characterizing the intermolecular interactions. Electron distribution is crucial for the stability of radicals and hence the antioxidant efficiency of flavonoid structures. The hydrogen bonding governs the formation of complexes of homoisoflavonoids with biological targets.

Three-Dimensional Molecular Modeling of a Diverse Range of SC Clan Serine Proteases

PubMed Central

Laskar, Aparna; Chatterjee, Aniruddha; Chatterjee, Somnath; Rodger, Euan J.

2012-01-01

Serine proteases are involved in a variety of biological processes and are classified into clans sharing structural homology. Although various three-dimensional structures of SC clan proteases have been experimentally determined, they are mostly bacterial and animal proteases, with some from archaea, plants, and fungi, and as yet no structures have been determined for protozoa. To bridge this gap, we have used molecular modeling techniques to investigate the structural properties of different SC clan serine proteases from a diverse range of taxa. Either SWISS-MODEL was used for homology-based structure prediction or the LOOPP server was used for threading-based structure prediction. The predicted models were refined using Insight II and SCRWL and validated against experimental structures. Investigation of secondary structures and electrostatic surface potential was performed using MOLMOL. The structural geometry of the catalytic core shows clear deviations between taxa, but the relative positions of the catalytic triad residues were conserved. Evolutionary divergence was also exhibited by large variation in secondary structure features outside the core, differences in overall amino acid distribution, and unique surface electrostatic potential patterns between species. Encompassing a wide range of taxa, our structural analysis provides an evolutionary perspective on SC clan serine proteases. PMID:23213528

Purely Structural Protein Scoring Functions Using Support Vector Machine and Ensemble Learning.

PubMed

Mirzaei, Shokoufeh; Sidi, Tomer; Keasar, Chen; Crivelli, Silvia

2016-08-24

The function of a protein is determined by its structure, which creates a need for efficient methods of protein structure determination to advance scientific and medical research. Because current experimental structure determination methods carry a high price tag, computational predictions are highly desirable. Given a protein sequence, computational methods produce numerous 3D structures known as decoys. However, selection of the best quality decoys is challenging as the end users can handle only a few ones. Therefore, scoring functions are central to decoy selection. They combine measurable features into a single number indicator of decoy quality. Unfortunately, current scoring functions do not consistently select the best decoys. Machine learning techniques offer great potential to improve decoy scoring. This paper presents two machine-learning based scoring functions to predict the quality of proteins structures, i.e., the similarity between the predicted structure and the experimental one without knowing the latter. We use different metrics to compare these scoring functions against three state-of-the-art scores. This is a first attempt at comparing different scoring functions using the same non-redundant dataset for training and testing and the same features. The results show that adding informative features may be more significant than the method used.

Expertise in Problem Solving.

DTIC Science & Technology

1981-05-18

determining our subsequent experimental procedure. Figures 2 - Ishow two samples of protocols, one from Expert R.E. and the oth,_ Irom Novice C.H., both on...in press). This is also true of older versus younger children (Chi, 1976), and fast as compared with slow learners. For example, good readers can...Using chunks as a defining unit of knowledge structure, Chase and Simon set out to experimentally identify the structure and size of chunks in the

Structural Insights into Bound Water in Crystalline Amino Acids: Experimental and Theoretical (17)O NMR.

PubMed

Michaelis, Vladimir K; Keeler, Eric G; Ong, Ta-Chung; Craigen, Kimberley N; Penzel, Susanne; Wren, John E C; Kroeker, Scott; Griffin, Robert G

2015-06-25

We demonstrate here that the (17)O NMR properties of bound water in a series of amino acids and dipeptides can be determined with a combination of nonspinning and magic-angle spinning experiments using a range of magnetic field strengths from 9.4 to 21.1 T. Furthermore, we propose a (17)O chemical shift fingerprint region for bound water molecules in biological solids that is well outside the previously determined ranges for carbonyl, carboxylic, and hydroxyl oxygens, thereby offering the ability to resolve multiple (17)O environments using rapid one-dimensional NMR techniques. Finally, we compare our experimental data against quantum chemical calculations using GIPAW and hybrid-DFT, finding intriguing discrepancies between the electric field gradients calculated from structures determined by X-ray and neutron diffraction.

SFG analysis of surface bound proteins: a route towards structure determination.

PubMed

Weidner, Tobias; Castner, David G

2013-08-14

The surface of a material is rapidly covered with proteins once that material is placed in a biological environment. The structure and function of these bound proteins play a key role in the interactions and communications of the material with the biological environment. Thus, it is crucial to gain a molecular level understanding of surface bound protein structure. While X-ray diffraction and solution phase NMR methods are well established for determining the structure of proteins in the crystalline or solution phase, there is not a corresponding single technique that can provide the same level of structural detail about proteins at surfaces or interfaces. However, recent advances in sum frequency generation (SFG) vibrational spectroscopy have significantly increased our ability to obtain structural information about surface bound proteins and peptides. A multi-technique approach of combining SFG with (1) protein engineering methods to selectively introduce mutations and isotopic labels, (2) other experimental methods such as time-of-flight secondary ion mass spectrometry (ToF-SIMS) and near edge X-ray absorption fine structure (NEXAFS) to provide complementary information, and (3) molecular dynamic (MD) simulations to extend the molecular level experimental results is a particularly promising route for structural characterization of surface bound proteins and peptides. By using model peptides and small proteins with well-defined structures, methods have been developed to determine the orientation of both backbone and side chains to the surface.

SFG analysis of surface bound proteins: A route towards structure determination

PubMed Central

Weidner, Tobias; Castner, David G.

2013-01-01

The surface of a material is rapidly covered with proteins once that material is placed in a biological environment. The structure and function of these bound proteins play a key role in the interactions and communications of the material with the biological environment. Thus, it is crucial to gain a molecular level understanding of surface bound protein structure. While X-ray diffraction and solution phase NMR methods are well established for determining the structure of proteins in the crystalline or solution phase, there is not a corresponding single technique that can provide the same level of structural detail about proteins at surfaces or interfaces. However, recent advances in sum frequency generation (SFG) vibrational spectroscopy have significantly increased our ability to obtain structural information about surface bound proteins and peptides. A multi-technique approach of combining SFG with (1) protein engineering methods to selectively introduce mutations and isotopic labels, (2) other experimental methods such as time-of-flight secondary ion mass spectrometry (ToF-SIMS) and near edge x-ray absorption fine structure (NEXAFS) to provide complementary information, and (3) molecular dynamic (MD) simulations to extend the molecular level experimental results is a particularly promising route for structural characterization of surface bound proteins and peptides. By using model peptides and small proteins with well-defined structures, methods have been developed to determine the orientation of both backbone and side chains to the surface. PMID:23727992

Accurate determination of interfacial protein secondary structure by combining interfacial-sensitive amide I and amide III spectral signals.

PubMed

Ye, Shuji; Li, Hongchun; Yang, Weilai; Luo, Yi

2014-01-29

Accurate determination of protein structures at the interface is essential to understand the nature of interfacial protein interactions, but it can only be done with a few, very limited experimental methods. Here, we demonstrate for the first time that sum frequency generation vibrational spectroscopy can unambiguously differentiate the interfacial protein secondary structures by combining surface-sensitive amide I and amide III spectral signals. This combination offers a powerful tool to directly distinguish random-coil (disordered) and α-helical structures in proteins. From a systematic study on the interactions between several antimicrobial peptides (including LKα14, mastoparan X, cecropin P1, melittin, and pardaxin) and lipid bilayers, it is found that the spectral profiles of the random-coil and α-helical structures are well separated in the amide III spectra, appearing below and above 1260 cm(-1), respectively. For the peptides with a straight backbone chain, the strength ratio for the peaks of the random-coil and α-helical structures shows a distinct linear relationship with the fraction of the disordered structure deduced from independent NMR experiments reported in the literature. It is revealed that increasing the fraction of negatively charged lipids can induce a conformational change of pardaxin from random-coil to α-helical structures. This experimental protocol can be employed for determining the interfacial protein secondary structures and dynamics in situ and in real time without extraneous labels.

Detonation product EOS studies: Using ISLS to refine CHEETAH

NASA Astrophysics Data System (ADS)

Zaug, Joseph; Fried, Larry; Hansen, Donald

2001-06-01

Knowledge of an effective interatomic potential function underlies any effort to predict or rationalize the properties of solids and liquids. The experiments we undertake are directed towards determination of equilibrium and dynamic properties of simple fluids at densities sufficiently high that traditional computational methods and semi-empirical forms successful at ambient conditions may require reconsideration. In this paper we present high-pressure and temperature experimental sound speed data on a suite of non-ideal simple fluids and fluid mixtures. Impulsive Stimulated Light Scattering conducted in the diamond-anvil cell offers an experimental approach to determine cross-pair potential interactions through equation of state determinations. In addition the kinetics of structural relaxation in fluids can be studied. We compare our experimental results with our thermochemical computational model CHEETAH. Computational models are systematically improved with each addition of experimental data. Experimentally grounded computational models provide a good basis to confidently understand the chemical nature of reactions at extreme conditions.

Transmission electron diffraction determination of the Ge(001)-(2 × 1) surface structure

NASA Astrophysics Data System (ADS)

Collazo-Davila, C.; Grozea, D.; Landree, E.; Marks, L. D.

1997-04-01

The lateral displacements in the Ge(001)-(2 × 1) surface reconstruction have been determined using transmission electron diffraction (TED). The best-fit model includes displacements extending six layers into the bulk. The atomic positions found agree with X-ray studies to within a few hundredths of an ångström. With the positions determined so precisely, it is suggested that the Ge(001)-(2 × 1) surface can now serve as a standard for comparison with theoretical surface structure calculations. The results from the currently available theoretical studies on the surface are compared with the experimentally determined structure.

Structural features of microRNA (miRNA) precursors and their relevance to miRNA biogenesis and small interfering RNA/short hairpin RNA design.

PubMed

Krol, Jacek; Sobczak, Krzysztof; Wilczynska, Urszula; Drath, Maria; Jasinska, Anna; Kaczynska, Danuta; Krzyzosiak, Wlodzimierz J

2004-10-01

We have established the structures of 10 human microRNA (miRNA) precursors using biochemical methods. Eight of these structures turned out to be different from those that were computer-predicted. The differences localized in the terminal loop region and at the opposite side of the precursor hairpin stem. We have analyzed the features of these structures from the perspectives of miRNA biogenesis and active strand selection. We demonstrated the different thermodynamic stability profiles for pre-miRNA hairpins harboring miRNAs at their 5'- and 3'-sides and discussed their functional implications. Our results showed that miRNA prediction based on predicted precursor structures may give ambiguous results, and the success rate is significantly higher for the experimentally determined structures. On the other hand, the differences between the predicted and experimentally determined structures did not affect the stability of termini produced through "conceptual dicing." This result confirms the value of thermodynamic analysis based on mfold as a predictor of strand section by RNAi-induced silencing complex (RISC).

Supervised Machine-Learning-Based Determination of Three-Dimensional Structure of Metallic Nanoparticles

DOE PAGES

Timoshenko, Janis; Lu, Deyu; Lin, Yuewei; ...

2017-09-29

Tracking the structure of heterogeneous catalysts under operando conditions remains a challenge due to the paucity of experimental techniques that can provide atomic-level information for catalytic metal species. Here we report on the use of X-ray absorption near edge structure (XANES) spectroscopy and supervised machine learning (SML) for refining the three-dimensional geometry of metal catalysts. SML is used to unravel the hidden relationship between the XANES features and catalyst geometry. To train our SML method, we rely on ab-initio XANES simulations. Our approach allows one to solve the structure of a metal catalyst from its experimental XANES, as demonstrated heremore » by reconstructing the average size, shape and morphology of well-defined platinum nanoparticles. This method is applicable to the determination of the nanoparticle structure in operando studies and can be generalized to other nanoscale systems. In conclusion, it also allows on-the-fly XANES analysis, and is a promising approach for high-throughput and time-dependent studies.« less

Supervised Machine-Learning-Based Determination of Three-Dimensional Structure of Metallic Nanoparticles

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

Timoshenko, Janis; Lu, Deyu; Lin, Yuewei

Tracking the structure of heterogeneous catalysts under operando conditions remains a challenge due to the paucity of experimental techniques that can provide atomic-level information for catalytic metal species. Here we report on the use of X-ray absorption near edge structure (XANES) spectroscopy and supervised machine learning (SML) for refining the three-dimensional geometry of metal catalysts. SML is used to unravel the hidden relationship between the XANES features and catalyst geometry. To train our SML method, we rely on ab-initio XANES simulations. Our approach allows one to solve the structure of a metal catalyst from its experimental XANES, as demonstrated heremore » by reconstructing the average size, shape and morphology of well-defined platinum nanoparticles. This method is applicable to the determination of the nanoparticle structure in operando studies and can be generalized to other nanoscale systems. In conclusion, it also allows on-the-fly XANES analysis, and is a promising approach for high-throughput and time-dependent studies.« less

On vital aid: the why, what and how of validation

PubMed Central

Kleywegt, Gerard J.

2009-01-01

Limitations to the data and subjectivity in the structure-determination process may cause errors in macromolecular crystal structures. Appropriate validation techniques may be used to reveal problems in structures, ideally before they are analysed, published or deposited. Additionally, such tech­niques may be used a posteriori to assess the (relative) merits of a model by potential users. Weak validation methods and statistics assess how well a model reproduces the information that was used in its construction (i.e. experimental data and prior knowledge). Strong methods and statistics, on the other hand, test how well a model predicts data or information that were not used in the structure-determination process. These may be data that were excluded from the process on purpose, general knowledge about macromolecular structure, information about the biological role and biochemical activity of the molecule under study or its mutants or complexes and predictions that are based on the model and that can be tested experimentally. PMID:19171968

Crystal structure of minoxidil at low temperature and polymorph prediction.

PubMed

Martín-Islán, Africa P; Martín-Ramos, Daniel; Sainz-Díaz, C Ignacio

2008-02-01

An experimental and theoretical investigation on crystal forms of the popular and ubiquitous pharmaceutical Minoxidil is presented here. A new crystallization method is presented for Minoxidil (6-(1-piperidinyl)-2,4-pyrimidinediamide 3-oxide) in ethanol-poly(ethylene glycol), yielding crystals with good quality. The crystal structure is determined at low temperature, with a final R value of 0.035, corresponding to space group P2(1) (monoclinic) with cell dimensions a = 9.357(1) A, b = 8.231(1) A, c = 12.931(2) A, and beta = 90.353(4) degrees . Theoretical calculations of the molecular structure of Minoxidil are set forward using empirical force fields and quantum-mechanical methods. A theoretical prediction for Minoxidil crystal structure shows many possible polymorphs. The predicted crystal structures are compared with X-ray experimental data obtained in our laboratory, and the experimental crystal form is found to be one of the lowest energy polymorphs.

Structural analysis of a set of proteins resulting from a bacterial genomics project.

PubMed

Badger, J; Sauder, J M; Adams, J M; Antonysamy, S; Bain, K; Bergseid, M G; Buchanan, S G; Buchanan, M D; Batiyenko, Y; Christopher, J A; Emtage, S; Eroshkina, A; Feil, I; Furlong, E B; Gajiwala, K S; Gao, X; He, D; Hendle, J; Huber, A; Hoda, K; Kearins, P; Kissinger, C; Laubert, B; Lewis, H A; Lin, J; Loomis, K; Lorimer, D; Louie, G; Maletic, M; Marsh, C D; Miller, I; Molinari, J; Muller-Dieckmann, H J; Newman, J M; Noland, B W; Pagarigan, B; Park, F; Peat, T S; Post, K W; Radojicic, S; Ramos, A; Romero, R; Rutter, M E; Sanderson, W E; Schwinn, K D; Tresser, J; Winhoven, J; Wright, T A; Wu, L; Xu, J; Harris, T J R

2005-09-01

The targets of the Structural GenomiX (SGX) bacterial genomics project were proteins conserved in multiple prokaryotic organisms with no obvious sequence homolog in the Protein Data Bank of known structures. The outcome of this work was 80 structures, covering 60 unique sequences and 49 different genes. Experimental phase determination from proteins incorporating Se-Met was carried out for 45 structures with most of the remainder solved by molecular replacement using members of the experimentally phased set as search models. An automated tool was developed to deposit these structures in the Protein Data Bank, along with the associated X-ray diffraction data (including refined experimental phases) and experimentally confirmed sequences. BLAST comparisons of the SGX structures with structures that had appeared in the Protein Data Bank over the intervening 3.5 years since the SGX target list had been compiled identified homologs for 49 of the 60 unique sequences represented by the SGX structures. This result indicates that, for bacterial structures that are relatively easy to express, purify, and crystallize, the structural coverage of gene space is proceeding rapidly. More distant sequence-structure relationships between the SGX and PDB structures were investigated using PDB-BLAST and Combinatorial Extension (CE). Only one structure, SufD, has a truly unique topology compared to all folds in the PDB. Copyright 2005 Wiley-Liss, Inc.

Application of Nuclear Magnetic Resonance and Hybrid Methods to Structure Determination of Complex Systems.

PubMed

Prischi, Filippo; Pastore, Annalisa

2016-01-01

The current main challenge of Structural Biology is to undertake the structure determination of increasingly complex systems in the attempt to better understand their biological function. As systems become more challenging, however, there is an increasing demand for the parallel use of more than one independent technique to allow pushing the frontiers of structure determination and, at the same time, obtaining independent structural validation. The combination of different Structural Biology methods has been named hybrid approaches. The aim of this review is to critically discuss the most recent examples and new developments that have allowed structure determination or experimentally-based modelling of various molecular complexes selecting them among those that combine the use of nuclear magnetic resonance and small angle scattering techniques. We provide a selective but focused account of some of the most exciting recent approaches and discuss their possible further developments.

Piezoceramic Actuator Placement for Acoustic Control of Panels

NASA Technical Reports Server (NTRS)

Bevan, Jeffrey S.; Turner, Travis L. (Technical Monitor)

2001-01-01

Optimum placement of multiple traditional piezoceramic actuators is determined for active structural acoustic control of flat panels. The structural acoustic response is determined using acoustic radiation filters and structural surface vibration characteristics. Linear Quadratic Regulator (LQR) control is utilized to determine the optimum state feedback gain for active structural acoustic control. The optimum actuator location is determined by minimizing the structural acoustic radiated noise using a modified genetic algorithm. Experimental tests are conducted and compared to analytical results. Anisotropic piezoceramic actuators exhibits enhanced performance when compared to traditional isotropic piezoceramic actuators. As a result of the inherent isotropy, these advanced actuators develop strain along the principal material axis. The orientation of anisotropic actuators is investigated on the effect of structural vibration and acoustic control of curved and flat panels. A fully coupled shallow shell finite element formulation is developed to include anisotropic piezoceramic actuators for shell structures.

Piezoceramic Actuator Placement for Acoustic Control of Panels

NASA Technical Reports Server (NTRS)

Bevan, Jeffrey S.

2000-01-01

Optimum placement of multiple traditional piezoceramic actuators is determined for active structural acoustic control of flat panels. The structural acoustic response is determined using acoustic radiation filters and structural surface vibration characteristics. Linear Quadratic Regulator (LQR) control is utilized to determine the optimum state feedback gain for active structural acoustic control. The optimum actuator location is determined by minimizing the structural acoustic radiated noise using a modified genetic algorithm. Experimental tests are conducted and compared to analytical results. Anisotropic piezoceramic actuators exhibit enhanced performance when compared to traditional isotropic piezoceramic actuators. As a result of the inherent isotropy, these advanced actuators develop strain along the principal material axis. The orientation of anisotropic actuators is investigated on the effect of structural vibration and acoustic control of curved and flat panels. A fully coupled shallow shell finite element formulation is developed to include anisotropic piezoceramic actuators for shell structures.

Stability and Interaction of Coherent Structure in Supersonic Reactive Wakes

NASA Technical Reports Server (NTRS)

Menon, Suresh

1983-01-01

A theoretical formulation and analysis is presented for a study of the stability and interaction of coherent structure in reacting free shear layers. The physical problem under investigation is a premixed hydrogen-oxygen reacting shear layer in the wake of a thin flat plate. The coherent structure is modeled as a periodic disturbance and its stability is determined by the application of linearized hydrodynamic stability theory which results in a generalized eigenvalue problem for reactive flows. Detailed stability analysis of the reactive wake for neutral, symmetrical and antisymmetrical disturbance is presented. Reactive stability criteria is shown to be quite different from classical non-reactive stability. The interaction between the mean flow, coherent structure and fine-scale turbulence is theoretically formulated using the von-Kaman integral technique. Both time-averaging and conditional phase averaging are necessary to separate the three types of motion. The resulting integro-differential equations can then be solved subject to initial conditions with appropriate shape functions. In the laminar flow transition region of interest, the spatial interaction between the mean motion and coherent structure is calculated for both non-reactive and reactive conditions and compared with experimental data wherever available. The fine-scale turbulent motion determined by the application of integral analysis to the fluctuation equations. Since at present this turbulence model is still untested, turbulence is modeled in the interaction problem by a simple algebraic eddy viscosity model. The applicability of the integral turbulence model formulated here is studied parametrically by integrating these equations for the simple case of self-similar mean motion with assumed shape functions. The effect of the motion of the coherent structure is studied and very good agreement is obtained with previous experimental and theoretical works for non-reactive flow. For the reactive case, lack of experimental data made direct comparison difficult. It was determined that the growth rate of the disturbance amplitude is lower for reactive case. The results indicate that the reactive flow stability is in qualitative agreement with experimental observation.

Structurally compliant rocket engine combustion chamber: Experimental and analytical validation

NASA Technical Reports Server (NTRS)

Jankovsky, Robert S.; Arya, Vinod K.; Kazaroff, John M.; Halford, Gary R.

1994-01-01

A new, structurally compliant rocket engine combustion chamber design has been validated through analysis and experiment. Subscale, tubular channel chambers have been cyclically tested and analytically evaluated. Cyclic lives were determined to have a potential for 1000 percent increase over those of rectangular channel designs, the current state of the art. Greater structural compliance in the circumferential direction gave rise to lower thermal strains during hot firing, resulting in lower thermal strain ratcheting and longer predicted fatigue lives. Thermal, structural, and durability analyses of the combustion chamber design, involving cyclic temperatures, strains, and low-cycle fatigue lives, have corroborated the experimental observations.

Determination of the nuclear level densities and radiative strength function for 43 nuclei in the mass interval 28≤A≤200

NASA Astrophysics Data System (ADS)

Knezevic, David; Jovancevic, Nikola; Sukhovoj, Anatoly M.; Mitsyna, Ludmila V.; Krmar, Miodrag; Cong, Vu D.; Hambsch, Franz-Josef; Oberstedt, Stephan; Revay, Zsolt; Stieghorst, Christian; Dragic, Aleksandar

2018-03-01

The determination of nuclear level densities and radiative strength functions is one of the most important tasks in low-energy nuclear physics. Accurate experimental values of these parameters are critical for the study of the fundamental properties of nuclear structure. The step-like structure in the dependence of the level densities p on the excitation energy of nuclei Eex is observed in the two-step gamma cascade measurements for nuclei in the 28 ≤ A ≤ 200 mass region. This characteristic structure can be explained only if a co-existence of quasi-particles and phonons, as well as their interaction in a nucleus, are taken into account in the process of gamma-decay. Here we present a new improvement to the Dubna practical model for the determination of nuclear level densities and radiative strength functions. The new practical model guarantees a good description of the available intensities of the two step gamma cascades, comparable to the experimental data accuracy.

Ellipsometric study of metal-organic chemically vapor deposited III-V semiconductor structures

NASA Technical Reports Server (NTRS)

Alterovitz, Samuel A.; Sekula-Moise, Patricia A.; Sieg, Robert M.; Drotos, Mark N.; Bogner, Nancy A.

1992-01-01

An ellipsometric study of MOCVD-grown layers of AlGaAs and InGaAs in thick films and strained layer complex structures is presented. It is concluded that the ternary composition of thick nonstrained layers can be accurately determined to within experimental errors using numerical algorithms. In the case of complex structures, thickness of all layers and the alloy composition of nonstrained layers can be determined simultaneously, provided that the correlations between parameters is no higher than 0.9.

Numerical modeling of the strain of elastic rubber elements

NASA Astrophysics Data System (ADS)

Moskvichev, E. N.; Porokhin, A. V.; Shcherbakov, I. V.

2017-11-01

A comparative analysis of the results of experimental investigation of mechanical behavior of the rubber sample during biaxial compression testing and numerical simulation results obtained by the finite element method was carried out to determine the correctness of the model applied in the engineering calculations of elastic structural elements made of the rubber. The governing equation represents the five-parameter Mooney-Rivlin model with the constants determined from experimental data. The investigation results showed that these constants reliably describe the mechanical behavior of the material under consideration. The divergence of experimental and numerical results does not exceed 15%.

Ortho and para hydrogen dimers on G/SiC(0001): combined STM and DFT study.

PubMed

Merino, P; Švec, M; Martínez, J I; Mutombo, P; Gonzalez, C; Martín-Gago, J A; de Andres, P L; Jelinek, P

2015-01-01

The hydrogen (H) dimer structures formed upon room-temperature H adsorption on single layer graphene (SLG) grown on SiC(0001) are addressed using a combined theoretical-experimental approach. Our study includes density functional theory (DFT) calculations for the full (6√3 × 6√3)R30° unit cell of the SLG/SiC(0001) substrate and atomically resolved scanning tunneling microscopy images determining simultaneously the graphene lattice and the internal structure of the H adsorbates. We show that H atoms normally group in chemisorbed coupled structures of different sizes and orientations. We make an atomic scale determination of the most stable experimental geometries, the small dimers and ellipsoid-shaped features, and we assign them to hydrogen adsorbed in para dimers and ortho dimers configuration, respectively, through comparison with the theory.

Optimal Experimental Design for Model Discrimination

PubMed Central

Myung, Jay I.; Pitt, Mark A.

2009-01-01

Models of a psychological process can be difficult to discriminate experimentally because it is not easy to determine the values of the critical design variables (e.g., presentation schedule, stimulus structure) that will be most informative in differentiating them. Recent developments in sampling-based search methods in statistics make it possible to determine these values, and thereby identify an optimal experimental design. After describing the method, it is demonstrated in two content areas in cognitive psychology in which models are highly competitive: retention (i.e., forgetting) and categorization. The optimal design is compared with the quality of designs used in the literature. The findings demonstrate that design optimization has the potential to increase the informativeness of the experimental method. PMID:19618983

Experimental determination of satellite bolted joints thermal resistance

NASA Technical Reports Server (NTRS)

Mantelli, Marcia Barbosa Henriques; Basto, Jose Edson

1990-01-01

The thermal resistance was experimentally determined of the bolted joints of the first Brazilian satellite (SCD 01). These joints, used to connect the satellite structural panels, are reproduced in an experimental apparatus, keeping, as much as possible, the actual dimensions and materials. A controlled amount of heat is forced to pass through the joint and the difference of temperature between the panels is measured. The tests are conducted in a vacuum chamber with liquid nitrogen cooled walls, that simulates the space environment. Experimental procedures are used to avoid much heat losses, which are carefully calculated. Important observations about the behavior of the joint thermal resistance with the variation of the mean temperature are made.

Experimental methods and transport models for drug delivery across the blood-brain barrier.

PubMed

Fu, Bingmei M

2012-06-01

The blood-brain barrier (BBB) is a dynamic barrier essential for maintaining the micro-environment of the brain. Although the special anatomical features of the BBB determine its protective role for the central nervous system (CNS) from blood-born neurotoxins, however, the BBB extremely limits the therapeutic efficacy of drugs into the CNS, which greatly hinders the treatment of major brain diseases. This review summarized the unique structures of the BBB, described a variety of in vivo and in vitro experimental methods for determining the transport properties of the BBB, e.g., the permeability of the BBB to water, ions, and solutes including nutrients, therapeutic agents and drug carriers, and presented newly developed mathematical models which quantitatively correlate the anatomical structures of the BBB with its barrier functions. Finally, on the basis of the experimental observations and the quantitative models, several strategies for drug delivery through the BBB were proposed.

Experimental Methods and Transport Models for Drug Delivery across the Blood-Brain Barrier

PubMed Central

Fu, Bingmei M

2017-01-01

The blood-brain barrier (BBB) is a dynamic barrier essential for maintaining the micro-environment of the brain. Although the special anatomical features of the BBB determine its protective role for the central nervous system (CNS) from blood-born neurotoxins, however, the BBB extremely limits the therapeutic efficacy of drugs into the CNS, which greatly hinders the treatment of major brain diseases. This review summarized the unique structures of the BBB, described a variety of in vivo and in vitro experimental methods for determining the transport properties of the BBB, e.g., the permeability of the BBB to water, ions, and solutes including nutrients, therapeutic agents and drug carriers, and presented newly developed mathematical models which quantitatively correlate the anatomical structures of the BBB with its barrier functions. Finally, on the basis of the experimental observations and the quantitative models, several strategies for drug delivery through the BBB were proposed. PMID:22201587

Theoretical and experimental studies of the structure and vibrational spectra of NTO

NASA Astrophysics Data System (ADS)

Sorescu, Dan C.; Sutton, Teressa R. L.; Thompson, Donald L.; Beardall, David; Wight, Charles A.

1996-10-01

The structure and vibrational spectra of the high explosive 5-nitro-2,4-dihydro-3H-1,2,4-triazol-3-one (NTO) have been determined by ab initio molecular orbital calculations at the Hartree-Fock and second-order Møller-Plesset levels and by density functional theory (B3LYP). Experimental frequencies for the molecule have been determined from infrared spectra of pure NTO films and NTO molecules isolated in an argon matrix at 21 K. A force field for gas phase NTO has been obtained based on calculated results at the MP2/6-311G∗∗ level. In addition, a force field for solid state NTO has been constructed using the experimental vibrational frequencies for NTO films and scaled ab initio vibrational frequencies. Differences between the solid state and gas phase results indicate that the environment and preparation procedure exert a marked influence on the spectral characteristics of the NTO molecule.

Detonation Product EOS Studies: Using ISLS to Refine Cheetah

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

Zaug, J M; Howard, W M; Fried, L E

2001-08-08

Knowledge of an effective interatomic potential function underlies any effort to predict or rationalize the properties of solids and liquids. The experiments we undertake are directed towards determination of equilibrium and dynamic properties of simple fluids at densities sufficiently high that traditional computational methods and semi-empirical forms successful at ambient conditions may require reconsideration. In this paper we present high-pressure and temperature experimental sound speed data on a simple fluid, methanol. Impulsive Stimulated Light Scattering (ISLS) conducted on diamond-anvil cell (DAC) encapsulated samples offers an experimental approach to determine cross-pair potential interactions through equation of state determinations. In addition themore » kinetics of structural relaxation in fluids can be studied. We compare our experimental results with our thermochemical computational model Cheetah. Computational models are systematically improved with each addition of experimental data.« less

Teaching Three-Dimensional Structural Chemistry Using Crystal Structure Databases. 4. Examples of Discovery-Based Learning Using the Complete Cambridge Structural Database

ERIC Educational Resources Information Center

Battle, Gary M.; Allen, Frank H.; Ferrence, Gregory M.

2011-01-01

Parts 1 and 2 of this series described the educational value of experimental three-dimensional (3D) chemical structures determined by X-ray crystallography and retrieved from the crystallographic databases. In part 1, we described the information content of the Cambridge Structural Database (CSD) and discussed a representative teaching subset of…

Teaching Three-Dimensional Structural Chemistry Using Crystal Structure Databases. 3. The Cambridge Structural Database System: Information Content and Access Software in Educational Applications

ERIC Educational Resources Information Center

Battle, Gary M.; Allen, Frank H.; Ferrence, Gregory M.

2011-01-01

Parts 1 and 2 of this series described the educational value of experimental three-dimensional (3D) chemical structures determined by X-ray crystallography and retrieved from the crystallographic databases. In part 1, we described the information content of the Cambridge Structural Database (CSD) and discussed a representative teaching subset of…

Leaving Group Ability Observably Affects Transition State Structure in a Single Enzyme Active Site.

PubMed

Roston, Daniel; Demapan, Darren; Cui, Qiang

2016-06-15

A reaction's transition state (TS) structure plays a critical role in determining reactivity and has important implications for the design of catalysts, drugs, and other applications. Here, we explore TS structure in the enzyme alkaline phosphatase using hybrid Quantum Mechanics/Molecular Mechanics simulations. We find that minor perturbations to the substrate have major effects on TS structure and the way the enzyme stabilizes the TS. Substrates with good leaving groups (LGs) have little cleavage of the phosphorus-LG bond at the TS, while substrates with poor LGs have substantial cleavage of that bond. The results predict nonlinear free energy relationships for a single rate-determining step, and substantial differences in kinetic isotope effects for different substrates; both trends were observed in previous experimental studies, although the original interpretations differed from the present model. Moreover, due to different degrees of phosphorus-LG bond cleavage at the TS for different substrates, the LG is stabilized by different interactions at the TS: while a poor LG is directly stabilized by an active site zinc ion, a good LG is mainly stabilized by active site water molecules. Our results demonstrate the considerable plasticity of TS structure and stabilization in enzymes. Furthermore, perturbations to reactivity that probe TS structure experimentally (i.e., substituent effects) may substantially perturb the TS they aim to probe, and thus classical experimental approaches such as free energy relations should be interpreted with care.

Optimal Experimental Design for Model Discrimination

ERIC Educational Resources Information Center

Myung, Jay I.; Pitt, Mark A.

2009-01-01

Models of a psychological process can be difficult to discriminate experimentally because it is not easy to determine the values of the critical design variables (e.g., presentation schedule, stimulus structure) that will be most informative in differentiating them. Recent developments in sampling-based search methods in statistics make it…

Models for the Immediate Environment of Ions in Aqueous Solutions of Neodymium Chloride

NASA Astrophysics Data System (ADS)

Smirnov, P. R.; Grechin, O. V.

2018-01-01

Radial distribution functions of neodymium chloride aqueous solutions in a wide range of concentrations under ambient conditions are calculated from experimental data obtained earlier via X-ray diffraction analysis. Different models of the structural organization of the system are developed. The optimum versions are determined by calculating theoretical functions for each model and comparing their fit to the experimental functions. Such quantitative characteristics of the immediate environment of Nd3+ and Cl- ions as coordination numbers, interparticle distances, and varieties of ion pairs are determined. It is shown that the average number of water molecules in the first coordination sphere of the cation falls from 9 to 6.2 as the concentration rises. The structure of the systems over the whole range of concentrations is determined by ion associates of the noncontact type.

Experimental determination of the inertia constants of an airplane or of a missile

NASA Technical Reports Server (NTRS)

Loiseau, H.

1983-01-01

The possibility to measure the inertia constants of an airplane or of a missile by a unique experimental set up without having to materialize axes of rotation was investigated. It is sufficient to suspend the structure appropriately, to obtain the six natural modes determined by the suspension and to introduce these results as data into a computer. If the structure is very flexible it is necessary to take into account the first natural modes of deformation. Experiments on rigid and flexible models led to precise results and allow consideration of full scale measurements. The final goal is to provide, by a standard ground vibration test completed by the measured characteristics of the suspension modes, the set of data necessary for flutter calculations and for the determination of all the inertia constants.

Solid iron-hydrogen alloys under high pressure by first principles

NASA Astrophysics Data System (ADS)

Umemoto, K.; Hirose, K.

2016-12-01

Hydrogen and iron are two of major constituents of the Earth and planetary interiors. The crystal structure of solid FeHx is one of the most fundamental information in order to understand properties of planetary cores. It is well known that FeH takes closed-packed structures: dhcp, hcp, and fcc. Recently, hydrogen-rich phases, FeH2 and FeH3, were experimentally synthesized [1]. Although a tetragonal structure of FeH2 was proposed, it could not explain experimental observations, energetic stability and compression curve. Here we propose a new crystal structure of FeH2. The symmetry of the new structure is completely identical to that in originally proposed one, but the hydrogen sublattice which cannot be directly determined by XRD experiments is different. It will be demonstrated by first principles that the new structure can be fully consistent with experimental observations. [1] C. M. Pépin, A. Dewaele, G. Geneste, P. Loubeyre, and M. Mezouar, Phys. Rev. Lett. 113, 265504 (2014).

Lattice and Valence Electronic Structures of Crystalline Octahedral Molybdenum Halide Clusters-Based Compounds, Cs2[Mo6X14] (X = Cl, Br, I), Studied by Density Functional Theory Calculations.

PubMed

Saito, Norio; Cordier, Stéphane; Lemoine, Pierric; Ohsawa, Takeo; Wada, Yoshiki; Grasset, Fabien; Cross, Jeffrey S; Ohashi, Naoki

2017-06-05

The electronic and crystal structures of Cs 2 [Mo 6 X 14 ] (X = Cl, Br, I) cluster-based compounds were investigated by density functional theory (DFT) simulations and experimental methods such as powder X-ray diffraction, ultraviolet-visible spectroscopy, and X-ray photoemission spectroscopy (XPS). The experimentally determined lattice parameters were in good agreement with theoretically optimized ones, indicating the usefulness of DFT calculations for the structural investigation of these clusters. The calculated band gaps of these compounds reproduced those experimentally determined by UV-vis reflectance within an error of a few tenths of an eV. Core-level XPS and effective charge analyses indicated bonding states of the halogens changed according to their sites. The XPS valence spectra were fairly well reproduced by simulations based on the projected electron density of states weighted with cross sections of Al K α , suggesting that DFT calculations can predict the electronic properties of metal-cluster-based crystals with good accuracy.

Toward a structure determination method for biomineral-associated protein using combined solid- state NMR and computational structure prediction.

PubMed

Masica, David L; Ash, Jason T; Ndao, Moise; Drobny, Gary P; Gray, Jeffrey J

2010-12-08

Protein-biomineral interactions are paramount to materials production in biology, including the mineral phase of hard tissue. Unfortunately, the structure of biomineral-associated proteins cannot be determined by X-ray crystallography or solution nuclear magnetic resonance (NMR). Here we report a method for determining the structure of biomineral-associated proteins. The method combines solid-state NMR (ssNMR) and ssNMR-biased computational structure prediction. In addition, the algorithm is able to identify lattice geometries most compatible with ssNMR constraints, representing a quantitative, novel method for investigating crystal-face binding specificity. We use this method to determine most of the structure of human salivary statherin interacting with the mineral phase of tooth enamel. Computation and experiment converge on an ensemble of related structures and identify preferential binding at three crystal surfaces. The work represents a significant advance toward determining structure of biomineral-adsorbed protein using experimentally biased structure prediction. This method is generally applicable to proteins that can be chemically synthesized. Copyright © 2010 Elsevier Ltd. All rights reserved.

Algorithm for selection of optimized EPR distance restraints for de novo protein structure determination

PubMed Central

Kazmier, Kelli; Alexander, Nathan S.; Meiler, Jens; Mchaourab, Hassane S.

2010-01-01

A hybrid protein structure determination approach combining sparse Electron Paramagnetic Resonance (EPR) distance restraints and Rosetta de novo protein folding has been previously demonstrated to yield high quality models (Alexander et al., 2008). However, widespread application of this methodology to proteins of unknown structures is hindered by the lack of a general strategy to place spin label pairs in the primary sequence. In this work, we report the development of an algorithm that optimally selects spin labeling positions for the purpose of distance measurements by EPR. For the α-helical subdomain of T4 lysozyme (T4L), simulated restraints that maximize sequence separation between the two spin labels while simultaneously ensuring pairwise connectivity of secondary structure elements yielded vastly improved models by Rosetta folding. 50% of all these models have the correct fold compared to only 21% and 8% correctly folded models when randomly placed restraints or no restraints are used, respectively. Moreover, the improvements in model quality require a limited number of optimized restraints, the number of which is determined by the pairwise connectivities of T4L α-helices. The predicted improvement in Rosetta model quality was verified by experimental determination of distances between spin labels pairs selected by the algorithm. Overall, our results reinforce the rationale for the combined use of sparse EPR distance restraints and de novo folding. By alleviating the experimental bottleneck associated with restraint selection, this algorithm sets the stage for extending computational structure determination to larger, traditionally elusive protein topologies of critical structural and biochemical importance. PMID:21074624

Experimental and computational thermochemical study and solid-phase structure of 5,5-dimethylbarbituric acid.

PubMed

Roux, María Victoria; Notario, Rafael; Foces-Foces, Concepción; Temprado, Manuel; Ros, Francisco; Emel'yanenko, Vladimir N; Verevkin, Sergey P

2010-03-18

This paper reports an experimental and computational thermochemical study on 5,5-dimethylbarbituric acid and the solid-phase structure of the compound. The value of the standard (p(o) = 0.1 MPa) molar enthalpy of formation in the gas phase at T = 298.15 K has been determined. The energy of combustion was measured by static bomb combustion calorimetry, and from the result obtained, the standard molar enthalpy of formation in the crystalline state at T = 298.15 K was calculated as -(706.4 +/- 2.2) kJ x mol(-1). The enthalpy of sublimation was determined using a transference (transpiration) method in a saturated NB(2) stream, and a value of the enthalpy of sublimation at T = 298.15 K was derived as (115.8 +/- 0.5) kJ x mol(-1). From these results a value of -(590.6 +/- 2.3) kJ x mol(-1) for the gas-phase enthalpy of formation at T = 298.15 K was determined. Theoretical calculations at the G3 level were performed, and a study on molecular and electronic structure of the compound has been carried out. Calculated enthalpies of formation are in reasonable agreement with the experimental value. 5,5-Dimethylbarbituric acid was characterized by single crystal X-ray diffraction analysis. In the crystal structure, N-H...O=C hydrogen bonds lead to the formation of ribbons connected further by weak C-H...O=C hydrogen bonds into a three-dimensional network. The molecular and supramolecular structures observed in the solid state were also investigated in the gas phase by DFT calculations.

Experimental vibration damping characteristics of the third-stage rotor of a three-stage transonic axial-flow compressor

NASA Technical Reports Server (NTRS)

Newman, Frederick A.

1988-01-01

Rotor blade aerodynamic damping is experimentally determined in a three-stage transonic axial flow compressor having design aerodynamic performance goals of 4.5:1 pressure ratio and 65.5 lbm/sec weight flow. The combined damping associated with each mode is determined by a least squares fit of a single degree of freedom system transfer function to the nonsynchronous portion of the rotor blade strain gage output power spectra. The combined damping consists of the aerodynanmic damping and the structural and mechanical damping. The aerodynamic damping varies linearly with the inlet total pressure for a given corrected speed, weight flow, and pressure ratio while the structural and mechanical damping is assumed to remain constant. The combined damping is determined at three inlet total pressure levels to obtain the aerodynamic damping. The third-stage rotor blade aerodynamic damping is presented and discussed for the design equivalent speed with the stator blades reset for maximum efficiency. The compressor overall performance and experimental Campbell diagrams for the third-stage rotor blade row are also presented.

Experimental Vibration Damping Characteristics of the Third-stage Rotor of a Three-stage Transonic Axial-flow Compressor

NASA Technical Reports Server (NTRS)

Newman, Frederick A.

1988-01-01

Rotor blade aerodynamic damping is experimentally determined in a three-stage transonic axial flow compressor having design aerodynamic performance goals of 4.5:1 pressure ratio and 65.5 lbm/sec weight flow. The combined damping associated with each mode is determined by a least squares fit of a single degree of freedom system transfer function to the nonsynchronous portion of the rotor blade strain gage output power spectra. The combined damping consists of the aerodynamic damping and the structural and mechanical damping. The aerodynamic damping varies linearly with the inlet total pressure for a given corrected speed, weight flow, and pressure ratio while the structural and mechanical damping is assumed to remain constant. The combined damping is determined at three inlet total pressure levels to obtain the aerodynamic damping. The third-stage rotor blade aerodynamic damping is presented and discussed for the design equivalent speed with the stator blades reset for maximum efficiency. The compressor overall preformance and experimental Campbell diagrams for the third-stage rotor blade row are also presented.

Workshop on Measurement Needs for Local-Structure Determination in Inorganic Materials

PubMed Central

Levin, Igor; Vanderah, Terrell

2008-01-01

The functional responses (e.g., dielectric, magnetic, catalytic, etc.) of many industrially-relevant materials are controlled by their local structure—a term that refers to the atomic arrangements on a scale ranging from atomic (sub-nanometer) to several nanometers. Thus, accurate knowledge of local structure is central to understanding the properties of nanostructured materials, thereby placing the problem of determining atomic positions on the nanoscale—the so-called “nanostructure problem”—at the center of modern materials development. Today, multiple experimental techniques exist for probing local atomic arrangements; nonetheless, finding accurate comprehensive, and robust structural solutions for the nanostructured materials still remains a formidable challenge because any one of these methods yields only a partial view of the local structure. The primary goal of this 2-day NIST-sponsored workshop was to bring together experts in the key experimental and theoretical areas relevant to local-structure determination to devise a strategy for the collaborative effort required to develop a comprehensive measurement solution on the local scale. The participants unanimously agreed that solving the nanostructure problem—an ultimate frontier in materials characterization—necessitates a coordinated interdisciplinary effort that transcends the existing capabilities of any single institution, including national laboratories, centers, and user facilities. The discussions converged on an institute dedicated to local structure determination as the most viable organizational platform for successfully addressing the nanostructure problem. The proposed “institute” would provide an intellectual infrastructure for local structure determination by (1) developing and maintaining relevant computer software integrated in an open-source global optimization framework (Fig. 2), (2) connecting industrial and academic users with experts in measurement techniques, (3) developing and maintaining pertinent databases, and (4) providing necessary education and training. PMID:27096131

SASSIE: A program to study intrinsically disordered biological molecules and macromolecular ensembles using experimental scattering restraints

NASA Astrophysics Data System (ADS)

Curtis, Joseph E.; Raghunandan, Sindhu; Nanda, Hirsh; Krueger, Susan

2012-02-01

A program to construct ensembles of biomolecular structures that are consistent with experimental scattering data are described. Specifically, we generate an ensemble of biomolecular structures by varying sets of backbone dihedral angles that are then filtered using experimentally determined restraints to rapidly determine structures that have scattering profiles that are consistent with scattering data. We discuss an application of these tools to predict a set of structures for the HIV-1 Gag protein, an intrinsically disordered protein, that are consistent with small-angle neutron scattering experimental data. We have assembled these algorithms into a program called SASSIE for structure generation, visualization, and analysis of intrinsically disordered proteins and other macromolecular ensembles using neutron and X-ray scattering restraints. Program summaryProgram title: SASSIE Catalogue identifier: AEKL_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEKL_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: GNU General Public License v3 No. of lines in distributed program, including test data, etc.: 3 991 624 No. of bytes in distributed program, including test data, etc.: 826 Distribution format: tar.gz Programming language: Python, C/C++, Fortran Computer: PC/Mac Operating system: 32- and 64-bit Linux (Ubuntu 10.04, Centos 5.6) and Mac OS X (10.6.6) RAM: 1 GB Classification: 3 External routines: Python 2.6.5, numpy 1.4.0, swig 1.3.40, scipy 0.8.0, Gnuplot-py-1.8, Tcl 8.5, Tk 8.5, Mac installation requires aquaterm 1.0 (or X window system) and Xcode 3 development tools. Nature of problem: Open source software to generate structures of disordered biological molecules that subsequently allow for the comparison of computational and experimental results is limiting the use of scattering resources. Solution method: Starting with an all atom model of a protein, for example, users can input regions to vary dihedral angles, ensembles of structures can be generated. Additionally, simple two-body rigid-body rotations are supported with and without disordered regions. Generated structures can then be used to calculate small-angle scattering profiles which can then be filtered against experimentally determined data. Filtered structures can be visualized individually or as an ensemble using density plots. In the modular and expandable program framework the user can easily access our subroutines and structural coordinates can be easily obtained for study using other computational physics methods. Additional comments: The distribution file for this program is over 159 Mbytes and therefore is not delivered directly when download or Email is requested. Instead an html file giving details of how the program can be obtained is sent. Running time: Varies depending on application. Typically 10 minutes to 24 hours depending on the number of generated structures.

STITCHER: Dynamic assembly of likely amyloid and prion β-structures from secondary structure predictions

PubMed Central

Bryan, Allen W; O’Donnell, Charles W; Menke, Matthew; Cowen, Lenore J; Lindquist, Susan; Berger, Bonnie

2012-01-01

The supersecondary structure of amyloids and prions, proteins of intense clinical and biological interest, are difficult to determine by standard experimental or computational means. In addition, significant conformational heterogeneity is known or suspected to exist in many amyloid fibrils. Previous work has demonstrated that probability-based prediction of discrete β-strand pairs can offer insight into these structures. Here, we devise a system of energetic rules that can be used to dynamically assemble these discrete β-strand pairs into complete amyloid β-structures. The STITCHER algorithm progressively ‘stitches’ strand-pairs into full β-sheets based on a novel free-energy model, incorporating experimentally observed amino-acid side-chain stacking contributions, entropic estimates, and steric restrictions for amyloidal parallel β-sheet construction. A dynamic program computes the top 50 structures and returns both the highest scoring structure and a consensus structure taken by polling this list for common discrete elements. Putative structural heterogeneity can be inferred from sequence regions that compose poorly. Predictions show agreement with experimental models of Alzheimer’s amyloid beta peptide and the Podospora anserina Het-s prion. Predictions of the HET-s homolog HET-S also reflect experimental observations of poor amyloid formation. We put forward predicted structures for the yeast prion Sup35, suggesting N-terminal structural stability enabled by tyrosine ladders, and C-terminal heterogeneity. Predictions for the Rnq1 prion and alpha-synuclein are also given, identifying a similar mix of homogenous and heterogeneous secondary structure elements. STITCHER provides novel insight into the energetic basis of amyloid structure, provides accurate structure predictions, and can help guide future experimental studies. Proteins 2012. © 2011 Wiley Periodicals, Inc. PMID:22095906

STITCHER: Dynamic assembly of likely amyloid and prion β-structures from secondary structure predictions.

PubMed

Bryan, Allen W; O'Donnell, Charles W; Menke, Matthew; Cowen, Lenore J; Lindquist, Susan; Berger, Bonnie

2012-02-01

The supersecondary structure of amyloids and prions, proteins of intense clinical and biological interest, are difficult to determine by standard experimental or computational means. In addition, significant conformational heterogeneity is known or suspected to exist in many amyloid fibrils. Previous work has demonstrated that probability-based prediction of discrete β-strand pairs can offer insight into these structures. Here, we devise a system of energetic rules that can be used to dynamically assemble these discrete β-strand pairs into complete amyloid β-structures. The STITCHER algorithm progressively 'stitches' strand-pairs into full β-sheets based on a novel free-energy model, incorporating experimentally observed amino-acid side-chain stacking contributions, entropic estimates, and steric restrictions for amyloidal parallel β-sheet construction. A dynamic program computes the top 50 structures and returns both the highest scoring structure and a consensus structure taken by polling this list for common discrete elements. Putative structural heterogeneity can be inferred from sequence regions that compose poorly. Predictions show agreement with experimental models of Alzheimer's amyloid beta peptide and the Podospora anserina Het-s prion. Predictions of the HET-s homolog HET-S also reflect experimental observations of poor amyloid formation. We put forward predicted structures for the yeast prion Sup35, suggesting N-terminal structural stability enabled by tyrosine ladders, and C-terminal heterogeneity. Predictions for the Rnq1 prion and alpha-synuclein are also given, identifying a similar mix of homogenous and heterogeneous secondary structure elements. STITCHER provides novel insight into the energetic basis of amyloid structure, provides accurate structure predictions, and can help guide future experimental studies. Copyright © 2011 Wiley Periodicals, Inc.

The hyperfine structure in the rotational spectra of D{sub 2}{sup 17}O and HD{sup 17}O: Confirmation of the absolute nuclear magnetic shielding scale for oxygen

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

Puzzarini, Cristina, E-mail: cristina.puzzarini@unibo.it; Cazzoli, Gabriele; Harding, Michael E.

2015-03-28

Guided by theoretical predictions, the hyperfine structures of the rotational spectra of mono- and bideuterated-water containing {sup 17}O have been experimentally investigated. To reach sub-Doppler resolution, required to resolve the hyperfine structure due to deuterium quadrupole coupling as well as to spin-rotation (SR) and dipolar spin-spin couplings, the Lamb-dip technique has been employed. The experimental investigation and in particular, the spectral analysis have been supported by high-level quantum-chemical computations employing coupled-cluster techniques and, for the first time, a complete experimental determination of the hyperfine parameters involved was possible. The experimentally determined {sup 17}O spin-rotation constants of D{sub 2}{sup 17}O andmore » HD{sup 17}O were used to derive the paramagnetic part of the corresponding nuclear magnetic shielding constants. Together with the computed diamagnetic contributions as well as the vibrational and temperature corrections, the latter constants have been employed to confirm the oxygen nuclear magnetic shielding scale, recently established on the basis of spin-rotation data for H{sub 2}{sup 17}O [Puzzarini et al., J. Chem. Phys. 131, 234304 (2009)].« less

The structure of small, vapor-deposited particles. II - Experimental study of particles with hexagonal profile

NASA Technical Reports Server (NTRS)

Yacaman, M. J.; Heinemann, K.; Yang, C. Y.; Poppa, H.

1979-01-01

'Multiply-twinned' gold particles with hexagonal bright field TEM profile were determined to be icosahedra composed of 20 identical and twin-related tetrahedral building units that do not have an fcc structure. The crystal structure of these slightly deformed tetrahedra is rhombohedral. Experimental evidence supporting this particle model was obtained by selected-zone dark field and weak beam dark field electron microscopy. In conjunction with the results of part I, it has been concluded that multiply-twinned gold particles of pentagonal or hexagonal profile that are found during the early stages of the vapor deposition growth process on alkali halide surfaces do not have an fcc crystal structure, which is in obvious contrast to the structure of bulk gold.

A reconfigurable robot with tensegrity structure using nylon artificial muscle

NASA Astrophysics Data System (ADS)

Wu, Lianjun; de Andrade, Monica Jung; Brahme, Tarang; Tadesse, Yonas; Baughman, Ray H.

2016-04-01

This paper describes the design and experimental investigation of a self-reconfigurable icosahedral robot for locomotion. The robot consists of novel and modular tensegrity structures, which can potentially maneuver in unstructured environments while carrying a payload. Twisted and Coiled Polymer (TCP) muscles were utilized to actuate the tensegrity structure as needed. The tensegrity system has rigid struts and flexible TCP muscles that allow keeping a payload in the central region. The TCP muscles provide large actuation stroke, high mechanical power per fiber mass and can undergo millions of highly reversible cycles. The muscles are electrothermally driven, and, upon stimulus, the heated muscles reconfigure the shape of the tensegrity structure. Here, we present preliminary experimental results that determine the rolling motion of the structure.

Molecular structure and the EPR calculation of the gas phase succinonitrile molecule

NASA Astrophysics Data System (ADS)

Kepceoǧlu, A.; Kılıç, H. Ş.; Dereli, Ö.

2017-02-01

Succinonitrile (i.e. butanedinitrile) is a colorless nitrile compound that can be used in the gel polymer batteries as a solid-state solvent electrolytes and has a plastic crystal structure. Prior to the molecular structure calculation of the succinonitrile molecule, the conformer analysis were calculated by using semi empirical method PM3 core type Hamiltonian and eight different conformer structures were determined. Molecular structure with energy related properties of these conformers having the lowest energy was calculated by using DFT (B3LYP) methods with 6-311++G(d,p) basis set. Possible radicals, can be formed experimentally, were modeled in this study. EPR parameters of these model radicals were calculated and then compared with that obtained experimentally.

A statistical analysis of RNA folding algorithms through thermodynamic parameter perturbation.

PubMed

Layton, D M; Bundschuh, R

2005-01-01

Computational RNA secondary structure prediction is rather well established. However, such prediction algorithms always depend on a large number of experimentally measured parameters. Here, we study how sensitive structure prediction algorithms are to changes in these parameters. We found already that for changes corresponding to the actual experimental error to which these parameters have been determined, 30% of the structure are falsely predicted whereas the ground state structure is preserved under parameter perturbation in only 5% of all the cases. We establish that base-pairing probabilities calculated in a thermal ensemble are viable although not a perfect measure for the reliability of the prediction of individual structure elements. Here, a new measure of stability using parameter perturbation is proposed, and its limitations are discussed.

The effect of data structures on INGRES performance

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

Creighton, J.R.

1987-01-01

Computer experiments were conducted to determine the effect of using Heap, ISAM, Hash and B-tree data structures for INGRES relations. Average times for retrieve, append and update were determined for searches by unique key and non-key data. The experiments were conducted on relations of approximately 1000 tuples of 332 byte width. Multiple operations were performed, where appropriate, to obtain average times. Simple models of the data structures are presented and shown to be consistent with experimental results. The models can be used to predict performance, and to select the appropriate data structure for various applications.

Physical–chemical determinants of coil conformations in globular proteins

PubMed Central

Perskie, Lauren L; Rose, George D

2010-01-01

We present a method with the potential to generate a library of coil segments from first principles. Proteins are built from α-helices and/or β-strands interconnected by these coil segments. Here, we investigate the conformational determinants of short coil segments, with particular emphasis on chain turns. Toward this goal, we extracted a comprehensive set of two-, three-, and four-residue turns from X-ray–elucidated proteins and classified them by conformation. A remarkably small number of unique conformers account for most of this experimentally determined set, whereas remaining members span a large number of rare conformers, many occurring only once in the entire protein database. Factors determining conformation were identified via Metropolis Monte Carlo simulations devised to test the effectiveness of various energy terms. Simulated structures were validated by comparison to experimental counterparts. After filtering rare conformers, we found that 98% of the remaining experimentally determined turn population could be reproduced by applying a hydrogen bond energy term to an exhaustively generated ensemble of clash-free conformers in which no backbone polar group lacks a hydrogen-bond partner. Further, at least 90% of longer coil segments, ranging from 5- to 20 residues, were found to be structural composites of these shorter primitives. These results are pertinent to protein structure prediction, where approaches can be divided into either empirical or ab initio methods. Empirical methods use database-derived information; ab initio methods rely on physical–chemical principles exclusively. Replacing the database-derived coil library with one generated from first principles would transform any empirically based method into its corresponding ab initio homologue. PMID:20512968

Structure and Sequence Search on Aptamer-Protein Docking

NASA Astrophysics Data System (ADS)

Xiao, Jiajie; Bonin, Keith; Guthold, Martin; Salsbury, Freddie

2015-03-01

Interactions between proteins and deoxyribonucleic acid (DNA) play a significant role in the living systems, especially through gene regulation. However, short nucleic acids sequences (aptamers) with specific binding affinity to specific proteins exhibit clinical potential as therapeutics. Our capillary and gel electrophoresis selection experiments show that specific sequences of aptamers can be selected that bind specific proteins. Computationally, given the experimentally-determined structure and sequence of a thrombin-binding aptamer, we can successfully dock the aptamer onto thrombin in agreement with experimental structures of the complex. In order to further study the conformational flexibility of this thrombin-binding aptamer and to potentially develop a predictive computational model of aptamer-binding, we use GPU-enabled molecular dynamics simulations to both examine the conformational flexibility of the aptamer in the absence of binding to thrombin, and to determine our ability to fold an aptamer. This study should help further de-novo predictions of aptamer sequences by enabling the study of structural and sequence-dependent effects on aptamer-protein docking specificity.

Vibrational and mechanical properties of single layer MXene structures: a first-principles investigation

NASA Astrophysics Data System (ADS)

Yorulmaz, Uğur; Özden, Ayberk; Perkgöz, Nihan K.; Ay, Feridun; Sevik, Cem

2016-08-01

MXenes, carbides, nitrides and carbonitrides of early transition metals are the new members of two dimensional materials family given with a formula of {{{M}}}n+1 X n . Recent advances in chemical exfoliation and CVD growth of these crystals together with their promising performance in electrochemical energy storage systems have triggered the interest in these two dimensional structures. In this work, we employ first principles calculations for n = 1 structures of Sc, Ti, Zr, Mo and Hf pristine MXenes and their fully surface terminated forms with F and O. We systematically investigated the dynamical and mechanical stability of both pristine and fully terminated MXene structures to determine the possible MXene candidates for experimental realization. In conjunction with an extensive stability analysis, we report Raman and infrared active mode frequencies for the first time, providing indispensable information for the experimental elaboration of MXene field. After determining dynamically stable MXenes, we provide their phonon dispersion relations, electronic and mechanical properties.

Vibrational and mechanical properties of single layer MXene structures: a first-principles investigation.

PubMed

Yorulmaz, Uğur; Özden, Ayberk; Perkgöz, Nihan K; Ay, Feridun; Sevik, Cem

2016-08-19

MXenes, carbides, nitrides and carbonitrides of early transition metals are the new members of two dimensional materials family given with a formula of [Formula: see text] X n . Recent advances in chemical exfoliation and CVD growth of these crystals together with their promising performance in electrochemical energy storage systems have triggered the interest in these two dimensional structures. In this work, we employ first principles calculations for n = 1 structures of Sc, Ti, Zr, Mo and Hf pristine MXenes and their fully surface terminated forms with F and O. We systematically investigated the dynamical and mechanical stability of both pristine and fully terminated MXene structures to determine the possible MXene candidates for experimental realization. In conjunction with an extensive stability analysis, we report Raman and infrared active mode frequencies for the first time, providing indispensable information for the experimental elaboration of MXene field. After determining dynamically stable MXenes, we provide their phonon dispersion relations, electronic and mechanical properties.

Officer Career Development: Analytic Strategy Recommendations

DTIC Science & Technology

1989-07-01

model is perhaps better suited to experimental designs where investigators determine discrete values for each Xi and then randomly sample subjects into... experimental designs . New York: McGraw-Hill. ,Terlove, 4. (1971). Further evidence on the estimation of dynamic economic relations from a time series of...Cunningham. W. R., & Birren, 1. E. (1980). Age chsane in the factor Newseroade. I R., & Labouvie. E V. 1985) Experimental design in structure of

Music in film and animation: experimental semiotics applied to visual, sound and musical structures

NASA Astrophysics Data System (ADS)

Kendall, Roger A.

2010-02-01

The relationship of music to film has only recently received the attention of experimental psychologists and quantificational musicologists. This paper outlines theory, semiotical analysis, and experimental results using relations among variables of temporally organized visuals and music. 1. A comparison and contrast is developed among the ideas in semiotics and experimental research, including historical and recent developments. 2. Musicological Exploration: The resulting multidimensional structures of associative meanings, iconic meanings, and embodied meanings are applied to the analysis and interpretation of a range of film with music. 3. Experimental Verification: A series of experiments testing the perceptual fit of musical and visual patterns layered together in animations determined goodness of fit between all pattern combinations, results of which confirmed aspects of the theory. However, exceptions were found when the complexity of the stratified stimuli resulted in cognitive overload.

Aromatic claw: A new fold with high aromatic content that evades structural prediction: Aromatic Claw

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

Sachleben, Joseph R.; Adhikari, Aashish N.; Gawlak, Grzegorz

2016-11-10

We determined the NMR structure of a highly aromatic (13%) protein of unknown function, Aq1974 from Aquifex aeolicus (PDB ID: 5SYQ). The unusual sequence of this protein has a tryptophan content five times the normal (six tryptophan residues of 114 or 5.2% while the average tryptophan content is 1.0%) with the tryptophans occurring in a WXW motif. It has no detectable sequence homology with known protein structures. Although its NMR spectrum suggested that the protein was rich in β-sheet, upon resonance assignment and solution structure determination, the protein was found to be primarily α-helical with a small two-stranded β-sheet withmore » a novel fold that we have termed an Aromatic Claw. As this fold was previously unknown and the sequence unique, we submitted the sequence to CASP10 as a target for blind structural prediction. At the end of the competition, the sequence was classified a hard template based model; the structural relationship between the template and the experimental structure was small and the predictions all failed to predict the structure. CSRosetta was found to predict the secondary structure and its packing; however, it was found that there was little correlation between CSRosetta score and the RMSD between the CSRosetta structure and the NMR determined one. This work demonstrates that even in relatively small proteins, we do not yet have the capacity to accurately predict the fold for all primary sequences. The experimental discovery of new folds helps guide the improvement of structural prediction methods.« less

Vegetation response to stand structure and prescribed fire in an interior ponderosa pine ecosystem

Treesearch

Jianwei Zhang; Martin W. Ritchie; William W. Oliver

2008-01-01

A large-scale interior ponderosa pine (Pinus ponderosa Dougl. ex P. & C. Laws.) study was conducted at the Blacks Mountain Experimental Forest in northeastern California. The primary purpose of the study was to determine the influence of structural diversity on the dynamics of interior pine forests at the landscape scale. High structural...

A Bayesian Approach for Determining Protein Side-Chain Rotamer Conformations Using Unassigned NOE Data

PubMed Central

Zeng, Jianyang; Roberts, Kyle E.; Zhou, Pei

2011-01-01

Abstract A major bottleneck in protein structure determination via nuclear magnetic resonance (NMR) is the lengthy and laborious process of assigning resonances and nuclear Overhauser effect (NOE) cross peaks. Recent studies have shown that accurate backbone folds can be determined using sparse NMR data, such as residual dipolar couplings (RDCs) or backbone chemical shifts. This opens a question of whether we can also determine the accurate protein side-chain conformations using sparse or unassigned NMR data. We attack this question by using unassigned nuclear Overhauser effect spectroscopy (NOESY) data, which records the through-space dipolar interactions between protons nearby in three-dimensional (3D) space. We propose a Bayesian approach with a Markov random field (MRF) model to integrate the likelihood function derived from observed experimental data, with prior information (i.e., empirical molecular mechanics energies) about the protein structures. We unify the side-chain structure prediction problem with the side-chain structure determination problem using unassigned NMR data, and apply the deterministic dead-end elimination (DEE) and A* search algorithms to provably find the global optimum solution that maximizes the posterior probability. We employ a Hausdorff-based measure to derive the likelihood of a rotamer or a pairwise rotamer interaction from unassigned NOESY data. In addition, we apply a systematic and rigorous approach to estimate the experimental noise in NMR data, which also determines the weighting factor of the data term in the scoring function derived from the Bayesian framework. We tested our approach on real NMR data of three proteins: the FF Domain 2 of human transcription elongation factor CA150 (FF2), the B1 domain of Protein G (GB1), and human ubiquitin. The promising results indicate that our algorithm can be applied in high-resolution protein structure determination. Since our approach does not require any NOE assignment, it can accelerate the NMR structure determination process. PMID:21970619

Detonation Product EOS Studies: Using ISLS to Refine Cheetah

NASA Astrophysics Data System (ADS)

Zaug, J. M.; Howard, W. M.; Fried, L. E.; Hansen, D. W.

2002-07-01

Knowledge of an effective interatomic potential function underlies any effort to predict or rationalize the properties of solids and liquids. The experiments we undertake are directed towards determination of equilibrium and dynamic properties of simple fluids at densities sufficiently high that traditional computational methods and semi-empirical forms successful at ambient conditions may require reconsideration. In this paper we present high-pressure and temperature experimental sound speed data on a simple fluid, methanol. Impulsive Stimulated Light Scattering (ISLS) conducted on diamond-anvil cell (DAC) encapsulated samples offers an experimental approach to determine cross-pair potential interactions through equation of state determinations. In addition the kinetics of structural relaxation in fluids can be studied. We compare our experimental results with our thermochemical computational model Cheetah. Experimentally grounded computational models provide a good basis to confidently understand the chemical nature of reactions at extreme conditions.

Experimental observation and determination of the laser-induced frequency shift of hyperfine levels of ultracold polar molecules

NASA Astrophysics Data System (ADS)

Liu, Wenliang; Wang, Xiaofeng; Wu, Jizhou; Su, Xingliang; Wang, Shen; Sovkov, Vladimir B.; Ma, Jie; Xiao, Liantuan; Jia, Suotang

2017-08-01

We report on the experimental observation and quantitative determination of the laser-induced frequency shift (LIFS) of the ultracold polar molecules formed by photoassociation (PA). The experiments are performed by detecting a series of double PA spectra with a molecular hyperfine structure, which are induced by two PA lasers with a precise and adjustable frequency reference. We find that the LIFS of the molecular hyperfine levels shows a linear dependence on PA laser intensity.

Ultra-small Ag clusters in zeolite A4: Antibacterial and thermochromic applications

NASA Astrophysics Data System (ADS)

Horta-Fraijo, P.; Cortez-Valadez, M.; Flores-Lopez, N. S.; Britto Hurtado, R.; Vargas-Ortiz, R. A.; Perez-Rodriguez, A.; Flores-Acosta, M.

2018-03-01

The physical and chemical properties of metal clusters depend on their atomic structure, therefore, it is important to determine the lowest-energy structures of the clusters in order to understand and utilize their properties. In this work, we use the Density Functional Theory (DFT) at the generalized gradient approximation level Becke's three-parameter and the gradient corrected functional of Lee, Yang and Puar (B3LYP) in combination with the basis set LANL2DZ (the effective core potentials and associated double-zeta valence) to determine some of the structural, electronic and vibrational properties of the planar silver clusters (Agn clusters n = 2-24). Additionally, the study reports the experimental synthesis of small silver clusters in synthetic zeolite A4. The synthesis was possible using the ion exchange method with some precursors like silver nitrate (AgNO3) and synthetic zeolite A4. The silver clusters in zeolite powder underwent thermal treatment at 450 °C to release the remaining water or humidity on it. The morphology of the particles was determined by Transmission Electron microscopy. The nanomaterials obtained show thermochromic properties. The structural parameters were correlated theoretically and experimentally.

Mathematical methods for protein science

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

Hart, W.; Istrail, S.; Atkins, J.

1997-12-31

Understanding the structure and function of proteins is a fundamental endeavor in molecular biology. Currently, over 100,000 protein sequences have been determined by experimental methods. The three dimensional structure of the protein determines its function, but there are currently less than 4,000 structures known to atomic resolution. Accordingly, techniques to predict protein structure from sequence have an important role in aiding the understanding of the Genome and the effects of mutations in genetic disease. The authors describe current efforts at Sandia to better understand the structure of proteins through rigorous mathematical analyses of simple lattice models. The efforts have focusedmore » on two aspects of protein science: mathematical structure prediction, and inverse protein folding.« less

Energetics and structural properties of twist grain boundaries in Cu

NASA Technical Reports Server (NTRS)

Karimi, Majid

1992-01-01

Structural and energetics properties of atoms near a grain boundary are of great importance from theoretical and experimental standpoints. From various experimental work it is concluded that diffusion at low temperatures at polycrystalline materials take place near grain boundary. Experimental and theoretical results also indicate changes of up to 70 percent in physical properties near a grain boundary. The Embedded Atom Method (EAM) calculations on structural properties of Au twist grain boundaries are in quite good agreement with their experimental counterparts. The EAM is believed to predict reliable values for the single vacancy formation energy as well as migration energy. However, it is not clear whether the EAM functions which are fitted to the bulk properties of a perfect crystalline solid can produce reliable results on grain boundaries. One of the objectives of this work is to construct the EAM functions for Cu and use them in conjunction with the molecular static simulation to study structures and energetics of atoms near twist grain boundaries in Cu. This provides tests of the EAM functions near a grain boundary. In particular, we determine structure, single vacancy formation energy, migration energy, single vacancy activation energy, and interlayer spacing as a function of distance from grain boundary. Our results are compared with the available experimental and theoretical results from grain boundaries and bulk.

Fracture modes in notched angleplied composite laminates

NASA Technical Reports Server (NTRS)

Irvine, T. B.; Ginty, C. A.

1984-01-01

The Composite Durability Structural Analysis (CODSTRAN) computer code is used to determine composite fracture. Fracture modes in solid and notched, unidirectional and angleplied graphite/epoxy composites were determined by using CODSTRAN. Experimental verification included both nondestructive (ultrasonic C-Scanning) and destructive (scanning electron microscopy) techniques. The fracture modes were found to be a function of ply orientations and whether the composite is notched or unnotched. Delaminations caused by stress concentrations around notch tips were also determined. Results indicate that the composite mechanics, structural analysis, laminate analysis, and fracture criteria modules embedded in CODSTRAN are valid for determining composite fracture modes.

Development of XAFS Into a Structure Determination Technique

NASA Astrophysics Data System (ADS)

Stern, E. A.

After the detection of diffraction of x-rays by M. Laue in 1912, the technique was soon applied to structure determination by Bragg within a year. On the other hand, although the edge steps in X-Ray absorption were discovered even earlier by Barkla and both the near edge (XANES) and extended X-Ray fine structure (EXAFS) past the edge were detected by 1929, it still took over 40 years to realize the structure information contained in this X-Ray absorption fine structure (XAFS). To understand this delay a brief historical review of the development of the scientific ideas that transformed XAFS into the premiere technique for local structure determination is given. The development includes both advances in theoretical understanding and calculational capabilities, and in experimental facilities, especially synchrotron radiation sources. The present state of the XAFS technique and its capabilities are summarized.

The structural, electronic and spectroscopic properties of 4FPBAPE molecule: Experimental and theoretical study

NASA Astrophysics Data System (ADS)

Tanış, Emine; Babur Sas, Emine; Kurban, Mustafa; Kurt, Mustafa

2018-02-01

The experimental and theoretical study of 4-Formyl Phenyl Boronic Acid Pinacol Ester (4FPBAPE) molecule were performed in this work. 1H, 13C NMR and UV-Vis spectra were tested in dimethyl sulfoxide (DMSO). The structural, spectroscopic properties and energies of 4FPBAPE were obtained for two potential conformers from density functional theory (DFT) with B3LYP/6-311G (d, p) and CAM-B3LYP/6-311G (d, p) basis sets. The optimal geometry of those structures was obtained according to the position of oxygen atom upon determining the scan coordinates for each conformation. The most stable conformer was found as the A2 form. The fundamental vibrations were determined based on optimized structure in terms of total energy distribution. Electronic properties such as oscillator strength, wavelength, excitation energy, HOMO, LUMO and molecular electrostatic potential and structural properties such as radial distribution functions (RDF) and probability density depending on coordination number are presented. Theoretical results of 4-FPBAPE spectra were found to be compatible with observed spectra.

Communication: Determining the structure of the N{sub 2}Ar van der Waals complex with laser-based channel-selected Coulomb explosion

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

Wu, Chengyin, E-mail: cywu@pku.edu.cn; Liu, Yunquan; Gong, Qihuang

2014-04-14

We experimentally reconstructed the structure of the N{sub 2}Ar van der Waals complex with the technique of laser-based channel-selected Coulomb explosion imaging. The internuclear distance between the N{sub 2} center of mass and the Ar atom, i.e., the length of the van der Waals bond, was determined to be 3.88 Å from the two-body explosion channels. The angle between the van der Waals bond and the N{sub 2} principal axis was determined to be 90° from the three-body explosion channels. The reconstructed structure was contrasted with our high level ab initio calculations. The agreement demonstrated the potential application of laser-basedmore » Coulomb explosion in imaging transient molecular structure, particularly for floppy van der Waals complexes, whose structures remain difficult to be determined by conventional spectroscopic methods.« less

Investigating energy-based pool structure selection in the structure ensemble modeling with experimental distance constraints: The example from a multidomain protein Pub1.

PubMed

Zhu, Guanhua; Liu, Wei; Bao, Chenglong; Tong, Dudu; Ji, Hui; Shen, Zuowei; Yang, Daiwen; Lu, Lanyuan

2018-05-01

The structural variations of multidomain proteins with flexible parts mediate many biological processes, and a structure ensemble can be determined by selecting a weighted combination of representative structures from a simulated structure pool, producing the best fit to experimental constraints such as interatomic distance. In this study, a hybrid structure-based and physics-based atomistic force field with an efficient sampling strategy is adopted to simulate a model di-domain protein against experimental paramagnetic relaxation enhancement (PRE) data that correspond to distance constraints. The molecular dynamics simulations produce a wide range of conformations depicted on a protein energy landscape. Subsequently, a conformational ensemble recovered with low-energy structures and the minimum-size restraint is identified in good agreement with experimental PRE rates, and the result is also supported by chemical shift perturbations and small-angle X-ray scattering data. It is illustrated that the regularizations of energy and ensemble-size prevent an arbitrary interpretation of protein conformations. Moreover, energy is found to serve as a critical control to refine the structure pool and prevent data overfitting, because the absence of energy regularization exposes ensemble construction to the noise from high-energy structures and causes a more ambiguous representation of protein conformations. Finally, we perform structure-ensemble optimizations with a topology-based structure pool, to enhance the understanding on the ensemble results from different sources of pool candidates. © 2018 Wiley Periodicals, Inc.

Deducing 2D Crystal Structure at the Solid/Liquid Interface with Atomic Resolution by Combined STM and SFG Study

NASA Astrophysics Data System (ADS)

McClelland, Arthur; Ahn, Seokhoon; Matzger, Adam J.; Chen, Zhan

2009-03-01

Supplemented by computed models, Scanning Tunneling Microscopy (STM) can provide detailed structure of 2D crystals formed at the liquid/solid interface with atomic resolution. However, some structural information such as functional group orientations in such 2D crystals needs to be tested experimentally to ensure the accuracy of the deduced structures. Due to the limited sensitivity, many other experimental techniques such as Raman and infrared spectroscopy have not been allowed to provide such structural information of 2D crystals. Here we showed that Sum Frequency Generation Vibrational Spectroscopy (SFG) can measure average orientation of functional groups in such 2D crystals, or physisorbed monolayers, providing key experimental data to aid in the modeling and interpretation of the STM images. The usefulness of combining these two techniques is demonstrated with a phthalate diesters monolayer formed at the 1-phenyloctane/ highly oriented pyrolytic graphite (HOPG) interface. The spatial orientation of the ester C=O of the monolayer was successfully determined using SFG.

Structural, spectral, NLO and MEP analysis of the [MgO2Ti2(OPri)6], [MgO2Ti2(OPri)2(acac)4] and [MgO2Ti2(OPri)2(bzac)4] by DFT method

NASA Astrophysics Data System (ADS)

Sayin, Koray; Karakaş, Duran

2015-06-01

Quantum chemical calculations are performed on [MgO2Ti2(OPri)6] and [MgO2Ti2(OPri)2(L)4] complexes. L is acetylacetonate (acac) and benzoylacetonate (bzac) anion. The crystal structures of these complexes have not been obtained as experimentally but optimized structures of these complexes are obtained as theoretically in this study. Universal force field (UFF) and DFT/B3LYP method are used to obtain optimized structures. Theoretical spectral analysis (IR, 1H and 13C NMR) is compared with their experimental values. A good agreement is found between experimental and theoretical spectral analysis. These results mean that the optimized structures of mentioned complexes are appropriate. Additionally, the active sites of mentioned complexes are determined by molecular electrostatic potential (MEP) diagrams and non-linear optical (NLO) properties are investigated.

Local and average structure of Mn- and La-substituted BiFeO{sub 3}

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

Jiang, Bo; Selbach, Sverre M., E-mail: selbach@ntnu.no

2017-06-15

The local and average structure of solid solutions of the multiferroic perovskite BiFeO{sub 3} is investigated by synchrotron X-ray diffraction (XRD) and electron density functional theory (DFT) calculations. The average experimental structure is determined by Rietveld refinement and the local structure by total scattering data analyzed in real space with the pair distribution function (PDF) method. With equal concentrations of La on the Bi site or Mn on the Fe site, La causes larger structural distortions than Mn. Structural models based on DFT relaxed geometry give an improved fit to experimental PDFs compared to models constrained by the space groupmore » symmetry. Berry phase calculations predict a higher ferroelectric polarization than the experimental literature values, reflecting that structural disorder is not captured in either average structure space group models or DFT calculations with artificial long range order imposed by periodic boundary conditions. Only by including point defects in a supercell, here Bi vacancies, can DFT calculations reproduce the literature results on the structure and ferroelectric polarization of Mn-substituted BiFeO{sub 3}. The combination of local and average structure sensitive experimental methods with DFT calculations is useful for illuminating the structure-property-composition relationships in complex functional oxides with local structural distortions. - Graphical abstract: The experimental and simulated partial pair distribution functions (PDF) for BiFeO{sub 3}, BiFe{sub 0.875}Mn{sub 0.125}O{sub 3}, BiFe{sub 0.75}Mn{sub 0.25}O{sub 3} and Bi{sub 0.9}La{sub 0.1}FeO{sub 3}.« less

Using experimental studies and theoretical calculations to analyze the molecular mechanism of coumarin, p-hydroxybenzoic acid, and cinnamic acid

NASA Astrophysics Data System (ADS)

Hsieh, Tiane-Jye; Su, Chia-Ching; Chen, Chung-Yi; Liou, Chyong-Huey; Lu, Li-Hwa

2005-05-01

Three natural products, Coumarin ( 1), p-hydroxybenzoic acid ( 2), trans-cinnamic acid ( 3) were isolated from the natural plant of indigenous cinnamon and the structures including relative stereochemistry were elucidated on the basis of spectroscopic data and theoretical calculations. Their sterochemical structures were determined by NMR spectroscopy, mass spectroscopy, and X-ray crystallography. The p-hydroxybenzoic acid complex with water is reported to show the existence of two hydrogen bonds. The two hydrogen bonds are formed in the water molecule of two hydrogen-accepting oxygen of carbonyl group of the p-hydroxybenzoic acid. The intermolecular interaction two hydrogen bond of the model system of the water- p-hydroxybenzoic acid was investigated. An experimental study and a theoretical analysis using the B3LYP/6-31G* method in the GAUSSIAN-03 package program were conducted on the three natural products. The theoretical results are supplemented by experimental data. Optimal geometric structures of three compounds were also determined. The calculated molecular mechanics compared quite well with those obtained from the experimental data. The ionization potentials, highest occupied molecular orbital energy, lowest unoccupied molecular orbital energy, energy gaps, heat of formation, atomization energies, and vibration frequencies of the compounds were also calculated. The results of the calculations show that three natural products are stable molecules with high reactive and various other physical properties. The study also provided an explicit understanding of the sterochemical structure and thermodynamic properties of the three natural products.

Structural, mechanical and vibrational study of uranyl silicate mineral soddyite by DFT calculations

NASA Astrophysics Data System (ADS)

Colmenero, Francisco; Bonales, Laura J.; Cobos, Joaquín; Timón, Vicente

2017-09-01

Uranyl silicate mineral soddyite, (UO2)2(SiO4)·2(H2O), is a fundamental component of the paragenetic sequence of secondary phases that arises from the weathering of uraninite ore deposits and corrosion of spent nuclear fuel. In this work, soddyite was studied by first principle calculations based on the density functional theory. As far as we know, this is the first time that soddyite structure is determined theoretically. The computed structure of soddyite reproduces the one determined experimentally by X-Ray diffraction (orthorhombic symmetry, spatial group Fddd O2; lattice parameters a = 8.334 Å, b = 11.212 Å; c = 18.668 Å). Lattice parameters, bond lengths, bond angles and X-Ray powder pattern were found to be in very good agreement with their experimental counterparts. Furthermore, the mechanical properties were obtained and the satisfaction of the Born conditions for mechanical stability of the structure was demonstrated by means of calculations of the elasticity tensor. The equation of state of soddyite was obtained by fitting lattice volumes and pressures to a fourth order Birch-Murnahan equation of state. The Raman spectrum was also computed by means of density functional perturbation theory and compared with the experimental spectrum obtained from a natural soddyite sample. The results were also found in agreement with the experimental data. A normal mode analysis of the theoretical spectra was carried out and used in order to assign the main bands of the Raman spectrum.

Monitoring the bending and twist of morphing structures

NASA Astrophysics Data System (ADS)

Smoker, J.; Baz, A.

2008-03-01

This paper presents the development of the theoretical basis for the design of sensor networks for determining the 2-dimensioal shape of morphing structures by monitoring simultaneously the bending and twist deflections. The proposed development is based on the non-linear theory of finite elements to extract the transverse linear and angular deflections of a plate-like structure. The sensors outputs are wirelessly transmitted to the command unit to simultaneously compute maps of the linear and angular deflections and maps of the strain distribution of the entire structure. The deflection and shape information are required to ascertain that the structure is properly deployed and that its surfaces are operating wrinkle-free. The strain map ensures that the structure is not loaded excessively to adversely affect its service life. The developed theoretical model is validated experimentally using a prototype of a variable cambered span morphing structure provided with a network of distributed sensors. The structure/sensor network system is tested under various static conditions to determine the response characteristics of the proposed sensor network as compared to other conventional sensor systems. The presented theoretical and experimental techniques can have a great impact on the safe deployment and effective operation of a wide variety of morphing and inflatable structures such as morphing aircraft, solar sails, inflatable wings, and large antennas.

Mutations that Cause Human Disease: A Computational/Experimental Approach

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

Beernink, P; Barsky, D; Pesavento, B

International genome sequencing projects have produced billions of nucleotides (letters) of DNA sequence data, including the complete genome sequences of 74 organisms. These genome sequences have created many new scientific opportunities, including the ability to identify sequence variations among individuals within a species. These genetic differences, which are known as single nucleotide polymorphisms (SNPs), are particularly important in understanding the genetic basis for disease susceptibility. Since the report of the complete human genome sequence, over two million human SNPs have been identified, including a large-scale comparison of an entire chromosome from twenty individuals. Of the protein coding SNPs (cSNPs), approximatelymore » half leads to a single amino acid change in the encoded protein (non-synonymous coding SNPs). Most of these changes are functionally silent, while the remainder negatively impact the protein and sometimes cause human disease. To date, over 550 SNPs have been found to cause single locus (monogenic) diseases and many others have been associated with polygenic diseases. SNPs have been linked to specific human diseases, including late-onset Parkinson disease, autism, rheumatoid arthritis and cancer. The ability to predict accurately the effects of these SNPs on protein function would represent a major advance toward understanding these diseases. To date several attempts have been made toward predicting the effects of such mutations. The most successful of these is a computational approach called ''Sorting Intolerant From Tolerant'' (SIFT). This method uses sequence conservation among many similar proteins to predict which residues in a protein are functionally important. However, this method suffers from several limitations. First, a query sequence must have a sufficient number of relatives to infer sequence conservation. Second, this method does not make use of or provide any information on protein structure, which can be used to understand how an amino acid change affects the protein. The experimental methods that provide the most detailed structural information on proteins are X-ray crystallography and NMR spectroscopy. However, these methods are labor intensive and currently cannot be carried out on a genomic scale. Nonetheless, Structural Genomics projects are being pursued by more than a dozen groups and consortia worldwide and as a result the number of experimentally determined structures is rising exponentially. Based on the expectation that protein structures will continue to be determined at an ever-increasing rate, reliable structure prediction schemes will become increasingly valuable, leading to information on protein function and disease for many different proteins. Given known genetic variability and experimentally determined protein structures, can we accurately predict the effects of single amino acid substitutions? An objective assessment of this question would involve comparing predicted and experimentally determined structures, which thus far has not been rigorously performed. The completed research leveraged existing expertise at LLNL in computational and structural biology, as well as significant computing resources, to address this question.« less

Regional mechanics determine collagen fiber structure in healing myocardial infarcts.

PubMed

Fomovsky, Gregory M; Rouillard, Andrew D; Holmes, Jeffrey W

2012-05-01

Following myocardial infarction, the mechanical properties of the healing infarct are an important determinant of heart function and the risk of progression to heart failure. In particular, mechanical anisotropy (having different mechanical properties in different directions) in the healing infarct can preserve pump function of the heart. Based on reports of different collagen structures and mechanical properties in various animal models, we hypothesized that differences in infarct size, shape, and/or location produce different patterns of mechanical stretch that guide evolving collagen fiber structure. We tested the effects of infarct shape and location using a combined experimental and computational approach. We studied mechanics and collagen fiber structure in cryoinfarcts in 53 Sprague-Dawley rats and found that regardless of shape or orientation, cryoinfarcts near the equator of the left ventricle stretched primarily in the circumferential direction and developed circumferentially aligned collagen, while infarcts at the apex stretched similarly in the circumferential and longitudinal directions and developed randomly oriented collagen. In a computational model of infarct healing, an effect of mechanical stretch on fibroblast and collagen alignment was required to reproduce the experimental results. We conclude that mechanical environment determines collagen fiber structure in healing myocardial infarcts. Our results suggest that emerging post-infarction therapies that alter regional mechanics will also alter infarct collagen structure, offering both potential risks and novel therapeutic opportunities. Copyright © 2012 Elsevier Ltd. All rights reserved.

Regional Mechanics Determine Collagen Fiber Structure in Healing Myocardial Infarcts

PubMed Central

Fomovsky, Gregory M.; Rouillard, Andrew D.; Holmes, Jeffrey W.

2012-01-01

Following myocardial infarction, the mechanical properties of the healing infarct are an important determinant of heart function and the risk of progression to heart failure. In particular, mechanical anisotropy (having different mechanical properties in different directions) in the healing infarct can preserve pump function of the heart. Based on reports of different collagen structures and mechanical properties in various animal models, we hypothesized that differences in infarct size, shape, and/or location produce different patterns of mechanical stretch that guide evolving collagen fiber structure. We tested the effects of infarct shape and location using a combined experimental and computational approach. We studied mechanics and collagen fiber structure in cryoinfarcts in 53 Sprague-Dawley rats and found that regardless of shape or orientation, cryoinfarcts near the equator of the left ventricle stretched primarily in the circumferential direction and developed circumferentially aligned collagen, while infarcts at the apex stretched similarly in the circumferential and longitudinal direction and developed randomly oriented collagen. In a computational model of infarct healing, an effect of mechanical stretch on fibroblast and collagen alignment was required to reproduce the experimental results. We conclude that mechanical environment determines collagen fiber structure in healing myocardial infarcts. Our results suggest that emerging post-infarction therapies that alter regional mechanics will also alter infarct collagen structure, offering both potential risks and novel therapeutic opportunities. PMID:22418281

Stiffness analysis of glued connection of the timber-concrete structure

NASA Astrophysics Data System (ADS)

Daňková, Jana; Mec, Pavel; Majstríková, Tereza

2016-01-01

This paper presents results of experimental and mathematical analysis of stiffness characteristics of a composite timber-concrete structure. The composite timberconcrete structure presented herein is non-typical compared to similar types of building structures. The interaction between the timber and concrete part of the composite cross-section is not based on metal connecting elements, but it is ensured by a glued-in perforated mesh made of plywood. The paper presents results of experimental and mathematical analysis for material alternatives of the solution of the glued joint. The slip modulus values were determined experimentally. Data obtained from the experiment evaluated by means of regression analysis. Test results were also used as input data for the compilation of a 3D model of a composite structure by means of the 3D finite element model. On the basis of result evaluation, it can be stated that the stress-deformation behaviour at shear loading of this specific timber-concrete composite structure can be affected by the type of glue used. Parameters of the 3D model of both alternative of the structure represent well the behaviour of the composite structure and the model can be used for predicting design parameters of a building structure.

Estimating structure quality trends in the Protein Data Bank by equivalent resolution.

PubMed

Bagaria, Anurag; Jaravine, Victor; Güntert, Peter

2013-10-01

The quality of protein structures obtained by different experimental and ab-initio calculation methods varies considerably. The methods have been evolving over time by improving both experimental designs and computational techniques, and since the primary aim of these developments is the procurement of reliable and high-quality data, better techniques resulted on average in an evolution toward higher quality structures in the Protein Data Bank (PDB). Each method leaves a specific quantitative and qualitative "trace" in the PDB entry. Certain information relevant to one method (e.g. dynamics for NMR) may be lacking for another method. Furthermore, some standard measures of quality for one method cannot be calculated for other experimental methods, e.g. crystal resolution or NMR bundle RMSD. Consequently, structures are classified in the PDB by the method used. Here we introduce a method to estimate a measure of equivalent X-ray resolution (e-resolution), expressed in units of Å, to assess the quality of any type of monomeric, single-chain protein structure, irrespective of the experimental structure determination method. We showed and compared the trends in the quality of structures in the Protein Data Bank over the last two decades for five different experimental techniques, excluding theoretical structure predictions. We observed that as new methods are introduced, they undergo a rapid method development evolution: within several years the e-resolution score becomes similar for structures obtained from the five methods and they improve from initially poor performance to acceptable quality, comparable with previously established methods, the performance of which is essentially stable. Copyright © 2013 Elsevier Ltd. All rights reserved.

Food-web models predict species abundances in response to habitat change.

PubMed

Gotelli, Nicholas J; Ellison, Aaron M

2006-10-01

Plant and animal population sizes inevitably change following habitat loss, but the mechanisms underlying these changes are poorly understood. We experimentally altered habitat volume and eliminated top trophic levels of the food web of invertebrates that inhabit rain-filled leaves of the carnivorous pitcher plant Sarracenia purpurea. Path models that incorporated food-web structure better predicted population sizes of food-web constituents than did simple keystone species models, models that included only autecological responses to habitat volume, or models including both food-web structure and habitat volume. These results provide the first experimental confirmation that trophic structure can determine species abundances in the face of habitat loss.

Determination of the mechanical indices of composite materials by testing multilayered samples

NASA Astrophysics Data System (ADS)

Teregulov, I. G.; Kayumov, R. A.; Butenko, Yu. I.; Safiullin, D. Kh.

1996-09-01

The mechanical indices of materials such as composites reinforced by braids and ribbons are difficult to determine by standard methods. Moreover, the indices of such materials may be greatly altered when they are converted into various structures. It has been suggested that these indices be determined by analyzing the structure testing data. The determination of linear and nonlinear elastic, plastic, and viscoelastic parameters of reinforced materials is discussed. A very simple structure, namely, cylindrical shells made by symmetric winding, is studied as an example. Equilibrium conditions are used to obtain resolving equations relative to the mechanical indices. Convergence of iteration methods is examined. The effect of the scatter of experimental data on the calculated results is analyzed.

Keto-enol tautomerism of (E)-2-[(3,4-dimethylphenylimino)methyl]-4-nitrophenol: Synthesis, X-ray, FT-IR, UV-Vis, NMR and quantum chemical characterizations

NASA Astrophysics Data System (ADS)

Özek Yıldırım, Arzu; Yıldırım, M. Hakkı; Albayrak Kaştaş, Çiǧdem

2017-01-01

(E)-2-((3,4-dimethylphenylimino)methyl)-4-nitrophenol, which is a new Schiff base compound, was synthesized and characterized by experimental and computational methods. Molecular geometry, harmonic oscillator model of aromaticity (HOMA) indices, intra- and inter-molecular interactions in the crystal structure were determined by using single crystal X-ray diffraction technique. The optimized structures, which are obtained by Gaussian and Slater type orbitals, were compared to experimental structures to determine how much correlation is found between the experimental and the calculated properties. Intramolecular and hyperconjugative interactions of bonds have been found by Natural Bond Orbital analysis. The experimental infrared spectrum of the compound has been analyzed in detail by the calculated infrared spectra and Potential Energy Distribution analysis. To find out about the correlation between the solvent polarity and the enol-keto equilibrium, experimental UV-Visible spectra of the compound were obtained in benzene, CHCl3, EtOH and DMSO solvents. In these solvents, the UV-Vis spectra and relaxed potential energy surface scan (PES) calculations have been performed to get more insight into the equilibrium dynamics. Solvent effects in UV-Vis and PES calculations have been taken into account by using Polarizable Continuum Modelling method. 1H and 13C NMR spectra of the compound (in DMSO) were analyzed. The computational study of nonlinear optical properties shows that the compound can be used for the development of nonlinear optical materials.

Crack identification method in beam-like structures using changes in experimentally measured frequencies and Particle Swarm Optimization

NASA Astrophysics Data System (ADS)

Khatir, Samir; Dekemele, Kevin; Loccufier, Mia; Khatir, Tawfiq; Abdel Wahab, Magd

2018-02-01

In this paper, a technique is presented for the detection and localization of an open crack in beam-like structures using experimentally measured natural frequencies and the Particle Swarm Optimization (PSO) method. The technique considers the variation in local flexibility near the crack. The natural frequencies of a cracked beam are determined experimentally and numerically using the Finite Element Method (FEM). The optimization algorithm is programmed in MATLAB. The algorithm is used to estimate the location and severity of a crack by minimizing the differences between measured and calculated frequencies. The method is verified using experimentally measured data on a cantilever steel beam. The Fourier transform is adopted to improve the frequency resolution. The results demonstrate the good accuracy of the proposed technique.

Building Quakes: Detection of Weld Fractures in Buildings using High-Frequency Seismic Techniques

NASA Astrophysics Data System (ADS)

Heckman, V.; Kohler, M. D.; Heaton, T. H.

2009-12-01

Catastrophic fracture of welded beam-column connections in buildings was observed in the Northridge and Kobe earthquakes. Despite the structural importance of such connections, it can be difficult to locate damage in structural members underneath superficial building features. We have developed a novel technique to locate fracturing welds in buildings in real time using high-frequency information from seismograms. Numerical and experimental methods were used to investigate an approach for detecting the brittle fracture of welds of beam-column connections in instrumented steel moment-frame buildings through the use of time-reversed Green’s functions and wave propagation reciprocity. The approach makes use of a prerecorded catalogue of Green’s functions for an instrumented building to detect high-frequency failure events in the building during a later earthquake by screening continuous data for the presence of one or more of the events. This was explored experimentally by comparing structural responses of a small-scale laboratory structure under a variety of loading conditions. Experimentation was conducted on a polyvinyl chloride frame model structure with data recorded at a sample rate of 2000 Hz using piezoelectric accelerometers and a 24-bit digitizer. Green’s functions were obtained by applying impulsive force loads at various locations along the structure with a rubber-tipped force transducer hammer. We performed a blind test using cross-correlation techniques to determine if it was possible to use the catalogue of Green’s functions to pinpoint the absolute times and locations of subsequent, induced failure events in the structure. A finite-element method was used to simulate the response of the model structure to various source mechanisms in order to determine the types of elastic waves that were produced as well as to obtain a general understanding of the structural response to localized loading and fracture.

DEVELOPMENT OF PREDICTIVE STRUCTURE-BIODEGRADATION RELATIONSHIP MODELS WITH THE USE OF RESPIROMETRICALLY GENERATED BIOKINETIC DATA

EPA Science Inventory

Biodegradation is an important mechanism determining the fate of chemicals in the aquatic environment. In this paper, experimental data, determined from electrolytic respirometry, for 27 compounds were analyzed using first order and Monod kinetics. Additional data from the lite...

Pedagogical Interaction in High School, the Structural and Functional Model of Pedagogical Interaction

ERIC Educational Resources Information Center

Semenova, Larissa A.; Kazantseva, Anastassiya I.; Sergeyeva, Valeriya V.; Raklova, Yekaterina M.; Baiseitova, Zhanar B.

2016-01-01

The study covers the problems of pedagogical technologies and their experimental implementation in the learning process. The theoretical aspects of the "student-teacher" interaction are investigated. A structural and functional model of pedagogical interaction is offered, which determines the conditions for improving pedagogical…

Determining the transition-state structure for different SN2 reactions using experimental nucleophile carbon and secondary alpha-deuterium kinetic isotope effects and theory.

PubMed

Westaway, Kenneth C; Fang, Yao-ren; MacMillar, Susanna; Matsson, Olle; Poirier, Raymond A; Islam, Shahidul M

2008-10-16

Nucleophile (11)C/ (14)C [ k (11)/ k (14)] and secondary alpha-deuterium [( k H/ k D) alpha] kinetic isotope effects (KIEs) were measured for the S N2 reactions between tetrabutylammonium cyanide and ethyl iodide, bromide, chloride, and tosylate in anhydrous DMSO at 20 degrees C to determine whether these isotope effects can be used to determine the structure of S N2 transition states. Interpreting the experimental KIEs in the usual fashion (i.e., that a smaller nucleophile KIE indicates the Nu-C alpha transition state bond is shorter and a smaller ( k H/ k D) alpha is found when the Nu-LG distance in the transition state is shorter) suggests that the transition state is tighter with a slightly shorter NC-C alpha bond and a much shorter C alpha-LG bond when the substrate has a poorer halogen leaving group. Theoretical calculations at the B3LYP/aug-cc-pVDZ level of theory support this conclusion. The results show that the experimental nucleophile (11)C/ (14)C KIEs can be used to determine transition-state structure in different reactions and that the usual method of interpreting these KIEs is correct. The magnitude of the experimental secondary alpha-deuterium KIE is related to the nucleophile-leaving group distance in the S N2 transition state ( R TS) for reactions with a halogen leaving group. Unfortunately, the calculated and experimental ( k H/ k D) alpha's change oppositely with leaving group ability. However, the calculated ( k H/ k D) alpha's duplicate both the trend in the KIE with leaving group ability and the magnitude of the ( k H/ k D) alpha's for the ethyl halide reactions when different scale factors are used for the high and the low energy vibrations. This suggests it is critical that different scaling factors for the low and high energy vibrations be used if one wishes to duplicate experimental ( k H/ k D) alpha's. Finally, neither the experimental nor the theoretical secondary alpha-deuterium KIEs for the ethyl tosylate reaction fit the trend found for the reactions with a halogen leaving group. This presumably is found because of the bulky (sterically hindered) leaving group in the tosylate reaction. From every prospective, the tosylate reaction is too different from the halogen reactions to be compared.

Solidification Based Grain Refinement in Steels

DTIC Science & Technology

2009-07-24

pearlite (See Figure 1). No evidence of the as-cast austenite dendrite structure was observed. The gating system for this sample resides at the thermal...possible nucleating compounds. 3) Extend grain refinement theory and solidification knowledge through experimental data. 4) Determine structure ...refine the structure of a casting through heat treatment. The energy required for grain refining via thermomechanical processes or heat treatment

Intermolecular shielding contributions studied by modeling the 13C chemical-shift tensors of organic single crystals with plane waves

PubMed Central

Johnston, Jessica C.; Iuliucci, Robbie J.; Facelli, Julio C.; Fitzgerald, George; Mueller, Karl T.

2009-01-01

In order to predict accurately the chemical shift of NMR-active nuclei in solid phase systems, magnetic shielding calculations must be capable of considering the complete lattice structure. Here we assess the accuracy of the density functional theory gauge-including projector augmented wave method, which uses pseudopotentials to approximate the nodal structure of the core electrons, to determine the magnetic properties of crystals by predicting the full chemical-shift tensors of all 13C nuclides in 14 organic single crystals from which experimental tensors have previously been reported. Plane-wave methods use periodic boundary conditions to incorporate the lattice structure, providing a substantial improvement for modeling the chemical shifts in hydrogen-bonded systems. Principal tensor components can now be predicted to an accuracy that approaches the typical experimental uncertainty. Moreover, methods that include the full solid-phase structure enable geometry optimizations to be performed on the input structures prior to calculation of the shielding. Improvement after optimization is noted here even when neutron diffraction data are used for determining the initial structures. After geometry optimization, the isotropic shift can be predicted to within 1 ppm. PMID:19831448

Neutral, ion gas-phase energetics and structural properties of hydroxybenzophenones.

PubMed

Dávalos, Juan Z; Guerrero, Andrés; Herrero, Rebeca; Jimenez, Pilar; Chana, Antonio; Abboud, José Luis M; Lima, Carlos F R A C; Santos, Luís M N B F; Lago, Alexsandre F

2010-04-16

We have carried out a study of the energetics, structural, and physical properties of o-, m-, and p-hydroxybenzophenone neutral molecules, C(13)H(10)O(2), and their corresponding anions. In particular, the standard enthalpies of formation in the gas phase at 298.15 K for all of these species were determined. A reliable experimental estimation of the enthalpy associated with intramolecular hydrogen bonding in chelated species was experimentally obtained. The gas-phase acidities (GA) of benzophenones, substituted phenols, and several aliphatic alcohols are compared with the corresponding aqueous acidities (pK(a)), covering a range of 278 kJ.mol(-1) in GA and 11.4 in pK(a). A computational study of the various species shed light on structural effects and further confirmed the self-consistency of the experimental results.

Structure and energetics of Cr(CO)6 and Cr(CO)5

NASA Technical Reports Server (NTRS)

Barnes, Leslie A.; Liu, Bowen; Lindh, Roland

1993-01-01

The geometric structures and energetics of Cr(CO)6 and Cr(CO)5 are determined at the modified coupled-pair functional, single and double excitation coupled-cluster (CCSD), and CCSD(T) levels of theory. For Cr(CO)6, the structure and force constants for the totally symmetric representation are in good agreement with experimental data once basis set constants are taken into account. In the largest basis set at the CCSD(T) level of theory, the total binding energy of CR(CO)6 is estimated at around 140 kcal/mol, or about 86 percent of the experimental value. In contrast, the first bond energy of Cr(CO)6 is very well described at the CCSD(T) level of theory, with the best estimated value of 38 kcal/mol being within the experimental uncertainty.

DFT and experimental studies of the structure and vibrational spectra of curcumin

NASA Astrophysics Data System (ADS)

Kolev, Tsonko M.; Velcheva, Evelina A.; Stamboliyska, Bistra A.; Spiteller, Michael

The potential energy surface of curcumin [1,7-bis(4-hydroxy-3-methoxyphenyl)-1,6-heptadiene-3,5-dione] was explored with the DFT correlation functional B3LYP method using 6-311G* basis. The single-point calculations were performed at levels up to B3LYP/6-311++G**//B3LYP/6-311G*. All isomers were located and relative energies determined. According to the calculation the planar enol form is more stable than the nonplanar diketo form. The results of the optimized molecular structure are presented and compared with the experimental X-ray diffraction. In addition, harmonic vibrational frequencies of the molecule were evaluated theoretically using B3LYP density functional methods. The computed vibrational frequencies were used to determine the types of molecular motions associated with each of the experimental bands observed. Our vibrational data show that in both the solid state and in all studied solutions curcumin exists in the enol form.

The effects of rigid motions on elastic network model force constants

PubMed Central

Lezon, Timothy R.

2012-01-01

Elastic network models provide an efficient way to quickly calculate protein global dynamics from experimentally determined structures. The model’s single parameter, its force constant, determines the physical extent of equilibrium fluctuations. The values of force constants can be calculated by fitting to experimental data, but the results depend on the type of experimental data used. Here we investigate the differences between calculated values of force constants _t to data from NMR and X-ray structures. We find that X-ray B factors carry the signature of rigid-body motions, to the extent that B factors can be almost entirely accounted for by rigid motions alone. When fitting to more refined anisotropic temperature factors, the contributions of rigid motions are significantly reduced, indicating that the large contribution of rigid motions to B factors is a result of over-fitting. No correlation is found between force constants fit to NMR data and those fit to X-ray data, possibly due to the inability of NMR data to accurately capture protein dynamics. PMID:22228562

Numerical validation of selected computer programs in nonlinear analysis of steel frame exposed to fire

NASA Astrophysics Data System (ADS)

Maślak, Mariusz; Pazdanowski, Michał; Woźniczka, Piotr

2018-01-01

Validation of fire resistance for the same steel frame bearing structure is performed here using three different numerical models, i.e. a bar one prepared in the SAFIR environment, and two 3D models developed within the framework of Autodesk Simulation Mechanical (ASM) and an alternative one developed in the environment of the Abaqus code. The results of the computer simulations performed are compared with the experimental results obtained previously, in a laboratory fire test, on a structure having the same characteristics and subjected to the same heating regimen. Comparison of the experimental and numerically determined displacement evolution paths for selected nodes of the considered frame during the simulated fire exposure constitutes the basic criterion applied to evaluate the validity of the numerical results obtained. The experimental and numerically determined estimates of critical temperature specific to the considered frame and related to the limit state of bearing capacity in fire have been verified as well.

Analysis of the Defect Structure of B2 Feal Alloys

NASA Technical Reports Server (NTRS)

Bozzolo, Guillermo; Ferrante, John; Noebe, Ronald D.; Amador, Carlos

1995-01-01

The Bozzolo, Ferrante and Smith (BFS) method for alloys is applied to the study of the defect structure of B2 FeAI alloys. First-principles Linear Muffin Tin Orbital calculations are used to determine the input parameters to the BFS method used in this work. The calculations successfully determine the phase field of the B2 structure, as well as the dependence with composition of the lattice parameter. Finally, the method is used to perform 'static' simulations where instead of determining the ground state configuration of the alloy with a certain concentration of vacancies, a large number of candidate ordered structures are studied and compared, in order to determine not only the lowest energy configurations but other possible metastable states as well. The results provide a description of the defect structure consistent with available experimental data. The simplicity of the BFS method also allows for a simple explanation of some of the essential features found in the concentration dependence of the heat of formation, lattice parameter and the defect structure.

Requirements on paramagnetic relaxation enhancement data for membrane protein structure determination by NMR.

PubMed

Gottstein, Daniel; Reckel, Sina; Dötsch, Volker; Güntert, Peter

2012-06-06

Nuclear magnetic resonance (NMR) structure calculations of the α-helical integral membrane proteins DsbB, GlpG, and halorhodopsin show that distance restraints from paramagnetic relaxation enhancement (PRE) can provide sufficient structural information to determine their structure with an accuracy of about 1.5 Å in the absence of other long-range conformational restraints. Our systematic study with simulated NMR data shows that about one spin label per transmembrane helix is necessary for obtaining enough PRE distance restraints to exclude wrong topologies, such as pseudo mirror images, if only limited other NMR restraints are available. Consequently, an experimentally realistic amount of PRE data enables α-helical membrane protein structure determinations that would not be feasible with the very limited amount of conventional NOESY data normally available for these systems. These findings are in line with our recent first de novo NMR structure determination of a heptahelical integral membrane protein, proteorhodopsin, that relied extensively on PRE data. Copyright © 2012 Elsevier Ltd. All rights reserved.

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

Schaeffel, J.A.; Mullinix, B.R.; Ranson, W.F.

An experimental technique to simulate and evaluate the effects of high concentrations of x-rays resulting from a nuclear detonation on missile structures is presented. Data from 34 tests are included to demonstrate the technique. The effects of variations in the foil thickness, capacitor voltage, and plate thickness on the total impulse and maximum strain in the structure were determined. The experimental technique utilizes a high energy capacitor discharge unit to explode an aluminum foil on the surface of the structure. The structural response is evaluated by optical methods using the grid slope deflection method. The fringe patterns were recorded usingmore » a high-speed framing camera. The data were digitized using an optical comparator with an x-y table. The analysis was performed on a CDC 6600 computer.« less

In search of a consensus model of the resting state of a voltage-sensing domain.

PubMed

Vargas, Ernesto; Bezanilla, Francisco; Roux, Benoît

2011-12-08

Voltage-sensing domains (VSDs) undergo conformational changes in response to the membrane potential and are the critical structural modules responsible for the activation of voltage-gated channels. Structural information about the key conformational states underlying voltage activation is currently incomplete. Through the use of experimentally determined residue-residue interactions as structural constraints, we determine and refine a model of the Kv channel VSD in the resting conformation. The resulting structural model is in broad agreement with results that originate from various labs using different techniques, indicating the emergence of a consensus for the structural basis of voltage sensing. Copyright © 2011 Elsevier Inc. All rights reserved.

Detection of free nickel monocarbonyl, NiCO: rotational spectrum and structure.

PubMed

Yamazaki, Emi; Okabayashi, Toshiaki; Tanimoto, Mitsutoshi

2004-02-04

Unsaturated transition metal carbonyls are important in processes such as organometallic synthesis, homogeneous catalysis, and photochemical decomposition of organometallics. In particular, a metal monocarbonyl offers a zeroth-order model for interpreting the chemisorption of a CO molecule on a metal surface in catalytic activation processes. Quite large numbers of theoretical papers have appeared which predict spectroscopic and structural properties of transition metal carbonyls. The nickel monocarbonyl NiCO has been one of the metal carbonyls most extensively studied by the theoretical calculations. At least 50 theoretical studies have been published on this simplest transition metal carbonyl up to the present time. However, experimental evidence of NiCO is much more sparse than theoretical predictions, and the actual structure of NiCO has never been determined by any experimental methods. This Communication reports the first preparation of free nickel monocarbonyl and observation of its rotational transitions. The NiCO molecule was generated by the sputtering reaction of a Ni cathode in the presence of CO. The accurate bond lengths of Ni-C and C-O were experimentally determined from isotopic data and were compared with the theoretical predictions for the first time.

Structure and properties of microporous titanosilicate determined by first-principles calculations

NASA Astrophysics Data System (ADS)

Ching, W. Y.; Xu, Yong-Nian; Gu, Zong-Quan

1996-12-01

The structure of EST-10, a member of synthetic microporous titanosilicates, was recently determined by an ingenious combination of experimental and simulational techniques. However, the locations of the alkali atoms in the framework remain elusive and its electronic structure is totally unknown. Based on first-principles local density calculations, the possible locations of the alkali atoms are identified and its electronic structure and bonding fully elucidated. ETS-10 is a semiconductor with a direct band gap of 2.33 eV. The Na atoms are likely to locate inside the seven-member ring pore adjacent to the one-dimensional Ti-O-Ti-O- chain.

Testing the effect of habitat structure and complexity on nekton assemblages using experimental oyster reefs

USGS Publications Warehouse

Humphries, Austin T.; LaPeyre, Megan K.; Kimball, Matthew E.; Rozas, Lawrence P.

2011-01-01

Structurally complex habitats are often associated with more diverse and abundant species assemblages in both aquatic and terrestrial ecosystems. Biogenic reefs formed by the eastern oyster (Crassostrea virginica) are complex in nature and are recognized for their potential habitat value in estuarine systems along the US Atlantic and Gulf of Mexico coasts. Few studies, however, have examined the response of nekton to structural complexity within oyster reefs. We used a quantitative sampling technique to examine how the presence and complexity of experimental oyster reefs influence the abundance, biomass, and distribution of nekton by sampling reefs 4 months and 16 months post-construction. Experimental oyster reefs were colonized immediately by resident fishes and decapod crustaceans, and reefs supported a distinct nekton assemblage compared to mud-bottom habitat. Neither increased reef complexity, nor age of the experimental reef resulted in further changes in nekton assemblages or increases in nekton abundance or diversity. The presence of oyster reefs per se was the most important factor determining nekton usage.

A thorough experimental study of CH/π interactions in water: quantitative structure-stability relationships for carbohydrate/aromatic complexes.

PubMed

Jiménez-Moreno, Ester; Jiménez-Osés, Gonzalo; Gómez, Ana M; Santana, Andrés G; Corzana, Francisco; Bastida, Agatha; Jiménez-Barbero, Jesus; Asensio, Juan Luis

2015-11-13

CH/π interactions play a key role in a large variety of molecular recognition processes of biological relevance. However, their origins and structural determinants in water remain poorly understood. In order to improve our comprehension of these important interaction modes, we have performed a quantitative experimental analysis of a large data set comprising 117 chemically diverse carbohydrate/aromatic stacking complexes, prepared through a dynamic combinatorial approach recently developed by our group. The obtained free energies provide a detailed picture of the structure-stability relationships that govern the association process, opening the door to the rational design of improved carbohydrate-based ligands or carbohydrate receptors. Moreover, this experimental data set, supported by quantum mechanical calculations, has contributed to the understanding of the main driving forces that promote complex formation, underlining the key role played by coulombic and solvophobic forces on the stabilization of these complexes. This represents the most quantitative and extensive experimental study reported so far for CH/π complexes in water.

Method of experimental and calculation determination of dissipative properties of carbon

NASA Astrophysics Data System (ADS)

Kazakova, Olga I.; Smolin, Igor Yu.; Bezmozgiy, Iosif M.

2017-12-01

This paper describes the process of definition of relations between the damping ratio and strain/state levels in a material. For these purposes, the experimental-calculation approach was applied. The experimental research was performed on plane composite specimens. The tests were accompanied by finite element modeling using the ANSYS software. Optimization was used as a tool for FEM property setting and for finding the above-mentioned relations. A difference between the calculation and experimental results was accepted as objective functions of this optimization. The optimization cycle was implemented using the pSeven DATADVANCE software platform. The developed approach makes it possible to determine the relations between the damping ratio and strain/state levels in the material, which can be used for computer modeling of the structure response under dynamic loading.

Phospholipid component volumes: determination and application to bilayer structure calculations.

PubMed

Armen, R S; Uitto, O D; Feller, S E

1998-08-01

We present a new method for the determination of bilayer structure based on a combination of computational studies and laboratory experiments. From molecular dynamics simulations, the volumes of submolecular fragments of saturated and unsaturated phosphatidylcholines in the liquid crystalline state have been extracted with a precision not available experimentally. Constancy of component volumes, both among different lipids and as a function of membrane position for a given lipid, have been examined. The component volumes were then incorporated into the liquid crystallographic method described by Wiener and White (1992. Biophys. J. 61:434-447, and references therein) for determining the structure of a fluid-phase dioleoylphosphatidylcholine bilayer from x-ray and neutron diffraction experiments.

Phospholipid component volumes: determination and application to bilayer structure calculations.

PubMed Central

Armen, R S; Uitto, O D; Feller, S E

1998-01-01

We present a new method for the determination of bilayer structure based on a combination of computational studies and laboratory experiments. From molecular dynamics simulations, the volumes of submolecular fragments of saturated and unsaturated phosphatidylcholines in the liquid crystalline state have been extracted with a precision not available experimentally. Constancy of component volumes, both among different lipids and as a function of membrane position for a given lipid, have been examined. The component volumes were then incorporated into the liquid crystallographic method described by Wiener and White (1992. Biophys. J. 61:434-447, and references therein) for determining the structure of a fluid-phase dioleoylphosphatidylcholine bilayer from x-ray and neutron diffraction experiments. PMID:9675175

Three key residues form a critical contact network in a protein folding transition state

NASA Astrophysics Data System (ADS)

Vendruscolo, Michele; Paci, Emanuele; Dobson, Christopher M.; Karplus, Martin

2001-02-01

Determining how a protein folds is a central problem in structural biology. The rate of folding of many proteins is determined by the transition state, so that a knowledge of its structure is essential for understanding the protein folding reaction. Here we use mutation measurements-which determine the role of individual residues in stabilizing the transition state-as restraints in a Monte Carlo sampling procedure to determine the ensemble of structures that make up the transition state. We apply this approach to the experimental data for the 98-residue protein acylphosphatase, and obtain a transition-state ensemble with the native-state topology and an average root-mean-square deviation of 6Å from the native structure. Although about 20 residues with small positional fluctuations form the structural core of this transition state, the native-like contact network of only three of these residues is sufficient to determine the overall fold of the protein. This result reveals how a nucleation mechanism involving a small number of key residues can lead to folding of a polypeptide chain to its unique native-state structure.

Experimental validation of tape springs to be used as thin-walled space structures

NASA Astrophysics Data System (ADS)

Oberst, S.; Tuttle, S. L.; Griffin, D.; Lambert, A.; Boyce, R. R.

2018-04-01

With the advent of standardised launch geometries and off-the-shelf payloads, space programs utilising nano-satellite platforms are growing worldwide. Thin-walled, flexible and self-deployable structures are commonly used for antennae, instrument booms or solar panels owing to their lightweight, ideal packaging characteristics and near zero energy consumption. However their behaviour in space, in particular in Low Earth Orbits with continually changing environmental conditions, raises many questions. Accurate numerical models, which are often not available due to the difficulty of experimental testing under 1g-conditions, are needed to answer these questions. In this study, we present on-earth experimental validations, as a starting point to study the response of a tape spring as a representative of thin-walled flexible structures under static and vibrational loading. Material parameters of tape springs in a singly (straight, open cylinder) and a doubly curved design, are compared to each other by combining finite element calculations, with experimental laser vibrometry within a single and multi-stage model updating approach. While the determination of the Young's modulus is unproblematic, the damping is found to be inversely proportional to deployment length. With updated material properties the buckling instability margin is calculated using different slenderness ratios. Results indicate a high sensitivity of thin-walled structures to miniscule perturbations, which makes proper experimental testing a key requirement for stability prediction on thin-elastic space structures. The doubly curved tape spring provides closer agreement with experimental results than a straight tape spring design.

A new potential for radiation studies of borosilicate glass

NASA Astrophysics Data System (ADS)

Alharbi, Amal F.; Jolley, Kenny; Smith, Roger; Archer, Andrew J.; Christie, Jamieson K.

2017-02-01

Borosilicate glass containing 70 mol% SiO2 and 30 mol% B2O3 is investigated theoretically using fixed charge potentials. An existing potential parameterisation for borosilicate glass is found to give good agreement for the bond angle and bond length distributions compared to experimental values but the optimal density is 30% higher than experiment. Therefore the potential parameters are refitted to give an optimal density of 2.1 g/cm3, in line with experiment. To determine the optimal density, a series of random initial structures are quenched at a rate of 5 × 1012 K/s using constant volume molecular dynamics. An average of 10 such quenches is carried out for each fixed volume. For each quenched structure, the bond angles, bond lengths, mechanical properties and melting points are determined. The new parameterisation is found to give the density, bond angles, bond lengths and Young's modulus comparable with experimental data, however, the melting points and Poisson's ratio are higher than the reported experimental values. The displacement energy thresholds are computed to be similar to those determined with the earlier parameterisation, which is lower than those for ionic crystalline materials.

Thermal desorption of metals from tungsten single crystal surfaces

NASA Technical Reports Server (NTRS)

Bauer, E.; Bonczek, F.; Poppa, H.; Todd, G.

1975-01-01

After a short review of experimental methods used to determine desorption energies and frequencies the assumptions underlying the theoretical analysis of experimental data are discussed. Recent experimental results on the flash desorption of Cu, Ag, and Au from clean, well characterized W (110) and (100) surfaces are presented and analyzed in detail with respect to the coverage dependence. The results obtained clearly reveal the limitations of previous analytical methods and of the experimental technique per se (such as structure and phase changes below and in the temperature region in which desorption occurs).

Two-photon absorption in oxazole derivatives: An experimental and quantum chemical study

NASA Astrophysics Data System (ADS)

Silva, D. L.; De Boni, L.; Correa, D. S.; Costa, S. C. S.; Hidalgo, A. A.; Zilio, S. C.; Canuto, S.; Mendonca, C. R.

2012-05-01

Experimental and theoretical studies on the two-photon absorption properties of two oxazole derivatives: 2,5-diphenyloxazole (PPO) and 2-(4-biphenylyl)-5-phenyl-1,3,4-oxadiazole (PBD) are presented. The two-photon absorption cross-section spectra were determined by means of the Z-scan technique, from 460 up to 650 nm, and reached peak values of 84 GM for PBD and 27 GM for PPO. Density Functional Theory and response function formalism are used to determine the molecular structures and the one- and two-photon absorption properties and to assist in the interpretation of the experimental results. The Polarizable Continuum Model in one-photon absorption calculations is used to estimate solvent effects.

Validation and upgrading of physically based mathematical models

NASA Technical Reports Server (NTRS)

Duval, Ronald

1992-01-01

The validation of the results of physically-based mathematical models against experimental results was discussed. Systematic techniques are used for: (1) isolating subsets of the simulator mathematical model and comparing the response of each subset to its experimental response for the same input conditions; (2) evaluating the response error to determine whether it is the result of incorrect parameter values, incorrect structure of the model subset, or unmodeled external effects of cross coupling; and (3) modifying and upgrading the model and its parameter values to determine the most physically appropriate combination of changes.

In Silico Analysis for the Study of Botulinum Toxin Structure

NASA Astrophysics Data System (ADS)

Suzuki, Tomonori; Miyazaki, Satoru

2010-01-01

Protein-protein interactions play many important roles in biological function. Knowledge of protein-protein complex structure is required for understanding the function. The determination of protein-protein complex structure by experimental studies remains difficult, therefore computational prediction of protein structures by structure modeling and docking studies is valuable method. In addition, MD simulation is also one of the most popular methods for protein structure modeling and characteristics. Here, we attempt to predict protein-protein complex structure and property using some of bioinformatic methods, and we focus botulinum toxin complex as target structure.

Modeling complexes of modeled proteins.

PubMed

Anishchenko, Ivan; Kundrotas, Petras J; Vakser, Ilya A

2017-03-01

Structural characterization of proteins is essential for understanding life processes at the molecular level. However, only a fraction of known proteins have experimentally determined structures. This fraction is even smaller for protein-protein complexes. Thus, structural modeling of protein-protein interactions (docking) primarily has to rely on modeled structures of the individual proteins, which typically are less accurate than the experimentally determined ones. Such "double" modeling is the Grand Challenge of structural reconstruction of the interactome. Yet it remains so far largely untested in a systematic way. We present a comprehensive validation of template-based and free docking on a set of 165 complexes, where each protein model has six levels of structural accuracy, from 1 to 6 Å C α RMSD. Many template-based docking predictions fall into acceptable quality category, according to the CAPRI criteria, even for highly inaccurate proteins (5-6 Å RMSD), although the number of such models (and, consequently, the docking success rate) drops significantly for models with RMSD > 4 Å. The results show that the existing docking methodologies can be successfully applied to protein models with a broad range of structural accuracy, and the template-based docking is much less sensitive to inaccuracies of protein models than the free docking. Proteins 2017; 85:470-478. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

Response of basic structural elements and B-52 structural components to simulated nuclear overpressure. Volume II-program data (basic structural elements). Final report, 1 June 1977-30 September 1979

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

Syring, R.P.; Grubb, R.L.

1979-09-30

This document reports on the following: (1) experimental determination of the response of 16 basic structural elements and 7 B-52 components to simulated nuclear overpressure environments (utilizing Sandia Corporation's Thunderpipe Shock Tube), (2) analysis of these test specimens utilizing the NOVA-2 computer program, and (3) correlation of test and analysis results.

Experimental Protocol to Determine the Chloride Threshold Value for Corrosion in Samples Taken from Reinforced Concrete Structures

PubMed Central

Angst, Ueli M.; Boschmann, Carolina; Wagner, Matthias; Elsener, Bernhard

2017-01-01

The aging of reinforced concrete infrastructure in developed countries imposes an urgent need for methods to reliably assess the condition of these structures. Corrosion of the embedded reinforcing steel is the most frequent cause for degradation. While it is well known that the ability of a structure to withstand corrosion depends strongly on factors such as the materials used or the age, it is common practice to rely on threshold values stipulated in standards or textbooks. These threshold values for corrosion initiation (Ccrit) are independent of the actual properties of a certain structure, which clearly limits the accuracy of condition assessments and service life predictions. The practice of using tabulated values can be traced to the lack of reliable methods to determine Ccrit on-site and in the laboratory. Here, an experimental protocol to determine Ccrit for individual engineering structures or structural members is presented. A number of reinforced concrete samples are taken from structures and laboratory corrosion testing is performed. The main advantage of this method is that it ensures real conditions concerning parameters that are well known to greatly influence Ccrit, such as the steel-concrete interface, which cannot be representatively mimicked in laboratory-produced samples. At the same time, the accelerated corrosion test in the laboratory permits the reliable determination of Ccrit prior to corrosion initiation on the tested structure; this is a major advantage over all common condition assessment methods that only permit estimating the conditions for corrosion after initiation, i.e., when the structure is already damaged. The protocol yields the statistical distribution of Ccrit for the tested structure. This serves as a basis for probabilistic prediction models for the remaining time to corrosion, which is needed for maintenance planning. This method can potentially be used in material testing of civil infrastructures, similar to established methods used for mechanical testing. PMID:28892023

Experimental Protocol to Determine the Chloride Threshold Value for Corrosion in Samples Taken from Reinforced Concrete Structures.

PubMed

Angst, Ueli M; Boschmann, Carolina; Wagner, Matthias; Elsener, Bernhard

2017-08-31

The aging of reinforced concrete infrastructure in developed countries imposes an urgent need for methods to reliably assess the condition of these structures. Corrosion of the embedded reinforcing steel is the most frequent cause for degradation. While it is well known that the ability of a structure to withstand corrosion depends strongly on factors such as the materials used or the age, it is common practice to rely on threshold values stipulated in standards or textbooks. These threshold values for corrosion initiation (Ccrit) are independent of the actual properties of a certain structure, which clearly limits the accuracy of condition assessments and service life predictions. The practice of using tabulated values can be traced to the lack of reliable methods to determine Ccrit on-site and in the laboratory. Here, an experimental protocol to determine Ccrit for individual engineering structures or structural members is presented. A number of reinforced concrete samples are taken from structures and laboratory corrosion testing is performed. The main advantage of this method is that it ensures real conditions concerning parameters that are well known to greatly influence Ccrit, such as the steel-concrete interface, which cannot be representatively mimicked in laboratory-produced samples. At the same time, the accelerated corrosion test in the laboratory permits the reliable determination of Ccrit prior to corrosion initiation on the tested structure; this is a major advantage over all common condition assessment methods that only permit estimating the conditions for corrosion after initiation, i.e., when the structure is already damaged. The protocol yields the statistical distribution of Ccrit for the tested structure. This serves as a basis for probabilistic prediction models for the remaining time to corrosion, which is needed for maintenance planning. This method can potentially be used in material testing of civil infrastructures, similar to established methods used for mechanical testing.

The Scottish Structural Proteomics Facility: targets, methods and outputs.

PubMed

Oke, Muse; Carter, Lester G; Johnson, Kenneth A; Liu, Huanting; McMahon, Stephen A; Yan, Xuan; Kerou, Melina; Weikart, Nadine D; Kadi, Nadia; Sheikh, Md Arif; Schmelz, Stefan; Dorward, Mark; Zawadzki, Michal; Cozens, Christopher; Falconer, Helen; Powers, Helen; Overton, Ian M; van Niekerk, C A Johannes; Peng, Xu; Patel, Prakash; Garrett, Roger A; Prangishvili, David; Botting, Catherine H; Coote, Peter J; Dryden, David T F; Barton, Geoffrey J; Schwarz-Linek, Ulrich; Challis, Gregory L; Taylor, Garry L; White, Malcolm F; Naismith, James H

2010-06-01

The Scottish Structural Proteomics Facility was funded to develop a laboratory scale approach to high throughput structure determination. The effort was successful in that over 40 structures were determined. These structures and the methods harnessed to obtain them are reported here. This report reflects on the value of automation but also on the continued requirement for a high degree of scientific and technical expertise. The efficiency of the process poses challenges to the current paradigm of structural analysis and publication. In the 5 year period we published ten peer-reviewed papers reporting structural data arising from the pipeline. Nevertheless, the number of structures solved exceeded our ability to analyse and publish each new finding. By reporting the experimental details and depositing the structures we hope to maximize the impact of the project by allowing others to follow up the relevant biology.

Precision measurement of the three 2(3)P(J) helium fine structure intervals.

PubMed

Zelevinsky, T; Farkas, D; Gabrielse, G

2005-11-11

The three 2(3)P fine structure intervals of 4H are measured at an improved accuracy that is sufficient to test two-electron QED theory and to determine the fine structure constant alpha to 14 parts in 10(9). The more accurate determination of alpha, to a precision higher than attained with the quantum Hall and Josephson effects, awaits the reconciliation of two inconsistent theoretical calculations now being compared term by term. A low pressure helium discharge presents experimental uncertainties quite different than for earlier measurements and allows direct measurements of light pressure shifts.

PDBsum new things.

PubMed

Laskowski, Roman A

2009-01-01

PDBsum (http://www.ebi.ac.uk/pdbsum) provides summary information about each experimentally determined structural model in the Protein Data Bank (PDB). Here we describe some of its most recent features, including figures from the structure's key reference, citation data, Pfam domain diagrams, topology diagrams and protein-protein interactions. Furthermore, it now accepts users' own PDB format files and generates a private set of analyses for each uploaded structure.

Isolation and structural proof of the large diamond molecule, cyclohexamantane (C26H30)

USGS Publications Warehouse

Dahl, J.E.P.; Moldowan, J.M.; Peakman, T.M.; Clardy, J.C.; Lobkovsky, E.; Olmstead, M.M.; May, P.W.; Davis, T.J.; Steeds, J.W.; Peters, K.E.; Pepper, A.; Ekuan, A.; Carlson, R.M.K.

2003-01-01

Ace of diamonds: Cyclohexamantane (C26H30), a large diamond-like molecule containing six peri-fused adamantane cages was identified in petroleum and its structure proven by X-ray crystallography (see picture), Never synthesized because of severe mechanistic difficulties, the structure of cyclohexamantane has appeared in theoretical molecular-simulation studies related to diamond; its experimentally determined properties are now discussed.

Hydrodynamic Impact of a System with a Single Elastic Mode II : Comparison of Experimental Force and Response with Theory

NASA Technical Reports Server (NTRS)

Miller, Robert W; Merten, Kenneth F

1952-01-01

Hydrodynamic impact tests were made on an elastic model approximating a two-mass spring system to determine experimentally the effects of structural flexibility on the hydrodynamic loads encountered during seaplane landing impacts and to correlate the results with theory. A flexible seaplane was represented by a two-mass spring system consisting of a rigid prismatic float connected to a rigid upper mass by an elastic structure. The model had a ratio of sprung mass to hull mass of 0.6 and a natural frequency of 3.0 cycles per second. The tests were conducted in smooth water at fixed trims and included both high and low flight-path angles and a range of velocity. Theoretical and experimental comparisons indicated that the theoretical results agreed well with the experimental results.

Solvent effects on the crystal growth structure and morphology of the pharmaceutical dirithromycin

NASA Astrophysics Data System (ADS)

Wang, Yuan; Liang, Zuozhong

2017-12-01

Solvent effects on the crystal structure and morphology of pharmaceutical dirithromycin molecules were systematically investigated using both experimental crystallization and theoretical simulation. Dirithromycin is one of the new generation of macrolide antibiotics with two polymorphic forms (Form I and Form II) and many solvate forms. Herein, six solvates of the dirithromycin, including acetonitrile, acetonitrile/water, acetone, 1-propanol, N,N-dimethylformamide (DMF) and cyclohexane, were studied. Experimentally, we crystallized the dirithromycin molecules in different solvents by the solvent evaporating method and measured the crystal structures with the X-ray diffraction (XRD). We compared these crystal structures of dirithromycin solvates and analyzed the solvent property-determined structure evolution. The solvents have a strong interaction with the dirithromycin molecule due to the formation of inter-molecular interactions (such as the hydrogen bonding and close contacts (sum of vdW radii)). Theoretically, we calculated the ideal crystal habit based on the solvated structures with the attachment growth (AE) model. The predicted morphologies and aspect ratios of dirithromycin solvates agree well with the experimental results. This work could be helpful to better understand the structure and morphology evolution of solvates controlled by solvents and guide the crystallization of active pharmaceutical ingredients in the pharmaceutical industry.

Use of the dynamic stiffness method to interpret experimental data from a nonlinear system

NASA Astrophysics Data System (ADS)

Tang, Bin; Brennan, M. J.; Gatti, G.

2018-05-01

The interpretation of experimental data from nonlinear structures is challenging, primarily because of dependency on types and levels of excitation, and coupling issues with test equipment. In this paper, the use of the dynamic stiffness method, which is commonly used in the analysis of linear systems, is used to interpret the data from a vibration test of a controllable compressed beam structure coupled to a test shaker. For a single mode of the system, this method facilitates the separation of mass, stiffness and damping effects, including nonlinear stiffness effects. It also allows the separation of the dynamics of the shaker from the structure under test. The approach needs to be used with care, and is only suitable if the nonlinear system has a response that is predominantly at the excitation frequency. For the structure under test, the raw experimental data revealed little about the underlying causes of the dynamic behaviour. However, the dynamic stiffness approach allowed the effects due to the nonlinear stiffness to be easily determined.

Structural refinement of vitreous silica bilayers

NASA Astrophysics Data System (ADS)

Sadjadi, Mahdi; Wilson, Mark; Thorpe, M. F.

The importance of glasses resides not only in their applications but in fundamental questions that they put forth. The continuous random network model can successfully describe the glass structure, but determining details, like ring statistics, has always been difficult using only diffraction data. But recent atomic images of 2D vitreous silica bilayers can offer valuable new insights which are hard to be observed directly in 3D silica models/experiments (for references see). However, the experimental results are prone to uncertainty in atomic positions, systematic errors, and being finite. We employ special boundary conditions developed for such networks to refine the experimental structures. We show the best structure can be found by using various potentials to maximize information gained from the experimental samples. We find a range of densities, the so-called flexibility window, in which tetrahedra are perfect. We compare results from simulations using harmonic potentials, MD with atomic polarizabilities included and DFT. We should thank David Drabold and Bishal Bhattarai for useful discussions. Support through NSF Grant # DMS 1564468 is gratefully acknowledged.

Experimental assessment and analysis of super-resolution in fluorescence microscopy based on multiple-point spread function fitting of spectrally demultiplexed images

NASA Astrophysics Data System (ADS)

Nishimura, Takahiro; Kimura, Hitoshi; Ogura, Yusuke; Tanida, Jun

2018-06-01

This paper presents an experimental assessment and analysis of super-resolution microscopy based on multiple-point spread function fitting of spectrally demultiplexed images using a designed DNA structure as a test target. For the purpose, a DNA structure was designed to have binding sites at a certain interval that is smaller than the diffraction limit. The structure was labeled with several types of quantum dots (QDs) to acquire their spatial information as spectrally encoded images. The obtained images are analyzed with a point spread function multifitting algorithm to determine the QD locations that indicate the binding site positions. The experimental results show that the labeled locations can be observed beyond the diffraction-limited resolution using three-colored fluorescence images that were obtained with a confocal fluorescence microscope. Numerical simulations show that labeling with eight types of QDs enables the positions aligned at 27.2-nm pitches on the DNA structure to be resolved with high accuracy.

Advancing Scientific Reasoning in Upper Elementary Classrooms: Direct Instruction Versus Task Structuring

NASA Astrophysics Data System (ADS)

Lazonder, Ard W.; Wiskerke-Drost, Sjanou

2015-02-01

Several studies found that direct instruction and task structuring can effectively promote children's ability to design unconfounded experiments. The present study examined whether the impact of these interventions extends to other scientific reasoning skills by comparing the inquiry activities of 55 fifth-graders randomly assigned to one of three conditions. Children in the control condition investigated a four-variable inquiry task without additional support. Performance of this task in the direct instruction condition was preceded by a short training in experimental design, whereas children in the task structuring condition, who did not receive the introductory training, were given a version of the task that addressed the four variables one at a time. Analysis of children's experimentation behavior confirmed that direct instruction and task structuring are equally effective and superior to unguided inquiry. Both interventions also evoked more determinate predictions and valid inferences. These findings demonstrate that the effect of short-term interventions designed to promote unconfounded experimentation extends beyond the control of variables.

New Trends on Green Buildings: Investigation of the Feasibility of Using Plastic Members in RC Buildings with SWs

NASA Astrophysics Data System (ADS)

Arslan, M. H.; Arslan, H. D.

2017-08-01

Shear walled (SW) reinforced concrete (RC) buildings are considered to be a type of high seismic safety building. Although this structural system has an important seismic advantage, it also has some disadvantages, especially in acoustic and thermal comfort. In this study, experimental studies have been conducted on RC members produced with plastic material having circular sections to determine structural performance. RC members have been produced with and without 6 cm diameter balls to analyze the structural behaviour under loading and to investigate the thermal performance and sound absorption behaviour of the members. In the study, structural parameters have been determined for RC members such as slabs and SWs produced with and without balls to discover the feasibility of the research and discuss the findings comparatively. The results obtained from the experimental studies show that PB used in RC with suitable positions do not significantly decrease strength but improve the thermal and acoustic features. It has been also seen that using plastic balls reduce the total concrete materials.

Improving RNA nearest neighbor parameters for helices by going beyond the two-state model.

PubMed

Spasic, Aleksandar; Berger, Kyle D; Chen, Jonathan L; Seetin, Matthew G; Turner, Douglas H; Mathews, David H

2018-06-01

RNA folding free energy change nearest neighbor parameters are widely used to predict folding stabilities of secondary structures. They were determined by linear regression to datasets of optical melting experiments on small model systems. Traditionally, the optical melting experiments are analyzed assuming a two-state model, i.e. a structure is either complete or denatured. Experimental evidence, however, shows that structures exist in an ensemble of conformations. Partition functions calculated with existing nearest neighbor parameters predict that secondary structures can be partially denatured, which also directly conflicts with the two-state model. Here, a new approach for determining RNA nearest neighbor parameters is presented. Available optical melting data for 34 Watson-Crick helices were fit directly to a partition function model that allows an ensemble of conformations. Fitting parameters were the enthalpy and entropy changes for helix initiation, terminal AU pairs, stacks of Watson-Crick pairs and disordered internal loops. The resulting set of nearest neighbor parameters shows a 38.5% improvement in the sum of residuals in fitting the experimental melting curves compared to the current literature set.

Determination of effective loss factors in reduced SEA models

NASA Astrophysics Data System (ADS)

Chimeno Manguán, M.; Fernández de las Heras, M. J.; Roibás Millán, E.; Simón Hidalgo, F.

2017-01-01

The definition of Statistical Energy Analysis (SEA) models for large complex structures is highly conditioned by the classification of the structure elements into a set of coupled subsystems and the subsequent determination of the loss factors representing both the internal damping and the coupling between subsystems. The accurate definition of the complete system can lead to excessively large models as the size and complexity increases. This fact can also rise practical issues for the experimental determination of the loss factors. This work presents a formulation of reduced SEA models for incomplete systems defined by a set of effective loss factors. This reduced SEA model provides a feasible number of subsystems for the application of the Power Injection Method (PIM). For structures of high complexity, their components accessibility can be restricted, for instance internal equipments or panels. For these cases the use of PIM to carry out an experimental SEA analysis is not possible. New methods are presented for this case in combination with the reduced SEA models. These methods allow defining some of the model loss factors that could not be obtained through PIM. The methods are validated with a numerical analysis case and they are also applied to an actual spacecraft structure with accessibility restrictions: a solar wing in folded configuration.

Thrust-wrench fault interference in a brittle medium: new insights from analogue modelling experiments

NASA Astrophysics Data System (ADS)

Rosas, Filipe; Duarte, Joao; Schellart, Wouter; Tomas, Ricardo; Grigorova, Vili; Terrinha, Pedro

2015-04-01

We present analogue modelling experimental results concerning thrust-wrench fault interference in a brittle medium, to try to evaluate the influence exerted by different prescribed interference angles in the formation of morpho-structural interference fault patterns. All the experiments were conceived to simulate simultaneous reactivation of confining strike-slip and thrust faults defining a (corner) zone of interference, contrasting with previously reported discrete (time and space) superposition of alternating thrust and strike-slip events. Different interference angles of 60°, 90° and 120° were experimentally investigated by comparing the specific structural configurations obtained in each case. Results show that a deltoid-shaped morpho-structural pattern is consistently formed in the fault interference (corner) zone, exhibiting a specific geometry that is fundamentally determined by the different prescribed fault interference angle. Such angle determines the orientation of the displacement vector shear component along the main frontal thrust direction, determining different fault confinement conditions in each case, and imposing a complying geometry and kinematics of the interference deltoid structure. Model comparison with natural examples worldwide shows good geometric and kinematic similarity, pointing to the existence of matching underlying dynamic process. Acknowledgments This work was sponsored by the Fundação para a Ciência e a Tecnologia (FCT) through project MODELINK EXPL/GEO-GEO/0714/2013.

Rapid and reliable protein structure determination via chemical shift threading.

PubMed

Hafsa, Noor E; Berjanskii, Mark V; Arndt, David; Wishart, David S

2018-01-01

Protein structure determination using nuclear magnetic resonance (NMR) spectroscopy can be both time-consuming and labor intensive. Here we demonstrate how chemical shift threading can permit rapid, robust, and accurate protein structure determination using only chemical shift data. Threading is a relatively old bioinformatics technique that uses a combination of sequence information and predicted (or experimentally acquired) low-resolution structural data to generate high-resolution 3D protein structures. The key motivations behind using NMR chemical shifts for protein threading lie in the fact that they are easy to measure, they are available prior to 3D structure determination, and they contain vital structural information. The method we have developed uses not only sequence and chemical shift similarity but also chemical shift-derived secondary structure, shift-derived super-secondary structure, and shift-derived accessible surface area to generate a high quality protein structure regardless of the sequence similarity (or lack thereof) to a known structure already in the PDB. The method (called E-Thrifty) was found to be very fast (often < 10 min/structure) and to significantly outperform other shift-based or threading-based structure determination methods (in terms of top template model accuracy)-with an average TM-score performance of 0.68 (vs. 0.50-0.62 for other methods). Coupled with recent developments in chemical shift refinement, these results suggest that protein structure determination, using only NMR chemical shifts, is becoming increasingly practical and reliable. E-Thrifty is available as a web server at http://ethrifty.ca .

Food-Web Models Predict Species Abundances in Response to Habitat Change

PubMed Central

Gotelli, Nicholas J; Ellison, Aaron M

2006-01-01

Plant and animal population sizes inevitably change following habitat loss, but the mechanisms underlying these changes are poorly understood. We experimentally altered habitat volume and eliminated top trophic levels of the food web of invertebrates that inhabit rain-filled leaves of the carnivorous pitcher plant Sarracenia purpurea. Path models that incorporated food-web structure better predicted population sizes of food-web constituents than did simple keystone species models, models that included only autecological responses to habitat volume, or models including both food-web structure and habitat volume. These results provide the first experimental confirmation that trophic structure can determine species abundances in the face of habitat loss. PMID:17002518

Restoring eastside ponderosa pine ecosystems at the Blacks Mountain Experimental Forest: a case study

Treesearch

Jianwei Zhang; Martin W. Ritchie

2008-01-01

The ecological research project of interior ponderosa pine forests at the Blacks Mountain Experimental Forest in northeastern California was initiated by an interdisciplinary team of scientists in the early 1990s. The objectives of this study were to determine the effect of stand structure, and prescribed fire on vegetation growth, resilience, and sustainability of...

Development and study of a heat pipe with dielectric properties

NASA Astrophysics Data System (ADS)

Semena, M. G.; Gershuni, A. N.; Chepurnoi, A. B.

Requirements for the structural elements of heat pipes with dielectric properties are examined. To obtain information necessary for the thermal analysis of heat pipes, a study is made of the capillary-transport characteristics of a dielectric capillary structure consisting of quartz fibers; the capillary pressure and the liquid penetration coefficient are determined. The results of the study are used to develop dielectric heat pipes for the cooling of a vacuum electronic instrument. Experimentally determined characteristics of the heat pipes are presented.

Time-Resolved Macromolecular Crystallography at Modern X-Ray Sources.

PubMed

Schmidt, Marius

2017-01-01

Time-resolved macromolecular crystallography unifies protein structure determination with chemical kinetics. With the advent of fourth generation X-ray sources the time-resolution can be on the order of 10-40 fs, which opens the ultrafast time scale to structure determination. Fundamental motions and transitions associated with chemical reactions in proteins can now be observed. Moreover, new experimental approaches at synchrotrons allow for the straightforward investigation of all kind of reactions in biological macromolecules. Here, recent developments in the field are reviewed.

Computational assessment of folding energy landscapes in heterodimeric coiled coils.

PubMed

André, Ingemar; Bjelic, Sinisa

2018-07-01

The coiled coil structural motif consists of alpha helices supercoiling around each other to form staggered knobs-into-holes packing. Such structures are deceptively simple, especially as they often can be described with parametric equations, but are known to exist in various conformations. Even the simplest systems, consisting of 2 monomers, can assemble into a wide range of states. They can form canonical as well as noncanonical coiled coils, be parallel or antiparallel, where helices associate with different degrees of shift, tilt, and rotation. Here, we investigate the energy landscape of heterodimeric coiled coils by carrying out de novo folding simulations starting from amino acid sequence. We folded a diverse set of 22 heterodimers and demonstrate that the approach is capable of identifying the atomic details in the experimental structure in the majority of cases. Our methodology also enables exploration of alternative states that can be accessible in solution beyond the experimentally determined structure. For many systems, we observe folding energy landscapes with multiple energy minima and several isoenergetic states. By comparing coiled coils from single domains and those extracted from larger proteins, we find that standalone coiled coils have deeper energy wells at the experimentally determined conformation. By folding the competing homodimeric states in addition to the heterodimers, we observe that the structural specificity towards the heteromeric state is often small. Taken together, our results demonstrate that de novo folding simulations can be a powerful tool to characterize structural specificity of coiled coils when coupled to assessment of energy landscapes. © 2018 Wiley Periodicals, Inc.

Damage level prediction of non-reshaped berm breakwater using ANN, SVM and ANFIS models

NASA Astrophysics Data System (ADS)

Mandal, Sukomal; Rao, Subba; N., Harish; Lokesha

2012-06-01

The damage analysis of coastal structure is very important as it involves many design parameters to be considered for the better and safe design of structure. In the present study experimental data for non-reshaped berm breakwater are collected from Marine Structures Laboratory, Department of Applied Mechanics and Hydraulics, NITK, Surathkal, India. Soft computing techniques like Artificial Neural Network (ANN), Support Vector Machine (SVM) and Adaptive Neuro Fuzzy Inference system (ANFIS) models are constructed using experimental data sets to predict the damage level of non-reshaped berm breakwater. The experimental data are used to train ANN, SVM and ANFIS models and results are determined in terms of statistical measures like mean square error, root mean square error, correla-tion coefficient and scatter index. The result shows that soft computing techniques i.e., ANN, SVM and ANFIS can be efficient tools in predicting damage levels of non reshaped berm breakwater.

Structural Acoustic Response of a Shape Memory Alloy Hybrid Composite Panel (Lessons Learned)

NASA Technical Reports Server (NTRS)

Turner, Travis L.

2002-01-01

This study presents results from an effort to fabricate a shape memory alloy hybrid composite (SMAHC) panel specimen and test the structure for dynamic response and noise transmission characteristics under the action of thermal and random acoustic loads. A method for fabricating a SMAHC laminate with bi-directional SMA reinforcement is described. Glass-epoxy unidirectional prepreg tape and Nitinol ribbon comprise the material system. Thermal activation of the Nitinol actuators was achieved through resistive heating. The experimental hardware required for mechanical support of the panel/actuators and for establishing convenient electrical connectivity to the actuators is presented. Other experimental apparatus necessary for controlling the panel temperature and acquiring structural acoustic data are also described. Deficiency in the thermal control system was discovered in the process of performing the elevated temperature tests. Discussion of the experimental results focuses on determining the causes for the deficiency and establishing means for rectifying the problem.

Structural acoustic response of a shape memory alloy hybrid composite panel (lessons learned)

NASA Astrophysics Data System (ADS)

Turner, Travis L.

2002-07-01

This study presents results from an effort to fabricate a shape memory alloy hybrid composite (SMAHC) panel specimen and test the structure for dynamic response and noise transmission characteristics under the action of thermal and random acoustic loads. A method for fabricating a SMAHC laminate with bi-directional SMA reinforcement is described. Glass-epoxy unidirectional prepreg tape and Nitinol ribbon comprise the material system. Thermal activation of the Nitinol actuators was achieved through resistive heating. The experimental hardware required for mechanical support of the panel/actuators and for establishing convenient electrical connectivity to the actuators is presented. Other experimental apparatus necessary for controlling the panel temperature and acquiring structural acoustic data are also described. Deficiency in the thermal control system was discovered in the process of performing the elevated temperature tests. Discussion of the experimental results focuses on determining the causes for the deficiency and establishing means for rectifying the problem.

Predicting the potentials, solubilities and stabilities of metal-acetylacetonates for non-aqueous redox flow batteries using density functional theory calculations

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

Kucharyson, J. F.; Cheng, L.; Tung, S. O.

New active materials are needed to improve the performance and reduce the cost of non-aqueous redox flow batteries (RFBs) for grid-scale energy storage applications. Efforts to develop better performing materials, which have largely been empirical, would benefit from a better understanding of relationships between structural, electronic and RFB-relevant functional properties. This paper focuses on metal-acetylacetonates, a class of metal coordination complexes that has shown promise for use in RFBs, and describes correlations between their experimentally measured standard potentials, solubilities, and stabilities (cycle lifes), and selected chemical, structural and electronic properties determined from Density Functional Theory (DFT) calculations. The training setmore » consisted of 16 complexes including 5 different metals and 11 different substituents on the acetylacetonate ligand. Standard potentials for those compounds were calculated and are in good agreement with experimentally measured results. A predictive equation based on the solvation energies and dipole moments, two easily computed properties, reasonably modeled the experimentally determined solubilities. Importantly, we were able to identify a descriptor for the stability of acetylacetonates. The experimentally determined stability, quantified as the cycle life to a given degree of degradation, correlated with the percentage of the highest occupied (HOMO) or lowest unoccupied molecular orbital (LUMO) on the metal of the complex. This percentage is influenced by the degree of ligand innocence (irreducibility), and complexes with the most innocent ligands yielded the most stable redox reactions. To this end, VO(acetylacetonate)(2) and Fe(acetylacetonate)(3), with nearly 80% of the HOMO and LUMO on the metal, possessed the most stable oxidation and reduction half-reactions, respectively. The structure-function relationships and correlations presented in this paper could be used to predict new, highly soluble and stable complexes for RFB applications.« less

Influence of structure properties on protein-protein interactions-QSAR modeling of changes in diffusion coefficients.

PubMed

Bauer, Katharina Christin; Hämmerling, Frank; Kittelmann, Jörg; Dürr, Cathrin; Görlich, Fabian; Hubbuch, Jürgen

2017-04-01

Information about protein-protein interactions provides valuable knowledge about the phase behavior of protein solutions during the biopharmaceutical production process. Up to date it is possible to capture their overall impact by an experimentally determined potential of mean force. For the description of this potential, the second virial coefficient B22, the diffusion interaction parameter kD, the storage modulus G', or the diffusion coefficient D is applied. In silico methods do not only have the potential to predict these parameters, but also to provide deeper understanding of the molecular origin of the protein-protein interactions by correlating the data to the protein's three-dimensional structure. This methodology furthermore allows a lower sample consumption and less experimental effort. Of all in silico methods, QSAR modeling, which correlates the properties of the molecule's structure with the experimental behavior, seems to be particularly suitable for this purpose. To verify this, the study reported here dealt with the determination of a QSAR model for the diffusion coefficient of proteins. This model consisted of diffusion coefficients for six different model proteins at various pH values and NaCl concentrations. The generated QSAR model showed a good correlation between experimental and predicted data with a coefficient of determination R2 = 0.9 and a good predictability for an external test set with R2 = 0.91. The information about the properties affecting protein-protein interactions present in solution was in agreement with experiment and theory. Furthermore, the model was able to give a more detailed picture of the protein properties influencing the diffusion coefficient and the acting protein-protein interactions. Biotechnol. Bioeng. 2017;114: 821-831. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

Electronic structure and orientation relationship of Li nanoclusters embedded in MgO studied by depth-selective positron annihilation two-dimensional angular correlation

NASA Astrophysics Data System (ADS)

Falub, C. V.; Mijnarends, P. E.; Eijt, S. W.; van Huis, M. A.; van Veen, A.; Schut, H.

2002-08-01

Quantum-confined positrons are sensitive probes for determining the electronic structure of nanoclusters embedded in materials. In this work, a depth-selective positron annihilation 2D-ACAR (two-dimensional angular correlation of annihilation radiation) method is used to determine the electronic structure of Li nanoclusters formed by implantation of 1016-cm-2 30-keV 6Li ions in MgO (100) and (110) crystals and by subsequent annealing at 950 K. Owing to the difference between the positron affinities of lithium and MgO, the Li nanoclusters act as quantum dots for positrons. 2D-ACAR distributions for different projections reveal a semicoherent fitting of the embedded metallic Li nanoclusters to the host MgO lattice. Ab initio Korringa-Kohn-Rostoker calculations of the momentum density show that the anisotropies of the experimental distributions are consistent with an fcc crystal structure of the Li nanoclusters. The observed reduction of the width of the experimental 2D-ACAR distribution is attributed to positron trapping in vacancies associated with Li clusters. This work proposes a method for studying the electronic structure of metallic quantum dots embedded in an insulating material.

Rotational Spectrum of 1,1-Difluoroethane: Internal Rotation Analysis and Structure

NASA Astrophysics Data System (ADS)

Villamanan, R. M.; Chen, W. D.; Wlodarczak, G.; Demaison, J.; Lesarri, A. G.; Lopez, J. C.; Alonso, J. L.

1995-05-01

The rotational spectrum of CH3CHF2 in its ground state was measured up to 653 GHz. Accurate rotational and centrifugal distortion constants were determined. The internal rotation splittings were analyzed using the internal axis method. An ab initio structure has been calculated and a near-equilibrium structure has been estimated using offsets derived empirically. This structure was compared to an experimental r0 structure. The four lowest excited states (including the methyl torsion) have also been assigned.

Nanoscopic diffusion studies on III-V compound semiconductor structures: Experiment and theory

NASA Astrophysics Data System (ADS)

Gonzalez Debs, Mariam

The electronic structure of multilayer semiconductor heterostructures is affected by the detailed compositional profiles throughout the structure and at critical interfaces. The extent of interdiffusion across these interfaces places limits on both the processing time and temperatures for many applications based on the resultant compositional profile and associated electronic structure. Atomic and phenomenological methods were used in this work through the combination of experiment and theory to understand the nanoscopic mechanisms in complex heterostructures. Two principal studies were conducted. Tin diffusion in GaAs was studied by fitting complex experimental diffusion profiles to a phenomenological model which involved the diffusion of substitutional and interstitial dopant atoms. A methodology was developed combining both the atomistic model and the use of key features within these experimentally-obtained diffusion profiles to determine meaningful values of the transport and defect reaction rate parameters. Interdiffusion across AlSb/GaSb multi-quantum well interfaces was also studied. The chemical diffusion coefficient characterizing the AlSb/GaSb diffusion couple was quantitatively determined by fitting the observed photoluminescence (PL) peak shifts to the solution of the Schrodinger equation using a potential derived from the solution of the diffusion equation to quantify the interband transition energy shifts. First-principles calculations implementing Density Functional Theory were performed to study the thermochemistry of point defects as a function of local environment, allowing a direct comparison of interfacial and bulk diffusion phenomena within these nanoscopic structures. Significant differences were observed in the Ga and Al vacancy formation energies at the AlSb/GaSb interface when compared to bulk AlSb and GaSb with the largest change found for Al vacancies. The AlSb/GaSb structures were further studied using positron annihilation spectroscopy (PAS) to investigate the role of vacancies in the interdiffusion of Al and Ga in the superlattices. The PL and PAS experimental techniques together with the phenomenological and atomistic modeling allowed for the determination of the underlying mass transport mechanisms at the nanoscale.

Experimental results of active control on a large structure to suppress vibration

NASA Technical Reports Server (NTRS)

Dunn, H. J.

1991-01-01

Three design methods, Linear Quadratic Gaussian with Loop Transfer Recovery (LQG/LTR), H-infinity, and mu-synthesis, are used to obtain compensators for suppressing the vibrations of a 10-bay vertical truss structure, a component typical of what may be used to build a large space structure. For the design process the plant dynamic characteristics of the structure were determined experimentally using an identification method. The resulting compensators were implemented on a digital computer and tested for their ability to suppress the first bending mode response of the 10-bay vertical truss. Time histories of the measured motion are presented, and modal damping obtained during the experiments are compared with analytical predictions. The advantages and disadvantages of using the various design methods are discussed.

Structural classification of CDR-H3 revisited: a lesson in antibody modeling.

PubMed

Kuroda, Daisuke; Shirai, Hiroki; Kobori, Masato; Nakamura, Haruki

2008-11-15

Among the six complementarity-determining regions (CDRs) in the variable domains of an antibody, the third CDR of the heavy chain (CDR-H3), which lies in the center of the antigen-binding site, plays a particularly important role in antigen recognition. CDR-H3 shows significant variability in its length, sequence, and structure. Although difficult, model building of this segment is the most critical step in antibody modeling. Since our first proposal of the "H3-rules," which classify CDR-H3 structure based on amino acid sequence, the number of experimentally determined antibody structures has increased. Here, we revise these H3-rules and propose an improved classification scheme for CDR-H3 structure modeling. In addition, we determine the common features of CDR-H3 in antibody drugs as well as discuss the concept of "antibody druggability," which can be applied as an indicator of antibody evaluation during drug discovery.

PREvaIL, an integrative approach for inferring catalytic residues using sequence, structural, and network features in a machine-learning framework.

PubMed

Song, Jiangning; Li, Fuyi; Takemoto, Kazuhiro; Haffari, Gholamreza; Akutsu, Tatsuya; Chou, Kuo-Chen; Webb, Geoffrey I

2018-04-14

Determining the catalytic residues in an enzyme is critical to our understanding the relationship between protein sequence, structure, function, and enhancing our ability to design novel enzymes and their inhibitors. Although many enzymes have been sequenced, and their primary and tertiary structures determined, experimental methods for enzyme functional characterization lag behind. Because experimental methods used for identifying catalytic residues are resource- and labor-intensive, computational approaches have considerable value and are highly desirable for their ability to complement experimental studies in identifying catalytic residues and helping to bridge the sequence-structure-function gap. In this study, we describe a new computational method called PREvaIL for predicting enzyme catalytic residues. This method was developed by leveraging a comprehensive set of informative features extracted from multiple levels, including sequence, structure, and residue-contact network, in a random forest machine-learning framework. Extensive benchmarking experiments on eight different datasets based on 10-fold cross-validation and independent tests, as well as side-by-side performance comparisons with seven modern sequence- and structure-based methods, showed that PREvaIL achieved competitive predictive performance, with an area under the receiver operating characteristic curve and area under the precision-recall curve ranging from 0.896 to 0.973 and from 0.294 to 0.523, respectively. We demonstrated that this method was able to capture useful signals arising from different levels, leveraging such differential but useful types of features and allowing us to significantly improve the performance of catalytic residue prediction. We believe that this new method can be utilized as a valuable tool for both understanding the complex sequence-structure-function relationships of proteins and facilitating the characterization of novel enzymes lacking functional annotations. Copyright © 2018 Elsevier Ltd. All rights reserved.

Periodic Density Functional Theory Study of the Structure, Raman Spectrum, and Mechanical Properties of Schoepite Mineral.

PubMed

Colmenero, Francisco; Cobos, Joaquín; Timón, Vicente

2018-04-16

The structure and Raman spectrum of schoepite mineral, [(UO 2 ) 8 O 2 (OH) 12 ]·12H 2 O, was studied by means of theoretical calculations. The computations were carried out by using density functional theory with plane waves and pseudopotentials. A norm-conserving pseudopotential specific for the U atom developed in a previous work was employed. Because it was not possible to locate H atoms directly from X-ray diffraction (XRD) data by structure refinement in previous experimental studies, all of the positions of the H atoms in the full unit cell were determined theoretically. The structural results, including the lattice parameters, bond lengths, bond angles, and powder XRD pattern, were found to be in good agreement with their experimental counterparts. However, the calculations performed using the unit cell designed by Ostanin and Zeller in 2007, involving half of the atoms of the full unit cell, led to significant errors in the computed powder XRD pattern. Furthermore, Ostanin and Zeller's unit cell contains hydronium ions, H 3 O + , which are incompatible with the experimental information. Therefore, while the use of this schoepite model may be a very useful approximation requiring a much smaller amount of computational effort, the full unit cell should be used to study this mineral accurately. The Raman spectrum was also computed by means of density functional perturbation theory and compared with the experimental spectrum. The results were also in agreement with the experimental data. A normal-mode analysis of the theoretical spectra was performed to assign the main bands of the Raman spectrum. This assignment significantly improved the current empirical assignment of the bands of the Raman spectrum of schoepite mineral. In addition, the equation of state and elastic properties of this mineral were determined. The crystal structure of schoepite was found to be stable mechanically and dynamically. Schoepite can be described as a brittle material exhibiting small anisotropy and large compressibility in the direction perpendicular to the layers, which characterize its structure. The calculated bulk modulus, B, was ∼35 GPa.

The three-dimensional genome organization of Drosophila melanogaster through data integration.

PubMed

Li, Qingjiao; Tjong, Harianto; Li, Xiao; Gong, Ke; Zhou, Xianghong Jasmine; Chiolo, Irene; Alber, Frank

2017-07-31

Genome structures are dynamic and non-randomly organized in the nucleus of higher eukaryotes. To maximize the accuracy and coverage of three-dimensional genome structural models, it is important to integrate all available sources of experimental information about a genome's organization. It remains a major challenge to integrate such data from various complementary experimental methods. Here, we present an approach for data integration to determine a population of complete three-dimensional genome structures that are statistically consistent with data from both genome-wide chromosome conformation capture (Hi-C) and lamina-DamID experiments. Our structures resolve the genome at the resolution of topological domains, and reproduce simultaneously both sets of experimental data. Importantly, this data deconvolution framework allows for structural heterogeneity between cells, and hence accounts for the expected plasticity of genome structures. As a case study we choose Drosophila melanogaster embryonic cells, for which both data types are available. Our three-dimensional genome structures have strong predictive power for structural features not directly visible in the initial data sets, and reproduce experimental hallmarks of the D. melanogaster genome organization from independent and our own imaging experiments. Also they reveal a number of new insights about genome organization and its functional relevance, including the preferred locations of heterochromatic satellites of different chromosomes, and observations about homologous pairing that cannot be directly observed in the original Hi-C or lamina-DamID data. Our approach allows systematic integration of Hi-C and lamina-DamID data for complete three-dimensional genome structure calculation, while also explicitly considering genome structural variability.

Experimental identification of the behaviour of and lateral forces from freely-walking pedestrians on laterally oscillating structures in a virtual reality environment.

PubMed

Bocian, Mateusz; Macdonald, John H G; Burn, Jeremy F; Redmill, David

2015-12-15

Modelling pedestrian loading on lively structures such as bridges remains a challenge. This is because pedestrians have the capacity to interact with vibrating structures which can lead to amplification of the structural response. Current design guidelines are often inaccurate and limiting as they do not sufficiently acknowledge this effect. This originates in scarcity of data on pedestrian behaviour on vibrating ground and uncertainty as to the accuracy of results from previous experimental campaigns aiming to quantify pedestrian behaviour in this case. To this end, this paper presents a novel experimental setup developed to evaluate pedestrian actions on laterally oscillating ground in the laboratory environment while avoiding the implications of artificiality and allowing for unconstrained gait. A biologically-inspired approach was adopted in its development, relying on appreciation of operational complexities of biological systems, in particular their adaptability and control requirements. In determination of pedestrian forces to the structure consideration was given to signal processing issues which have been neglected in past studies. The results from tests conducted on the setup are related to results from previous experimental investigations and outputs of the inverted pendulum pedestrian model for walking on laterally oscillating ground, which is capable of generating self-excited forces.

X-ray crystallography over the past decade for novel drug discovery - where are we heading next?

PubMed

Zheng, Heping; Handing, Katarzyna B; Zimmerman, Matthew D; Shabalin, Ivan G; Almo, Steven C; Minor, Wladek

2015-01-01

Macromolecular X-ray crystallography has been the primary methodology for determining the three-dimensional structures of proteins, nucleic acids and viruses. Structural information has paved the way for structure-guided drug discovery and laid the foundations for structural bioinformatics. However, X-ray crystallography still has a few fundamental limitations, some of which may be overcome and complemented using emerging methods and technologies in other areas of structural biology. This review describes how structural knowledge gained from X-ray crystallography has been used to advance other biophysical methods for structure determination (and vice versa). This article also covers current practices for integrating data generated by other biochemical and biophysical methods with those obtained from X-ray crystallography. Finally, the authors articulate their vision about how a combination of structural and biochemical/biophysical methods may improve our understanding of biological processes and interactions. X-ray crystallography has been, and will continue to serve as, the central source of experimental structural biology data used in the discovery of new drugs. However, other structural biology techniques are useful not only to overcome the major limitation of X-ray crystallography, but also to provide complementary structural data that is useful in drug discovery. The use of recent advancements in biochemical, spectroscopy and bioinformatics methods may revolutionize drug discovery, albeit only when these data are combined and analyzed with effective data management systems. Accurate and complete data management is crucial for developing experimental procedures that are robust and reproducible.

Structure and properties of microporous titanosilicate determined by first-principles calculations

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

Ching, W.Y.; Xu, Y.; Gu, Z.

1996-12-01

The structure of EST-10, a member of synthetic microporous titanosilicates, was recently determined by an ingenious combination of experimental and simulational techniques. However, the locations of the alkali atoms in the framework remain elusive and its electronic structure is totally unknown. Based on first-principles local density calculations, the possible locations of the alkali atoms are identified and its electronic structure and bonding fully elucidated. ETS-10 is a semiconductor with a direct band gap of 2.33 eV. The Na atoms are likely to locate inside the seven-member ring pore adjacent to the one-dimensional Ti-O-Ti-O- chain. {copyright} {ital 1996 The American Physicalmore » Society.}« less

Determining the size dependence of structural properties of clusters

NASA Astrophysics Data System (ADS)

Dong, Yi; Springborg, Michael

2012-12-01

Problems related to the determination of the structure of the global total-energy minimum for clusters are discussed through three examples. For isolated gold clusters it is shown that low-symmetry structures result due to covalent bonding. Subsequently, SiNGeN and (HAlO)N clusters are treated for which the occurrence of so called homotops leads to additional computational complexity. For the former it is found that the structures are not directly related to those of the pure monatomic clusters, and for the latter the results are shown to be in agreement with available experimental information on nanostructured HAlO. In order to illustrate and analyze the results, various descriptors are introduced and applied.

Composite laminate failure parameter optimization through four-point flexure experimentation and analysis

DOE PAGES

Nelson, Stacy; English, Shawn; Briggs, Timothy

2016-05-06

Fiber-reinforced composite materials offer light-weight solutions to many structural challenges. In the development of high-performance composite structures, a thorough understanding is required of the composite materials themselves as well as methods for the analysis and failure prediction of the relevant composite structures. However, the mechanical properties required for the complete constitutive definition of a composite material can be difficult to determine through experimentation. Therefore, efficient methods are necessary that can be used to determine which properties are relevant to the analysis of a specific structure and to establish a structure's response to a material parameter that can only be definedmore » through estimation. The objectives of this paper deal with demonstrating the potential value of sensitivity and uncertainty quantification techniques during the failure analysis of loaded composite structures; and the proposed methods are applied to the simulation of the four-point flexural characterization of a carbon fiber composite material. Utilizing a recently implemented, phenomenological orthotropic material model that is capable of predicting progressive composite damage and failure, a sensitivity analysis is completed to establish which material parameters are truly relevant to a simulation's outcome. Then, a parameter study is completed to determine the effect of the relevant material properties' expected variations on the simulated four-point flexural behavior as well as to determine the value of an unknown material property. This process demonstrates the ability to formulate accurate predictions in the absence of a rigorous material characterization effort. Finally, the presented results indicate that a sensitivity analysis and parameter study can be used to streamline the material definition process as the described flexural characterization was used for model validation.« less

Electronic structures of C u 2 O , C u 4 O 3 , and CuO: A joint experimental and theoretical study

DOE PAGES

Wang, Y.; Lany, S.; Ghanbaja, J.; ...

2016-12-14

We present a joint experimental and theoretical study for the electronic structures of copper oxides including Cu 2O, CuO, and the metastable mixed-valence oxide Cu 4O 3. The optical band gap is determined by experimental optical absorption coefficient, and the electronic structure in valence and conduction bands is probed by photoemission and electron energy loss spectroscopies, respectively. Furthermore, we compare our experimental results with many-body GW calculations utilizing an additional on-site potential for d-orbital energies that facilitates tractable and predictive computations. The side-by-side comparison between the three oxides, including a band insulator (Cu2O) and two Mott/charge-transfer insulators (CuO, Cu 4Omore » 3) leads to a consistent picture for the optical and band-structure properties of the Cu oxides, strongly supporting indirect band gaps of about 1.2 and 0.8 eV in CuO and Cu 4O 3, respectively. This comparison also points towards surface oxidation and reduction effects that can complicate the interpretation of the photoemission spectra.« less

High-throughput determination of RNA structure by proximity ligation.

PubMed

Ramani, Vijay; Qiu, Ruolan; Shendure, Jay

2015-09-01

We present an unbiased method to globally resolve RNA structures through pairwise contact measurements between interacting regions. RNA proximity ligation (RPL) uses proximity ligation of native RNA followed by deep sequencing to yield chimeric reads with ligation junctions in the vicinity of structurally proximate bases. We apply RPL in both baker's yeast (Saccharomyces cerevisiae) and human cells and generate contact probability maps for ribosomal and other abundant RNAs, including yeast snoRNAs, the RNA subunit of the signal recognition particle and the yeast U2 spliceosomal RNA homolog. RPL measurements correlate with established secondary structures for these RNA molecules, including stem-loop structures and long-range pseudoknots. We anticipate that RPL will complement the current repertoire of computational and experimental approaches in enabling the high-throughput determination of secondary and tertiary RNA structures.

Structural Assembly of Multidomain Proteins and Protein Complexes Guided by the Overall Rotational Diffusion Tensor

PubMed Central

Ryabov, Yaroslav; Fushman, David

2008-01-01

We present a simple and robust approach that uses the overall rotational diffusion tensor as a structural constraint for domain positioning in multidomain proteins and protein-protein complexes. This method offers the possibility to use NMR relaxation data for detailed structure characterization of such systems provided the structures of individual domains are available. The proposed approach extends the concept of using long-range information contained in the overall rotational diffusion tensor. In contrast to the existing approaches, we use both the principal axes and principal values of protein’s rotational diffusion tensor to determine not only the orientation but also the relative positioning of the individual domains in a protein. This is achieved by finding the domain arrangement in a molecule that provides the best possible agreement with all components of the overall rotational diffusion tensor derived from experimental data. The accuracy of the proposed approach is demonstrated for two protein systems with known domain arrangement and parameters of the overall tumbling: the HIV-1 protease homodimer and Maltose Binding Protein. The accuracy of the method and its sensitivity to domain positioning is also tested using computer-generated data for three protein complexes, for which the experimental diffusion tensors are not available. In addition, the proposed method is applied here to determine, for the first time, the structure of both open and closed conformations of Lys48-linked di-ubiquitin chain, where domain motions render impossible accurate structure determination by other methods. The proposed method opens new avenues for improving structure characterization of proteins in solution. PMID:17550252

Response of basic structural elements and B-52 structural components to simulated nuclear overpressure. Volume I-program description and results (basic structural elements). Final report, 1 June 1977-30 September 1979

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

Syring, R.P.; Grubb, R.L.

1979-09-30

This document reports on the following: (1) experimental determination of the response of 16 basic structural elements and 7 B-52 components to simulated nuclear overpressure environments (utilizing Sandia Corporation's Thunderpipe Shock Tube), (2) analysis of these test specimens utilizing the NOVA-2 computer program, and (3) correlation of test and analysis results.

Method for determining optimal supercell representation of interfaces

NASA Astrophysics Data System (ADS)

Stradi, Daniele; Jelver, Line; Smidstrup, Søren; Stokbro, Kurt

2017-05-01

The geometry and structure of an interface ultimately determines the behavior of devices at the nanoscale. We present a generic method to determine the possible lattice matches between two arbitrary surfaces and to calculate the strain of the corresponding matched interface. We apply this method to explore two relevant classes of interfaces for which accurate structural measurements of the interface are available: (i) the interface between pentacene crystals and the (1 1 1) surface of gold, and (ii) the interface between the semiconductor indium-arsenide and aluminum. For both systems, we demonstrate that the presented method predicts interface geometries in good agreement with those measured experimentally, which present nontrivial matching characteristics and would be difficult to guess without relying on automated structure-searching methods.

Fine- and hyperfine structure investigations of even configuration system of atomic terbium

NASA Astrophysics Data System (ADS)

Stefanska, D.; Elantkowska, M.; Ruczkowski, J.; Furmann, B.

2017-03-01

In this work a parametric study of the fine structure (fs) and the hyperfine structure (hfs) for the even-parity configurations of atomic terbium (Tb I) is presented, based in considerable part on the new experimental results. Measurements on 134 spectral lines were performed by laser induced fluorescence (LIF) in a hollow cathode discharge lamp; on this basis, the hyperfine structure constants A and B were determined for 52 even-parity levels belonging to the configurations 4f85d6s2, 4f85d26s or 4f96s6p; in all the cases those levels were involved in the transitions investigated as the lower levels. For 40 levels the hfs was examined for the first time, and for the remaining 12 levels the new measurements supplement our earlier results. As a by-product, also preliminary values of the hfs constants for 84 odd-parity levels were determined (the investigations of the odd-parity levels system in the terbium atom are still in progress). This huge amount of new experimental data, supplemented by our earlier published results, were considered for the fine and hyperfine structure analysis. A multi-configuration fit of 7 configurations was performed, taking into account second-order of perturbation theory, including the effects of closed shell-open shell excitations. Predicted values of the level energies, as well as of magnetic dipole and electric quadrupole hyperfine structure constants A and B, are quoted in cases when no experimental values are available. By combining our experimental data with our own semi-empirical procedure it was possible to identify correctly the lower and upper level of the line 544.1440 nm measured by Childs with the use of the atomic-beam laser-rf double-resonance technique (Childs, J Opt Soc Am B 9;1992:191-6).

Electronic structure of the organic semiconductor copper phthalocyanine: experiment and theory.

PubMed

Aristov, V Yu; Molodtsova, O V; Maslyuk, V V; Vyalikh, D V; Zhilin, V M; Ossipyan, Yu A; Bredow, T; Mertig, I; Knupfer, M

2008-01-21

The electronic structure of the organic semiconductor copper-phthalocyanine (CuPc) has been determined by a combination of conventional and resonant photoemission, near-edge x-ray absorption, as well as by the first-principles calculations. The experimentally obtained electronic valence band structure of CuPc is in very good agreement with the calculated density of states results, allowing the derivation of detailed site specific information.

An Integrated Approach Linking Process to Structural Modeling With Microstructural Characterization for Injections-Molded Long-Fiber Thermoplastics

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

Nguyen, Ba Nghiep; Bapanapalli, Satish K.; Smith, Mark T.

2008-09-01

The objective of our work is to enable the optimum design of lightweight automotive structural components using injection-molded long fiber thermoplastics (LFTs). To this end, an integrated approach that links process modeling to structural analysis with experimental microstructural characterization and validation is developed. First, process models for LFTs are developed and implemented into processing codes (e.g. ORIENT, Moldflow) to predict the microstructure of the as-formed composite (i.e. fiber length and orientation distributions). In parallel, characterization and testing methods are developed to obtain necessary microstructural data to validate process modeling predictions. Second, the predicted LFT composite microstructure is imported into amore » structural finite element analysis by ABAQUS to determine the response of the as-formed composite to given boundary conditions. At this stage, constitutive models accounting for the composite microstructure are developed to predict various types of behaviors (i.e. thermoelastic, viscoelastic, elastic-plastic, damage, fatigue, and impact) of LFTs. Experimental methods are also developed to determine material parameters and to validate constitutive models. Such a process-linked-structural modeling approach allows an LFT composite structure to be designed with confidence through numerical simulations. Some recent results of our collaborative research will be illustrated to show the usefulness and applications of this integrated approach.« less

Structure determination of butylone as a new psychoactive substance using chiroptical and vibrational spectroscopies.

PubMed

Spálovská, Dita; Králík, František; Kohout, Michal; Jurásek, Bronislav; Habartová, Lucie; Kuchař, Martin; Setnička, Vladimír

2018-05-01

Recently, there has been a worldwide substantial increase in the consumption of new psychoactive substances (NPS), compounds that mimic the structure of illicit drugs, such as amphetamines or ecstasy. The producers try to avoid the law by a slight modification of illicit structures, thereby developing dozens of temporarily legal NPS every year. The current trends in the detection and monitoring of such substances demand a fast and reliable analysis. Molecular spectroscopy represents a highly effective tool for the identification of NPS and chiroptical methods can provide further information on their 3D structure, which is the key for the determination of their biological activity. We present the first systematic study of NPS, specifically butylone, combining chiroptical and vibrational spectroscopies with ab initio calculations. According to density functional theory calculations, 6 stable lowest energy conformers of butylone were found and their molecular structure was described. For each conformer, the relative abundance based on the Boltzmann distribution was estimated, their population weighted spectra predicted and compared to the experimental results. Very good agreement between the experimental and the simulated spectra was achieved, which allowed not only the assignment of the absolute configuration, but also a precise description of the molecular structure. © 2018 Wiley Periodicals, Inc.

Structural bioinformatics of the human spliceosomal proteome

PubMed Central

Korneta, Iga; Magnus, Marcin; Bujnicki, Janusz M.

2012-01-01

In this work, we describe the results of a comprehensive structural bioinformatics analysis of the spliceosomal proteome. We used fold recognition analysis to complement prior data on the ordered domains of 252 human splicing proteins. Examples of newly identified domains include a PWI domain in the U5 snRNP protein 200K (hBrr2, residues 258–338), while examples of previously known domains with a newly determined fold include the DUF1115 domain of the U4/U6 di-snRNP protein 90K (hPrp3, residues 540–683). We also established a non-redundant set of experimental models of spliceosomal proteins, as well as constructed in silico models for regions without an experimental structure. The combined set of structural models is available for download. Altogether, over 90% of the ordered regions of the spliceosomal proteome can be represented structurally with a high degree of confidence. We analyzed the reduced spliceosomal proteome of the intron-poor organism Giardia lamblia, and as a result, we proposed a candidate set of ordered structural regions necessary for a functional spliceosome. The results of this work will aid experimental and structural analyses of the spliceosomal proteins and complexes, and can serve as a starting point for multiscale modeling of the structure of the entire spliceosome. PMID:22573172

SAbDab: the structural antibody database

PubMed Central

Dunbar, James; Krawczyk, Konrad; Leem, Jinwoo; Baker, Terry; Fuchs, Angelika; Georges, Guy; Shi, Jiye; Deane, Charlotte M.

2014-01-01

Structural antibody database (SAbDab; http://opig.stats.ox.ac.uk/webapps/sabdab) is an online resource containing all the publicly available antibody structures annotated and presented in a consistent fashion. The data are annotated with several properties including experimental information, gene details, correct heavy and light chain pairings, antigen details and, where available, antibody–antigen binding affinity. The user can select structures, according to these attributes as well as structural properties such as complementarity determining region loop conformation and variable domain orientation. Individual structures, datasets and the complete database can be downloaded. PMID:24214988

Anisotropy of machine building materials

NASA Technical Reports Server (NTRS)

Ashkenazi, Y. K.

1981-01-01

The results of experimental studies of the anisotropy of elastic and strength characteristics of various structural materials, including pressure worked metals and alloys, laminated fiberglass plastics, and laminated wood plastics, are correlated and classified. Strength criteria under simple and complex stresses are considered as applied to anisotropic materials. Practical application to determining the strength of machine parts and structural materials is discussed.

Cation distribution in NiZn-ferrite films via extended x-ray absorption fine structure

NASA Astrophysics Data System (ADS)

Harris, V. G.; Koon, N. C.; Williams, C. M.; Zhang, Q.; Abe, M.; Kirkland, J. P.

1996-04-01

We have applied extended x-ray absorption fine structure (EXAFS) spectroscopy to study the cation distribution in a series of spin-sprayed NiZn-ferrite films. A least-squares fitting of experimental EXAFS data with theoretical, multiple-scattering, EXAFS data allowed the quantitative determination of site distributions for all transition metal cations.

Study of complex molecular systems by probe vibrational spectroscopy method

NASA Astrophysics Data System (ADS)

Boldeskul, A. E.; Zatsepin, V. M.; Atakhodjaev, A. K.; Shermatov, A. N.; Ashburiev, R.

1984-03-01

Experimental study of benzonitril as a probe in aqueous solution of sodium lauril sulphate /SDS/ by Raman spectroscopy technique showed integral moments of √ /C X N/ line to be extremely sensitive to the structural transitions in micellar systems. The central part of the experimental contour was used to determine integral moments with the help of line shape approximant received by Mori method

Application of Powder Diffraction Methods to the Analysis of Short- and Long-Range Atomic Order in Nanocrystalline Diamond and SiC: The Concept of the Apparent Lattice Parameter (alp)

NASA Technical Reports Server (NTRS)

Palosz, B.; Grzanka, E.; Gierlotka, S.; Stelmakh, S.; Pielaszek, R.; Bismayer, U.; Weber, H.-P.; Palosz, W.

2003-01-01

Two methods of the analysis of powder diffraction patterns of diamond and SiC nanocrystals are presented: (a) examination of changes of the lattice parameters with diffraction vector Q ('apparent lattice parameter', alp) which refers to Bragg scattering, and (b), examination of changes of inter-atomic distances based on the analysis of the atomic Pair Distribution Function, PDF. Application of these methods was studied based on the theoretical diffraction patterns computed for models of nanocrystals having (i) a perfect crystal lattice, and (ii), a core-shell structure, i.e. constituting a two-phase system. The models are defined by the lattice parameter of the grain core, thickness of the surface shell, and the magnitude and distribution of the strain field in the shell. X-ray and neutron experimental diffraction data of nanocrystalline SiC and diamond powders of the grain diameter from 4 nm up to micrometers were used. The effects of the internal pressure and strain at the grain surface on the structure are discussed based on the experimentally determined dependence of the alp values on the Q-vector, and changes of the interatomic distances with the grain size determined experimentally by the atomic Pair Distribution Function (PDF) analysis. The experimental results lend a strong support to the concept of a two-phase, core and the surface shell structure of nanocrystalline diamond and SiC.

Using experimental and computational energy equilibration to understand hierarchical self-assembly of Fmoc-dipeptide amphiphiles.

PubMed

Sasselli, I R; Pappas, C G; Matthews, E; Wang, T; Hunt, N T; Ulijn, R V; Tuttle, T

2016-10-12

Despite progress, a fundamental understanding of the relationships between the molecular structure and self-assembly configuration of Fmoc-dipeptides is still in its infancy. In this work, we provide a combined experimental and computational approach that makes use of free energy equilibration of a number of related Fmoc-dipeptides to arrive at an atomistic model of Fmoc-threonine-phenylalanine-amide (Fmoc-TF-NH 2 ) which forms twisted fibres. By using dynamic peptide libraries where closely related dipeptide sequences are dynamically exchanged to eventually favour the formation of the thermodynamically most stable configuration, the relative importance of C-terminus modifications (amide versus methyl ester) and contributions of aliphatic versus aromatic amino acids (phenylalanine F vs. leucine L) is determined (F > L and NH 2 > OMe). The approach enables a comparative interpretation of spectroscopic data, which can then be used to aid the construction of the atomistic model of the most stable structure (Fmoc-TF-NH 2 ). The comparison of the relative stabilities of the models using molecular dynamic simulations and the correlation with experimental data using dynamic peptide libraries and a range of spectroscopy methods (FTIR, CD, fluorescence) allow for the determination of the nanostructure with atomistic resolution. The final model obtained through this process is able to reproduce the experimentally observed formation of intertwining fibres for Fmoc-TF-NH 2 , providing information of the interactions involved in the hierarchical supramolecular self-assembly. The developed methodology and approach should be of general use for the characterization of supramolecular structures.

Temperature dependence of local structural changes around transition metal centers Cr3+ and Mn2+ in RAl3(BO3)4 crystals studied by EMR

NASA Astrophysics Data System (ADS)

Açıkgöz, Muhammed; Rudowicz, Czesław; Gnutek, Paweł

2017-11-01

Theoretical investigations are carried out to determine the temperature dependence of the local structural parameters of Cr3+ and Mn2+ ions doped into RAl3(BO3)4 (RAB, R = Y, Eu, Tm) crystals. The zero-field splitting (ZFS) parameters (ZFSPs) obtained from the spin Hamiltonian (SH) analysis of EMR (EPR) spectra serve for fine-tuning the theoretically predicted ZFSPs obtained using the semi-empirical superposition model (SPM). The SPM analysis enables to determine the local structure changes around Cr3+ and Mn2+ centers in RAB crystals and explain the observed temperature dependence of the ZFSPs. The local monoclinic C2 site symmetry of all Al sites in YAB necessitates consideration of one non-zero monoclinic ZFSP (in the Stevens notation, b21) for Cr3+ ions. However, the experimental second-rank ZFSPs (D =b20 , E = 1 / 3b22) were expressed in a nominal principal axis system. To provide additional insight into low symmetry aspects, the distortions (ligand's distances ΔRi and angular distortions Δθi) have been varied while preserving monoclinic site symmetry, in such way as to obtain the calculated values (D, E) close to the experimental ones, while keeping b21 close to zero. This procedure yields good matching of the calculated ZFSPs and the experimental ones, and enables determination of the corresponding local distortions. The present results may be useful in future studies aimed at technological applications of the Huntite-type borates with the formula RM3(BO3)4. The model parameters determined here may be utilized for ZFSP calculations for Cr3+ and Mn2+ ions at octahedral sites in single-molecule magnets and single-chain magnets.

Properties of iron under core conditions

NASA Astrophysics Data System (ADS)

Brown, J. M.

2003-04-01

Underlying an understanding of the geodynamo and evolution of the core is knowledge of the physical and chemical properties of iron and iron mixtures under high pressure and temperature conditions. Key properties include the viscosity of the fluid outer core, thermal diffusivity, equations-of-state, elastic properties of solid phases, and phase equilibria for iron and iron-dominated mixtures. As is expected for work that continues to tax technological and intellectual limits, controversy has followed both experimental and theoretical progress in this field. However, estimates for the melting temperature of the inner core show convergence and the equation-of-state for iron as determined in independent experiments and theories are in remarkable accord. Furthermore, although the structure and elastic properties of the solid inner-core phase remains uncertain, theoretical and experimental underpinnings are better understood and substantial progress is likely in the near future. This talk will focus on an identification of properties that are reasonably well known and those that merit further detailed study. In particular, both theoretical and experimental (static and shock wave) determinations of the density of iron under extreme conditions are in agreement at the 1% or better level. The behavior of the Gruneisen parameter (which determines the geothermal gradient and controls much of the outer core heat flux) is constrained by experiment and theory under core conditions for both solid and liquid phases. Recent experiments and theory are suggestive of structure or structures other than the high-pressure hexagonal close-packed (HCP) phase. Various theories and experiments for the elasticity of HCP iron remain in poor accord. Uncontroversial constraints on core chemistry will likely never be possible. However, reasonable bounds are possible on the basis of seismic profiles, geochemical arguments, and determinations of sound velocities and densities at high pressure and temperature.

Ab initio study on structural stability of uranium carbide

NASA Astrophysics Data System (ADS)

Sahoo, B. D.; Joshi, K. D.; Gupta, Satish C.

2013-06-01

First principles calculations have been performed using plane wave pseudopotential and full potential linearized augmented plane wave (FP-LAPW) methods to analyze structural, elastic and dynamic stability of UC under hydrostatic compression. Our calculations within pseudopotential method suggest that the rocksalt (B1) structure will transform to body centered orthorhombic (bco) structure at ˜21.5 GPa. The FP-LAPW calculations put this transition at 23 GPa. The transition pressures determined from our calculations though agree reasonably with the experimental value of 27 GPa, the high pressure bco structure suggested by theory differs slightly from the experimentally reported pseudo bco phase. The elastic stability analysis of B1 phase suggests that the B1 to bco transition is driven by the failure of C44 modulus. This finding is further substantiated by the lattice dynamic calculations which demonstrate that the B1 phase becomes dynamically unstable around the transition pressure and the instability is of long wavelength nature.

Matching experimental and three dimensional numerical models for structural vibration problems with uncertainties

NASA Astrophysics Data System (ADS)

Langer, P.; Sepahvand, K.; Guist, C.; Bär, J.; Peplow, A.; Marburg, S.

2018-03-01

The simulation model which examines the dynamic behavior of real structures needs to address the impact of uncertainty in both geometry and material parameters. This article investigates three-dimensional finite element models for structural dynamics problems with respect to both model and parameter uncertainties. The parameter uncertainties are determined via laboratory measurements on several beam-like samples. The parameters are then considered as random variables to the finite element model for exploring the uncertainty effects on the quality of the model outputs, i.e. natural frequencies. The accuracy of the output predictions from the model is compared with the experimental results. To this end, the non-contact experimental modal analysis is conducted to identify the natural frequency of the samples. The results show a good agreement compared with experimental data. Furthermore, it is demonstrated that geometrical uncertainties have more influence on the natural frequencies compared to material parameters and material uncertainties are about two times higher than geometrical uncertainties. This gives valuable insights for improving the finite element model due to various parameter ranges required in a modeling process involving uncertainty.

In situ determination of crystal structure and chemistry of minerals at Earth's deep lower mantle conditions

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

Yuan, Hongsheng; Zhang, Li

Recent advances in experimental techniques and data processing allow in situ determination of mineral crystal structure and chemistry up to Mbar pressures in a laser-heated diamond anvil cell (DAC), providing the fundamental information of the mineralogical constitution of our Earth's interior. This work highlights several recent breakthroughs in the field of high-pressure mineral crystallography, including the stability of bridgmanite, the single-crystal structure studies of post-perovskite and H-phase as well as the identification of hydrous minerals and iron oxides in the deep lower mantle. The future development of high-pressure crystallography is also discussed.

The effects of rigid motions on elastic network model force constants.

PubMed

Lezon, Timothy R

2012-04-01

Elastic network models provide an efficient way to quickly calculate protein global dynamics from experimentally determined structures. The model's single parameter, its force constant, determines the physical extent of equilibrium fluctuations. The values of force constants can be calculated by fitting to experimental data, but the results depend on the type of experimental data used. Here, we investigate the differences between calculated values of force constants and data from NMR and X-ray structures. We find that X-ray B factors carry the signature of rigid-body motions, to the extent that B factors can be almost entirely accounted for by rigid motions alone. When fitting to more refined anisotropic temperature factors, the contributions of rigid motions are significantly reduced, indicating that the large contribution of rigid motions to B factors is a result of over-fitting. No correlation is found between force constants fit to NMR data and those fit to X-ray data, possibly due to the inability of NMR data to accurately capture protein dynamics. Copyright © 2011 Wiley Periodicals, Inc.

Development of Computer Models for the Assessment of Foreign Body Impact Events on Composite Structures

NASA Technical Reports Server (NTRS)

Bucinell, Ronald B.

1997-01-01

The objective of this project was to model the 5-3/4 inch pressure vessels used on the NASA RTOP program in an attempt to learn more about how impact damage forms and what are the residual effects of the resulting damage. A global-local finite element model was developed for the bottle and the states of stress in the bottles were determined down to the constituent level. The experimental data that was generated on the NASA RTOP program was not in a form that enabled the model developed under this grant to be correlated with the experimental data. As a result of this exercise it is recommended that an experimental program be designed using statistical design of experiment techniques to generate data that can be used to isolate the phenomenon that control the formation of impact damage. This data should include residual property determinations so that models for post impact structural integrity can be developed. It is also recommended that the global-local methodology be integrated directly into the finite element code. This will require considerable code development.

Structural characterization of a first-generation articulated-truss joint for space crane application

NASA Technical Reports Server (NTRS)

Sutter, Thomas R.; Wu, K. Chauncey; Riutort, Kevin T.; Laufer, Joseph B.; Phelps, James E.

1992-01-01

A first-generation space crane articulated-truss joint was statically and dynamically characterized in a configuration that approximated an operational environment. The articulated-truss joint was integrated into a test-bed for structural characterization. Static characterization was performed by applying known loads and measuring the corresponding deflections to obtain load-deflection curves. Dynamic characterization was performed using modal testing to experimentally determine the first six mode shapes, frequencies, and modal damping values. Static and dynamic characteristics were also determined for a reference truss that served as a characterization baseline. Load-deflection curves and experimental frequency response functions are presented for the reference truss and the articulated-truss joint mounted in the test-bed. The static and dynamic experimental results are compared with analytical predictions obtained from finite element analyses. Load-deflection response is also presented for one of the linear actuators used in the articulated-truss joint. Finally, an assessment is presented for the predictability of the truss hardware used in the reference truss and articulated-truss joint based upon hardware stiffness properties that were previously obtained during the Precision Segmented Reflector (PSR) Technology Development Program.

Bridging the Resolution Gap in Structural Modeling of 3D Genome Organization

PubMed Central

Marti-Renom, Marc A.; Mirny, Leonid A.

2011-01-01

Over the last decade, and especially after the advent of fluorescent in situ hybridization imaging and chromosome conformation capture methods, the availability of experimental data on genome three-dimensional organization has dramatically increased. We now have access to unprecedented details of how genomes organize within the interphase nucleus. Development of new computational approaches to leverage this data has already resulted in the first three-dimensional structures of genomic domains and genomes. Such approaches expand our knowledge of the chromatin folding principles, which has been classically studied using polymer physics and molecular simulations. Our outlook describes computational approaches for integrating experimental data with polymer physics, thereby bridging the resolution gap for structural determination of genomes and genomic domains. PMID:21779160

The Effect of Quantum-Mechanical Interference on Precise Measurements of the n = 2 Triplet P Fine Structure of Helium

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

Marsman, A.; Horbatsch, M.; Hessels, E. A., E-mail: hessels@yorku.ca

2015-09-15

For many decades, improvements in both theory and experiment of the fine structure of the n = 2 triplet P levels of helium have allowed for an increasingly precise determination of the fine-structure constant. Recently, it has been observed that quantum-mechanical interference between neighboring resonances can cause significant shifts, even if such neighboring resonances are separated by thousands of natural widths. The shifts depend in detail on the experimental method used for the measurement, as well as the specific experimental parameters employed. Here, we review how these shifts apply for the most precise measurements of the helium 2{sup 3}P fine-structuremore » intervals.« less

Experimental determination of the field shift factor and the mass shift coefficient for the 1S0-3P1 spin-forbidden transition at 791 nm in neutral barium

NASA Astrophysics Data System (ADS)

Yu, Geng-Hua; Yan, Hui; Zhong, Jia-Qi; Liu, Hong; Zhu, Xiao-Ling; Yang, Wei

2018-01-01

The experimental measurements of the isotope shifts (ISs) for the 1S0-3P1 spin-forbidden transition at 791 nm in neutral barium have been carried out with a thermal barium atom beam. The hyperfine structure (HFS) constants a and b of the odd isotopes 137Ba and 135Ba for this transition have been extracted from the experimental results: a(137Ba) = 1149.9(1.0) MHz, b(137Ba)= -41.6(0.5) MHz, a(135Ba) = 1028.0(1.0) MHz, b(135Ba) = -27.5(0.5) MHz. The measured IS results with the reference isotope 138Ba are 183.7(1.0) MHz (137Ba-138Ba), 108.5(0.3) MHz (136Ba-138Ba) and 218.9(1.0) MHz (135Ba-138Ba). Our IS measurements are in good agreement with the previous experiments. The field shift (FS) factor Fk and the mass shift (MS) coefficient ΔKMS for this spin-forbidden transition have be determined experimentally as -3.19(4) GHz ṡ fm-2 and -242(20) GHz ṡ amu, respectively. The results provided herein could be used for further checks theoretically and experimentally, and could also contribute to the study on the nuclear structure of the barium isotopic nuclei.

Quantitative Understanding of SHAPE Mechanism from RNA Structure and Dynamics Analysis.

PubMed

Hurst, Travis; Xu, Xiaojun; Zhao, Peinan; Chen, Shi-Jie

2018-05-10

The selective 2'-hydroxyl acylation analyzed by primer extension (SHAPE) method probes RNA local structural and dynamic information at single nucleotide resolution. To gain quantitative insights into the relationship between nucleotide flexibility, RNA 3D structure, and SHAPE reactivity, we develop a 3D Structure-SHAPE Relationship model (3DSSR) to rebuild SHAPE profiles from 3D structures. The model starts from RNA structures and combines nucleotide interaction strength and conformational propensity, ligand (SHAPE reagent) accessibility, and base-pairing pattern through a composite function to quantify the correlation between SHAPE reactivity and nucleotide conformational stability. The 3DSSR model shows the relationship between SHAPE reactivity and RNA structure and energetics. Comparisons between the 3DSSR-predicted SHAPE profile and the experimental SHAPE data show correlation, suggesting that the extracted analytical function may have captured the key factors that determine the SHAPE reactivity profile. Furthermore, the theory offers an effective method to sieve RNA 3D models and exclude models that are incompatible with experimental SHAPE data.

Structural Genomics of Protein Phosphatases

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

Almo,S.; Bonanno, J.; Sauder, J.

The New York SGX Research Center for Structural Genomics (NYSGXRC) of the NIGMS Protein Structure Initiative (PSI) has applied its high-throughput X-ray crystallographic structure determination platform to systematic studies of all human protein phosphatases and protein phosphatases from biomedically-relevant pathogens. To date, the NYSGXRC has determined structures of 21 distinct protein phosphatases: 14 from human, 2 from mouse, 2 from the pathogen Toxoplasma gondii, 1 from Trypanosoma brucei, the parasite responsible for African sleeping sickness, and 2 from the principal mosquito vector of malaria in Africa, Anopheles gambiae. These structures provide insights into both normal and pathophysiologic processes, including transcriptionalmore » regulation, regulation of major signaling pathways, neural development, and type 1 diabetes. In conjunction with the contributions of other international structural genomics consortia, these efforts promise to provide an unprecedented database and materials repository for structure-guided experimental and computational discovery of inhibitors for all classes of protein phosphatases.« less

Education Catching up with Science: Preparing Students for Three-Dimensional Literacy in Cell Biology

ERIC Educational Resources Information Center

Kramer, IJsbrand M.; Dahmani, Hassen-Reda; Delouche, Pamina; Bidabe, Marissa; Schneeberger, Patricia

2012-01-01

The large number of experimentally determined molecular structures has led to the development of a new semiotic system in the life sciences, with increasing use of accurate molecular representations. To determine how this change impacts students' learning, we incorporated image tests into our introductory cell biology course. Groups of students…

Asymmetric scoring functions for proteins

NASA Astrophysics Data System (ADS)

Lezon, Timothy; Holter, Neal; Maritan, Amos; Banavar, Jayanth

2003-03-01

The protein folding problem entails the prediction of the native state structure of a protein given the sequence of amino acids. In a coarse-grained description of a protein, an important ingredient for attempting this task is the determination of the effective energies of interaction between amino acids. We will discuss a simple approach for determining such interaction potentials from a training set of protein sequences and their experimentally determined native state structures. The key new ingredient in our study is the incorporation of the lack of symmetry in the effective interactions between amino acids. Our results, obtained using a set of 513 proteins, and their implications will be discussed.

Frequency-independent radiation modes of interior sound radiation: Experimental study and global active control

NASA Astrophysics Data System (ADS)

Hesse, C.; Papantoni, V.; Algermissen, S.; Monner, H. P.

2017-08-01

Active control of structural sound radiation is a promising technique to overcome the poor passive acoustic isolation performance of lightweight structures in the low-frequency region. Active structural acoustic control commonly aims at the suppression of the far-field radiated sound power. This paper is concerned with the active control of sound radiation into acoustic enclosures. Experimental results of a coupled rectangular plate-fluid system under stochastic excitation are presented. The amplitudes of the frequency-independent interior radiation modes are determined in real-time using a set of structural vibration sensors, for the purpose of estimating their contribution to the acoustic potential energy in the enclosure. This approach is validated by acoustic measurements inside the cavity. Utilizing a feedback control approach, a broadband reduction of the global acoustic response inside the enclosure is achieved.

Dynamic analysis for shuttle design verification

NASA Technical Reports Server (NTRS)

Fralich, R. W.; Green, C. E.; Rheinfurth, M. H.

1972-01-01

Two approaches that are used for determining the modes and frequencies of space shuttle structures are discussed. The first method, direct numerical analysis, involves finite element mathematical modeling of the space shuttle structure in order to use computer programs for dynamic structural analysis. The second method utilizes modal-coupling techniques of experimental verification made by vibrating only spacecraft components and by deducing modes and frequencies of the complete vehicle from results obtained in the component tests.

Comparison of the Experimental Performance of Ferroelectric CPW Circuits with Method of Moment Simulations and Conformal Mapping

NASA Technical Reports Server (NTRS)

VanKeuls, Fred W.; Chevalier, Chris T.; Miranda, Felix A.; Carlson, C. M.; Rivkin, T. V.; Parilla, P. A.; Perkins, J. D.; Ginley, D. S.

2001-01-01

Experimental measurements of coplanar waveguide (CPW) circuits atop thin films of ferroelectric Ba(x)Sr(1-x)TiO3 (BST) were made as a function bias from 0 to 200 V and frequency from 0.045 to 20 GHz. The resulting phase shifts are compared with method of moments electromagnetic simulations and a conformal mapping analysis to determine the dielectric constant of the BST films. Based on the correlation between the experimental and the modeled data, an analysis of the extent to which the electromagnetic simulators provide reliable values for the dielectric constant of the ferroelectric in these structures has been performed. In addition, to determine how well the modeled data compare with experimental data, the dielectric constant values were also compared to low frequency measurements of interdigitated capacitor circuits on the same films. Results of these comparisons will be presented.

How precise are reported protein coordinate data?

PubMed

Konagurthu, Arun S; Allison, Lloyd; Abramson, David; Stuckey, Peter J; Lesk, Arthur M

2014-03-01

Atomic coordinates in the Worldwide Protein Data Bank (wwPDB) are generally reported to greater precision than the experimental structure determinations have actually achieved. By using information theory and data compression to study the compressibility of protein atomic coordinates, it is possible to quantify the amount of randomness in the coordinate data and thereby to determine the realistic precision of the reported coordinates. On average, the value of each C(α) coordinate in a set of selected protein structures solved at a variety of resolutions is good to about 0.1 Å.

The structure of SpnF a standalone enzyme that catalyzes [4 + 2] cycloaddition

DOE PAGES

Fage, Christopher D.; Isiorho, Eta A.; Liu, Yungnan; ...

2015-03-02

In the biosynthetic pathway of the spinosyn insecticides, the tailoring enzyme SpnF performs a [4 + 2] cycloaddition on a 22-membered macrolactone to forge an embedded cyclohexene ring. To learn more about this reaction, which could potentially proceed through a Diels-Alder mechanism, in this paper we determined the 1.50-Å-resolution crystal structure of SpnF bound to S-adenosylhomocysteine. Finally, this sets the stage for advanced experimental and computational studies to determine the precise mechanism of SpnF-mediated cyclization.

Using Entropy Maximization to Understand the Determinants of Structural Dynamics beyond Native Contact Topology

PubMed Central

Lezon, Timothy R.; Bahar, Ivet

2010-01-01

Comparison of elastic network model predictions with experimental data has provided important insights on the dominant role of the network of inter-residue contacts in defining the global dynamics of proteins. Most of these studies have focused on interpreting the mean-square fluctuations of residues, or deriving the most collective, or softest, modes of motions that are known to be insensitive to structural and energetic details. However, with increasing structural data, we are in a position to perform a more critical assessment of the structure-dynamics relations in proteins, and gain a deeper understanding of the major determinants of not only the mean-square fluctuations and lowest frequency modes, but the covariance or the cross-correlations between residue fluctuations and the shapes of higher modes. A systematic study of a large set of NMR-determined proteins is analyzed using a novel method based on entropy maximization to demonstrate that the next level of refinement in the elastic network model description of proteins ought to take into consideration properties such as contact order (or sequential separation between contacting residues) and the secondary structure types of the interacting residues, whereas the types of amino acids do not play a critical role. Most importantly, an optimal description of observed cross-correlations requires the inclusion of destabilizing, as opposed to exclusively stabilizing, interactions, stipulating the functional significance of local frustration in imparting native-like dynamics. This study provides us with a deeper understanding of the structural basis of experimentally observed behavior, and opens the way to the development of more accurate models for exploring protein dynamics. PMID:20585542

Using entropy maximization to understand the determinants of structural dynamics beyond native contact topology.

PubMed

Lezon, Timothy R; Bahar, Ivet

2010-06-17

Comparison of elastic network model predictions with experimental data has provided important insights on the dominant role of the network of inter-residue contacts in defining the global dynamics of proteins. Most of these studies have focused on interpreting the mean-square fluctuations of residues, or deriving the most collective, or softest, modes of motions that are known to be insensitive to structural and energetic details. However, with increasing structural data, we are in a position to perform a more critical assessment of the structure-dynamics relations in proteins, and gain a deeper understanding of the major determinants of not only the mean-square fluctuations and lowest frequency modes, but the covariance or the cross-correlations between residue fluctuations and the shapes of higher modes. A systematic study of a large set of NMR-determined proteins is analyzed using a novel method based on entropy maximization to demonstrate that the next level of refinement in the elastic network model description of proteins ought to take into consideration properties such as contact order (or sequential separation between contacting residues) and the secondary structure types of the interacting residues, whereas the types of amino acids do not play a critical role. Most importantly, an optimal description of observed cross-correlations requires the inclusion of destabilizing, as opposed to exclusively stabilizing, interactions, stipulating the functional significance of local frustration in imparting native-like dynamics. This study provides us with a deeper understanding of the structural basis of experimentally observed behavior, and opens the way to the development of more accurate models for exploring protein dynamics.

Real-Time Examination of Atomistic Mechanisms during Shock-Induced Structural Transformation in Silicon

DOE PAGES

Turneaure, Stefan J.; Sinclair, N.; Gupta, Y. M.

2016-07-20

Experimental determination of atomistic mechanisms linking crystal structures during a compression driven solid-solid phase transformation is a long standing and challenging scientific objective. Also, when using new capabilities at the Dynamic Compression Sector at the Advanced Photon Source, the structure of shocked Si at 19 GPa was identified as simple hexagonal and the lattice orientations between ambient cubic diamond and simple hexagonal structures were related. Furthermore, this approach is general and provides a powerful new method for examining atomistic mechanisms during stress-induced structural changes.

The experimental-theoretical model of the jet HF induction discharge of atmospheric pressure

NASA Astrophysics Data System (ADS)

Gainullin, R.; Kirpichnikov, A.

2017-11-01

The paper considers theexperimental-theoretical model devised to determine the regularities of the quasi-stationary electromagnetic field structure of the HFI discharge burning in the inductor of finite dimensions at atmospheric pressure.

Microwave Spectrum of Hydrogen Bonded HEXAFLUOROISOPROPANOL•••WATER Complex

NASA Astrophysics Data System (ADS)

Shahi, Abhishek; Arunan, Elangannan

2014-06-01

Stabilizing α-helical structure of protein and dissolving a hard to dissolve polymer, polythene terphthalete, are some of the unique properties of the organic solvent Hexafluoroisopropanol (HFIP). After determining the complete microwave spectrum of HFIP monomer, we have recorded the spectrum of HFIP***H_2O complex. Ab initio calculations were used to optimize three different possible structures. The global minimum, structure 1, had HFIP as proton donor. Another promising structure, Structure 2, has been obtained from a molecular dynamic study. A total of 46 observed lines have been fitted well for obtaining the rotational and distortion constants within experimental uncertainty. The observed rotational constants are A = 1134.53898(77) MHz, B = 989.67594(44) MHz and C = 705.26602(20) MHz. Interestingly, the rotational constants of structure 1, structure 2 and experiments were very close. Experimentally observed distortion constants were close to structure 1. b-type transitions were stronger than c-type which is also consistent with the calculated dipole moment components of structure 1. Calculations predict a non-zero a-dipole moment but experimentally a-type transitions were absent. Microwave spectra of two of the deuterium isotopologues of this complex i.e. HFIP***D_2O (30 transitions) and HFIP***HOD (33 transitions) have been also observed. Search for other isotopologues are in progress. To characterize the nature of hydrogen bonding, Atoms in Molecules and Natural Bond Orbital theoretical analysis have been done. Experimental structure and these theoretical analyses indicate that the hydrogen bonding in HFIP***H_2O complex is stronger than that in water dimer. A. Shahi and E. Arunan, Talk number RK16, 68th International Symposium on Molecular Spectroscopy 2013, Ohio, USA. Yamaguchi, T.; Imura, S.; Kai, T.; Yoshida, K. Zeitschrift für Naturforsch. A 2013, 68a, 145.

Challenging the state-of-the-art in protein structure prediction: Highlights of experimental target structures for the 10th Critical Assessment of Techniques for Protein Structure Prediction Experiment CASP10

PubMed Central

Kryshtafovych, Andriy; Moult, John; Bales, Patrick; Bazan, J. Fernando; Biasini, Marco; Burgin, Alex; Chen, Chen; Cochran, Frank V.; Craig, Timothy K.; Das, Rhiju; Fass, Deborah; Garcia-Doval, Carmela; Herzberg, Osnat; Lorimer, Donald; Luecke, Hartmut; Ma, Xiaolei; Nelson, Daniel C.; van Raaij, Mark J.; Rohwer, Forest; Segall, Anca; Seguritan, Victor; Zeth, Kornelius; Schwede, Torsten

2014-01-01

For the last two decades, CASP has assessed the state of the art in techniques for protein structure prediction and identified areas which required further development. CASP would not have been possible without the prediction targets provided by the experimental structural biology community. In the latest experiment, CASP10, over 100 structures were suggested as prediction targets, some of which appeared to be extraordinarily difficult for modeling. In this paper, authors of some of the most challenging targets discuss which specific scientific question motivated the experimental structure determination of the target protein, which structural features were especially interesting from a structural or functional perspective, and to what extent these features were correctly reproduced in the predictions submitted to CASP10. Specifically, the following targets will be presented: the acid-gated urea channel, a difficult to predict trans-membrane protein from the important human pathogen Helicobacter pylori; the structure of human interleukin IL-34, a recently discovered helical cytokine; the structure of a functionally uncharacterized enzyme OrfY from Thermoproteus tenax formed by a gene duplication and a novel fold; an ORFan domain of mimivirus sulfhydryl oxidase R596; the fibre protein gp17 from bacteriophage T7; the Bacteriophage CBA-120 tailspike protein; a virus coat protein from metagenomic samples of the marine environment; and finally an unprecedented class of structure prediction targets based on engineered disulfide-rich small proteins. PMID:24318984

Investigation of gamma ray shielding, structural and dissolution rate properties of Bi2O3-BaO-B2O3-Na2O glass system

NASA Astrophysics Data System (ADS)

Dogra, Mridula; Singh, K. J.; Kaur, Kulwinder; Anand, Vikas; Kaur, Parminder; Singh, Prabhjot; Bajwa, B. S.

2018-03-01

In the present study, quaternary system of the composition (0.45 + x) Bi2O3-(0.25 - x) BaO-0.15 B2O3-0.15 Na2O (where 0 ≤ x ≤ 0.2 mol fraction) has been prepared by using melt-quenching technique for investigation of gamma ray shielding properties. Mass attenuation coefficients and half value layer parameters have been determined experimentally at 662 keV by using 137Cs source. It has been found that experimental results of these parameters hold good agreement with theoretical values. The density, molar volume, XRD, FTIR, Raman and UV-visible studies have been used to determine structural properties of the prepared glass samples. Dissolution rate of the samples has also been measured to check their utility as long term durable glasses.

Generation of laser-induced periodic surface structures on transparent material-fused silica

NASA Astrophysics Data System (ADS)

Schwarz, Simon; Rung, Stefan; Hellmann, Ralf

2016-05-01

We report on a comparison between simulated and experimental results for the generation of laser-induced periodic surface structures with low spatial frequency on dielectrics. Using the established efficacy factor theory extended by a Drude model, we determine the required carrier density for the generation of low spatial frequency LIPSS (LSFL) and forecast their periodicity and orientation. In a subsequent calculative step, we determine the fluence of ultrashort laser pulses necessary to excite this required carrier density in due consideration of the pulse number dependent ablation threshold. The later calculation is based on a rate equation including photo- and avalanche ionization and derives appropriate process parameters for a selective generation of LSFL. Exemplarily, we apply this approach to the generation of LSFL on fused silica using a 1030 nm femtosecond laser. The experimental results for the orientation and spatial periodicity of LSFL reveal excellent agreement with the simulation.

Generation of laser-induced periodic surface structures on transparent material-fused silica

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

Schwarz, Simon; Rung, Stefan; Hellmann, Ralf

2016-05-02

We report on a comparison between simulated and experimental results for the generation of laser-induced periodic surface structures with low spatial frequency on dielectrics. Using the established efficacy factor theory extended by a Drude model, we determine the required carrier density for the generation of low spatial frequency LIPSS (LSFL) and forecast their periodicity and orientation. In a subsequent calculative step, we determine the fluence of ultrashort laser pulses necessary to excite this required carrier density in due consideration of the pulse number dependent ablation threshold. The later calculation is based on a rate equation including photo- and avalanche ionizationmore » and derives appropriate process parameters for a selective generation of LSFL. Exemplarily, we apply this approach to the generation of LSFL on fused silica using a 1030 nm femtosecond laser. The experimental results for the orientation and spatial periodicity of LSFL reveal excellent agreement with the simulation.« less

Time zero determination for FEL pump-probe studies based on ultrafast melting of bismuth.

PubMed

Epp, S W; Hada, M; Zhong, Y; Kumagai, Y; Motomura, K; Mizote, S; Ono, T; Owada, S; Axford, D; Bakhtiarzadeh, S; Fukuzawa, H; Hayashi, Y; Katayama, T; Marx, A; Müller-Werkmeister, H M; Owen, R L; Sherrell, D A; Tono, K; Ueda, K; Westermeier, F; Miller, R J D

2017-09-01

A common challenge for pump-probe studies of structural dynamics at X-ray free-electron lasers (XFELs) is the determination of time zero (T 0 )-the time an optical pulse (e.g., an optical laser) arrives coincidently with the probe pulse (e.g., a XFEL pulse) at the sample position. In some cases, T 0 might be extracted from the structural dynamics of the sample's observed response itself, but generally, an independent robust method is required or would be superior to the inferred determination of T 0 . In this paper, we present how the structural dynamics in ultrafast melting of bismuth can be exploited for a quickly performed, reliable and accurate determination of T 0 with a precision below 20 fs and an overall experimental accuracy of 50 fs to 150 fs (estimated). Our approach is potentially useful and applicable for fixed-target XFEL experiments, such as serial femtosecond crystallography, utilizing an optical pump pulse in the ultraviolet to near infrared spectral range and a pixelated 2D photon detector for recording crystallographic diffraction patterns in transmission geometry. In comparison to many other suitable approaches, our method is fairly independent of the pumping wavelength (UV-IR) as well as of the X-ray energy and offers a favorable signal contrast. The technique is exploitable not only for the determination of temporal characteristics of the experiment at the interaction point but also for investigating important conditions affecting experimental control such as spatial overlap and beam spot sizes.

Experimental strategies for imaging bioparticles with femtosecond hard X-ray pulses

DOE Data Explorer

Daurer, Benedikt, J.

2016-12-09

Facilitating the very short and intense pulses from an X-ray laser for the purpose of imaging small bioparticles carries the potential for structure determination at atomic resolution without the need for crystallization. In this study, we explore experimental strategies for this idea based on data collected at the Linac Coherent Light Source from 40 nm virus particles injected into a hard X-ray beam.

Protein Denaturation on p-T Axes--Thermodynamics and Analysis.

PubMed

Smeller, László

2015-01-01

Proteins are essential players in the vast majority of molecular level life processes. Since their structure is in most cases substantial for their correct function, study of their structural changes attracted great interest in the past decades. The three dimensional structure of proteins is influenced by several factors including temperature, pH, presence of chaotropic and cosmotropic agents, or presence of denaturants. Although pressure is an equally important thermodynamic parameter as temperature, pressure studies are considerably less frequent in the literature, probably due to the technical difficulties associated to the pressure studies. Although the first steps in the high-pressure protein study have been done 100 years ago with Bridgman's ground breaking work, the field was silent until the modern spectroscopic techniques allowed the characterization of the protein structural changes, while the protein was under pressure. Recently a number of proteins were studied under pressure, and complete pressure-temperature phase diagrams were determined for several of them. This review summarizes the thermodynamic background of the typical elliptic p-T phase diagram, its limitations and the possible reasons for deviations of the experimental diagrams from the theoretical one. Finally we show some examples of experimentally determined pressure-temperature phase diagrams.

Rigidity of transmembrane proteins determines their cluster shape

NASA Astrophysics Data System (ADS)

Jafarinia, Hamidreza; Khoshnood, Atefeh; Jalali, Mir Abbas

2016-01-01

Protein aggregation in cell membrane is vital for the majority of biological functions. Recent experimental results suggest that transmembrane domains of proteins such as α -helices and β -sheets have different structural rigidities. We use molecular dynamics simulation of a coarse-grained model of protein-embedded lipid membranes to investigate the mechanisms of protein clustering. For a variety of protein concentrations, our simulations under thermal equilibrium conditions reveal that the structural rigidity of transmembrane domains dramatically affects interactions and changes the shape of the cluster. We have observed stable large aggregates even in the absence of hydrophobic mismatch, which has been previously proposed as the mechanism of protein aggregation. According to our results, semiflexible proteins aggregate to form two-dimensional clusters, while rigid proteins, by contrast, form one-dimensional string-like structures. By assuming two probable scenarios for the formation of a two-dimensional triangular structure, we calculate the lipid density around protein clusters and find that the difference in lipid distribution around rigid and semiflexible proteins determines the one- or two-dimensional nature of aggregates. It is found that lipids move faster around semiflexible proteins than rigid ones. The aggregation mechanism suggested in this paper can be tested by current state-of-the-art experimental facilities.

Underestimated Halogen Bonds Forming with Protein Backbone in Protein Data Bank.

PubMed

Zhang, Qian; Xu, Zhijian; Shi, Jiye; Zhu, Weiliang

2017-07-24

Halogen bonds (XBs) are attracting increasing attention in biological systems. Protein Data Bank (PDB) archives experimentally determined XBs in biological macromolecules. However, no software for structure refinement in X-ray crystallography takes into account XBs, which might result in the weakening or even vanishing of experimentally determined XBs in PDB. In our previous study, we showed that side-chain XBs forming with protein side chains are underestimated in PDB on the basis of the phenomenon that the proportion of side-chain XBs to overall XBs decreases as structural resolution becomes lower and lower. However, whether the dominant backbone XBs forming with protein backbone are overlooked is still a mystery. Here, with the help of the ratio (R F ) of the observed XBs' frequency of occurrence to their frequency expected at random, we demonstrated that backbone XBs are largely overlooked in PDB, too. Furthermore, three cases were discovered possessing backbone XBs in high resolution structures while losing the XBs in low resolution structures. In the last two cases, even at 1.80 Å resolution, the backbone XBs were lost, manifesting the urgent need to consider XBs in the refinement process during X-ray crystallography study.

Combined Approach for the Structural Characterization of Alkali Fluoroscandates: Solid-State NMR, Powder X-ray Diffraction, and Density Functional Theory Calculations.

PubMed

Rakhmatullin, Aydar; Polovov, Ilya B; Maltsev, Dmitry; Allix, Mathieu; Volkovich, Vladimir; Chukin, Andrey V; Boča, Miroslav; Bessada, Catherine

2018-02-05

The structures of several fluoroscandate compounds are presented here using a characterization approach combining powder X-ray diffraction and solid-state NMR. The structure of K 5 Sc 3 F 14 was fully determined from Rietveld refinement performed on powder X-ray diffraction data. Moreover, the local structures of NaScF 4 , Li 3 ScF 6 , KSc 2 F 7 , and Na 3 ScF 6 compounds were studied in detail from solid-state 19 F and 45 Sc NMR experiments. The 45 Sc chemical shift ranges for six- and seven-coordinated scandium environments were defined. The 19 F chemical shift ranges for bridging and terminal fluorine atoms were also determined. First-principles calculations of the 19 F and 45 Sc NMR parameters were carried out using plane-wave basis sets and periodic boundary conditions (CASTEP), and the results were compared with the experimental data. A good agreement between the calculated shielding constants and experimental chemical shifts was obtained. This demonstrates the good potential of computational methods in spectroscopic assignments of solid-state 45 Sc NMR spectroscopy.

A sensorless method for measuring the point mobility of mechanical structures

NASA Astrophysics Data System (ADS)

Boulandet, R.; Michau, M.; Herzog, P.; Micheau, P.; Berry, A.

2016-09-01

This paper presents a convenient and cost-effective experimental tool for measuring the mobility characteristics of a mechanical structure. The objective is to demonstrate that the point mobility measurement can be performed using only an electrodynamic inertial exciter. Unlike previous work based on voice coil actuators, no load cell or accelerometer is needed. Instead, it is theoretically shown that the mobility characteristics of the structure can be estimated from variations in the electrical input impedance of the actuator fixed onto it, provided that the electromechanical parameters of the actuator are known. The proof of concept is made experimentally using a cheap commercially available actuator on a simply supported plate, leading to a good dynamic range from 100 Hz to 1 kHz. The methodology to assess the basic parameters of the actuator is also given. Measured data are compared to a standard shaker testing and the strengths and weaknesses of the sensorless mobility measuring device are discussed. It is believed that this sensorless mobility measuring device can be a convenient experimental tool to determine the dynamic characteristics of a wide range of mechanical structures.

Determination of the structural properties of the aqueous electrolyte LiCl6H 2 O at the supercooled state using the Reverse Monte Carlo (RMC) simulation

NASA Astrophysics Data System (ADS)

ZIANE, M.; HABCHI, M.; DEROUICHE, A.; MESLI, S. M.; BENZOUINE, F.; KOTBI, M.

2017-03-01

A structural study of an aqueous electrolyte whose experimental results are available. It is a solution of A structural study of an aqueous electrolyte whose experimental results are available. It is a solution LiCl6H 2 O type at supercooled state (162K) contrasted with pure water at room temperature by means of Partial Distribution Functions (PDF) issue from neutron scattering technique. The aqueous electrolyte solution of the chloride lithium LiCl presents interesting properties which is studied by different methods at different concentration and thermodynamical states: This system possesses the property to become a glass through a metastable supercooled state when the temperature decreases. Based on these partial functions, the Reverse Monte Carlo method (RMC) computes radial correlation functions which allow exploring a number of structural features of the system. The purpose of the RMC is to produce a consistent configuration with the experimental data. They are usually the most important in the limit of systematic errors (of unknown distribution).

Crystal structure of a designed, thermostable, heterotrimeric coiled coil.

PubMed Central

Nautiyal, S.; Alber, T.

1999-01-01

Electrostatic interactions are often critical for determining the specificity of protein-protein complexes. To study the role of electrostatic interactions for assembly of helical bundles, we previously designed a thermostable, heterotrimeric coiled coil, ABC, in which charged residues were employed to drive preferential association of three distinct, 34-residue helices. To investigate the basis for heterotrimer specificity, we have used multiwavelength anomalous diffraction (MAD) analysis to determine the 1.8 A resolution crystal structure of ABC. The structure shows that ABC forms a heterotrimeric coiled coil with the intended arrangement of parallel chains. Over half of the ion pairs engineered to restrict helix associations were apparent in the experimental electron density map. As seen in other trimeric coiled coils, ABC displays acute knobs-into-holes packing and a buried anion coordinated by core polar amino acids. These interactions validate the design strategy and illustrate how packing and polar contacts determine structural uniqueness. PMID:10210186

X-ray crystallography over the past decade for novel drug discovery – where are we heading next?

PubMed Central

Zheng, Heping; Handing, Katarzyna B; Zimmerman, Matthew D; Shabalin, Ivan G; Almo, Steven C; Minor, Wladek

2015-01-01

Introduction Macromolecular X-ray crystallography has been the primary methodology for determining the three-dimensional structures of proteins, nucleic acids and viruses. Structural information has paved the way for structure-guided drug discovery and laid the foundations for structural bioinformatics. However, X-ray crystallography still has a few fundamental limitations, some of which may be overcome and complemented using emerging methods and technologies in other areas of structural biology. Areas covered This review describes how structural knowledge gained from X-ray crystallography has been used to advance other biophysical methods for structure determination (and vice versa). This article also covers current practices for integrating data generated by other biochemical and biophysical methods with those obtained from X-ray crystallography. Finally, the authors articulate their vision about how a combination of structural and biochemical/biophysical methods may improve our understanding of biological processes and interactions. Expert opinion X-ray crystallography has been, and will continue to serve as, the central source of experimental structural biology data used in the discovery of new drugs. However, other structural biology techniques are useful not only to overcome the major limitation of X-ray crystallography, but also to provide complementary structural data that is useful in drug discovery. The use of recent advancements in biochemical, spectroscopy and bioinformatics methods may revolutionize drug discovery, albeit only when these data are combined and analyzed with effective data management systems. Accurate and complete data management is crucial for developing experimental procedures that are robust and reproducible. PMID:26177814

VoroMQA: Assessment of protein structure quality using interatomic contact areas.

PubMed

Olechnovič, Kliment; Venclovas, Česlovas

2017-06-01

In the absence of experimentally determined protein structure many biological questions can be addressed using computational structural models. However, the utility of protein structural models depends on their quality. Therefore, the estimation of the quality of predicted structures is an important problem. One of the approaches to this problem is the use of knowledge-based statistical potentials. Such methods typically rely on the statistics of distances and angles of residue-residue or atom-atom interactions collected from experimentally determined structures. Here, we present VoroMQA (Voronoi tessellation-based Model Quality Assessment), a new method for the estimation of protein structure quality. Our method combines the idea of statistical potentials with the use of interatomic contact areas instead of distances. Contact areas, derived using Voronoi tessellation of protein structure, are used to describe and seamlessly integrate both explicit interactions between protein atoms and implicit interactions of protein atoms with solvent. VoroMQA produces scores at atomic, residue, and global levels, all in the fixed range from 0 to 1. The method was tested on the CASP data and compared to several other single-model quality assessment methods. VoroMQA showed strong performance in the recognition of the native structure and in the structural model selection tests, thus demonstrating the efficacy of interatomic contact areas in estimating protein structure quality. The software implementation of VoroMQA is freely available as a standalone application and as a web server at http://bioinformatics.lt/software/voromqa. Proteins 2017; 85:1131-1145. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

Modelling and Simulation of the Dynamics of the Antigen-Specific T Cell Response Using Variable Structure Control Theory.

PubMed

Anelone, Anet J N; Spurgeon, Sarah K

2016-01-01

Experimental and mathematical studies in immunology have revealed that the dynamics of the programmed T cell response to vigorous infection can be conveniently modelled using a sigmoidal or a discontinuous immune response function. This paper hypothesizes strong synergies between this existing work and the dynamical behaviour of engineering systems with a variable structure control (VSC) law. These findings motivate the interpretation of the immune system as a variable structure control system. It is shown that dynamical properties as well as conditions to analytically assess the transition from health to disease can be developed for the specific T cell response from the theory of variable structure control. In particular, it is shown that the robustness properties of the specific T cell response as observed in experiments can be explained analytically using a VSC perspective. Further, the predictive capacity of the VSC framework to determine the T cell help required to overcome chronic Lymphocytic Choriomeningitis Virus (LCMV) infection is demonstrated. The findings demonstrate that studying the immune system using variable structure control theory provides a new framework for evaluating immunological dynamics and experimental observations. A modelling and simulation tool results with predictive capacity to determine how to modify the immune response to achieve healthy outcomes which may have application in drug development and vaccine design.

Elucidation of Peptide-Directed Palladium Surface Structure for Biologically Tunable Nanocatalysts

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

Bedford, Nicholas M.; Ramezani-Dakhel, Hadi; Slocik, Joseph M.

Peptide-enabled synthesis of inorganic nanostructures represents an avenue to access catalytic materials with tunable and optimized properties. This is achieved via peptide complexity and programmability that is missing in traditional ligands for catalytic nanomaterials. Unfortunately, there is limited information available to correlate peptide sequence to particle structure and catalytic activity to date. As such, the application of peptide-enabled nanocatalysts remains limited to trial and error approaches. In this paper, a hybrid experimental and computational approach is introduced to systematically elucidate biomolecule-dependent structure/function relationships for peptide-capped Pd nanocatalysts. Synchrotron X-ray techniques were used to uncover substantial particle surface structural disorder, whichmore » was dependent upon the amino acid sequence of the peptide capping ligand. Nanocatalyst configurations were then determined directly from experimental data using reverse Monte Carlo methods and further refined using molecular dynamics simulation, obtaining thermodynamically stable peptide-Pd nanoparticle configurations. Sequence-dependent catalytic property differences for C-C coupling and olefin hydrogenation were then eluddated by identification of the catalytic active sites at the atomic level and quantitative prediction of relative reaction rates. This hybrid methodology provides a clear route to determine peptide-dependent structure/function relationships, enabling the generation of guidelines for catalyst design through rational tailoring of peptide sequences« less

Linking molecular models with ion mobility experiments. Illustration with a rigid nucleic acid structure

PubMed Central

D'Atri, Valentina; Porrini, Massimiliano; Rosu, Frédéric; Gabelica, Valérie

2015-01-01

Ion mobility spectrometry experiments allow the mass spectrometrist to determine an ion's rotationally averaged collision cross section ΩEXP. Molecular modelling is used to visualize what ion three-dimensional structure(s) is(are) compatible with the experiment. The collision cross sections of candidate molecular models have to be calculated, and the resulting ΩCALC are compared with the experimental data. Researchers who want to apply this strategy to a new type of molecule face many questions: (1) What experimental error is associated with ΩEXP determination, and how to estimate it (in particular when using a calibration for traveling wave ion guides)? (2) How to generate plausible 3D models in the gas phase? (3) Different collision cross section calculation models exist, which have been developed for other analytes than mine. Which one(s) can I apply to my systems? To apply ion mobility spectrometry to nucleic acid structural characterization, we explored each of these questions using a rigid structure which we know is preserved in the gas phase: the tetramolecular G-quadruplex [dTGGGGT]4, and we will present these detailed investigation in this tutorial. © 2015 The Authors. Journal of Mass Spectrometry published by John Wiley & Sons Ltd. PMID:26259654

Elucidation of peptide-directed palladium surface structure for biologically tunable nanocatalysts.

PubMed

Bedford, Nicholas M; Ramezani-Dakhel, Hadi; Slocik, Joseph M; Briggs, Beverly D; Ren, Yang; Frenkel, Anatoly I; Petkov, Valeri; Heinz, Hendrik; Naik, Rajesh R; Knecht, Marc R

2015-05-26

Peptide-enabled synthesis of inorganic nanostructures represents an avenue to access catalytic materials with tunable and optimized properties. This is achieved via peptide complexity and programmability that is missing in traditional ligands for catalytic nanomaterials. Unfortunately, there is limited information available to correlate peptide sequence to particle structure and catalytic activity to date. As such, the application of peptide-enabled nanocatalysts remains limited to trial and error approaches. In this paper, a hybrid experimental and computational approach is introduced to systematically elucidate biomolecule-dependent structure/function relationships for peptide-capped Pd nanocatalysts. Synchrotron X-ray techniques were used to uncover substantial particle surface structural disorder, which was dependent upon the amino acid sequence of the peptide capping ligand. Nanocatalyst configurations were then determined directly from experimental data using reverse Monte Carlo methods and further refined using molecular dynamics simulation, obtaining thermodynamically stable peptide-Pd nanoparticle configurations. Sequence-dependent catalytic property differences for C-C coupling and olefin hydrogenation were then elucidated by identification of the catalytic active sites at the atomic level and quantitative prediction of relative reaction rates. This hybrid methodology provides a clear route to determine peptide-dependent structure/function relationships, enabling the generation of guidelines for catalyst design through rational tailoring of peptide sequences.

Text Mining for Protein Docking

PubMed Central

Badal, Varsha D.; Kundrotas, Petras J.; Vakser, Ilya A.

2015-01-01

The rapidly growing amount of publicly available information from biomedical research is readily accessible on the Internet, providing a powerful resource for predictive biomolecular modeling. The accumulated data on experimentally determined structures transformed structure prediction of proteins and protein complexes. Instead of exploring the enormous search space, predictive tools can simply proceed to the solution based on similarity to the existing, previously determined structures. A similar major paradigm shift is emerging due to the rapidly expanding amount of information, other than experimentally determined structures, which still can be used as constraints in biomolecular structure prediction. Automated text mining has been widely used in recreating protein interaction networks, as well as in detecting small ligand binding sites on protein structures. Combining and expanding these two well-developed areas of research, we applied the text mining to structural modeling of protein-protein complexes (protein docking). Protein docking can be significantly improved when constraints on the docking mode are available. We developed a procedure that retrieves published abstracts on a specific protein-protein interaction and extracts information relevant to docking. The procedure was assessed on protein complexes from Dockground (http://dockground.compbio.ku.edu). The results show that correct information on binding residues can be extracted for about half of the complexes. The amount of irrelevant information was reduced by conceptual analysis of a subset of the retrieved abstracts, based on the bag-of-words (features) approach. Support Vector Machine models were trained and validated on the subset. The remaining abstracts were filtered by the best-performing models, which decreased the irrelevant information for ~ 25% complexes in the dataset. The extracted constraints were incorporated in the docking protocol and tested on the Dockground unbound benchmark set, significantly increasing the docking success rate. PMID:26650466

Experimental and theoretical investigation of three-dimensional nitrogen-doped aluminum clusters AI 8N - and AI 8N

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

Wang, Leiming; Huang, Wei; Wang, Lai S.

The structure and electronic properties of the Al 8N - and Al 8N clusters were investigated by combined photoelectron spectroscopy and ab initio studies. Congested photoelectron spectra were observed and experimental evidence was obtained for the presence of multiple isomers for Al 8N - Global minimum searches revealed several structures for Al 8N - with close energies. The calculated vertical detachment energies of the two lowest-lying isomers, which are of C 2v and C s symmetry, respectively, were shown to agree well with the experimental data. Unlike the three-dimensional structures of Al 6N - and Al 7N -, in whichmore » the dopant N atom has a high coordination number of 6,the dopant N atom in the two low-lying isomers of Al 8N - has a lower coordination number of 4 and 5, respectively. The competition between the Al–Al and Al–N interactions are shown to determine the global minimum structures of the doped aluminum clusters and results in the structural diversity for both Al 8N - and Al8N. © 2009 American Institute of Physics« less

Numerical modelling and experimental analysis of acoustic emission

NASA Astrophysics Data System (ADS)

Gerasimov, S. I.; Sych, T. V.

2018-05-01

In the present paper, the authors report on the application of non-destructive acoustic waves technologies to determine the structural integrity of engineering components. In particular, a finite element (FE) system COSMOS/M is used to investigate propagation characteristics of ultrasonic waves in linear, plane and three-dimensional structures without and with geometric concentrators. In addition, the FE results obtained are compared to the analytical and experimental ones. The study illustrates the efficient use of the FE method to model guided wave propagation problems and demonstrates the FE method’s potential to solve problems when an analytical solution is not possible due to “complicated” geometry.

Experimental determination of Ramsey numbers.

PubMed

Bian, Zhengbing; Chudak, Fabian; Macready, William G; Clark, Lane; Gaitan, Frank

2013-09-27

Ramsey theory is a highly active research area in mathematics that studies the emergence of order in large disordered structures. Ramsey numbers mark the threshold at which order first appears and are extremely difficult to calculate due to their explosive rate of growth. Recently, an algorithm that can be implemented using adiabatic quantum evolution has been proposed that calculates the two-color Ramsey numbers R(m,n). Here we present results of an experimental implementation of this algorithm and show that it correctly determines the Ramsey numbers R(3,3) and R(m,2) for 4≤m≤8. The R(8,2) computation used 84 qubits of which 28 were computational qubits. This computation is the largest experimental implementation of a scientifically meaningful adiabatic evolution algorithm that has been done to date.

Experimental Determination of Ramsey Numbers

NASA Astrophysics Data System (ADS)

Bian, Zhengbing; Chudak, Fabian; Macready, William G.; Clark, Lane; Gaitan, Frank

2013-09-01

Ramsey theory is a highly active research area in mathematics that studies the emergence of order in large disordered structures. Ramsey numbers mark the threshold at which order first appears and are extremely difficult to calculate due to their explosive rate of growth. Recently, an algorithm that can be implemented using adiabatic quantum evolution has been proposed that calculates the two-color Ramsey numbers R(m,n). Here we present results of an experimental implementation of this algorithm and show that it correctly determines the Ramsey numbers R(3,3) and R(m,2) for 4≤m≤8. The R(8,2) computation used 84 qubits of which 28 were computational qubits. This computation is the largest experimental implementation of a scientifically meaningful adiabatic evolution algorithm that has been done to date.

Method of fan sound mode structure determination

NASA Technical Reports Server (NTRS)

Pickett, G. F.; Sofrin, T. G.; Wells, R. W.

1977-01-01

A method for the determination of fan sound mode structure in the Inlet of turbofan engines using in-duct acoustic pressure measurements is presented. The method is based on the simultaneous solution of a set of equations whose unknowns are modal amplitude and phase. A computer program for the solution of the equation set was developed. An additional computer program was developed which calculates microphone locations the use of which results in an equation set that does not give rise to numerical instabilities. In addition to the development of a method for determination of coherent modal structure, experimental and analytical approaches are developed for the determination of the amplitude frequency spectrum of randomly generated sound models for use in narrow annulus ducts. Two approaches are defined: one based on the use of cross-spectral techniques and the other based on the use of an array of microphones.

Biological and functional relevance of CASP predictions

PubMed Central

Liu, Tianyun; Ish‐Shalom, Shirbi; Torng, Wen; Lafita, Aleix; Bock, Christian; Mort, Matthew; Cooper, David N; Bliven, Spencer; Capitani, Guido; Mooney, Sean D.

2017-01-01

Abstract Our goal is to answer the question: compared with experimental structures, how useful are predicted models for functional annotation? We assessed the functional utility of predicted models by comparing the performances of a suite of methods for functional characterization on the predictions and the experimental structures. We identified 28 sites in 25 protein targets to perform functional assessment. These 28 sites included nine sites with known ligand binding (holo‐sites), nine sites that are expected or suggested by experimental authors for small molecule binding (apo‐sites), and Ten sites containing important motifs, loops, or key residues with important disease‐associated mutations. We evaluated the utility of the predictions by comparing their microenvironments to the experimental structures. Overall structural quality correlates with functional utility. However, the best‐ranked predictions (global) may not have the best functional quality (local). Our assessment provides an ability to discriminate between predictions with high structural quality. When assessing ligand‐binding sites, most prediction methods have higher performance on apo‐sites than holo‐sites. Some servers show consistently high performance for certain types of functional sites. Finally, many functional sites are associated with protein‐protein interaction. We also analyzed biologically relevant features from the protein assemblies of two targets where the active site spanned the protein‐protein interface. For the assembly targets, we find that the features in the models are mainly determined by the choice of template. PMID:28975675

Single-crystal diffraction at megabar conditions by synchrotron radiation

NASA Astrophysics Data System (ADS)

Merlini, Marco; Hanfland, Michael

2013-08-01

Crystal structure determination at extreme pressures is currently possible at synchrotron beamlines optimized for such a purpose. We report the description of the experimental setup available at European Synchrotron Radiation Facility ID09 beamline (Grenoble, France) and, with two examples, we illustrate the state-of-the-art experiments currently performed at third-generation synchrotrons. The first example concerns the determination of the equation of state and the structural behavior of low-spin Fe-bearing siderite in the megabar pressure range. Siderite, in fact, undergoes a first-order isosymmetric transition at 45 GPa, and, above this pressure, it features Fe2+ in electronic low-spin configuration. The local configuration of Fe coordination polyhedra, determined by structural refinements, significantly deviates from a regular octahedron. Nevertheless, no further structural transition is detected up to the maximum pressure reached in our experiments, 135 GPa. The analysis of the Fe-O bond length extrapolated to ambient pressure, which indicates that the difference in ionic radii between the high- and the low-spin state of Fe2+ is 0.172 Å, in excellent agreement with the tabulated data by Shannon and Prewitt [Effective ionic radii in oxides and fluorides. Acta Crystallogr. 1969;B25:925-946]. The second example concerns the determination and refinement of the oP8 structure adopted by sodium in the pressure interval 118-125 GPa, using an experimental dataset collected at 118 GPa. The orthorhombic [a=4.7687(15) Å, b=3.0150(6) Å, c=5.2423(7) Å, V=75.4(3) Å3] oP8 structure is topologically related to the MnP structure, with two non-equivalent atoms in the unit cell. Despite the weak scattering factor of Na atoms, the quality of the data also allows meaningful displacement parameters refinements (R1=4.6%, 14 parameters, 190 diffractions, and 105 unique) demonstrating that the current accuracy of diffraction data at extreme pressures can be comparable with ambient condition measurements.

Experimental and theoretical studies of the crystal structures of bis-isoxazole-bis-methylene dinitrate (BIDN) and bis-isoxazole tetramethylene tetranitrate (BITN) by x-ray crystallography and density functional theory

NASA Astrophysics Data System (ADS)

Taylor, Decarlos E.; Sausa, Rosario C.

2018-06-01

The determination of crystal structures plays an important role for model testing and validation, and understanding intra and intermolecular interactions that influence crystal packing. Here, we report the molecular structure of two recently synthesized energetic molecules, 3,3-bis-isoxazole-5,5‧-bis-methylene dinitrate (C8H6N4O8, BIDN) and bis-isoxazole tetramethylene tetranitrate (C10H8N6O14, BITN) determined by single crystal x-ray diffraction and solid state density functional theory (DFT). BIDN is composed of two planar alkyl nitrate groups (r.m.s deviation = 0.0004 (1) Å) bonded to two planar azole rings (r.m.s deviation = 0.001 (1) Å, whereas BITN is composed of four planar alkyl nitrate groups (average r.m.s deviation = 0.002 (1) Å) bonded to two planar azole rings (average r.m.s deviation = 0.002 (1) Å). The theoretical calculations predict very well the planarity of both the alkyl nitrate groups and rings for both compounds. Furthermore, they predict well the bond lengths and angles of both molecules with mean deviation values of 0.018 Å (BIDN) and 0.017 Å (BITN) and 0.481° (BIDN) and 0.747° (BITN). Overall, the DFT determined torsion angles agree well with those determined experimentally for both BIDN (average deviation = 1.139°) and BITN (average deviation = 0.604°). The theoretical cell constant values are in excellent agreement with those determined experimentally for both molecules, with the BIDN a cell value and β angle showing the largest deviation, 2.1% and -1.3%, respectively. Contacts between the atoms N and H dominate the intermolecular interactions of BIDN, whereas contacts involving the atoms O and H dominate the BITN intermolecular interactions. Electrostatic potential calculations at the B3LYP/6-31G* level reveal BIDN exhibits a lower sensitivity to impact compared to BITN.

Biological and functional relevance of CASP predictions.

PubMed

Liu, Tianyun; Ish-Shalom, Shirbi; Torng, Wen; Lafita, Aleix; Bock, Christian; Mort, Matthew; Cooper, David N; Bliven, Spencer; Capitani, Guido; Mooney, Sean D; Altman, Russ B

2018-03-01

Our goal is to answer the question: compared with experimental structures, how useful are predicted models for functional annotation? We assessed the functional utility of predicted models by comparing the performances of a suite of methods for functional characterization on the predictions and the experimental structures. We identified 28 sites in 25 protein targets to perform functional assessment. These 28 sites included nine sites with known ligand binding (holo-sites), nine sites that are expected or suggested by experimental authors for small molecule binding (apo-sites), and Ten sites containing important motifs, loops, or key residues with important disease-associated mutations. We evaluated the utility of the predictions by comparing their microenvironments to the experimental structures. Overall structural quality correlates with functional utility. However, the best-ranked predictions (global) may not have the best functional quality (local). Our assessment provides an ability to discriminate between predictions with high structural quality. When assessing ligand-binding sites, most prediction methods have higher performance on apo-sites than holo-sites. Some servers show consistently high performance for certain types of functional sites. Finally, many functional sites are associated with protein-protein interaction. We also analyzed biologically relevant features from the protein assemblies of two targets where the active site spanned the protein-protein interface. For the assembly targets, we find that the features in the models are mainly determined by the choice of template. © 2017 The Authors Proteins: Structure, Function and Bioinformatics Published by Wiley Periodicals, Inc.

Experimental analysis and constitutive modelling of steel of A-IIIN strength class

NASA Astrophysics Data System (ADS)

Kruszka, Leopold; Janiszewski, Jacek

2015-09-01

Fundamentally important is the better understanding of behaviour of new building steels under impact loadings, including plastic deformations. Results of the experimental analysis in wide range of strain rates in compression at room temperature, as well as constitutive modelling for and B500SP structural steels of new A-IIIN Polish strength class, examined dynamically by split Hopkinson pressure bar technique at high strain rates, are presented in table and graphic forms. Dynamic mechanical characteristics of compressive strength for tested building structural steel are determined as well as dynamic mechanical properties of this material are compared with 18G2-b steel of A-II strength class, including effects of the shape of tested specimens, i.e. their slenderness. The paper focuses the attention on those experimental tests, their interpretation, and constitutive semi-empirical modelling of the behaviour of tested steels based on Johnson-Cook's model. Obtained results of analyses presented here are used for designing and numerical simulations of reinforced concrete protective structures.

Experimental evidence of locally resonant sonic band gap in two-dimensional phononic stubbed plates

NASA Astrophysics Data System (ADS)

Oudich, Mourad; Senesi, Matteo; Assouar, M. Badreddine; Ruzenne, Massimo; Sun, Jia-Hong; Vincent, Brice; Hou, Zhilin; Wu, Tsung-Tsong

2011-10-01

We provide experimental evidence of the existence of a locally resonant sonic band gap in a two-dimensional stubbed plate. Structures consisting of a periodic arrangement of silicone rubber stubs deposited on a thin aluminium plate were fabricated and characterized. Brillouin spectroscopy analysis is carried out to determine the elastic constants of the used rubber. The constants are then implemented in an efficient finite-element model that predicts the band structure and transmission to identify the theoretical band gap. We measure a complete sonic band gap for the out-of-plane Lamb wave modes propagating in various samples fabricated with different stub heights. Frequency domain measurements of full wave field and transmission are performed through a scanning laser Doppler vibrometer. A complete band gap from 1.9 to 2.6 kHz is showed using a sample with 6-mm stub diameter, 5-mm thickness, and 1-cm structure periodicity. Very good agreement between numerical and experimental results is obtained.

Interactions between Ether Phospholipids and Cholesterol as Determined by Scattering and Molecular Dynamics Simulations

PubMed Central

Pan, Jianjun; Cheng, Xiaolin; Heberle, Frederick A.; Mostofian, Barmak; Kučerka, Norbert; Drazba, Paul; Katsaras, John

2012-01-01

Cholesterol and ether lipids are ubiquitous in mammalian cell membranes, and their interactions are crucial in ether lipid mediated cholesterol trafficking. We report on cholesterol’s molecular interactions with ether lipids as determined using a combination of small-angle neutron and X-ray scattering, and all-atom molecular dynamics (MD) simulations. A scattering density profile model for an ether lipid bilayer was developed using MD simulations, which was then used to simultaneously fit the different experimental scattering data. From the analysis of the data the various bilayer structural parameters were obtained. Surface area constrained MD simulations were also performed to reproduce the experimental data. This iterative analysis approach resulted in good agreement between the experimental and simulated form factors. The molecular interactions taking place between cholesterol and ether lipids were then determined from the validated MD simulations. We found that in ether membranes, cholesterol primarily hydrogen bonds with the lipid headgroup phosphate oxygen, while in their ester membrane counterparts, cholesterol hydrogen bonds with the backbone ester carbonyls. This different mode of interaction between ether lipids and cholesterol induces cholesterol to reside closer to the bilayer surface, dehydrating the headgroup’s phosphate moiety. Moreover, the three-dimensional lipid chain spatial density distribution around cholesterol indicates anisotropic chain packing, causing cholesterol to tilt. These insights lend a better understanding of ether lipid mediated cholesterol trafficking and the roles that the different lipid species have in determining the structural and dynamical properties of membrane associated biomolecules. PMID:23199292

Phase Transitions of MgO Along the Hugoniot (Invited)

NASA Astrophysics Data System (ADS)

Root, S.; Shulenburger, L.; Lemke, R. W.; Cochrane, K. R.; Mattsson, T. R.

2013-12-01

The formation of terrestrial planets and planetary structure has become of great interest because of recent exoplanet discoveries of super earths. MgO is a major constituent of Earth's mantle, the rocky cores of gas giants such as Jupiter, and likely constitutes the interiors of many exoplanets. The high pressure - high temperature behavior of MgO directly affects equation of state models for planetary structure and formation. In this work, we examine single crystal MgO under shock compression utilizing experimental and density functional theory (DFT) methods to determine phase transformations along the Hugoniot. We perform plate impact experiments using Sandia's Z - facility on MgO up to 11.6 Mbar. The plate impact experiments generate highly accurate Hugoniot state data. The experimental results show the B1 - B2 solid - solid phase transition occurs near 4 Mbar on the Hugoniot. The solid - liquid transition is determined to be near 7 Mbar with a large region of B2-liquid coexistence. Using DFT methods, we also determine melt along the B1 and B2 solid phase boundaries as well as along the Hugoniot. The combined experimental and DFT results have determined the phase boundaries along the Hugoniot, which can be implemented into new planetary and EOS models. Sandia National Laboratories is a multi-program laboratory managed and operated by Sandia Corporation, a wholly owned subsidiary of Lockheed Martin Corporation, for the U.S. Department of Energy's National Nuclear Securities Administration under Contract No. DE-AC04-94AL85000.

Exploring GPCR-Lipid Interactions by Molecular Dynamics Simulations: Excitements, Challenges, and the Way Forward.

PubMed

Sengupta, Durba; Prasanna, Xavier; Mohole, Madhura; Chattopadhyay, Amitabha

2018-06-07

Gprotein-coupled receptors (GPCRs) are seven transmembrane receptors that mediate a large number of cellular responses and are important drug targets. One of the current challenges in GPCR biology is to analyze the molecular signatures of receptor-lipid interactions and their subsequent effects on GPCR structure, organization, and function. Molecular dynamics simulation studies have been successful in predicting molecular determinants of receptor-lipid interactions. In particular, predicted cholesterol interaction sites appear to correspond well with experimentally determined binding sites and estimated time scales of association. In spite of several success stories, the methodologies in molecular dynamics simulations are still emerging. In this Feature Article, we provide a comprehensive overview of coarse-grain and atomistic molecular dynamics simulations of GPCR-lipid interaction in the context of experimental observations. In addition, we discuss the effect of secondary and tertiary structural constraints in coarse-grain simulations in the context of functional dynamics and structural plasticity of GPCRs. We envision that this comprehensive overview will help resolve differences in computational studies and provide a way forward.

Structural Efficiency of Composite Struts for Aerospace Applications

NASA Technical Reports Server (NTRS)

Jegley, Dawn C.; Wu, K. Chauncey; McKenney, Martin J.; Oremont, Leonard

2011-01-01

The structural efficiency of carbon-epoxy tapered struts is considered through trade studies, detailed analysis, manufacturing and experimentation. Since some of the lunar lander struts are more highly loaded than struts used in applications such as satellites and telescopes, the primary focus of the effort is on these highly loaded struts. Lunar lander requirements include that the strut has to be tapered on both ends, complicating the design and limiting the manufacturing process. Optimal stacking sequences, geometries, and materials are determined and the sensitivity of the strut weight to each parameter is evaluated. The trade study results indicate that the most efficient carbon-epoxy struts are 30 percent lighter than the most efficient aluminum-lithium struts. Structurally efficient, highly loaded struts were fabricated and loaded in tension and compression to determine if they met the design requirements and to verify the accuracy of the analyses. Experimental evaluation of some of these struts demonstrated that they could meet the greatest Altair loading requirements in both tension and compression. These results could be applied to other vehicles requiring struts with high loading and light weight.

Biology Notes

ERIC Educational Resources Information Center

Holt, S.

1972-01-01

Short articles describing a model of protein synthesis, a simple constant temperature incubator, techniques for determining the age structure of populations from qualitative characters, an experimental demonstration of proteolytic enzyme action, and apparatus for demonstrating hydrotrophic response of roots and for measuring photosynthetic rate of…

Experimental determination of release fields in cut railroad car wheels

DOT National Transportation Integrated Search

1999-02-01

A new approach to the measurement of residual stresses in railroad wheels is investigated using a saw cut method of releasing stresses in the structure. High-sensitivity moire interferometry combined with Michelson interferometry provides full-field ...

Aggregates, broccoli and cauliflower

NASA Astrophysics Data System (ADS)

Grey, Francois; Kjems, Jørgen K.

1989-09-01

Naturally grown structures with fractal characters like broccoli and cauliflower are discussed and compared with DLA-type aggregates. It is suggested that the branching density can be used to characterize the growth process and an experimental method to determine this parameter is proposed.

Thermoelastic characteristics testing on kevlar samples for spacecraft structures

NASA Astrophysics Data System (ADS)

Crema, L. Balis; Barboni, R.; Castellani, A.; Peroni, I.

The tensile properties, the thermal expansion coefficient and the thermal conductivity of woven roving (WR) reinforced Kevlar fabrics were experimentally determined. Theoretical values for tensile Young's modulus were calculated by simulating a fabric as an equivalent cross-ply laminate. As thermal expansion coefficient concerns the fabrics have shown an isotropic behaviour. The thermal conductivity normal to fabric plane has also been determined.

Hydrogen-Bonding Network and OH Stretch Vibration of Cellulose: Comparison of Computational Modeling with Polarized IR and SFG Spectra.

PubMed

Lee, Christopher M; Kubicki, James D; Fan, Bingxin; Zhong, Linghao; Jarvis, Michael C; Kim, Seong H

2015-12-10

Hydrogen bonds play critical roles in noncovalent directional interactions determining the crystal structure of cellulose. Although diffraction studies accurately determined the coordinates of carbon and oxygen atoms in crystalline cellulose, the structural information on hydrogen atoms involved in hydrogen-bonding is still elusive. This could be complemented by vibrational spectroscopy; but the assignment of the OH stretch peaks has been controversial. In this study, we performed calculations using density functional theory with dispersion corrections (DFT-D2) for the cellulose Iβ crystal lattices with the experimentally determined carbon and oxygen coordinates. DFT-D2 calculations revealed that the OH stretch vibrations of cellulose are highly coupled and delocalized through intra- and interchain hydrogen bonds involving all OH groups in the crystal. Additionally, molecular dynamics (MD) simulations of a single cellulose microfibril showed that the conformations of OH groups exposed at the microfibril surface are not well-defined. Comparison of the computation results with the experimentally determined IR dichroism of uniaxially aligned cellulose microfibrils and the peak positions of various cellulose crystals allowed unambiguous identification of OH stretch modes observed in the vibrational spectra of cellulose.

Simplified Model to Predict Deflection and Natural Frequency of Steel Pole Structures

NASA Astrophysics Data System (ADS)

Balagopal, R.; Prasad Rao, N.; Rokade, R. P.

2018-04-01

Steel pole structures are suitable alternate to transmission line towers, due to difficulty encountered in finding land for the new right of way for installation of new lattice towers. The steel poles have tapered cross section and they are generally used for communication, power transmission and lighting purposes. Determination of deflection of steel pole is important to decide its functionality requirement. The excessive deflection of pole may affect the signal attenuation and short circuiting problems in communication/transmission poles. In this paper, a simplified method is proposed to determine both primary and secondary deflection based on dummy unit load/moment method. The predicted deflection from proposed method is validated with full scale experimental investigation conducted on 8 m and 30 m high lighting mast, 132 and 400 kV transmission pole and found to be in close agreement with each other. Determination of natural frequency is an important criterion to examine its dynamic sensitivity. A simplified semi-empirical method using the static deflection from the proposed method is formulated to determine its natural frequency. The natural frequency predicted from proposed method is validated with FE analysis results. Further the predicted results are validated with experimental results available in literature.

Two Growth Modes of Graphitic Carbon Nanofibers with Herring-Bone Structure

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

Merkulov, Igor A; Melechko, Anatoli Vasilievich; Wells, Jack C

2005-01-01

A simple mathematical model of the carbon nanofiber catalytic growth process is presented. Two major types of the fiber-catalyst interface shapes have been identified and described having qualitatively different structure in the center of a nanofiber. Presently, we discuss that the appearance of the irregular structure in the nanofiber central area is a result of curved-interface-growth kinematics. We suggest the method to determine the phenomenological parameters of the developed model from experimental data.

Two growth modes of graphitic carbon nanofibers with herring-bone structure

NASA Astrophysics Data System (ADS)

Merkulov, I. A.; Meleshko, A. V.; Wells, J. C.; Cui, H.; Merkulov, V. I.; Simpson, M. L.; Lowndes, D. H.

2005-07-01

A simple mathematical model of the carbon nanofiber catalytic growth process is presented. Two major types of the fiber-catalyst interface shapes have been identified and described having qualitatively different structure in the center of a nanofiber. Presently, we discuss that the appearance of the irregular structure in the nanofiber central area is a result of curved-interface-growth kinematics. We suggest the method to determine the phenomenological parameters of the developed model from experimental data.

Spectroscopic investigation on structure (monomer and dimer), molecular characteristics and comparative study on vibrational analysis of picolinic and isonicotinic acids using experimental and theoretical (DFT & IVP) methods

NASA Astrophysics Data System (ADS)

Ramesh, Gaddam; Reddy, Byru Venkatram

2018-05-01

In this investigation, the monomeric structure is determined for picolinic and isonicotinic acids based on geometry optimization for one of the four possible conformers and intramolecular hydrogen bond of Osbnd H⋯O using density functional theory (DFT) employing B3LYP functional supplemented with 6-311++G(d,p) basis set. Using this optimized monomeric form, the dimer structure is determined based on minimum energy and length of hydrogen bonds obtained for two possible dimeric forms yielded due to head-to-tail intermolecular Osbnd H⋯N hydrogen bond (dimer 1) linkage and tail-to -tail intermolecular Osbnd H⋯O hydrogen bond (dimer 2) linkage between pyridine ring and carboxyl group. The structure parameters obtained for monomer and dimer forms are in good agreement with the experimental literature values. The vibrational assignments have been made unambiguously for all the vibrations from FTIR and FT-Raman spectra based on the potential energy distribution (PED) and eigen vectors obtained in DFT and inverse vibrational problem (IVP) computations. The rms error between the observed and scaled frequencies is 7.7 and 9.4 cm-1 for PIA and INA, respectively. A 74-element modified valence force field is derived by Wilson's GF matrix method using 58 experimental frequencies of the two molecules in overlay least-squares technique. The average error between observed and computed frequencies by this method is calculated to be 10.39 cm-1. The results of both DFT and IVP computations yielded good agreement between observed and calculated frequencies. The NLO behaviour using hyperpolarizability values; and HOMO and LUMO energies; of the two molecules are investigated by DFT. Charge density distribution and site of chemical reactivity of the molecules are studied by molecular electrostatic surface potential (MESP). Stability of the molecules arising from hyper conjugative interactions and charge delocalization has been analyzed using natural bond orbital (NBO) analysis. The 13C and 1H NMR chemical shifts of the molecules are calculated by the gauge independent atomic orbital (GIAO) method and compared with experimental results. UV-visible (UV-Vis) spectra of the compounds are also recorded in the region 200-400 nm. Thermodynamic parameters and rotational constants are also determined and found that they are comparable with experimental literature values for these molecules.

Linking amphibian call structure to the environment: the interplay between phenotypic flexibility and individual attributes.

PubMed

Ziegler, Lucía; Arim, Matías; Narins, Peter M

2011-05-01

The structure of the environment surrounding signal emission produces different patterns of degradation and attenuation. The expected adjustment of calls to ensure signal transmission in an environment was formalized in the acoustic adaptation hypothesis. Within this framework, most studies considered anuran calls as fixed attributes determined by local adaptations. However, variability in vocalizations as a product of phenotypic expression has also been reported. Empirical evidence supporting the association between environment and call structure has been inconsistent, particularly in anurans. Here, we identify a plausible causal structure connecting environment, individual attributes, and temporal and spectral adjustments as direct or indirect determinants of the observed variation in call attributes of the frog Hypsiboas pulchellus. For that purpose, we recorded the calls of 40 males in the field, together with vegetation density and other environmental descriptors of the calling site. Path analysis revealed a strong effect of habitat structure on the temporal parameters of the call, and an effect of site temperature conditioning the size of organisms calling at each site and thus indirectly affecting the dominant frequency of the call. Experimental habitat modification with a styrofoam enclosure yielded results consistent with field observations, highlighting the potential role of call flexibility on detected call patterns. Both, experimental and correlative results indicate the need to incorporate the so far poorly considered role of phenotypic plasticity in the complex connection between environmental structure and individual call attributes.

Structure and magnetism of epitaxially strained Pd(001) films on Fe(001): Experiment and theory

NASA Astrophysics Data System (ADS)

Fullerton, Eric E.; Stoeffler, D.; Ounadjela, K.; Heinrich, B.; Celinski, Z.; Bland, J. A. C.

1995-03-01

We present an experimental and theoretical description of the structure and magnetism of epitaxially strained Pd(001) films on Fe(001) and in Fe/Pd/Fe(001) trilayers. The structure is determined by combining reflection high-energy electron diffraction and x-ray diffraction. For Fe/Au(001) bilayers and Fe/Pd/Au(001) trilayers grown by molecular-beam epitaxy on Ag(001), the Fe and Au layers are well represented by their bulk structure, whereas, thin Pd layers have a face-centered tetragonal structure with an in-plane expansion of 4.2% and an out-of-plane contraction of 7.2% (c/a=0.89). Theoretical ab initio studies of the interfacial structure indicate that the structural ground state of the epitaxially strained Pd layer is well described by a fct structure which maintains the bulk Pd atomic volume with small deviations at the interface. For Fe/Pd/Fe trilayers, the interlayer coupling oscillates with a period of 4 monolayers (ML) on a ferromagnetic background that crosses to weak antiferromagnetic coupling for thicknesses >12 ML of Pd. Strong ferromagnetic coupling observed below 5 ML of Pd indicates that 2 ML of Pd at each interface are ferromagnetically ordered. Theoretical studies of Fe3Pdn superlattices (where n is the number of Pd atomic layers) determine the polarization of the Pd layer and the interlayer magnetic coupling to depend strongly on the c/a ratio of the Pd layers. Modeling of a Pd layer with a constant-volume fct structure and one monolayer interfacial roughness find that the first 2 ML of the Pd is polarized in close agreement with the experimental results. Polarized neutron reflectivity results on an Fe(5.6 ML)/Pd(7 ML)/Au(20 ML) sample determine the average moment per Fe atom of 2.66+/-0.05μB. Calculations for the same structure show that this value is consistent with the induced Pd polarization.

Sum Frequency Generation Vibrational Spectroscopy Studies on ModelPeptide Adsorption at the Hydrophobic Solid-Water and HydrophilicSolid-Water Interfaces

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

York, Roger L.

2007-01-01

Sum frequency generation (SFG) vibrational spectroscopy has been used to study the interfacial structure of several polypeptides and amino acids adsorbed to hydrophobic and hydrophilic surfaces under a variety of experimental conditions. Peptide sequence, peptide chain length, peptide hydrophobicity, peptide side-chain type, surface hydrophobicity, and solution ionic strength all affect an adsorbed peptide's interfacial structure. Herein, it is demonstrated that with the choice of simple, model peptides and amino acids, surface specific SFG vibrational spectroscopy can be a powerful tool to elucidate the interfacial structure of these adsorbates. Herein, four experiments are described. In one, a series of isosequential amphiphilicmore » peptides are synthesized and studied when adsorbed to both hydrophobic and hydrophilic surfaces. On hydrophobic surfaces of deuterated polystyrene, it was determined that the hydrophobic part of the peptide is ordered at the solid-liquid interface, while the hydrophilic part of the peptide appears to have a random orientation at this interface. On a hydrophilic surface of silica, it was determined that an ordered peptide was only observed if a peptide had stable secondary structure in solution. In another experiment, the interfacial structure of a model amphiphilic peptide was studied as a function of the ionic strength of the solution, a parameter that could change the peptide's secondary structure in solution. It was determined that on a hydrophobic surface, the peptide's interfacial structure was independent of its structure in solution. This was in contrast to the adsorbed structure on a hydrophilic surface, where the peptide's interfacial structure showed a strong dependence on its solution secondary structure. In a third experiment, the SFG spectra of lysine and proline amino acids on both hydrophobic and hydrophilic surfaces were obtained by using a different experimental geometry that increases the SFG signal. Upon comparison of these spectra to the SFG spectra of interfacial polylysine and polyproline it was determined that the interfacial structure of a peptide is strongly dependent on its chain length. Lastly, SFG spectroscopy has been extended to the Amide I vibrational mode of a peptide (which is sensitive to peptide secondary structure) by building a new optical parametric amplifier based on lithium thioindate. Evidence is presented that suggests that the interfacial secondary structure of a peptide can be perturbed by a surface.« less

Destabilization of Human Serum Albumin by Ionic Liquids Studied Using Enhanced Molecular Dynamics Simulations.

PubMed

Jaeger, Vance W; Pfaendtner, Jim

2016-12-01

Ionic liquid (IL) containing solvents can change the structure, dynamics, function, and stability of proteins. In order to investigate the mechanisms by which ILs induce structural changes in a large multidomain protein, we study the interactions of human serum albumin (HSA) with two different ILs, 1-butyl-3-methylimidazolium tetrafluoroborate and choline dihydrogen phosphate. Root mean square deviation and fluctuation calculations indicate that high concentrations of ILs in mixtures with water lead to protein structures that remain close to their crystallographic structures on time scales of hundreds of nanoseconds. To overcome potential time scale limitations due to the high viscosity of the solvent, we employed enhanced sampling techniques to estimate the free energy of an experimentally determined important transition within the protein structure. Metadynamics simulations show that the free energy landscape of the unfolding of loop 1 of domain I is different in the presence of ILs than it is in water, consistent with previously published experimental evidence. We then apply essential dynamics coarse graining to systematically predict differences in the dynamics of proteins solvated in IL-water mixtures versus pure water systems. We also demonstrate that the presence of ionic liquids changes the distribution of intermolecular distances among several ligands, indicating that the protein structure swells in the presence of certain ILs, consistent with experimental evidence.

Detection of Non-Symmetrical Damage in Smart Plate-Like Structures

NASA Technical Reports Server (NTRS)

Blanks, H. T.; Emeric, P. R.

1998-01-01

A two-dimensional model for in-plane vibrations of a cantilever plate with a non-symmetrical damage is used in the context of defect identification in materials with piezoelectric ceramic patches bonded to their surface. These patches can act both as actuators and sensors in a self-analyzing fashion, which is a characteristic of smart materials. A Galerkin method is used to approximate the dynamic response of these structures. The natural frequency shifts due to the damage are estimated numerically and compared to experimental data obtained from tests on cantilever aluminum plate-like structures damaged at different locations with defects of different depths. The damage location and extent are determined by an enhanced least square identification method. Efficacy of the frequency shift based algorithms is demonstrated using experimental data.

Strain measurement on stiff structures: experimental evaluation of three integrated measurement principles

NASA Astrophysics Data System (ADS)

Rausch, J.; Hatzfeld, C.; Karsten, R.; Kraus, R.; Millitzer, J.; Werthschützky, R.

2012-06-01

This paper presents an experimental evaluation of three different strain measuring principles. Mounted on a steel beam resembling a car engine mount, metal foil strain gauges, piezoresistive silicon strain gauges and piezoelectric patches are investigated to measure structure-borne forces to control an active mounting structure. FEA simulation determines strains to be measured in the range of 10-8 up to 10-5 m × m-1. These low strains cannot be measured with conventional metal foil strain gauges, as shown in the experiment conducted. Both piezoresistive and piezoelectric gauges show good results compared to a conventional piezoelectric force sensor. Depending on bandwidth, overload capacity and primary electronic costs, these principles seem to be worth considering in an adaptronic system design. These parameters are described in detail for the principles investigated.

Assessment of PIV-based unsteady load determination of an airfoil with actuated flap

NASA Astrophysics Data System (ADS)

Sterenborg, J. J. H. M.; Lindeboom, R. C. J.; Simão Ferreira, C. J.; van Zuijlen, A. H.; Bijl, H.

2014-02-01

For complex experimental setups involving movable structures it is not trivial to directly measure unsteady loads. An alternative is to deduce unsteady loads indirectly from measured velocity fields using Noca's method. The ultimate aim is to use this method in future work to determine unsteady loads for fluid-structure interaction problems. The focus in this paper is first on the application and assessment of Noca's method for an airfoil with an oscillating trailing edge flap. To our best knowledge Noca's method has not been applied yet to airfoils with moving control surfaces or fluid-structure interaction problems. In addition, wind tunnel corrections for this type of unsteady flow problem are considered.

Ab initio simulations of the dynamic ion structure factor of warm dense lithium

DOE PAGES

Witte, B. B. L.; Shihab, M.; Glenzer, S. H.; ...

2017-04-06

Here, we present molecular dynamics simulations based on finite-temperature density functional theory that determine self-consistently the dynamic ion structure factor and the electronic form factor in lithium. Our comprehensive data set allows for the calculation of the dispersion relation for collective excitations, the calculation of the sound velocity, and the determination of the ion feature from the total electronic form factor and the ion structure factor. The results are compared with available experimental x-ray and neutron scattering data. Good agreement is found for both the liquid metal and warm dense matter domain. Finally, we study the impact of possible targetmore » inhomogeneities on x-ray scattering spectra.« less

Ab initio simulations of the dynamic ion structure factor of warm dense lithium

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

Witte, B. B. L.; Shihab, M.; Glenzer, S. H.

Here, we present molecular dynamics simulations based on finite-temperature density functional theory that determine self-consistently the dynamic ion structure factor and the electronic form factor in lithium. Our comprehensive data set allows for the calculation of the dispersion relation for collective excitations, the calculation of the sound velocity, and the determination of the ion feature from the total electronic form factor and the ion structure factor. The results are compared with available experimental x-ray and neutron scattering data. Good agreement is found for both the liquid metal and warm dense matter domain. Finally, we study the impact of possible targetmore » inhomogeneities on x-ray scattering spectra.« less

Resonance rotational level crossing in the fluorosulfate radical FSO3rad and experimental determination of the rotational A and the centrifugal distortion DK constants

NASA Astrophysics Data System (ADS)

Kolesniková, Lucie; Koucký, Jan; Kania, Patrik; Uhlíková, Tereza; Beckers, Helmut; Urban, Štěpán

2018-01-01

The resonance crossing of rotational levels with different fine-structure components and different k rotational quantum numbers was observed in the rotational spectra of the symmetric top fluorosulfate radical FSO3rad. Detailed measurements were performed to analyze these weak resonances as well as the A1-A2 splittings of the K = 3 and K = 6 transitions. The resonance level crossing enabled the experimental determination of "forbidden" parameters, the rotational A and the centrifugal distortion DK constants as well as the corresponding resonance off-diagonal matrix element.

IPET and FETR: Experimental Approach for Studying Molecular Structure Dynamics by Cryo-Electron Tomography of a Single-Molecule Structure

PubMed Central

Zhang, Lei; Ren, Gang

2012-01-01

The dynamic personalities and structural heterogeneity of proteins are essential for proper functioning. Structural determination of dynamic/heterogeneous proteins is limited by conventional approaches of X-ray and electron microscopy (EM) of single-particle reconstruction that require an average from thousands to millions different molecules. Cryo-electron tomography (cryoET) is an approach to determine three-dimensional (3D) reconstruction of a single and unique biological object such as bacteria and cells, by imaging the object from a series of tilting angles. However, cconventional reconstruction methods use large-size whole-micrographs that are limited by reconstruction resolution (lower than 20 Å), especially for small and low-symmetric molecule (<400 kDa). In this study, we demonstrated the adverse effects from image distortion and the measuring tilt-errors (including tilt-axis and tilt-angle errors) both play a major role in limiting the reconstruction resolution. Therefore, we developed a “focused electron tomography reconstruction” (FETR) algorithm to improve the resolution by decreasing the reconstructing image size so that it contains only a single-instance protein. FETR can tolerate certain levels of image-distortion and measuring tilt-errors, and can also precisely determine the translational parameters via an iterative refinement process that contains a series of automatically generated dynamic filters and masks. To describe this method, a set of simulated cryoET images was employed; to validate this approach, the real experimental images from negative-staining and cryoET were used. Since this approach can obtain the structure of a single-instance molecule/particle, we named it individual-particle electron tomography (IPET) as a new robust strategy/approach that does not require a pre-given initial model, class averaging of multiple molecules or an extended ordered lattice, but can tolerate small tilt-errors for high-resolution single “snapshot” molecule structure determination. Thus, FETR/IPET provides a completely new opportunity for a single-molecule structure determination, and could be used to study the dynamic character and equilibrium fluctuation of macromolecules. PMID:22291925

Characterization of TEM Moiré Patterns Originating from Two Monolayer Graphenes Grown on the Front and Back Sides of a Copper Substrate by CVD Method

NASA Astrophysics Data System (ADS)

Yamazaki, Kenji; Maehara, Yosuke; Gohara, Kazutoshi

2018-06-01

The number of layers affects the electronic properties of graphene owing to its unique band structure, called the Dirac corn. Raman spectroscopy is a key diagnostic tool for identifying the number of graphene layers and for determining their physical properties. Here, we observed moiré structures in transmission electron microscopy (TEM) observations; these are signature patterns in multilayer, although Raman spectra showed the typical intensity of the 2D/G peak in the monolayer. We also performed a multi-slice TEM image simulation to compare the 3D atomic structures of the two graphene membranes with experimental TEM images. We found that the experimental moiré image was constructed with a 9-12 Å interlayer distance between graphene membranes. This structure was constructed by transferring CVD-grown graphene films that formed on both sides of the Cu substrate at once.

Influence of Al grain boundaries segregations and La-doping on embrittlement of intermetallic NiAl

NASA Astrophysics Data System (ADS)

Kovalev, Anatoly I.; Wainstein, Dmitry L.; Rashkovskiy, Alexander Yu.

2015-11-01

The microscopic nature of intergranular fracture of NiAl was experimentally investigated by the set of electron spectroscopy techniques. The paper demonstrates that embrittlement of NiAl intermetallic compound is caused by ordering of atomic structure that leads to formation of structural aluminum segregations at grain boundaries (GB). Such segregations contain high number of brittle covalent interatomic bonds. The alloying by La increases the ductility of material avoiding Al GB enrichment and disordering GB atomic structure. The influence of La alloying on NiAl mechanical properties was investigated. GB chemical composition, atomic and electronic structure transformations after La doping were investigated by AES, XPS and EELFS techniques. To qualify the interatomic bonds metallicity the Fermi level (EF) position and electrons density (neff) in conduction band were determined in both undoped and doped NiAl. Basing on experimental results the physical model of GB brittleness formation was proposed.

Experimental and Numerical Analysis of Structural Acousticcontrol Interior Noise Reduction

NASA Technical Reports Server (NTRS)

Mei, Chuh; Bevan, Jeffrey S.

1999-01-01

The research results contained in this technical report were performed under the NASA grant entitled "Experimental and Numerical Structural Acoustic Control for Interior Noise Reduction". The report is based essentially on partial progress of the Ph.D. dissertation prepared by Jeffrey S. Bevan under direct guidance of Dr. Chuh Mei. The document presents a finite element formulation and control of sound radiated from cylindrical panels embedded with piezoceramic actuators. The extended MIN6 shallow shell element is fully electrical-structural coupled. A piezoelectric modal actuator participation (PMAP) is defined which indicates the actuator performance to each of the offending modes. Genetic algorithm is also employed to validate the sensor and actuator locations determined by the PMAP criteria. The work was conducted at the Department of Aerospace Engineering, Old Dominion University. Mr. Travis L. Turner, Structural Acoustics Branch, NASA Langley Research Center is the technical monitor.

Hydrothermal Synthesis of Nanostructured MnO2 and Gamma Radiation Effects on Rechargeable Lithium Battery Performance.

PubMed

Seo, Sang-Ei; Kang, Yun Ok; Jung, Sung-Hee; Choi, Seong-Ho

2015-09-01

Nanostructured manganese dioxide (MnO2) was synthesized by the hydrothermal method under various experimental conditions such as reaction time and concentration in order to obtain nanostructure material with different morphologies, and it was found that the morphology of the MnO2 obtained had a nanoparticle-like structure, urchin-like structure, or nanorod-like structure depending on the experimental conditions. Among the as-prepared MnO2 samples, the highest surface area was seen for the urchin-like structure, and this was irradiated by γ-rays with a total radiation dose of 30 kGy at a rate 1.0 x 10(4) Gy/h in order to determine the effect of γ-irradiation on battery performance. There was a decrease in battery performance in terms of capacity and stability for irradiated samples during 100 cycles.

Fine- and hyperfine structure investigations of the even-parity configuration system of the atomic holmium

NASA Astrophysics Data System (ADS)

Stefanska, D.; Ruczkowski, J.; Elantkowska, M.; Furmann, B.

2018-04-01

In this work new experimental results concerning the hyperfine structure (hfs) for the even-parity level system of the holmium atom (Ho I) were obtained; additionally, hfs data obtained recently as a by-product in investigations of the odd-parity level system were summarized. In the present work the values of the magnetic dipole and the electric quadrupole hfs constants A and B were determined for 24 even-parity levels, for 14 of them for the first time. On the basis of these results, as well as on available literature data, a parametric study of the fine structure and the hyperfine structure for the even-parity configurations of atomic holmium was performed. A multi-configuration fit of 7 configurations was carried out, taking into account second-order of the perturbation theory. For unknown electronic levels predicted values of the level energies and hfs constants are given, which can facilitate further experimental investigations.

A Practical Engineering Approach to Predicting Fatigue Crack Growth in Riveted Lap Joints

NASA Technical Reports Server (NTRS)

Harris, Charles E.; Piascik, Robert S.; Newman, James C., Jr.

1999-01-01

An extensive experimental database has been assembled from very detailed teardown examinations of fatigue cracks found in rivet holes of fuselage structural components. Based on this experimental database, a comprehensive analysis methodology was developed to predict the onset of widespread fatigue damage in lap joints of fuselage structure. Several computer codes were developed with specialized capabilities to conduct the various analyses that make up the comprehensive methodology. Over the past several years, the authors have interrogated various aspects of the analysis methods to determine the degree of computational rigor required to produce numerical predictions with acceptable engineering accuracy. This study led to the formulation of a practical engineering approach to predicting fatigue crack growth in riveted lap joints. This paper describes the practical engineering approach and compares predictions with the results from several experimental studies.

A Practical Engineering Approach to Predicting Fatigue Crack Growth in Riveted Lap Joints

NASA Technical Reports Server (NTRS)

Harris, C. E.; Piascik, R. S.; Newman, J. C., Jr.

2000-01-01

An extensive experimental database has been assembled from very detailed teardown examinations of fatigue cracks found in rivet holes of fuselage structural components. Based on this experimental database, a comprehensive analysis methodology was developed to predict the onset of widespread fatigue damage in lap joints of fuselage structure. Several computer codes were developed with specialized capabilities to conduct the various analyses that make up the comprehensive methodology. Over the past several years, the authors have interrogated various aspects of the analysis methods to determine the degree of computational rigor required to produce numerical predictions with acceptable engineering accuracy. This study led to the formulation of a practical engineering approach to predicting fatigue crack growth in riveted lap joints. This paper describes the practical engineering approach and compares predictions with the results from several experimental studies.

Quasiparticle trapping and the density of states in superconducting proximity structures

NASA Astrophysics Data System (ADS)

Warburton, P. A.; Blamire, M. G.

1994-08-01

An experimental study of quasiparticle trapping in epitaxial and polycrystalline Ta films on epitaxial Nb is presented using three-terminal double tunnel junction devices. It is shown that polycrystalline Ta is a more effective trap than epitaxial Ta. The experimentally measured tunneling density of states is used to calculate the inelastic quasiparticle scattering rates in the two types of Ta using the standard theory of Kaplan et a. (1976).The agreement of this calculation with the experimental results shows that the tunneling density of states may be used to determine scattering rates in proximitized superconducting films whose thickness is greater than the coherence length. This result is important since no existing theory satisfactorily describes the density of states in such proximity structures, which are currently being developed for use in high-resolution particle spectrometers.

Conformational analysis, spectroscopic, structure-activity relations and quantum chemical simulation studies of 4-(trifluoromethyl)benzylamine

NASA Astrophysics Data System (ADS)

Arjunan, V.; Devi, L.; Mohan, S.

2018-05-01

The FT-IR and FT-Raman spectra of 4-trifluoromethylbenzylamine (TFMBA) have been recorded in the range 4000-450 and 4000-100 cm-1 respectively. The conformational analysis of the compound has been carried out to attain stable geometry of the compound. The complete vibrational assignment and analysis of the fundamental modes of the compound are carried out using the experimental FTIR and FT-Raman data and quantum chemical studies. The experimental vibrational frequencies are compared with the wavenumbers obtained theoretically from the B3LYP gradient calculations employing the standard high level 6-311++G** and cc-pVTZ basis sets for the optimised geometry of the compound. The structural parameters, thermodynamic properties and vibrational frequencies of the normal modes obtained from the B3LYP methods are in good agreement with the experimental data. The 1H (400 MHz; CDCl3) and 13C (100 MHz; CDCl3) nuclear magnetic resonance (NMR) spectra were also recorded. The electronic properties, highest occupied molecular orbital and lowest unoccupied molecular orbital energies are measured by DFT approach. The charges of the atoms by natural bond orbital (NBO) analysis are determined by B3LYP/cc-pVTZ method. The structure-chemical reactivity relations of the compound are determined through chemical potential, global hardness, global softness, electronegativity, electrophilicity and local reactivity descriptors by conceptual DFT methods.

Experimental and numerical study of underwater beam propagation in a Rayleigh-Bénard turbulence tank.

PubMed

Nootz, Gero; Matt, Silvia; Kanaev, Andrey; Judd, Kyle P; Hou, Weilin

2017-08-01

The propagation of a laser beam through Rayleigh-Bénard (RB) turbulence is investigated experimentally and by way of numerical simulation. For the experimental part, a focused laser beam transversed a 5  m×0.5  m×0.5  m water filled tank lengthwise. The tank is heated from the bottom and cooled from the top to produce convective RB turbulence. The effect of the turbulence on the beam is recorded on the exit of the beam from the tank. From the centroid motion of the beam, the index of refraction structure constant Cn2 is determined. For the numerical efforts RB turbulence is simulated for a tank of the same geometry. The simulated temperature fields are converted to the index of refraction distributions, and Cn2 is extracted from the index of refraction structure functions, as well as from the simulated beam wander. To model the effect on beam propagation, the simulated index of refraction fields are converted to discrete index of refraction phase screens. These phase screens are then used in a split-step beam propagation method to investigate the effect of the turbulence on a laser beam. The beam wander as well as the index of refraction structure parameter Cn2 determined from the experiment and simulation are compared and found to be in good agreement.

Simplified Calculation of the Electrical Conductivity of Composites with Carbon Nanotubes

NASA Astrophysics Data System (ADS)

Ivanov, S. G.; Aniskevich, A.; Kulakov, V.

2018-03-01

The electrical conductivity of two groups of polymer nanocomposites filled with the same NC7000 carbon nanotubes (CNTs) beyond the percolation threshold is described with the help of simple formulas. Different manufacturing process of the nanocomposites led to different CNT network structures, and, as a consequence, their electrical conductivity, at the same CNT volume, differed by two orders of magnitude. The relation between the electrical conductivity and the volume content of CNTs of the first group of composites (with a higher electrical conductivity) is described assuming that the CNT network structure is close to a statistically homogeneous one. The formula for this case, derived on the basis of a self-consistent model, includes only two parameters: the effective longitudinal electrical conductivity of CNT and the percolation threshold (the critical value of CNT volume content). These parameters were determined from two experimental points of electrical conductivity as a function of the volume fraction of CNTs. The second group of nanocomposites had a pronounced agglomerative structure, which was confirmed by microscopy data. To describe the low electrical conductivity of this group of nanocomposites, a formula based on known models of micromechanics is proposed. Two parameters of this formula were determined from experimental data of the first group, but the other two — of the second group of nanocomposites. A comparison of calculation and experimental relations confirmed the practical expediency of using the approach described.

The architecture of PrPSc: Threading secondary structure elements into the 4-rung ß-solenoid scaffold

USDA-ARS?s Scientific Manuscript database

Aims: We propose to exploit the wealth of theoretical and experimental constraints to develop a structure of the infectious prion (hamster PrP27-30). Recent cryo-EM based evidence has determined that PrPSc is a 4-rung ß-solenoid (Vázquez-Fernández et al. 2016, PLoS Pathog. 12(9): e1005835). This ev...

Biologically Inspired, Anisoptropic Flexible Wing for Optimal Flapping Flight

DTIC Science & Technology

2013-01-31

Anisotropic Flexible Wing for Optimal Flapping Flight FA9550-07-1-0547 Sb. GRANT NUMBER Sc. PROGRAM ELEMENT NUMBER 6. AUTHOR(S) Sd. PROJECT NUMBER...anisotropic structural flexibility ; c) Conducted coordinated experimental and computational modeling to determine the roles of aerodynamic loading, wing inertia...and structural flexibility and elasticity; and d) Developed surrogate tools for flapping wing MA V design and optimization. Detailed research

Protein folding, protein structure and the origin of life: Theoretical methods and solutions of dynamical problems

NASA Technical Reports Server (NTRS)

Weaver, D. L.

1982-01-01

Theoretical methods and solutions of the dynamics of protein folding, protein aggregation, protein structure, and the origin of life are discussed. The elements of a dynamic model representing the initial stages of protein folding are presented. The calculation and experimental determination of the model parameters are discussed. The use of computer simulation for modeling protein folding is considered.

The Scottish Structural Proteomics Facility: targets, methods and outputs

PubMed Central

Oke, Muse; Carter, Lester G.; Johnson, Kenneth A.; Liu, Huanting; McMahon, Stephen A.; Yan, Xuan; Kerou, Melina; Weikart, Nadine D.; Kadi, Nadia; Sheikh, Md. Arif; Schmelz, Stefan; Dorward, Mark; Zawadzki, Michal; Cozens, Christopher; Falconer, Helen; Powers, Helen; Overton, Ian M.; van Niekerk, C. A. Johannes; Peng, Xu; Patel, Prakash; Garrett, Roger A.; Prangishvili, David; Botting, Catherine H.; Coote, Peter J.; Dryden, David T. F.; Barton, Geoffrey J.; Schwarz-Linek, Ulrich; Challis, Gregory L.; Taylor, Garry L.; White, Malcolm F.

2010-01-01

The Scottish Structural Proteomics Facility was funded to develop a laboratory scale approach to high throughput structure determination. The effort was successful in that over 40 structures were determined. These structures and the methods harnessed to obtain them are reported here. This report reflects on the value of automation but also on the continued requirement for a high degree of scientific and technical expertise. The efficiency of the process poses challenges to the current paradigm of structural analysis and publication. In the 5 year period we published ten peer-reviewed papers reporting structural data arising from the pipeline. Nevertheless, the number of structures solved exceeded our ability to analyse and publish each new finding. By reporting the experimental details and depositing the structures we hope to maximize the impact of the project by allowing others to follow up the relevant biology. Electronic supplementary material The online version of this article (doi:10.1007/s10969-010-9090-y) contains supplementary material, which is available to authorized users. PMID:20419351

Computing approximate solutions of the protein structure determination problem using global constraints on discrete crystal lattices.

PubMed

Dal Palù, Alessandro; Dovier, Agostino; Pontelli, Enrico

2010-01-01

Crystal lattices are discrete models of the three-dimensional space that have been effectively employed to facilitate the task of determining proteins' natural conformation. This paper investigates alternative global constraints that can be introduced in a constraint solver over discrete crystal lattices. The objective is to enhance the efficiency of lattice solvers in dealing with the construction of approximate solutions of the protein structure determination problem. Some of them (e.g., self-avoiding-walk) have been explicitly or implicitly already used in previous approaches, while others (e.g., the density constraint) are new. The intrinsic complexities of all of them are studied and preliminary experimental results are discussed.

Linking microbial community structure and microbial processes: An empirical and conceptual overview

USGS Publications Warehouse

Bier, R.L.; Bernhardt, Emily S.; Boot, Claudia M.; Graham, Emily B.; Hall, Edward K.; Lennon, Jay T.; Nemergut, Diana R.; Osborne, Brooke B.; Ruiz-Gonzalez, Clara; Schimel, Joshua P.; Waldrop, Mark P.; Wallenstein, Matthew D.

2015-01-01

A major goal of microbial ecology is to identify links between microbial community structure and microbial processes. Although this objective seems straightforward, there are conceptual and methodological challenges to designing studies that explicitly evaluate this link. Here, we analyzed literature documenting structure and process responses to manipulations to determine the frequency of structure-process links and whether experimental approaches and techniques influence link detection. We examined nine journals (published 2009–13) and retained 148 experimental studies measuring microbial community structure and processes. Many qualifying papers (112 of 148) documented structure and process responses, but few (38 of 112 papers) reported statistically testing for a link. Of these tested links, 75% were significant and typically used Spearman or Pearson's correlation analysis (68%). No particular approach for characterizing structure or processes was more likely to produce significant links. Process responses were detected earlier on average than responses in structure or both structure and process. Together, our findings suggest that few publications report statistically testing structure-process links. However, when links are tested for they often occur but share few commonalities in the processes or structures that were linked and the techniques used for measuring them.

New Computer Automated Holo-Photoelastic Method For Measuring Planar Principal Stress Magnitudes And Orientation

NASA Astrophysics Data System (ADS)

Brown, G. M.; Sullivan, J. L.

1987-09-01

A complete experimental determination of the stress and strain fields in an arbitrary deformed structure is generally unavailable. However, for two dimensional elasticity problems, such determinations are possible since in those cases one needs only to solve for three stresses (two normal and one shear). In fact, such determinations have been conducted quite often. By using isochromatic and isoclinic photoelastic data, the shear difference and numerical iteration techniques (1) and the least squares techniques (2) have been successfully used for complete stress field determinations of two dimensional elasticity problems. Though the shear difference technique can be particularly sensitive to cumulative errors resulting from numerical integration, the least squares technique is not affected by this and appears to yield better accuracy. The methods just cited use both experimental data and one or more mechanics conditions(e.g., the equations of equilibrium) to determine the stress field. However, the stress field can also be obtained from experimental data alone for planar elasticity problems, if there is enough of it to solve for the three stresses. For example, the Moire* technique or the combination of isochromatic, isoclinic, and isopachic data (for transparent models) can be used for such determinations. Further, with the marriage of advanced image processing equipment to computers, such analyses using this type of data can be conveniently conducted. It is even possible that such analyses could be more accurate than those using the combined experimental/numerical techniques cited above. The purposes of this report are two fold: i) to describe a single apparatus for obtaining isochromatic, isopachic, and isoclinic results for complete stress field determinations of two dimensional transparent models, and ii) to compare experimental and theoretical stress field values for an antisymmetrically loaded beam obtained using that apparatus.

Prototyping of Dental Structures Using Laser Milling

NASA Astrophysics Data System (ADS)

Andreev, A. O.; Kosenko, M. S.; Petrovskiy, V. N.; Mironov, V. D.

2016-02-01

The results of experimental studies of the effect of an ytterbium fiber laser radiation parameters on processing efficiency and quality of ZrO2 ceramics widely used in stomatology are presented. Laser operating conditions with optimum characteristics for obtaining high quality final surfaces and rapid material removal of dental structures are determined. The ability of forming thin-walled ceramic structures by laser milling technology (a minimum wall thickness of 50 μm) is demonstrated. The examples of three-dimensional dental structures created in computer 3D-models of human teeth using laser milling are shown.

Generalized fluid impulse functions for oscillating marine structures

NASA Astrophysics Data System (ADS)

Janardhanan, K.; Price, W. G.; Wu, Y.

1992-03-01

A selection of generalized impulse response functions is presented for a variety of rigid and flexible marine structures (i.e. mono-hull, SWATH, floating drydock and twin dock, fixed flexible pile). These functions are determined from calculated and experimental frequency-dependent hydrodynamic data, and the characteristics of these data depend on the type of structure considered. This information is reflected in the shape and duration of the generalized impulse response functions which are pre-requisites for a generalized integro-differential mathematical model describing the dynamic behaviour of the structures to seaway excitation.

Combining functional and structural genomics to sample the essential Burkholderia structome.

PubMed

Baugh, Loren; Gallagher, Larry A; Patrapuvich, Rapatbhorn; Clifton, Matthew C; Gardberg, Anna S; Edwards, Thomas E; Armour, Brianna; Begley, Darren W; Dieterich, Shellie H; Dranow, David M; Abendroth, Jan; Fairman, James W; Fox, David; Staker, Bart L; Phan, Isabelle; Gillespie, Angela; Choi, Ryan; Nakazawa-Hewitt, Steve; Nguyen, Mary Trang; Napuli, Alberto; Barrett, Lynn; Buchko, Garry W; Stacy, Robin; Myler, Peter J; Stewart, Lance J; Manoil, Colin; Van Voorhis, Wesley C

2013-01-01

The genus Burkholderia includes pathogenic gram-negative bacteria that cause melioidosis, glanders, and pulmonary infections of patients with cancer and cystic fibrosis. Drug resistance has made development of new antimicrobials critical. Many approaches to discovering new antimicrobials, such as structure-based drug design and whole cell phenotypic screens followed by lead refinement, require high-resolution structures of proteins essential to the parasite. We experimentally identified 406 putative essential genes in B. thailandensis, a low-virulence species phylogenetically similar to B. pseudomallei, the causative agent of melioidosis, using saturation-level transposon mutagenesis and next-generation sequencing (Tn-seq). We selected 315 protein products of these genes based on structure-determination criteria, such as excluding very large and/or integral membrane proteins, and entered them into the Seattle Structural Genomics Center for Infection Disease (SSGCID) structure determination pipeline. To maximize structural coverage of these targets, we applied an "ortholog rescue" strategy for those producing insoluble or difficult to crystallize proteins, resulting in the addition of 387 orthologs (or paralogs) from seven other Burkholderia species into the SSGCID pipeline. This structural genomics approach yielded structures from 31 putative essential targets from B. thailandensis, and 25 orthologs from other Burkholderia species, yielding an overall structural coverage for 49 of the 406 essential gene families, with a total of 88 depositions into the Protein Data Bank. Of these, 25 proteins have properties of a potential antimicrobial drug target i.e., no close human homolog, part of an essential metabolic pathway, and a deep binding pocket. We describe the structures of several potential drug targets in detail. This collection of structures, solubility and experimental essentiality data provides a resource for development of drugs against infections and diseases caused by Burkholderia. All expression clones and proteins created in this study are freely available by request.

CHAMELEON AUTOMATED RESIDENTIAL ENERGY MANAGEMENT SYSTEM

EPA Science Inventory

The expected output of the project will be an experimentally determined Chameleon specification. The expected outcomes will include 1) a set of guidelines for implementing Chameleon in residential structures from both a retrofit and original design perspective and 2) a cost a...

Mathematical Model Formulation And Validation Of Water And Solute Transport In Whole Hamster Pancreatic Islets

PubMed Central

Benson, Charles T.; Critser, John K.

2014-01-01

Optimization of cryopreservation protocols for cells and tissues requires accurate models of heat and mass transport. Model selection often depends on the configuration of the tissue. Here, a mathematical and conceptual model of water and solute transport for whole hamster pancreatic islets has been developed and experimentally validated incorporating fundamental biophysical data from previous studies on individual hamster islet cells while retaining whole-islet structural information. It describes coupled transport of water and solutes through the islet by three methods: intracellularly, intercellularly, and in combination. In particular we use domain decomposition techniques to couple a transmembrane flux model with an interstitial mass transfer model. The only significant undetermined variable is the cellular surface area which is in contact with the intercellularly transported solutes, Ais. The model was validated and Ais determined using a 3 × 3 factorial experimental design blocked for experimental day. Whole islet physical experiments were compared with model predictions at three temperatures, three perfusing solutions, and three islet size groups. A mean of 4.4 islets were compared at each of the 27 experimental conditions and found to correlate with a coefficient of determination of 0.87 ± 0.06 (mean ± S.D.). Only the treatment variable of perfusing solution was found to be significant (p < 0.05). We have devised a model that retains much of the intrinsic geometric configuration of the system, and thus fewer laboratory experiments are needed to determine model parameters and thus to develop new optimized cryopreservation protocols. Additionally, extensions to ovarian follicles and other concentric tissue structures may be made. PMID:24950195

Biotic and Abiotic Properties Mediating Plant Diversity Effects on Soil Microbial Communities in an Experimental Grassland

PubMed Central

Lange, Markus; Habekost, Maike; Eisenhauer, Nico; Roscher, Christiane; Bessler, Holger; Engels, Christof; Oelmann, Yvonne; Scheu, Stefan; Wilcke, Wolfgang; Schulze, Ernst-Detlef; Gleixner, Gerd

2014-01-01

Plant diversity drives changes in the soil microbial community which may result in alterations in ecosystem functions. However, the governing factors between the composition of soil microbial communities and plant diversity are not well understood. We investigated the impact of plant diversity (plant species richness and functional group richness) and plant functional group identity on soil microbial biomass and soil microbial community structure in experimental grassland ecosystems. Total microbial biomass and community structure were determined by phospholipid fatty acid (PLFA) analysis. The diversity gradient covered 1, 2, 4, 8, 16 and 60 plant species and 1, 2, 3 and 4 plant functional groups (grasses, legumes, small herbs and tall herbs). In May 2007, soil samples were taken from experimental plots and from nearby fields and meadows. Beside soil texture, plant species richness was the main driver of soil microbial biomass. Structural equation modeling revealed that the positive plant diversity effect was mainly mediated by higher leaf area index resulting in higher soil moisture in the top soil layer. The fungal-to-bacterial biomass ratio was positively affected by plant functional group richness and negatively by the presence of legumes. Bacteria were more closely related to abiotic differences caused by plant diversity, while fungi were more affected by plant-derived organic matter inputs. We found diverse plant communities promoted faster transition of soil microbial communities typical for arable land towards grassland communities. Although some mechanisms underlying the plant diversity effect on soil microorganisms could be identified, future studies have to determine plant traits shaping soil microbial community structure. We suspect differences in root traits among different plant communities, such as root turnover rates and chemical composition of root exudates, to structure soil microbial communities. PMID:24816860

Protein Models Docking Benchmark 2

PubMed Central

Anishchenko, Ivan; Kundrotas, Petras J.; Tuzikov, Alexander V.; Vakser, Ilya A.

2015-01-01

Structural characterization of protein-protein interactions is essential for our ability to understand life processes. However, only a fraction of known proteins have experimentally determined structures. Such structures provide templates for modeling of a large part of the proteome, where individual proteins can be docked by template-free or template-based techniques. Still, the sensitivity of the docking methods to the inherent inaccuracies of protein models, as opposed to the experimentally determined high-resolution structures, remains largely untested, primarily due to the absence of appropriate benchmark set(s). Structures in such a set should have pre-defined inaccuracy levels and, at the same time, resemble actual protein models in terms of structural motifs/packing. The set should also be large enough to ensure statistical reliability of the benchmarking results. We present a major update of the previously developed benchmark set of protein models. For each interactor, six models were generated with the model-to-native Cα RMSD in the 1 to 6 Å range. The models in the set were generated by a new approach, which corresponds to the actual modeling of new protein structures in the “real case scenario,” as opposed to the previous set, where a significant number of structures were model-like only. In addition, the larger number of complexes (165 vs. 63 in the previous set) increases the statistical reliability of the benchmarking. We estimated the highest accuracy of the predicted complexes (according to CAPRI criteria), which can be attained using the benchmark structures. The set is available at http://dockground.bioinformatics.ku.edu. PMID:25712716

Calorimetric Studies and Structural Aspects of Ionic Liquids in Designing Sorption Materials for Thermal Energy Storage.

PubMed

Brünig, Thorge; Krekić, Kristijan; Bruhn, Clemens; Pietschnig, Rudolf

2016-11-02

The thermal properties of a series of twenty-four ionic liquids (ILs) have been determined by isothermal titration calorimetry (ITC) with the aim of simulating processes involving water sorption. For eleven water-free ILs, the molecular structures have been determined by X-ray crystallography in the solid state, which have been used to derive the molecular volumes of the ionic components of the ILs. Moreover, the structures reveal a high prevalence of hydrogen bonding in these compounds. A relationship between the molecular volumes and the experimentally determined energies of dilution could be established. The highest energies of dilution observed in this series were obtained for the acetate-based ILs, which underlines their potential as working fluids in sorption-based thermal energy storage systems. © 2016 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Structures, phase stabilities, and electrical potentials of Li-Si battery anode materials

NASA Astrophysics Data System (ADS)

Tipton, William W.; Bealing, Clive R.; Mathew, Kiran; Hennig, Richard G.

2013-05-01

The Li-Si materials system holds promise for use as an anode in Li-ion battery applications. For this system, we determine the charge capacity, voltage profiles, and energy storage density solely by ab initio methods without any experimental input. We determine the energetics of the stable and metastable Li-Si phases likely to form during the charging and discharging of a battery. Ab initio molecular dynamics simulations are used to model the structure of amorphous Li-Si as a function of composition, and a genetic algorithm coupled to density-functional theory searches the Li-Si binary phase diagram for small-cell, metastable crystal structures. Calculations of the phonon densities of states using density-functional perturbation theory for selected structures determine the importance of vibrational, including zero-point, contributions to the free energies. The energetics and local structural motifs of these metastable Li-Si phases closely resemble those of the amorphous phases, making these small unit cell crystal phases good approximants of the amorphous phase for use in further studies. The charge capacity is estimated, and the electrical potential profiles and the energy density of Li-Si anodes are predicted. We find, in good agreement with experimental measurements, that the formation of amorphous Li-Si only slightly increases the anode potential. Additionally, the genetic algorithm identifies a previously unreported member of the Li-Si binary phase diagram with composition Li5Si2 which is stable at 0 K with respect to previously known phases. We discuss its relationship to the partially occupied Li7Si3 phase.

Swellix: a computational tool to explore RNA conformational space.

PubMed

Sloat, Nathan; Liu, Jui-Wen; Schroeder, Susan J

2017-11-21

The sequence of nucleotides in an RNA determines the possible base pairs for an RNA fold and thus also determines the overall shape and function of an RNA. The Swellix program presented here combines a helix abstraction with a combinatorial approach to the RNA folding problem in order to compute all possible non-pseudoknotted RNA structures for RNA sequences. The Swellix program builds on the Crumple program and can include experimental constraints on global RNA structures such as the minimum number and lengths of helices from crystallography, cryoelectron microscopy, or in vivo crosslinking and chemical probing methods. The conceptual advance in Swellix is to count helices and generate all possible combinations of helices rather than counting and combining base pairs. Swellix bundles similar helices and includes improvements in memory use and efficient parallelization. Biological applications of Swellix are demonstrated by computing the reduction in conformational space and entropy due to naturally modified nucleotides in tRNA sequences and by motif searches in Human Endogenous Retroviral (HERV) RNA sequences. The Swellix motif search reveals occurrences of protein and drug binding motifs in the HERV RNA ensemble that do not occur in minimum free energy or centroid predicted structures. Swellix presents significant improvements over Crumple in terms of efficiency and memory use. The efficient parallelization of Swellix enables the computation of sequences as long as 418 nucleotides with sufficient experimental constraints. Thus, Swellix provides a practical alternative to free energy minimization tools when multiple structures, kinetically determined structures, or complex RNA-RNA and RNA-protein interactions are present in an RNA folding problem.

Ambient Vibration Tests of an Arch Dam with Different Reservoir Water Levels: Experimental Results and Comparison with Finite Element Modelling

PubMed Central

Ranieri, Gaetano

2014-01-01

This paper deals with the ambient vibration tests performed in an arch dam in two different working conditions in order to assess the effect produced by two different reservoir water levels on the structural vibration properties. The study consists of an experimental part and a numerical part. The experimental tests were carried out in two different periods of the year, at the beginning of autumn (October 2012) and at the end of winter (March 2013), respectively. The measurements were performed using a fast technique based on asynchronous records of microtremor time-series. In-contact single-station measurements were done by means of one single high resolution triaxial tromometer and two low-frequency seismometers, placed in different points of the structure. The Standard Spectral Ratio method has been used to evaluate the natural frequencies of vibration of the structure. A 3D finite element model of the arch dam-reservoir-foundation system has been developed to verify analytically determined vibration properties, such as natural frequencies and mode shapes, and their changes linked to water level with the experimental results. PMID:25003146

Implementation and Development of the Incremental Hole Drilling Method for the Measurement of Residual Stress in Thermal Spray Coatings

NASA Astrophysics Data System (ADS)

Valente, T.; Bartuli, C.; Sebastiani, M.; Loreto, A.

2005-12-01

The experimental measurement of residual stresses originating within thick coatings deposited by thermal spray on solid substrates plays a role of fundamental relevance in the preliminary stages of coating design and process parameters optimization. The hole-drilling method is a versatile and widely used technique for the experimental determination of residual stress in the most superficial layers of a solid body. The consolidated procedure, however, can only be implemented for metallic bulk materials or for homogeneous, linear elastic, and isotropic materials. The main objective of the present investigation was to adapt the experimental method to the measurement of stress fields built up in ceramic coatings/metallic bonding layers structures manufactured by plasma spray deposition. A finite element calculation procedure was implemented to identify the calibration coefficients necessary to take into account the elastic modulus discontinuities that characterize the layered structure through its thickness. Experimental adjustments were then proposed to overcome problems related to the low thermal conductivity of the coatings. The number of calculation steps and experimental drilling steps were finally optimized.

Poisson-Nernst-Planck Models of Nonequilibrium Ion Electrodiffusion through a Protegrin Transmembrane Pore

PubMed Central

Bolintineanu, Dan S.; Sayyed-Ahmad, Abdallah; Davis, H. Ted; Kaznessis, Yiannis N.

2009-01-01

Protegrin peptides are potent antimicrobial agents believed to act against a variety of pathogens by forming nonselective transmembrane pores in the bacterial cell membrane. We have employed 3D Poisson-Nernst-Planck (PNP) calculations to determine the steady-state ion conduction characteristics of such pores at applied voltages in the range of −100 to +100 mV in 0.1 M KCl bath solutions. We have tested a variety of pore structures extracted from molecular dynamics (MD) simulations based on an experimentally proposed octomeric pore structure. The computed single-channel conductance values were in the range of 290–680 pS. Better agreement with the experimental range of 40–360 pS was obtained using structures from the last 40 ns of the MD simulation, where conductance values range from 280 to 430 pS. We observed no significant variation of the conductance with applied voltage in any of the structures that we tested, suggesting that the voltage dependence observed experimentally is a result of voltage-dependent channel formation rather than an inherent feature of the open pore structure. We have found the pore to be highly selective for anions, with anionic to cationic current ratios (ICl−/IK+) on the order of 103. This is consistent with the highly cationic nature of the pore but surprisingly in disagreement with the experimental finding of only slight anionic selectivity. We have additionally tested the sensitivity of our PNP model to several parameters and found the ion diffusion coefficients to have a significant influence on conductance characteristics. The best agreement with experimental data was obtained using a diffusion coefficient for each ion set to 10% of the bulk literature value everywhere inside the channel, a scaling used by several other studies employing PNP calculations. Overall, this work presents a useful link between previous work focused on the structure of protegrin pores and experimental efforts aimed at investigating their conductance characteristics. PMID:19180178

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

Pan, Jianjun; Cheng, Xiaolin; Heberle, Frederick A

Cholesterol and ether lipids are ubiquitous in mammalian cell membranes, and their interactions are crucial in ether lipid mediated cholesterol trafficking. We report on cholesterol s molecular interactions with ether lipids as determined using a combination of small-angle neutron and Xray scattering, and all-atom molecular dynamics (MD) simulations. A scattering density profile model for an ether lipid bilayer was developed using MD simulations, which was then used to simultaneously fit the different experimental scattering data. From analysis of the data the various bilayer structural parameters were obtained. Surface area constrained MD simulations were also performed to reproduce the experimental data.more » This iterative analysis approach resulted in good agreement between the experimental and simulated form factors. The molecular interactions taking place between cholesterol and ether lipids were then determined from the validated MD simulations. We found that in ether membranes cholesterol primarily hydrogen bonds with the lipid headgroup phosphate oxygen, while in their ester membrane counterparts cholesterol hydrogen bonds with the backbone ester carbonyls. This different mode of interaction between ether lipids and cholesterol induces cholesterol to reside closer to the bilayer surface, dehydrating the headgroup s phosphate moiety. Moreover, the three-dimensional lipid chain spatial density distribution around cholesterol indicates anisotropic chain packing, causing cholesterol to tilt. These insights lend a better understanding of ether lipid-mediated cholesterol trafficking and the roles that the different lipid species have in determining the structural and dynamical properties of membrane associated biomolecules.« less

Dynamic Testing of a Pre-stretched Flexible Tube for Identifying the Factors Affecting Modal Parameter Estimation

NASA Astrophysics Data System (ADS)

Unnikrishnan, Madhusudanan; Rajan, Akash; Basanthvihar Raghunathan, Binulal; Kochupillai, Jayaraj

2017-08-01

Experimental modal analysis is the primary tool for obtaining the fundamental dynamic characteristics like natural frequency, mode shape and modal damping ratio that determine the behaviour of any structure under dynamic loading conditions. This paper discusses about a carefully designed experimental method for calculating the dynamic characteristics of a pre-stretched horizontal flexible tube made of polyurethane material. The factors that affect the modal parameter estimation like the application time of shaker excitation, pause time between successive excitation cycles, averaging and windowing of measured signal, as well as the precautions to be taken during the experiment are explained in detail. The modal parameter estimation is done using MEscopeVESTM software. A finite element based pre-stressed modal analysis of the flexible tube is also done using ANSYS ver.14.0 software. The experimental and analytical results agreed well. The proposed experimental methodology may be extended for carrying out the modal analysis of many flexible structures like inflatables, tires and membranes.

Refinement of the experimental dynamic structure factor for liquid para-hydrogen and ortho-deuterium using semi-classical quantum simulation.

PubMed

Smith, Kyle K G; Poulsen, Jens Aage; Cunsolo, A; Rossky, Peter J

2014-01-21

The dynamic structure factor of liquid para-hydrogen and ortho-deuterium in corresponding thermodynamic states (T = 20.0 K, n = 21.24 nm(-3)) and (T = 23.0 K, n = 24.61 nm(-3)), respectively, has been computed by both the Feynman-Kleinert linearized path-integral (FK-LPI) and Ring-Polymer Molecular Dynamics (RPMD) methods and compared with Inelastic X Ray Scattering spectra. The combined use of computational and experimental methods enabled us to reduce experimental uncertainties in the determination of the true sample spectrum. Furthermore, the refined experimental spectrum of para-hydrogen and ortho-deuterium is consistently reproduced by both FK-LPI and RPMD results at momentum transfers lower than 12.8 nm(-1). At larger momentum transfers the FK-LPI results agree with experiment much better for ortho-deuterium than for para-hydrogen. More specifically we found that for k ∼ 20.0 nm(-1) para-hydrogen provides a test case for improved approximations to quantum dynamics.

Feasibility of using phase change materials to control the heat of hydration in massive concrete structures.

PubMed

Choi, Won-Chang; Khil, Bae-Soo; Chae, Young-Seok; Liang, Qi-Bo; Yun, Hyun-Do

2014-01-01

This paper presents experimental results that can be applied to select a possible phase change material (PCM), such as a latent heat material (LHM), to control the hydration heat in mass concrete structures. Five experimental tests (microconduction, simplified adiabatic temperature rise, heat, and compressive strength tests) were conducted to select the most desirable LHM out of seven types of inorganic PCM used in cement mortar and to determine the most suitable mix design. The results of these experimental tests were used to assess the feasibility of using PCM to reduce hydration heat in mass concrete that was examined. The experimental results show that cement mortar containing barium- [Ba(OH)2 · 8H2O] based PCM has the lowest amount of total hydration heat of the cement pastes. The barium-based PCM provides good latent heat properties that help to prevent volume change and microcracks caused by thermal stress in mass concrete.

Structural control and health monitoring of building structures with unknown ground excitations: Experimental investigation

NASA Astrophysics Data System (ADS)

He, Jia; Xu, You-Lin; Zhan, Sheng; Huang, Qin

2017-03-01

When health monitoring system and vibration control system both are required for a building structure, it will be beneficial and cost-effective to integrate these two systems together for creating a smart building structure. Recently, on the basis of extended Kalman filter (EKF), a time-domain integrated approach was proposed for the identification of structural parameters of the controlled buildings with unknown ground excitations. The identified physical parameters and structural state vectors were then utilized to determine the control force for vibration suppression. In this paper, the possibility of establishing such a smart building structure with the function of simultaneous damage detection and vibration suppression was explored experimentally. A five-story shear building structure equipped with three magneto-rheological (MR) dampers was built. Four additional columns were added to the building model, and several damage scenarios were then simulated by symmetrically cutting off these columns in certain stories. Two sets of earthquakes, i.e. Kobe earthquake and Northridge earthquake, were considered as seismic input and assumed to be unknown during the tests. The structural parameters and the unknown ground excitations were identified during the tests by using the proposed identification method with the measured control forces. Based on the identified structural parameters and system states, a switching control law was employed to adjust the current applied to the MR dampers for the purpose of vibration attenuation. The experimental results show that the presented approach is capable of satisfactorily identifying structural damages and unknown excitations on one hand and significantly mitigating the structural vibration on the other hand.

Challenging the state of the art in protein structure prediction: Highlights of experimental target structures for the 10th Critical Assessment of Techniques for Protein Structure Prediction Experiment CASP10.

PubMed

Kryshtafovych, Andriy; Moult, John; Bales, Patrick; Bazan, J Fernando; Biasini, Marco; Burgin, Alex; Chen, Chen; Cochran, Frank V; Craig, Timothy K; Das, Rhiju; Fass, Deborah; Garcia-Doval, Carmela; Herzberg, Osnat; Lorimer, Donald; Luecke, Hartmut; Ma, Xiaolei; Nelson, Daniel C; van Raaij, Mark J; Rohwer, Forest; Segall, Anca; Seguritan, Victor; Zeth, Kornelius; Schwede, Torsten

2014-02-01

For the last two decades, CASP has assessed the state of the art in techniques for protein structure prediction and identified areas which required further development. CASP would not have been possible without the prediction targets provided by the experimental structural biology community. In the latest experiment, CASP10, more than 100 structures were suggested as prediction targets, some of which appeared to be extraordinarily difficult for modeling. In this article, authors of some of the most challenging targets discuss which specific scientific question motivated the experimental structure determination of the target protein, which structural features were especially interesting from a structural or functional perspective, and to what extent these features were correctly reproduced in the predictions submitted to CASP10. Specifically, the following targets will be presented: the acid-gated urea channel, a difficult to predict transmembrane protein from the important human pathogen Helicobacter pylori; the structure of human interleukin (IL)-34, a recently discovered helical cytokine; the structure of a functionally uncharacterized enzyme OrfY from Thermoproteus tenax formed by a gene duplication and a novel fold; an ORFan domain of mimivirus sulfhydryl oxidase R596; the fiber protein gene product 17 from bacteriophage T7; the bacteriophage CBA-120 tailspike protein; a virus coat protein from metagenomic samples of the marine environment; and finally, an unprecedented class of structure prediction targets based on engineered disulfide-rich small proteins. Copyright © 2013 The Authors. Wiley Periodicals, Inc.

Hygrothermal effects on the mechanical behaviour of graphite fibre-reinforced epoxy laminates beyond initial failure

NASA Technical Reports Server (NTRS)

Ishai, O.; Garg, A.; Nelson, H. G.

1986-01-01

The critical load levels and associated cracking beyond which a multidirectional laminate can be considered as structurally failed has been determined by loading graphite fiber-reinforced epoxy laminates to different strain levels up to ultimate failure. Transverse matrix cracking was monitored by acoustic and optical methods. The residual stiffness and strength parallel and perpendicular to the cracks were determined and related to the environmental/loading history. Within the range of experimental conditions studied, it is concluded that the transverse cracking process does not have a crucial effect on the structural performance of multidirectional composite laminates.

Hypothesis: spring-loaded boomerang mechanism of influenza hemagglutinin-mediated membrane fusion.

PubMed

Tamm, Lukas K

2003-07-11

Substantial progress has been made in recent years to augment the current understanding of structures and interactions that promote viral membrane fusion. This progress is reviewed with a particular emphasis on recently determined structures of viral fusion domains and their interactions with lipid membranes. The results from the different structural and thermodynamic experimental approaches are synthesized into a new proposed mechanism, termed the "spring-loaded boomerang" mechanism of membrane fusion, which is presented here as a hypothesis.

SimRNA: a coarse-grained method for RNA folding simulations and 3D structure prediction.

PubMed

Boniecki, Michal J; Lach, Grzegorz; Dawson, Wayne K; Tomala, Konrad; Lukasz, Pawel; Soltysinski, Tomasz; Rother, Kristian M; Bujnicki, Janusz M

2016-04-20

RNA molecules play fundamental roles in cellular processes. Their function and interactions with other biomolecules are dependent on the ability to form complex three-dimensional (3D) structures. However, experimental determination of RNA 3D structures is laborious and challenging, and therefore, the majority of known RNAs remain structurally uncharacterized. Here, we present SimRNA: a new method for computational RNA 3D structure prediction, which uses a coarse-grained representation, relies on the Monte Carlo method for sampling the conformational space, and employs a statistical potential to approximate the energy and identify conformations that correspond to biologically relevant structures. SimRNA can fold RNA molecules using only sequence information, and, on established test sequences, it recapitulates secondary structure with high accuracy, including correct prediction of pseudoknots. For modeling of complex 3D structures, it can use additional restraints, derived from experimental or computational analyses, including information about secondary structure and/or long-range contacts. SimRNA also can be used to analyze conformational landscapes and identify potential alternative structures. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

Exploring the atomic structure and conformational flexibility of a 320 Å long engineered viral fiber using X-ray crystallography.

PubMed

Bhardwaj, Anshul; Casjens, Sherwood R; Cingolani, Gino

2014-02-01

Protein fibers are widespread in nature, but only a limited number of high-resolution structures have been determined experimentally. Unlike globular proteins, fibers are usually recalcitrant to form three-dimensional crystals, preventing single-crystal X-ray diffraction analysis. In the absence of three-dimensional crystals, X-ray fiber diffraction is a powerful tool to determine the internal symmetry of a fiber, but it rarely yields atomic resolution structural information on complex protein fibers. An 85-residue-long minimal coiled-coil repeat unit (MiCRU) was previously identified in the trimeric helical core of tail needle gp26, a fibrous protein emanating from the tail apparatus of the bacteriophage P22 virion. Here, evidence is provided that an MiCRU can be inserted in frame inside the gp26 helical core to generate a rationally extended fiber (gp26-2M) which, like gp26, retains a trimeric quaternary structure in solution. The 2.7 Å resolution crystal structure of this engineered fiber, which measures ∼320 Å in length and is only 20-35 Å wide, was determined. This structure, the longest for a trimeric protein fiber to be determined to such a high resolution, reveals the architecture of 22 consecutive trimerization heptads and provides a framework to decipher the structural determinants for protein fiber assembly, stability and flexibility.

Effect of oxygen impurities on properties of the ternary superconductor SnMo/sub 6/S/sub 8/: Extended x-ray-absorption fine-structure determination of bond distances and local-density cluster calculations

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

Guenzburger, D.; Ellis, D.E.; Montano, P.A.

1985-10-01

Electronic structure calculations were performed for clusters representing the Chevrel-phase SnMo/sub 6/S/sub 8/, with and without oxygen doping. In order to obtain the local structure around the Sn atom, extended x-ray-absorption fine-structure (EXAFS) measurements were made with synchro- tron radiation. The interatomic distances obtained experimentally were used in the calculations. The effect of oxygen doping on the Moessbauer isomer shift and quadrupole splitting values of /sup 119/Sn was investigated theoretically and compared with reported experimental values. The effect of oxygen substitution on the density of states at the Fermi energy of the (Mo/sub 6/S/sub 8/)/sup 2 -/ cluster was alsomore » studied. The results suggest that oxygen doping does not alter significantly the electronic structure of SnMo/sub 6/S/sub 8/.« less

Effects of cutouts on the behavior of symmetric composite laminates subjected to bending and twisting loads

NASA Technical Reports Server (NTRS)

Prasad, C. B.; Shuart, M. J.; Bains, N. J.; Rouse, M.

1993-01-01

Composite structures are used for a wide variety of aerospace applications. Practical structures contain cutouts and these structures are subjected to in-plane and out-of-plane loading conditions. Structurally efficient designs for composite structures require a thorough understanding of the effects of cutouts on the response of composite plates subjected to inplane or out-of-plane loadings. Most investigations of the behavior of composite plates with cutouts have considered in-plane loadings only. Out-of-plane loadings suchas bending or twisting have received very limited attention. The response of homogeneous plates (e.g., isotropic or orthotropic plates) subjected to bending or twisting moments has been studied analytically. These analyses are for infinite plates and neglect finite-plate effects. Recently, analytical and experimental studies were conducted to determine the effects of cutouts on the response of laminated composite plates subjected to bending moments. No analytical or experimental results are currently available for the effects of cutouts on the response of composite laminates subjected to twisting moments.

Experimental Protein Structure Verification by Scoring with a Single, Unassigned NMR Spectrum.

PubMed

Courtney, Joseph M; Ye, Qing; Nesbitt, Anna E; Tang, Ming; Tuttle, Marcus D; Watt, Eric D; Nuzzio, Kristin M; Sperling, Lindsay J; Comellas, Gemma; Peterson, Joseph R; Morrissey, James H; Rienstra, Chad M

2015-10-06

Standard methods for de novo protein structure determination by nuclear magnetic resonance (NMR) require time-consuming data collection and interpretation efforts. Here we present a qualitatively distinct and novel approach, called Comparative, Objective Measurement of Protein Architectures by Scoring Shifts (COMPASS), which identifies the best structures from a set of structural models by numerical comparison with a single, unassigned 2D (13)C-(13)C NMR spectrum containing backbone and side-chain aliphatic signals. COMPASS does not require resonance assignments. It is particularly well suited for interpretation of magic-angle spinning solid-state NMR spectra, but also applicable to solution NMR spectra. We demonstrate COMPASS with experimental data from four proteins--GB1, ubiquitin, DsbA, and the extracellular domain of human tissue factor--and with reconstructed spectra from 11 additional proteins. For all these proteins, with molecular mass up to 25 kDa, COMPASS distinguished the correct fold, most often within 1.5 Å root-mean-square deviation of the reference structure. Copyright © 2015 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 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

Valence electronic structure of cobalt phthalocyanine from an optimally tuned range-separated hybrid functional.

PubMed

Brumboiu, Iulia Emilia; Prokopiou, Georgia; Kronik, Leeor; Brena, Barbara

2017-07-28

We analyse the valence electronic structure of cobalt phthalocyanine (CoPc) by means of optimally tuning a range-separated hybrid functional. The tuning is performed by modifying both the amount of short-range exact exchange (α) included in the hybrid functional and the range-separation parameter (γ), with two strategies employed for finding the optimal γ for each α. The influence of these two parameters on the structural, electronic, and magnetic properties of CoPc is thoroughly investigated. The electronic structure is found to be very sensitive to the amount and range in which the exact exchange is included. The electronic structure obtained using the optimal parameters is compared to gas-phase photo-electron data and GW calculations, with the unoccupied states additionally compared with inverse photo-electron spectroscopy measurements. The calculated spectrum with tuned γ, determined for the optimal value of α = 0.1, yields a very good agreement with both experimental results and with GW calculations that well-reproduce the experimental data.

Experimental Protein Structure Verification by Scoring with a Single, Unassigned NMR Spectrum

PubMed Central

Courtney, Joseph M.; Ye, Qing; Nesbitt, Anna E.; Tang, Ming; Tuttle, Marcus D.; Watt, Eric D.; Nuzzio, Kristin M.; Sperling, Lindsay J.; Comellas, Gemma; Peterson, Joseph R.; Morrissey, James H.; Rienstra, Chad M.

2016-01-01

Standard methods for de novo protein structure determination by nuclear magnetic resonance (NMR) require time-consuming data collection and interpretation efforts. Here we present a qualitatively distinct and novel approach, called Comparative, Objective Measurement of Protein Architectures by Scoring Shifts (COMPASS), which identifies the best structures from a set of structural models by numerical comparison with a single, unassigned 2D 13C-13C NMR spectrum containing backbone and side-chain aliphatic signals. COMPASS does not require resonance assignments. It is particularly well suited for interpretation of magic-angle spinning solid-state NMR spectra, but also applicable to solution NMR spectra. We demonstrate COMPASS with experimental data from four proteins—GB1, ubiquitin, DsbA, and the extracellular domain of human tissue factor—and with reconstructed spectra from 11 additional proteins. For all these proteins, with molecular mass up to 25 kDa, COMPASS distinguished the correct fold, most often within 1.5 Å root-mean-square deviation of the reference structure. PMID:26365800

Multishaker modal testing

NASA Technical Reports Server (NTRS)

Craig, R. R., Jr.

1983-01-01

Procedures for improving the modal modeling of structures using test data and to determine appropriate analytical models based on substructure experimental data were explored. Two related research topics were considered in modal modeling: using several independently acquired columns of frequency response data, and modal modeling using simultaneous multi-point excitation. In component mode synthesis modeling, the emphasis is on determining the best way to employ complex modes and residuals.

Physics Of Variable-Polarity Plasma Arc Welding

NASA Technical Reports Server (NTRS)

Walsh, Daniel W.; Nunes, Arthur C., Jr.

1990-01-01

Report describes experimental study of some of the physical and chemical effects that occur during variable-polarity plasma arc (VPPA) keyhole welding of 2219 aluminum alloy. Comprised three major programs: (1) determination of effects of chemical additions (i.e., impurities) on structure and shape of bead and keyhole; (2) determination of flow in regions surrounding keyhole; (3) development of analog used easily to study flow in keyhole region.

A Concept of Thermographic Method for Non-Destructive Testing of Polymeric Composite Structures Using Self-Heating Effect

PubMed Central

2017-01-01

Traditional techniques of active thermography require an external source of energy used for excitation, usually in the form of high power lamps or ultrasonic devices. In this paper, the author presents an alternative approach based on the self-heating effect observable in polymer-based structures during cyclic loading. The presented approach is based on, firstly, determination of bending resonance frequencies of a tested structure, and then, on excitation of a structure with a multi-harmonic signal constructed from the harmonics with frequencies of determined resonances. Following this, heating-up of a tested structure occurs in the location of stress concentration and mechanical energy dissipation due to the viscoelastic response of a structure. By applying multi-harmonic signal, one ensures coverage of the structure by such heated regions. The concept is verified experimentally on artificially damaged composite specimens. The results demonstrate the presented approach and indicate its potential, especially when traditional methods of excitation with an external structure for thermographic inspection cannot be applied. PMID:29283430

A Concept of Thermographic Method for Non-Destructive Testing of Polymeric Composite Structures Using Self-Heating Effect.

PubMed

Katunin, Andrzej

2017-12-28

Traditional techniques of active thermography require an external source of energy used for excitation, usually in the form of high power lamps or ultrasonic devices. In this paper, the author presents an alternative approach based on the self-heating effect observable in polymer-based structures during cyclic loading. The presented approach is based on, firstly, determination of bending resonance frequencies of a tested structure, and then, on excitation of a structure with a multi-harmonic signal constructed from the harmonics with frequencies of determined resonances. Following this, heating-up of a tested structure occurs in the location of stress concentration and mechanical energy dissipation due to the viscoelastic response of a structure. By applying multi-harmonic signal, one ensures coverage of the structure by such heated regions. The concept is verified experimentally on artificially damaged composite specimens. The results demonstrate the presented approach and indicate its potential, especially when traditional methods of excitation with an external structure for thermographic inspection cannot be applied.

Experimental determination of material damping using vibration analyzer

NASA Technical Reports Server (NTRS)

Chowdhury, Mostafiz R.; Chowdhury, Farida

1990-01-01

Structural damping is an important dynamic characteristic of engineering materials that helps to damp vibrations by reducing their amplitudes. In this investigation, an experimental method is illustrated to determine the damping characteristics of engineering materials using a dual channel Fast Fourier Transform (FFT) analyzer. A portable Compaq III computer which houses the analyzer, is used to collect the dynamic responses of three metal rods. Time-domain information is analyzed to obtain the logarithmic decrement of their damping. The damping coefficients are then compared to determine the variation of damping from material to material. The variations of damping from one point to another of the same material, due to a fixed point excitation, and the variable damping at a fixed point due to excitation at different points, are also demonstrated.

Long-term experimental warming alters nitrogen-cycling communities but site factors remain the primary drivers of community structure in high arctic tundra soils.

PubMed

Walker, Jennifer K M; Egger, Keith N; Henry, Gregory H R

2008-09-01

Arctic air temperatures are expected to rise significantly over the next century. Experimental warming of arctic tundra has been shown to increase plant productivity and cause community shifts and may also alter microbial community structure. Hence, the objective of this study was to determine whether experimental warming caused shifts in soil microbial communities by measuring changes in the frequency, relative abundance and/or richness of nosZ and nifH genotypes. Five sites at a high arctic coastal lowland were subjected to a 13-year warming experiment using open-top chambers (OTCs). Sites differed by dominant plant community, soil parent material and/or moisture regimen. Six soil cores were collected from each of four replicate OTC and ambient plots at each site and subdivided into upper and lower samples. Differences in frequency and relative abundance of terminal restriction fragments were assessed graphically by two-way cluster analysis and tested statistically with permutational multivariate analysis of variance (ANOVA). Genotypic richness was compared using factorial ANOVA. The genotype frequency, relative abundance and genotype richness of both nosZ and nifH communities differed significantly by site, and by OTC treatment and/or depth at some sites. The site that showed the most pronounced treatment effect was a wet sedge meadow, where community structure and genotype richness of both nosZ and nifH were significantly affected by warming. Although warming was an important factor affecting these communities at some sites at this high arctic lowland, overall, site factors were the main determinants of community structure.

DFT simulation, quantum chemical electronic structure, spectroscopic and structure-activity investigations of 2-benzothiazole acetonitrile.

PubMed

Arjunan, V; Thillai Govindaraja, S; Jose, Sujin P; Mohan, S

2014-07-15

The Fourier transform infrared and FT-Raman spectra of 2-benzothiazole acetonitrile (BTAN) have been recorded in the range 4000-450 and 4000-100 cm(-1) respectively. The conformational analysis of the compound has been carried out to obtain the stable geometry of the compound. The complete vibrational assignment and analysis of the fundamental modes of the compound are carried out using the experimental FTIR and FT-Raman data and quantum chemical studies. The experimental vibrational frequencies are compared with the wavenumbers derived theoretically by B3LYP gradient calculations employing the standard 6-31G(**), high level 6-311++G(**) and cc-pVTZ basis sets. The structural parameters, thermodynamic properties and vibrational frequencies of the normal modes obtained from the B3LYP methods are in good agreement with the experimental data. The (1)H (400 MHz; CDCl3) and (13)C (100 MHz;CDCl3) nuclear magnetic resonance (NMR) spectra are also recorded. The electronic properties, the energies of the highest occupied and lowest unoccupied molecular orbitals are measured by DFT approach. The kinetic stability of the molecule has been determined from the frontier molecular orbital energy gap. The charges of the atoms and the structure-chemical reactivity relations of the compound are determined by its chemical potential, global hardness, global softness, electronegativity, electrophilicity and local reactivity descriptors by conceptual DFT methods. The non-linear optical properties of the compound have been discussed by measuring the polarisability and hyperpolarisability tensors. Copyright © 2014 Elsevier B.V. All rights reserved.

Experimental verification of distributed piezoelectric actuators for use in precision space structures

NASA Technical Reports Server (NTRS)

Crawley, E. F.; De Luis, J.

1986-01-01

An analytic model for structures with distributed piezoelectric actuators is experimentally verified for the cases of both surface-bonded and embedded actuators. A technique for the selection of such piezoelectric actuators' location has been developed, and is noted to indicate that segmented actuators are always more effective than continuous ones, since the output of each can be individually controlled. Manufacturing techniques for the bonding or embedding of segmented piezoelectric actuators are also developed which allow independent electrical contact to be made with each actuator. Static tests have been conducted to determine how the elastic properties of the composite are affected by the presence of an embedded actuator, for the case of glass/epoxy laminates.

Electronic structure and optical band gap determination of NiFe2O4.

PubMed

Meinert, Markus; Reiss, Günter

2014-03-19

In a theoretical study we investigate the electronic structure and band gap of the inverse spinel ferrite NiFe2O4. The experimental optical absorption spectrum is accurately reproduced by fitting the Tran-Blaha parameter in the modified Becke-Johnson potential. The accuracy of the commonly applied Tauc plot to find the optical gap is assessed based on the computed spectra and we find that this approach can lead to a misinterpretation of the experimental data. The minimum gap of NiFe2O4 is found to be a 1.53 eV wide indirect gap, which is located in the minority spin channel.

Experimental Study of Axially Tension Cold Formed Steel Channel Members

NASA Astrophysics Data System (ADS)

Apriani, Widya; Lubis, Fadrizal; Angraini, Muthia

2017-12-01

Experimental testing is commonly used as one of the steps to determine the cause of the collapse of a building structure. The collapse of structures can be due to low quality materials. Although material samples have passed laboratory tests and the existing technical specifications have been met but there may be undetected defects and known material after failure. In this paper will be presented Experimental Testing of Axially Tension Cold Formed Steel Channel Members to determine the cause of the collapse of a building roof truss x in Pekanbaru. Test of tensile strength material cold formed channel sections was performed to obtain the main characteristics of Cold Formed steel material, namely ultimate tensile strength loads that can be held by members and the yield stress possessed by channel sections used in construction. Analysis of axially tension cold formed steel channel section presents in this paper was conducted through experimental study based on specificationsAnnualBook of ASTM Standards: Metal Test methods and Analitical Procedures, Section 3 (1991). The result of capacity loads experimental test was compared with design based on SNI 03-7971-2013standard of Indonesia for the design of cold formed steel structural members. The results of the yield stress of the material will be seen against the minimum allowable allowable stress range. After the test, the percentace of ultimate axial tension capacity theory has a result that is 16.46% larger than the ultimate axial tension capacity experimental. When compared with the load that must be borne 5.673 kN/m it can be concluded that 2 specimens do not meet. Yield stress of member has fulfilled requirement that wass bigger than 550 MPa. Based on the curve obtained ultimate axial tension capacity theory, results greater than experimental. The greatest voltage value (fu) is achieved under the same conditions as its yield stress. For this specimen with a melting voltage value fy = 571.5068 MPa has fulfilled the minimum melting point value of 550 MPa required for standard mild steel materials in accordance with the code SNI 03-7971-2013 about Cold formed steel.

Experimental Study of Axially Tension Cold Formed Steel Channel Members

NASA Astrophysics Data System (ADS)

Apriani, Widya; Lubis, Fadrizal; Angraini, Muthia

2017-12-01

Experimental testing is commonly used as one of the steps to determine the cause of the collapse of a building structure. The collapse of structures can be due to low quality materials. Although material samples have passed laboratory tests and the existing technical specifications have been met but there may be undetected defects and known material after failure. In this paper will be presented Experimental Testing of Axially Tension Cold Formed Steel Channel Members to determine the cause of the collapse of a building roof truss x in Pekanbaru. Test of tensile strength material cold formed channel sections was performed to obtain the main characteristics of Cold Formed steel material, namely ultimate tensile strength loads that can be held by members and the yield stress possessed by channel sections used in construction. Analysis of axially tension cold formed steel channel section presents in this paper was conducted through experimental study based on specificationsAnnualBook of ASTM Standards: Metal Test methods and Analitical Procedures, Section 3 (1991). The result of capacity loads experimental test was compared with design based on SNI 03-7971- 2013standard of Indonesia for the design of cold formed steel structural members. The results of the yield stress of the material will be seen against the minimum allowable allowable stress range. After the test, the percentace of ultimate axial tension capacity theory has a result that is 16.46% larger than the ultimate axial tension capacity experimental. When compared with the load that must be borne 5.673 kN/m it can be concluded that 2 specimens do not meet. Yield stress of member has fulfilled requirement that wass bigger than 550 MPa. Based on the curve obtained ultimate axial tension capacity theory, results greater than experimental. The greatest voltage value (fu) is achieved under the same conditions as its yield stress. For this specimen with a melting voltage value fy = 571.5068 MPa has fulfilled the minimum melting point value of 550 MPa required for standard mild steel materials in accordance with the code SNI 03- 7971-2013 about Cold formed steel.

NMR in structural genomics to increase structural coverage of the protein universe: Delivered by Prof. Kurt Wüthrich on 7 July 2013 at the 38th FEBS Congress in St. Petersburg, Russia.

PubMed

Serrano, Pedro; Dutta, Samit K; Proudfoot, Andrew; Mohanty, Biswaranjan; Susac, Lukas; Martin, Bryan; Geralt, Michael; Jaroszewski, Lukasz; Godzik, Adam; Elsliger, Marc; Wilson, Ian A; Wüthrich, Kurt

2016-11-01

For more than a decade, the Joint Center for Structural Genomics (JCSG; www.jcsg.org) worked toward increased three-dimensional structure coverage of the protein universe. This coordinated quest was one of the main goals of the four high-throughput (HT) structure determination centers of the Protein Structure Initiative (PSI; www.nigms.nih.gov/Research/specificareas/PSI). To achieve the goals of the PSI, the JCSG made use of the complementarity of structure determination by X-ray crystallography and nuclear magnetic resonance (NMR) spectroscopy to increase and diversify the range of targets entering the HT structure determination pipeline. The overall strategy, for both techniques, was to determine atomic resolution structures for representatives of large protein families, as defined by the Pfam database, which had no structural coverage and could make significant contributions to biological and biomedical research. Furthermore, the experimental structures could be leveraged by homology modeling to further expand the structural coverage of the protein universe and increase biological insights. Here, we describe what could be achieved by this structural genomics approach, using as an illustration the contributions from 20 NMR structure determinations out of a total of 98 JCSG NMR structures, which were selected because they are the first three-dimensional structure representations of the respective Pfam protein families. The information from this small sample is representative for the overall results from crystal and NMR structure determination in the JCSG. There are five new folds, which were classified as domains of unknown functions (DUF), three of the proteins could be functionally annotated based on three-dimensional structure similarity with previously characterized proteins, and 12 proteins showed only limited similarity with previous deposits in the Protein Data Bank (PDB) and were classified as DUFs. © 2016 Federation of European Biochemical Societies.

First-Principles Predictions of Near-Edge X-ray Absorption Fine Structure Spectra of Semiconducting Polymers

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

Su, Gregory M.; Patel, Shrayesh N.; Pemmaraju, C. D.

The electronic structure and molecular orientation of semiconducting polymers in thin films determine their ability to transport charge. Methods based on near-edge X-ray absorption fine structure (NEXAFS) spectroscopy can be used to probe both the electronic structure and microstructure of semiconducting polymers in both crystalline and amorphous films. However, it can be challenging to interpret NEXAFS spectra on the basis of experimental data alone, and accurate, predictive calculations are needed to complement experiments. Here, we show that first-principles density functional theory (DFT) can be used to model NEXAFS spectra of semiconducting polymers and to identify the nature of transitions inmore » complicated NEXAFS spectra. Core-level X-ray absorption spectra of a set of semiconducting polymers were calculated using the excited electron and core-hole (XCH) approach based on constrained-occupancy DFT. A comparison of calculations on model oligomers and periodic structures with experimental data revealed the requirements for accurate prediction of NEXAFS spectra of both conjugated homopolymers and donor–acceptor polymers. The NEXAFS spectra predicted by the XCH approach were applied to study molecular orientation in donor–acceptor polymers using experimental spectra and revealed the complexity of using carbon edge spectra in systems with large monomeric units. The XCH approach has sufficient accuracy in predicting experimental NEXAFS spectra of polymers that it should be considered for design and analysis of measurements using soft X-ray techniques, such as resonant soft X-ray scattering and scanning transmission X-ray microscopy.« less

COMBREX-DB: an experiment centered database of protein function: knowledge, predictions and knowledge gaps.

PubMed

Chang, Yi-Chien; Hu, Zhenjun; Rachlin, John; Anton, Brian P; Kasif, Simon; Roberts, Richard J; Steffen, Martin

2016-01-04

The COMBREX database (COMBREX-DB; combrex.bu.edu) is an online repository of information related to (i) experimentally determined protein function, (ii) predicted protein function, (iii) relationships among proteins of unknown function and various types of experimental data, including molecular function, protein structure, and associated phenotypes. The database was created as part of the novel COMBREX (COMputational BRidges to EXperiments) effort aimed at accelerating the rate of gene function validation. It currently holds information on ∼ 3.3 million known and predicted proteins from over 1000 completely sequenced bacterial and archaeal genomes. The database also contains a prototype recommendation system for helping users identify those proteins whose experimental determination of function would be most informative for predicting function for other proteins within protein families. The emphasis on documenting experimental evidence for function predictions, and the prioritization of uncharacterized proteins for experimental testing distinguish COMBREX from other publicly available microbial genomics resources. This article describes updates to COMBREX-DB since an initial description in the 2011 NAR Database Issue. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

Experimental determinations of the eigenmodes for composite bars made with carbon and Kevlar-carbon fibers

NASA Astrophysics Data System (ADS)

Miriţoiu, C. M.; Stănescu, M. M.; Burada, C. O.; Bolcu, D.; Roşca, V.

2015-11-01

For modal identification, the single-point excitation method has been widely used in modal tests and it consists in applying a force in a given point and recording the vibratory structure response in all interest points, including the excitation point. There will be presented the experimental recordings for the studied bars (with Kevlar-carbon or carbon fibers), the frequency response function in Cartesian and polar coordinates. By using the frequency response functions we determine the eigenparameters for each bar. We present the final panel of the eigenmodes (with the damping factors, eigenfrequencies and critical damping) for each considered bar. Using the eigenfrequency of the first determined eigenmode, the bars stiffness has been determined. The presented bars can be used in practical engineering for: car or bus body parts, planes body parts, bullet-proof vests, reinforcements for sandwich beams, and so on.

Crack propagation modelling for high strength steel welded structural details

NASA Astrophysics Data System (ADS)

Mecséri, B. J.; Kövesdi, B.

2017-05-01

Nowadays the barrier of applying HSS (High Strength Steel) material in bridge structures is their low fatigue strength related to yield strength. This paper focuses on the fatigue behaviour of a structural details (a gusset plate connection) made from NSS and HSS material, which is frequently used in bridges in Hungary. An experimental research program is carried out at the Budapest University of Technology and Economics to investigate the fatigue lifetime of this structural detail type through the same test specimens made from S235 and S420 steel grades. The main aim of the experimental research program is to study the differences in the crack propagation and the fatigue lifetime between normal and high strength steel structures. Based on the observed fatigue crack pattern the main direction and velocity of the crack propagation is determined. In parallel to the tests finite element model (FEM) are also developed, which model can handle the crack propagation. Using the measured strain data in the tests and the calculated values from the FE model, the approximation of the material parameters of the Paris law are calculated step-by-step, and their calculated values are evaluated. The same material properties are determined for NSS and also for HSS specimens as well, and the differences are discussed. In the current paper, the results of the experiments, the calculation method of the material parameters and the calculated values are introduced.

Novel Yersinia Pestis Toxin that Resembles Bacillus Anthracis Edema Factor: Study of Activity and Structural Modeling

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

Motin, V; Garcia, E; Barsky, D

2003-02-05

The goal of this project was to begin both experimental and computational studies of the novel plague toxin to establish its biological properties and create its 3D-model. The project was divided into two parts. (1) Experimental--This part was devoted to determine distribution of the genes encoding novel plague toxin among different isolates of Y.pestis. If the EF-like activity is important for Y.pestis pathogenicity, it is anticipated that all highly virulent strains will contain the toxin genes. Also, they proposed to initiate research to investigate the functionality of the novel Y.pestis toxin that they hypothesize is likely to significantly contribute tomore » the virulence of this dangerous microbe. this research design consisted of amplification, cloning and expression in E.coli the toxin genes followed by affinity purification of the recombinant protein that can be further used for testing of enzymatic activity. (2) Computational--The structural modeling of the putative EF of Y.pestis was based on multiple sequence alignments, secondary structure predictions, and comparison with 3D models of the EF of B. anthracis. The x-ray structure of the last has been recently published [Nature. 2002. 415(Jan):396-402]. The final model was selected after detailed analysis to determine if the structure is consistent with the biological function.« less

Electronic origin of structural transition in 122 Fe based superconductors

NASA Astrophysics Data System (ADS)

Ghosh, Haranath; Sen, Smritijit; Ghosh, Abyay

2017-03-01

Direct quantitative correlations between the orbital order and orthorhombicity is achieved in a number of Fe-based superconductors of 122 family. The former (orbital order) is calculated from first principles simulations using experimentally determined doping and temperature dependent structural parameters while the latter (the orthorhombicity) is taken from already established experimental studies; when normalized, both the above quantities quantitatively corresponds to each other in terms of their doping as well as temperature variations. This proves that the structural transition in Fe-based materials is electronic in nature due to orbital ordering. An universal correlations among various structural parameters and electronic structure are also obtained. Most remarkable among them is the mapping of two Fe-Fe distances in the low temperature orthorhombic phase, with the band energies Edxz, Edyz of Fe at the high symmetry points of the Brillouin zone. The fractional co-ordinate zAs of As which essentially determines anion height is inversely (directly) proportional to Fe-As bond distances (with exceptions of K doped BaFe2As2) for hole (electron) doped materials as a function of doping. On the other hand, Fe-As bond-distance is found to be inversely (directly) proportional to the density of states at the Fermi level for hole (electron) doped systems. Implications of these results to current issues of Fe based superconductivity are discussed.

Near-field microwave tomography of planar semiconductor microstructures

NASA Astrophysics Data System (ADS)

Reznik, A. N.; Vostokov, N. V.; Vdovicheva, N. K.; Korolyov, S. A.; Shashkin, V. I.

2017-12-01

A method for determining the parameters of a layered semiconductor structure, using the data obtained by near-field microwave probing with a micron-size lateral resolution, was developed and tested experimentally. We have measured a frequency spectrum of the impedance of a coaxial antenna formed on a test structure surface. The corresponding inverse problem has been solved based on the quasistatic theory for the impedance of a monopole antenna interacting with a layered medium, which was proposed earlier [A. N. Reznik and S. A. Korolyov, J. Appl. Phys. 119, 094504 (2016)]. This method was applied to a low-barrier Mott diode structure with a nearly 100 nm thick undoped layer grown on a conducting substrate GaAs. Computer simulation allowed us to establish the optimal frequency intervals and estimate the accuracy of determining the structure parameters. Measurements were taken in the frequency range of 0.1-67 GHz on commercially available equipment. Three antennas with a radius of the central conductor of 5.5, 11, and 25 μm, respectively, were used. The accuracy of the experimental evaluation of the layer thickness d and conductivity σ was ˜1-3%, and for the substrate conductivity, it came to about 15%. As an example, we also present the parameters σ and d in four points of the sample surface image. These data show strong lateral inhomogeneity of the structure under study.

Experimental Verification of Integrity of Low-Pressure Injection Piles Structure - Pile Internal Capacity

NASA Astrophysics Data System (ADS)

Pachla, Henryk

2017-12-01

The idea of strengthening the foundation using injection piles lies in transferring loads from the foundation to the piles anchorage in existing structure and formed in the soil. Such a system has to be able to transfer loads from the foundation to the pile and from the pile onto the soil. Pile structure often reinforced with steel element has to also be able to transfer such a loading. According to the rules of continuum mechanics, the bearing capacity of such a system and a deformation of its individual elements can be determined by way of an analysis of the contact problem of three interfaces. Each of these surfaces is determined by different couples of materials. Those surfaces create: pile-foundation anchorage, bonding between reinforcement and material from which the pile is formed and pilesoil interface. What is essential is that on the contact surfaces the deformation of materials which adhere to each other can vary and depends on the mechanical properties and geometry of these surfaces. Engineering practice and experimental research point out that the failure in such structures occurs at interfaces. The paper is concentrating on presenting the experiments on interaction between cement grout and various types of steel reinforcement. The tests were conducted on the special low pressure injection piles widely used to strengthen foundations of already existing structures of historical buildings due to the technology of formation and injection pressure.

Investigation of the Effect of the Tortuous Pore Structure on Water Diffusion through a Polymer Film Using Lattice Boltzmann Simulations.

PubMed

Gebäck, Tobias; Marucci, Mariagrazia; Boissier, Catherine; Arnehed, Johan; Heintz, Alexei

2015-04-23

Understanding how the pore structure influences the mass transport through a porous material is important in several applications, not the least in the design of polymer film coatings intended to control drug release. In this study, a polymer film made of ethyl cellulose and hydroxypropyl cellulose was investigated. The 3D structure of the films was first experimentally characterized using confocal laser scanning microscopy data and then mathematically reconstructed for the whole film thickness. Lattice Boltzmann simulations were performed to compute the effective diffusion coefficient of water in the film and the results were compared to experimental data. The local porosities and pore sizes were also analyzed to determine how the properties of the internal film structure affect the water effective diffusion coefficient. The results show that the top part of the film has lower porosity, lower pore size, and lower connectivity, which results in a much lower effective diffusion coefficient in this part, largely determining the diffusion rate through the entire film. Furthermore, the local effective diffusion coefficients were not proportional to the local film porosity, indicating that the results cannot be explained by a single tortuosity factor. In summary, the proposed methodology of combining microscopy data, mass transport simulations, and pore space analysis can give valuable insights on how the film structure affects the mass transport through the film.

A Magic-Angle Spinning NMR Method for the Site-Specific Measurement of Proton Chemical-Shift Anisotropy in Biological and Organic Solids.

PubMed

Hou, Guangjin; Gupta, Rupal; Polenova, Tatyana; Vega, Alexander J

2014-02-01

Proton chemical shifts are a rich probe of structure and hydrogen bonding environments in organic and biological molecules. Until recently, measurements of 1 H chemical shift tensors have been restricted to either solid systems with sparse proton sites or were based on the indirect determination of anisotropic tensor components from cross-relaxation and liquid-crystal experiments. We have introduced an MAS approach that permits site-resolved determination of CSA tensors of protons forming chemical bonds with labeled spin-1/2 nuclei in fully protonated solids with multiple sites, including organic molecules and proteins. This approach, originally introduced for the measurements of chemical shift tensors of amide protons, is based on three RN -symmetry based experiments, from which the principal components of the 1 H CS tensor can be reliably extracted by simultaneous triple fit of the data. In this article, we expand our approach to a much more challenging system involving aliphatic and aromatic protons. We start with a review of the prior work on experimental-NMR and computational-quantum-chemical approaches for the measurements of 1 H chemical shift tensors and for relating these to the electronic structures. We then present our experimental results on U- 13 C, 15 N-labeled histdine demonstrating that 1 H chemical shift tensors can be reliably determined for the 1 H 15 N and 1 H 13 C spin pairs in cationic and neutral forms of histidine. Finally, we demonstrate that the experimental 1 H(C) and 1 H(N) chemical shift tensors are in agreement with Density Functional Theory calculations, therefore establishing the usefulness of our method for characterization of structure and hydrogen bonding environment in organic and biological solids.

Attractive S⋯π and π-π interactions in the pyrazine-2-thiocarboxamide structure: Experimental and computational studies in the context of crystal engineering and microbiological properties

NASA Astrophysics Data System (ADS)

Chylewska, Agnieszka; Sikorski, Artur; Ogryzek, Małgorzata; Makowski, Mariusz

2016-02-01

Pyrazine-2-thiocarboxamide (PTCA) was obtained after recrystallization and was characterised by elemental analysis, IR spectroscopy and thermogravimetry. Five dimers of PTCA were found in X-ray diffraction studies. These results were then compared with the known structures of a popular drug, i.e. pyrazine-2-carboxamide (PZA). S⋯π and π-π interactions were observed in the PTCA crystal structure as a novelty in X-ray measurements and our attention was focused on their role in stabilizing the PCTA structure. The geometry, energy and IR spectra for two conformers (E, Z) of PTCA and five dimers (D1-D5) were calculated for the gas phase with the DFT method at 6-311 + G(d,p) basis set. The results of calculations showed that D1 is the most stable dimer among five dimers of PTCA which were found experimentally. Thermal decomposition of PTCA was examined with the use of the TG/IR analysis (20-1000 °C) and the results were discussed. To test the antimicrobial activity of PTCA a biological assay was performed to determine its potentially pharmaceutical applications. The minimum inhibitory (MIC) and minimal bactericidal (fungicidal) concentrations (MBC) for PTCA were determined against six microorganisms.

A combined experimental and in silico characterization to highlight additional structural features and properties of a potentially new drug

NASA Astrophysics Data System (ADS)

Bastos, Isadora T. S.; Costa, Fanny N.; Silva, Tiago F.; Barreiro, Eliezer J.; Lima, Lídia M.; Braz, Delson; Lombardo, Giuseppe M.; Punzo, Francesco; Ferreira, Fabio F.; Barroso, Regina C.

2017-10-01

LASSBio-1755 is a new cycloalkyl-N-acylhydrazone parent compound designed for the development of derivatives with antinociceptive and anti-inflammatory activities. Although single crystal X-ray diffraction has been considered as the golden standard in structure determination, we successfully used X-ray powder diffraction data in the structural determination of new synthesized compounds, in order to overcome the bottle-neck due to the difficulties experienced in harvesting good quality single crystals of the compounds. We therefore unequivocally assigned the relative configuration (E) to the imine double bond and a s-cis conformation of the amide function of the N-acylhydrazone compound. These features are confirmed by a computational analysis performed on the basis of molecular dynamics calculations, which are extended not only to the structural characteristics but also to the analysis of the anisotropic atomic displacement parameters, a further information - missed in a typical powder diffraction analysis. The so inferred data were used to perform additional cycles of refinement and eventually generate a new cif file with additional physical information. Furthermore, crystal morphology prediction was performed, which is in agreement with the experimental images acquired by scanning electron microscopy, thus providing useful information on possible alternative paths for better crystallization strategies.

Current challenges in genome annotation through structural biology and bioinformatics.

PubMed

Furnham, Nicholas; de Beer, Tjaart A P; Thornton, Janet M

2012-10-01

With the huge volume in genomic sequences being generated from high-throughout sequencing projects the requirement for providing accurate and detailed annotations of gene products has never been greater. It is proving to be a huge challenge for computational biologists to use as much information as possible from experimental data to provide annotations for genome data of unknown function. A central component to this process is to use experimentally determined structures, which provide a means to detect homology that is not discernable from just the sequence and permit the consequences of genomic variation to be realized at the molecular level. In particular, structures also form the basis of many bioinformatics methods for improving the detailed functional annotations of enzymes in combination with similarities in sequence and chemistry. Copyright © 2012. Published by Elsevier Ltd.

Conformational flexibility and packing plausibility of repaglinide polymorphs

NASA Astrophysics Data System (ADS)

Rani, Dimpy; Goyal, Parnika; Chadha, Renu

2018-04-01

The present manuscript highlights the structural insight into the repaglinide polymorphs. The experimental screening for the possible crystal forms were carried out using various solvents, which generated three forms. The crystal structure of Form II and III was determined using PXRD pattern whereas structural analysis of Form I has already been reported. Form I, II and II was found to exist in P212121, PNA21 and P21/c space groups respectively. Conformational analysis was performed to account the conformational flexibility of RPG. The obtained conformers were further utilized to obtain the information about the crystal packing pattern of RPG polymorphs by polymorph prediction module. The lattice energy landscape, depicting the relationship between lattice energy and density of the polymorphs has been obtained for various possible polymorphs. The experimentally isolated polymorphs were successfully fitted into lattice energy landscape.

Survey of NASA research on crash dynamics

NASA Technical Reports Server (NTRS)

Thomson, R. G.; Carden, H. D.; Hayduk, R. J.

1984-01-01

Ten years of structural crash dynamics research activities conducted on general aviation aircraft by the National Aeronautics and Space Administration (NASA) are described. Thirty-two full-scale crash tests were performed at Langley Research Center, and pertinent data on airframe and seat behavior were obtained. Concurrent with the experimental program, analytical methods were developed to help predict structural behavior during impact. The effects of flight parameters at impact on cabin deceleration pulses at the seat/occupant interface, experimental and analytical correlation of data on load-limiting subfloor and seat configurations, airplane section test results for computer modeling validation, and data from emergency-locator-transmitter (ELT) investigations to determine probable cause of false alarms and nonactivations are assessed. Computer programs which provide designers with analytical methods for predicting accelerations, velocities, and displacements of collapsing structures are also discussed.

A general model-based design of experiments approach to achieve practical identifiability of pharmacokinetic and pharmacodynamic models.

PubMed

Galvanin, Federico; Ballan, Carlo C; Barolo, Massimiliano; Bezzo, Fabrizio

2013-08-01

The use of pharmacokinetic (PK) and pharmacodynamic (PD) models is a common and widespread practice in the preliminary stages of drug development. However, PK-PD models may be affected by structural identifiability issues intrinsically related to their mathematical formulation. A preliminary structural identifiability analysis is usually carried out to check if the set of model parameters can be uniquely determined from experimental observations under the ideal assumptions of noise-free data and no model uncertainty. However, even for structurally identifiable models, real-life experimental conditions and model uncertainty may strongly affect the practical possibility to estimate the model parameters in a statistically sound way. A systematic procedure coupling the numerical assessment of structural identifiability with advanced model-based design of experiments formulations is presented in this paper. The objective is to propose a general approach to design experiments in an optimal way, detecting a proper set of experimental settings that ensure the practical identifiability of PK-PD models. Two simulated case studies based on in vitro bacterial growth and killing models are presented to demonstrate the applicability and generality of the methodology to tackle model identifiability issues effectively, through the design of feasible and highly informative experiments.

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

Quennet, Marcel, E-mail: marcel.quennet@fu-berlin.de; Institut für Chemie und Biochemie, Freie Universität Berlin, Takustraße 3, 14195 Berlin; Ritscher, Anna

In this work the Cu/Zn order-disorder transition in Cu{sub 2}ZnSnS{sub 4} kesterites on Wyckoff positions 2c and 2d was investigated by a structural and electronic analysis in theory and experiment. For experimental investigations stoichiometric samples with different Cu/Zn order, annealed in the temperature range of 473–623 K and afterwards quenched, were used. The optical gaps were determined using the Derivation of Absorption Spectrum Fitting (DASF) method. Furthermore, the order-disorder transition was examined by DFT calculations for a closer analysis of the origins of the reduced band gap, showing a good agreement with experimental data with respect to structural and electronicmore » properties. Our studies show a slight increase of lattice parameter c in the kesterite lattice with increasing disorder. Additionally, a reduced band gap was observed with increasing disorder, which is an effect of newly occurring binding motifs in the disordered kesterite structure. - Highlights: • Experimental and theoretical investigation on the order-disorder transition in kesterites. • Slight enlargements of lattice constants due to disorder in experiment and theory. • Strong band gap fluctuations with decreasing order. • Electronic structure deviations due to changing binding motifs. • Disorder as possible main source of low open-circuit voltages.« less

Structural architecture of the human long non-coding RNA, steroid receptor RNA activator

PubMed Central

Novikova, Irina V.; Hennelly, Scott P.; Sanbonmatsu, Karissa Y.

2012-01-01

While functional roles of several long non-coding RNAs (lncRNAs) have been determined, the molecular mechanisms are not well understood. Here, we report the first experimentally derived secondary structure of a human lncRNA, the steroid receptor RNA activator (SRA), 0.87 kB in size. The SRA RNA is a non-coding RNA that coactivates several human sex hormone receptors and is strongly associated with breast cancer. Coding isoforms of SRA are also expressed to produce proteins, making the SRA gene a unique bifunctional system. Our experimental findings (SHAPE, in-line, DMS and RNase V1 probing) reveal that this lncRNA has a complex structural organization, consisting of four domains, with a variety of secondary structure elements. We examine the coevolution of the SRA gene at the RNA structure and protein structure levels using comparative sequence analysis across vertebrates. Rapid evolutionary stabilization of RNA structure, combined with frame-disrupting mutations in conserved regions, suggests that evolutionary pressure preserves the RNA structural core rather than its translational product. We perform similar experiments on alternatively spliced SRA isoforms to assess their structural features. PMID:22362738

Experimental and Theoretical Investigation of Sodiated Multimers of Steroid Epimers with Ion Mobility-Mass Spectrometry

NASA Astrophysics Data System (ADS)

Chouinard, Christopher D.; Cruzeiro, Vinícius Wilian D.; Roitberg, Adrian E.; Yost, Richard A.

2017-02-01

Ion mobility-mass spectrometry (IM-MS) has recently seen increased use in the analysis of small molecules, especially in the field of metabolomics, for increased breadth of information and improved separation of isomers. In this study, steroid epimers androsterone and trans-androsterone were analyzed with IM-MS to investigate differences in their relative mobilities. Although sodiated monomers exhibited very similar collision cross-sections (CCS), baseline separation was observed for the sodiated dimer species (RS = 1.81), with measured CCS of 242.6 and 256.3 Å2, respectively. Theoretical modeling was performed to determine the most energetically stable structures of solution-phase and gas-phase monomer and dimer structures. It was revealed that these epimers differ in their preferred dimer binding mode in solution phase: androsterone adopts a R=O - Na+ - OH—R' configuration, whereas trans-androsterone adopts a R=O - Na+ - O=R' configuration. This difference contributes to a significant structural variation, and subsequent CCS calculations based on these structures relaxed in the gas phase were in agreement with experimentally measured values (ΔCCS 5%). Additionally, these calculations accurately predicted the relative difference in mobility between the epimers. This study illustrates the power of combining experimental and theoretical results to better elucidate gas-phase structures.

Failure analysis of thick composite cylinders under external pressure

NASA Technical Reports Server (NTRS)

Caiazzo, A.; Rosen, B. W.

1992-01-01

Failure of thick section composites due to local compression strength and overall structural instability is treated. Effects of material nonlinearity, imperfect fiber architecture, and structural imperfections upon anticipated failure stresses are determined. Comparisons with experimental data for a series of test cylinders are described. Predicting the failure strength of composite structures requires consideration of stability and material strength modes of failure using linear and nonlinear analysis techniques. Material strength prediction requires the accurate definition of the local multiaxial stress state in the material. An elasticity solution for the linear static analysis of thick anisotropic cylinders and rings is used herein to predict the axisymmetric stress state in the cylinders. Asymmetric nonlinear behavior due to initial cylinder out of roundness and the effects of end closure structure are treated using finite element methods. It is assumed that local fiber or ply waviness is an important factor in the initiation of material failure. An analytical model for the prediction of compression failure of fiber composites, which includes the effects of fiber misalignments, matrix inelasticity, and multiaxial applied stresses is used for material strength calculations. Analytical results are compared to experimental data for a series of glass and carbon fiber reinforced epoxy cylinders subjected to external pressure. Recommendations for pretest characterization and other experimental issues are presented. Implications for material and structural design are discussed.

Interplay between theory and experiment: computational organometallic and transition metal chemistry.

PubMed

Lin, Zhenyang

2010-05-18

Computational and theoretical chemistry provide fundamental insights into the structures, properties, and reactivities of molecules. As a result, theoretical calculations have become indispensable in various fields of chemical research and development. In this Account, we present our research in the area of computational transition metal chemistry, using examples to illustrate how theory impacts our understanding of experimental results and how close collaboration between theoreticians and experimental chemists can be mutually beneficial. We begin by examining the use of computational chemistry to elucidate the details of some unusual chemical bonds. We consider the three-center, two-electron bonding in titanocene sigma-borane complexes and the five-center, four-electron bonding in a rhodium-bismuth complex. The bonding in metallabenzene complexes is also examined. In each case, theoretical calculations provide particular insight into the electronic structure of the chemical bonds. We then give an example of how theoretical calculations aided the structural determination of a kappa(2)-N,N chelate ruthenium complex formed upon heating an intermediate benzonitrile-coordinated complex. An initial X-ray diffraction structure proposed on the basis of a reasonable mechanism appeared to fit well, with an apparently acceptable R value of 0.0478. But when DFT calculations were applied, the optimized geometry differed significantly from the experimental data. By combining experimental and theoretical outlooks, we posited a new structure. Remarkably, a re-refining of the X-ray diffraction data based on the new structure resulted in a slightly lower R value of 0.0453. We further examine the use of computational chemistry in providing new insight into C-H bond activation mechanisms and in understanding the reactivity properties of nucleophilic boryl ligands, addressing experimental difficulties with calculations and vice versa. Finally, we consider the impact of theoretical insights in three very specific experimental studies of chemical reactions, illustrating how theoretical results prompt further experimental studies: (i) diboration of aldehydes catalyzed by copper(I) boryl complexes, (ii) ruthenium-catalyzed C-H amination of arylazides, and (iii) zinc reduction of a vinylcarbyne complex. The concepts and examples presented here are intended for nonspecialists, particularly experimentalists. Together, they illustrate some of the achievements that are possible with a fruitful union of experiment and theory.

Simultaneous determination of micellar structure and drag reduction in a surfactant solution flow using the fluorescence probe method

NASA Astrophysics Data System (ADS)

Wakimoto, Tatsuro; Araga, Koichi; Katoh, Kenji

2018-03-01

As widely known, the addition of a specific type of surfactant to water reduces drag in a pipe flow. This effect is considered to be a result of the suppression of turbulent transition caused by the ordered structure of rod-like micelles that is referred to as a shear-induced structure (SIS). However, it is typically difficult to determine the SIS since it is necessary to noninvasively detect the SIS with several hundred nanometers in the actual moving flow. In this study, we used the fluorescence probe method to locally determine the SIS in a pipe flow. When hydrophobic fluorescence molecules are added to the surfactant solution, the fluorescence molecules are trapped in micelles. Thus, fluorescence intensity varies based on the change in the micellar structure. We verified the applicability of the fluorescence probe method to the SIS detection and determined the relationship between the micellar structure and the drag reduction in the pipe flow by simultaneously measuring the fluorescence intensity and pipe friction factor. The experimental result demonstrates that the SIS formation in the near-wall region is closely correlated with the drag reduction and suggests that the near-wall SIS suppresses the turbulent transition.

Dominant modal decomposition method

NASA Astrophysics Data System (ADS)

Dombovari, Zoltan

2017-03-01

The paper deals with the automatic decomposition of experimental frequency response functions (FRF's) of mechanical structures. The decomposition of FRF's is based on the Green function representation of free vibratory systems. After the determination of the impulse dynamic subspace, the system matrix is formulated and the poles are calculated directly. By means of the corresponding eigenvectors, the contribution of each element of the impulse dynamic subspace is determined and the sufficient decomposition of the corresponding FRF is carried out. With the presented dominant modal decomposition (DMD) method, the mode shapes, the modal participation vectors and the modal scaling factors are identified using the decomposed FRF's. Analytical example is presented along with experimental case studies taken from machine tool industry.

Linking amphibian call structure to the environment: the interplay between phenotypic flexibility and individual attributes

PubMed Central

Arim, Matías; Narins, Peter M.

2011-01-01

The structure of the environment surrounding signal emission produces different patterns of degradation and attenuation. The expected adjustment of calls to ensure signal transmission in an environment was formalized in the acoustic adaptation hypothesis. Within this framework, most studies considered anuran calls as fixed attributes determined by local adaptations. However, variability in vocalizations as a product of phenotypic expression has also been reported. Empirical evidence supporting the association between environment and call structure has been inconsistent, particularly in anurans. Here, we identify a plausible causal structure connecting environment, individual attributes, and temporal and spectral adjustments as direct or indirect determinants of the observed variation in call attributes of the frog Hypsiboas pulchellus. For that purpose, we recorded the calls of 40 males in the field, together with vegetation density and other environmental descriptors of the calling site. Path analysis revealed a strong effect of habitat structure on the temporal parameters of the call, and an effect of site temperature conditioning the size of organisms calling at each site and thus indirectly affecting the dominant frequency of the call. Experimental habitat modification with a styrofoam enclosure yielded results consistent with field observations, highlighting the potential role of call flexibility on detected call patterns. Both, experimental and correlative results indicate the need to incorporate the so far poorly considered role of phenotypic plasticity in the complex connection between environmental structure and individual call attributes. PMID:22479134

Predictive Methodology for Delamination Growth in Laminated Composites Part 1: Theoretical Development and Preliminary Experimental Results

DOT National Transportation Integrated Search

1998-04-01

A methodology is presented for the prediction of delamination growth in laminated structures. The methodology is aimed at overcoming computational difficulties in the determination of energy release rate and mode mix. It also addresses the issue that...

Experimental analysis for fabrication of high-aspect-ratio piezoelectric ceramic structure by micro-powder injection molding process

NASA Astrophysics Data System (ADS)

Han, Jun Sae; Gal, Chang Woo; Park, Jae Man; Kim, Jong Hyun; Park, Seong Jin

2018-04-01

Aspect ratio effects in the micro-powder injection molding process were experimentally analyzed for fabrication of high-aspect-ratio piezoelectric ceramic structure. The mechanisms of critical defects have been studied according to individual manufacturing steps. In the molding process, incomplete filling phenomenon determines the critical aspect ratios of a micro pattern. According to mold temperature, an incomplete filling phenomenon has been analyzed with respect to different pattern sizes and aspect ratio. In demolding and drying process, the capillary behavior of sacrificial polymeric mold insert determines the critical aspect ratio of a micro pattern. With respect to pattern dimensions, slumping behavior has been analyzed. Based on our current systems, micro PZT feature has stability when it has lower aspect ratio than 5. Under optimized processing conditions, 20 μm and 40 μm ceramic rod array feature which has 5 of aspect ratio were successfully fabricated by the developed process. Further modification points to fabricate the smaller and higher feature were specifically addressed.

Synthesis, vibrational, NMR, quantum chemical and structure-activity relation studies of 2-hydroxy-4-methoxyacetophenone.

PubMed

Arjunan, V; Devi, L; Subbalakshmi, R; Rani, T; Mohan, S

2014-09-15

The stable geometry of 2-hydroxy-4-methoxyacetophenone is optimised by DFT/B3LYP method with 6-311++G(∗∗) and cc-pVTZ basis sets. The structural parameters, thermodynamic properties and vibrational frequencies of the optimised geometry have been determined. The effects of substituents (hydroxyl, methoxy and acetyl groups) on the benzene ring vibrational frequencies are analysed. The vibrational frequencies of the fundamental modes of 2-hydroxy-4-methoxyacetophenone have been precisely assigned and analysed and the theoretical results are compared with the experimental vibrations. 1H and 13C NMR isotropic chemical shifts are calculated and assignments made are compared with the experimental values. The energies of important MO's, the total electron density and electrostatic potential of the compound are determined. Various reactivity and selectivity descriptors such as chemical hardness, chemical potential, softness, electrophilicity, nucleophilicity and the appropriate local quantities are calculated. Copyright © 2014 Elsevier B.V. All rights reserved.

Specific features of the flow structure in a reactive type turbine stage

NASA Astrophysics Data System (ADS)

Chernikov, V. A.; Semakina, E. Yu.

2017-04-01

The results of experimental studies of the gas dynamics for a reactive type turbine stage are presented. The objective of the studies is the measurement of the 3D flow fields in reference cross sections, experimental determination of the stage characteristics, and analysis of the flow structure for detecting the sources of kinetic energy losses. The integral characteristics of the studied stage are obtained by averaging the results of traversing the 3D flow over the area of the reference cross sections before and behind the stage. The averaging is performed using the conservation equations for mass, total energy flux, angular momentum with respect to the axis z of the turbine, entropy flow, and the radial projection of the momentum flux equation. The flow parameter distributions along the channel height behind the stage are obtained in the same way. More thorough analysis of the flow structure is performed after interpolation of the experimentally measured point parameter values and 3D flow velocities behind the stage. The obtained continuous velocity distributions in the absolute and relative coordinate systems are presented in the form of vector fields. The coordinates of the centers and the vectors of secondary vortices are determined using the results of point measurements of velocity vectors in the cross section behind the turbine stage and their subsequent interpolation. The approach to analysis of experimental data on aerodynamics of the turbine stage applied in this study allows one to find the detailed space structure of the working medium flow, including secondary coherent vortices at the root and peripheral regions of the air-gas part of the stage. The measured 3D flow parameter fields and their interpolation, on the one hand, point to possible sources of increased power losses, and, on the other hand, may serve as the basis for detailed testing of CFD models of the flow using both integral and local characteristics. The comparison of the numerical and experimental results, as regards local characteristics, using statistical methods yields the quantitative estimate of their agreement.

Investigation of piezoelectric impedance-based health monitoring of structure interface debonding

NASA Astrophysics Data System (ADS)

Xiao, Li; Chen, Guofeng; Chen, Xiaoming; Qu, Wenzhong

2016-04-01

Various damages might occur during the solid rocket motor (SRM) manufacturing/operational phase, and the debonding of propellant/insulator/composite case interfaces is one of damage types which determine the life of a motor. The detection of such interface debonding damage will be beneficial for developing techniques for reliable nondestructive evaluation (NDE) and structural health monitoring (SHM). Piezoelectric sensors are widely used for structural health monitoring technique. In particular, electromechanical impedance (EMI) techniques give simple and low-cost solutions for detecting damage in various structures. In this work, piezoelectric EMI structural health monitoring technique is applied to identify the debonding condition of propellant/insulator interface structure using finite element method and experimental investigation. A three-dimensional coupled field finite element model is developed using the software ANSYS and the harmonic analysis is conducted for high-frequency impedance analysis procedure. In the experimental study, the impedance signals were measured from PZT and MFC sensors outside attached to composite case monitoring the different debonding conditions between the propellant and insulator. Root mean square deviation (RMSD) based damage index is conducted to quantify the changes i n impedance for different de bonding conditions and frequency range. Simulation and experimental results confirmed that the EMI technique can be used effectively for detecting the debonding damage in SRM and is expected to be useful for future application of real SRM's SHM.

Determination of ensemble-average pairwise root mean-square deviation from experimental B-factors.

PubMed

Kuzmanic, Antonija; Zagrovic, Bojan

2010-03-03

Root mean-square deviation (RMSD) after roto-translational least-squares fitting is a measure of global structural similarity of macromolecules used commonly. On the other hand, experimental x-ray B-factors are used frequently to study local structural heterogeneity and dynamics in macromolecules by providing direct information about root mean-square fluctuations (RMSF) that can also be calculated from molecular dynamics simulations. We provide a mathematical derivation showing that, given a set of conservative assumptions, a root mean-square ensemble-average of an all-against-all distribution of pairwise RMSD for a single molecular species, (1/2), is directly related to average B-factors () and (1/2). We show this relationship and explore its limits of validity on a heterogeneous ensemble of structures taken from molecular dynamics simulations of villin headpiece generated using distributed-computing techniques and the Folding@Home cluster. Our results provide a basis for quantifying global structural diversity of macromolecules in crystals directly from x-ray experiments, and we show this on a large set of structures taken from the Protein Data Bank. In particular, we show that the ensemble-average pairwise backbone RMSD for a microscopic ensemble underlying a typical protein x-ray structure is approximately 1.1 A, under the assumption that the principal contribution to experimental B-factors is conformational variability. 2010 Biophysical Society. Published by Elsevier Inc. All rights reserved.